@prefix rdf: . @prefix owl: . @prefix rdfs: . @prefix xml: . @prefix xsd: . a owl:Ontology; rdfs:label "ro_bfo_bridge", "relationship"; owl:versionInfo "0.1", "1.1.1", "$Revision$"@en; "2012-09-06"; "Alan Ruttenberg", "Andrew Spear", "Carlo Torniai", "Melissa Haendel", "Nicole Vasilevsky", "Pierre Grenon"; "Barry Smith and Pierre Grenon: \"The Cornucopia of Formal Ontological Relations\"", "Barry Smith: \"Against Fantology\"", "Barry Smith: \"Basic Tools of Formal Ontology\"", "Barry Smith: \"Beyond Concepts: Ontology as Reality Representation\"", "Pierre Grenon and Barry Smith: \"SNAP and SPAN: Towards Geospatial Dynamics\"", "Pierre Grenon, Barry Smith and Louis Goldberg: \"Biodynamic Ontology: Applying BFO in the Biomedical Domain\"", "Pierre Grenon: \"BFO in a Nutshell: A Bi-categorial Axiomatization of BFO and Comparison with DOLCE\"", "Pierre Grenon: \"Nuts in BFO's Nutshell: Revisions to the Bi-categorial Axiomatization of BFO\"", "Pierre Grenon: \"Spatio-temporality in Basic Formal Ontology: SNAP and SPAN, Upper-Level Ontology, and Framework for Formalization\""; "Basic Formal Ontology (BFO)"; "Holger Stenzhorn", "Matthew Brush"; "Institute for Formal Ontology and Medical Information Science (IFOMIS)"; rdfs:comment """The Reagent Ontology (ReO) is currently under development by the Ontology Development Group at Oregon Health and Science University. Expected release data is in September 2012. This pre-release version contains many temporary and test classes, as well as annotations meant to support development and documentation needs. Please post any comments, feedback, or requests to the tracker at our Google Code site (http://code.google.com/p/reagent-ontology/) , and contact Matthew Brush with any additional questions (brushm@ohsu.edu). Thanks!""", "release version 1.01", "cvs version $Revision: 1.5 $", """ This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi """, "Domain and range constraints for OBO_REL, in terms of BFO", "

This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology

In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes

For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see http://genomebiology.com/2005/6/5/R46 or the OBO relations page hosted at http://obo.sourceforge.net/relationship

"; "application/rdf+xml"; "en"; "en"; "http://www.ifomis.org/bfo/1.1"; "ro_bfo_bridge", "relationship"; "14:07:2006 00:00"; "http://creativecommons.org/licenses/by/3.0"; "cjm" . a owl:AnnotationProperty; rdfs:label "derives_from"@en; rdfs:comment "Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant."; """OBO/BFO? derives_from is used in many different ways: 1. Something large deriving from something smaller which contributes material to it (cell line derives from some cell) . . . i would say this is akin to an 'originates_from' relation 2. Something small deriving from larger entity of which it was a part . . . would be akin to a 'was_once_part_of' relation (biological specimen derives from some organism, monoclonal antiody derives from some hybridoma) 3. derivation at similar scale (eg a modified cell derives from an unmodified cell. mRNA deriving from pre-mRNA. a protein complex derives from an individual protein) . . . many of these are arguable transformations And in ReO I have an example of both #1 and #2 in the same axiom, which really highlights the issue : monoclonal antibody: derives_from some ('hybridoma cell line' and (derives_from some ('B cell' and (part_of some organism)))) NOTE THAT THE ABOVE IS NOT QUITE RIGHT, BUT SMITH ET ALL CAME UP SIMILARLY WITH THREE TYPES OF DERIVATION IN FIGURE 3 OF THEIR 2005 GENOME BIOLOGY PAPER (Relations in Biomedical Ontologies, 2005, Genome Biology 3A: 1 from 1 DERIVATION - blastula deriveing from zygote) 3B: 1 from many derivation - zygote deriving from sperm and egg) 3C: many from 1 derivation - promyleocytes deriving from a precursor myeloblast)"""; "ro_bfo_bridge", "relationship"; "OBO_REL:0000015"; rdfs:domain ; _:2dc5e9; _:2dc609 . _:2dc5e9 a ; rdfs:label "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'."@en; _:2dc5f9 . _:2dc5f9 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . _:2dc609 a ; rdfs:label "derived_from"@en . a owl:AnnotationProperty; rdfs:label "reo_exploratory_class_or_axiom"; rdfs:comment "no need to fill a value for this annotation - will be used to flag classes that need to be moved to a dev or ext layer"; "a class or axiom implemented to as a test class, or to test or record some new modeling approach/pattern, but that requires further review and consideration. such classes are often out of scope for ReO, but record ideas/classes that might be useful for the general OBO community"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "term replaced by"@en; "Add as annotation triples in the granting ontology"@en, "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en; "Person:Alan Ruttenberg"@en; "Person:Alan Ruttenberg"@en; "term replaced by"@en; . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "curator note", "curator note"@en; "An administrative note of use for a curator but of no use for a user"@en; "PERSON:Alan Ruttenberg"@en; "curator note"@en; . a owl:AnnotationProperty; rdfs:label "OBO foundry unique label"@en; "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ."; "An alternative name for a class or property which is unique across the OBO Foundry."@en; "GROUP:OBO Foundry "@en; "OBO foundry unique label"@en; "PERSON:Alan Ruttenberg"@en, "PERSON:Bjoern Peters"@en, "PERSON:Chris Mungall"@en, "PERSON:Melanie Courtot"@en; . a owl:AnnotationProperty; rdfs:label "has obsolescence reason"@en; "PERSON:Alan Ruttenberg"@en, "PERSON:Melanie Courtot"@en; "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en; "has obsolescence reason"@en . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "has axiom label"@en; "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI"@en; "Person:Alan Ruttenberg"@en; "Person:Alan Ruttenberg"@en; "has axiom id"@en . a owl:AnnotationProperty; rdfs:label "reo_developer_note"@en; "place to record modeling questions, issues, alternative approaches, and other 'action items' to be addressed by developers, and meant for eyes of core developers only. These annotations should not be visible for end users or other developers outside the current ontology project (as opposed to 'IAO:editor notes' which are more concrete and visible to all). This annotation property should live in a separate layer reserved for 'developer-only' annotaitons and comments."; rdfs:comment "In some cases these may not be directly 'about' the class they are appended to, but rather more genreal/high level modeling concerns or suggestions. For example, the usage on the investigation class, to outline a potential rationale behind distinguishing assays, experiments, and investigations, and how this relates to defining specimens and reagents."; "On chemical reagent class : For now only model a high level structure to house chemical reagents, If we decide to populate downward with more specific examples of chemical reagents, this can be done on a case by case basis manually, or we can talk with the ChEBI people about their semi-automated text mining tools/approach for assigning roles to chemical entities based on assertions in the literature. Their tools/algorithms could conceivable be used to mine the literature and/or vendor catalogs and assign reagent roles to those chemical entities that appear in some pre-defined context in these resources that would suggest them to be reagents. Refer back to Janna Hastings ICBO 2011 talk for more on this approach. "; "Regarding display of annotations using this property to end-users: intention was to use the 'editor note' for annoations to be showed to end users, and this 'ReO-development editor note' to record 'action items' intended only for ReO developers. However, in practice, many of the annotations I have made with this would be useful to show to end-users. Perhaps as I address each of these notes before an official resease, I should convert any ones that would be useful for end users to 'editor notes', so they will be displayed."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_development_convention"; """On 'experimentally modified cell' (and/or cell modification technique?): to get experimentally modified cell hierarchy to classify correctly, all material processing techniques that achieve a cell modification objective (or a material modification objective and have specified output some cell) need to have an axiom indicating this.""", "another good example is the use of this annotation on 'research material role'"; "ReO modeling convention"; """Describes conventions and rules to follow when IMPLEMENTING classes in ReO. This includes conventions for : (1) Hierarchy Classification Guidelines: design patterns and axiomitization conventions that should be applied to the annotated class in order to achieve consistent and complete modeling and desired inferencing (2) Logical Dependencies: any dependencies/implications that should be noted when implementing or removing a class of the type annotated (including how the class may be used in logical axioms for describing other classes in the ontology). Again, these conventions are useful for achieving consistency in modeling and in order to assure realization of all desired logical entailments by the reasoner."""; rdfs:comment "may overlap with intention of 'explanation of class usage' . . . possibly merge or redefine these?"; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "participates_in"@en; "relationship", "ro_bfo_bridge"; "OBO_REL:0000020"; rdfs:domain . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty; rdfs:label "transformed_into"@en; rdfs:comment "Obsoleted"; "relationship", "ro_bfo_bridge"; "OBO_REL:0000014"; "obsolete_transformed_into"; rdfs:domain . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "definition", "textual definition", "definition"@en; """2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. """@en; "Definition"; "GROUP:OBI:"@en; "PERSON:Daniel Schober"@en; "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en, "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en; "definition"@en; . a owl:AnnotationProperty; rdfs:label "expand expression to"@en; "Chris Mungall"; "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en; """ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" """@en; "expand expression to"@en . a owl:AnnotationProperty, owl:ObjectProperty; rdfs:label "has_specified_input"@en; "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works."; "PERSON: Bjoern Peters", "PERSON: Larry Hunter", "PERSON: Melanie Coutot", "PERSON: Alan Ruttenberg"@en; "has_specified_input"; "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en; "see is_input_of example_of_usage"@en; ; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "editor note"@en; "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en; "GROUP:OBI:"@en; "PERSON:Daniel Schober"@en; "editor note"@en; . a owl:AnnotationProperty; rdfs:label "in branch"@en; "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet."@en; "GROUP:OBI"@en; "OBI_0000277"@en; "in branch"@en . a owl:AnnotationProperty; rdfs:label "has curation status"@en; "OBI_0000281"@en; "PERSON:Alan Ruttenberg"@en, "PERSON:Bill Bug"@en, "PERSON:Melanie Courtot"@en; "has curation status"@en . a owl:AnnotationProperty; rdfs:label "definition source", "definition source"@en; "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w", "GROUP:OBI:"@en; "definition_source"; "PERSON:Daniel Schober"@en; "definition source"@en; "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en; . a owl:AnnotationProperty; rdfs:label "antisymmetric property"@en; "Alan Ruttenberg"@en; "antisymmetric property"@en; "part_of antisymmetric property xsd:true"@en; "use boolean value xsd:true to indicate that the property is an antisymmetric property"@en . a owl:AnnotationProperty; rdfs:label "definition editor", "definition editor"@en, "term editor"@en; "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115."@en; "definition_editor"; "GROUP:OBI:"@en; "Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en, "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en; "PERSON:Daniel Schober"@en; "definition editor"@en, "term editor"@en; . a owl:AnnotationProperty; rdfs:label "first order logic expression"@en; "PERSON:Alan Ruttenberg"@en; "first order logic expression"@en . a owl:AnnotationProperty, owl:ObjectProperty; rdfs:label "has_specified_output"@en; "PERSON: Bjoern Peters", "PERSON: Larry Hunter", "PERSON: Melanie Courtot", "PERSON: Alan Ruttenberg"@en; "has_specified_output"; "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en; ; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "alternative term"@en; "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en; "GROUP:OBI:"@en; "PERSON:Daniel Schober"@en; "alternative term"@en; . a owl:AnnotationProperty; rdfs:label "expand assertion to"@en; "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en; "Chris Mungall"@en; """ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" """@en; "expand assertion to"@en . a owl:AnnotationProperty; rdfs:label "transformation_of"@en; rdfs:comment "When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes."; "ro_bfo_bridge", "relationship"; "OBO_REL:0000013"; rdfs:domain ; _:2dc619 . _:2dc619 a ; rdfs:label "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2."@en; _:2dc629 . _:2dc629 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty; rdfs:label "editor preferred label"@en, "editor preferred term"@en; "GROUP:OBI:"@en; """IAO, OBI (unclear what the need/proepr usage for this term is, given the existence of an alternative term annotation, as well as other synonym-related annotation properties. If a term is the 'editor-preferred term', it should be the 'label' of the class. Where this type of annotation is needed is when one ontology, O1, wishes to re-use a class from another ontology (O2), and the developers of O1 wish to use a different label in their ontology from that used in O2. This could be a meaningful and beneficial use of an annotation property such as this, if it were definedand/or renamed to be used in such a way. At present, ontologies such as OBI seem to use it simply to restate that the 'label' on a class is also the 'editor-preferred term'. """; "PERSON:Daniel Schober"@en; "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en; "editor preferred term"@en; . a owl:AnnotationProperty; rdfs:label "example of usage"@en; "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not"@en; "GROUP:OBI:"@en; "PERSON:Daniel Schober"@en; "example"@en; . a owl:AnnotationProperty; rdfs:label "has_agent"@en; "OBO_REL:0000021"; "ro_bfo_bridge", "relationship"; rdfs:domain ; _:2dc639 . _:2dc639 a ; rdfs:label "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process"@en; _:2dc649 . _:2dc649 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:AnnotationProperty; rdfs:label "out of scope class"; "a flag annotation for classes/modeling that I dont want/need in reo, but want to keep as it may be in scope for related ontologies such as OBI of ERO (or i may want to put it in ReO at some point)."; rdfs:comment "Fill this property with the name of the ontology or ontologies where the class/modeling might fit (e.g. 'OBI', or 'ERO')"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "ReO alternative term"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "is denotator type"; "Alan Ruttenberg"; "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')"; "relates an class defined in an ontology, to the type of it's denotator"; rdfs:comment """describes how a class should be interpreted from an ontological perspective. (ie as a defined class, universal, or named class expression). See 'denotator type' IAO class for more. Value should be one of three individuals : 'defined', 'universal', or 'named class expression'. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Defined classes are non-universals, or classes based on some secondary axis of classification that may or may not result in complete and disjoint partitioning of its parent class."""; "is denotator type"@en . a owl:AnnotationProperty; rdfs:label "has ID policy for"; "Relating an ontology used to record id policy to the ontology namespace whose policy it manages"; "Person:Alan Ruttenberg"; """Ontology: Annotations: 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" 'has ID digit count' : 7, rdfs:label \"RO id policy\" 'has ID policy for': \"RO\"""" . a owl:AnnotationProperty; rdfs:label "has ID range allocated to"@en; "Person:Alan Ruttenberg"; "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms"; """Datatype: idrange:1 Annotations: 'has ID range allocated to': \"Chris Mungall\" EquivalentTo: xsd:integer[> 2151 , <= 2300] """ . a owl:AnnotationProperty; rdfs:label "imported from"@en; "For external terms/classes, the ontology from which the term was imported"@en; "GROUP:OBI:"@en; "PERSON:Alan Ruttenberg"@en, "PERSON:Melanie Courtot"@en; "imported from"@en; . a owl:AnnotationProperty; rdfs:label "has ID digit count"@en; """Ontology: Annotations: 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" 'has ID digit count' : 7, rdfs:label \"RO id policy\" 'has ID policy for': \"RO\""""; "Person:Alan Ruttenberg"; "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty; rdfs:label "reo_noteworthy_annotation"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_modeling_approach"@en; "another very good example of how this property is used differently than the generic 'comment' property is found on the 'cell subculturing' class", "Another example clarifies the scope of the techniques branch : 'techniques in scope here should be those related to reagents (ie material processing techniques used to generate a reagent or techniques/assays in which reagents are used). These classes are referenced as such in logical definitions of reagent classes.'", "A perfect example of the benefit/use of this annotation property is seen on the 'cell line' class, as it is not immediately intuitive how this branch is structured and how it should be used. To facilitate user understanding , we describe in an 'explanation of modeling approach' annotation the rationale behind the cell line hierarchy: \" the primary axis of classification for the cell line hierarchy is based on the distinction between permanent vs primary cell lines, as these represent mutually exclusive categories under which all cell line classes can be asserted. Accordingly, classes representing established, named cell lines (eg HeLa, PC-12, NIH-3T3) are asserted as children of 'permanent cell line' or 'primary cell line'. A range of additional equivalent classes (e.g. clonal cell line, expression cell line, disease-model cell line) have also been created and logically defined, such that asserted classes representing named cell lines can be classified into multiple categories based on the axioms describing their respective attributes. Similarly, instances of cell lines described in databases or catalogs using this model can be similarly classified in along multiple dimensions.", "another example of this annotation is on 'research material role'", "An example of this annotation applied to recording modeling rules or conventions is found on the 'research material role' class : All research materials described in this ontology should be asserted to have some kind of research material role (a reagent role, a specimen role, a scientific instrument or device role, or a research agent role). This is important for the planned processes used to generate them to classify as material processing technique, whcih is defined as having output some research material."; rdfs:comment "This information is intended to aid both end users and developers in understanding at a higher level the approach behind modeling choices in the ontology. Such annotations are most commonly used for more general classes representing core categories in our ontology (e.g. reagent, cell line, technique), to illuminate the modeling approach where it is not immediately obvious from viewing the class structure in the ontology itself."; """Used to explain high level modeling approaches regarding a certain class or hierarchy - in particular, the rationale for decisions regarding: (1) Class definitions (ie explains key definitional criteria and intended scope/usage of the class in the context of the global modeling approach or in relation to other classes) (vs IAO:comment which is to be used to clarify the textual definition without such global context) (2) Expected logical entailments (ie how the modeling approach facilitates desired logical inferencing) (3) Hierarchy design (ie explains axes choosen for asserted vs equivalent class implementation, significance of hierarchical modeling in context of the ontology, why a particular class structure was choosen over alternative approaches)"""; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "ReO-preferred_definition_editor"@en; "records editor who provides a ReO-preferred definition"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "ReO-preferred_definition_source"@en; "records source for a ReO-preferred definition, where this source comes from an external resource"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "equivalent class example"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_requires_feedback_to"@en; """SO/SOM (align with SO:0000440 vector replicon) CLO (discuss design pattern for defining derivation/origin of cell line. CLO approach for htis class is suspect as it states the cell line derives form cells that are part of an embryo that is part of a mouse. Here, we replace with our ReO axiom.)"""; rdfs:comment "Convention for values of this property : Indicate the appropriate ontology(ies) as the value of this property, followed by a brief description of the question or issue in parentheses ( ) follwoing the name of the ontology. In addition, the issue may be described in a 'comment' annotation on the class. "; "FLAG to record classes where we have issues or suggestions to feedback to an external ontology regarding a class imported into the home/current ontology (ie ReO). Most often used to address cases where imported term definitions are felt to be unclear, incomplete, erroneous, or inconsistent."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "preceded_by"@en; rdfs:comment "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."; "ro_bfo_bridge", "relationship"; "OBO_REL:0000017"; rdfs:domain ; _:2dc659 . _:2dc659 a ; rdfs:label "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. "@en; _:2dc669 . _:2dc669 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "reo_possible_alternate_labels"; "used to record developer ideas for other/possible better labels for a given class - but not to be used as official alternate terms. this is a developer annotation."; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "ReO-preferred_definition"@en; "records an alternate, ReO-preferred derfinition for classes imported from external ontologies. This definition may extend that in a source ontology, but should ultimtely be consistent with its original meaning (otherwise a new class should be created)."; rdfs:comment "This definition is included/written to be consistent with the role of the class in the current ontology, and/or to make distincitons important in the context of the current ontology. In some cases, may involve simple converting to appropriate aristotelian format for the current ontology."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_exploratory_axiom"; "A flag to mark exploratory axioms."; "Was previously using the reo_class_role : exploratory class or axiom approach, but noted that when moving annotations on axioms to a new layer, the axioms come along. so needed an annotaiton property to use only for axioms that will not be moved to the reo-dev layer."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_class_role"; rdfs:comment """To be filled by one of the following individuals that are instances of ReO:class purpose {'primary classification axis', 'secondary classification axis', 'example defined class' , 'example particular class', 'shortcut relation'} Example defined and particular classes may ultimately be moved to a separte layer (reo-example.owl?), so as not to obscure the core hierarchical structure and logic of ReO."""; "Annotation that indicates the role of a given class from an ontological perspective, as representing the primary or secondary axis of classification, or its reason for inclusion in the ontology, as an example of the types of defined classes that ReO can be used to create, or an example of a more granular class that ReO can accommodate."; rdfs:subPropertyOf ; rdfs:range . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "agent_in"@en; "relationship", "ro_bfo_bridge"; "OBO_REL:0000022"; rdfs:domain . a owl:AnnotationProperty; rdfs:label "reo_modeling_dependency"; "used to record dependency or need for modeling to be addressed by some external ontology (or other part of ReO), in order to complete modeling of the annotated class/hierarchy"; "June 2012 - waiting for OBI to resolve data item modeling with respect to measured vs planned/specified vs predicted data, to import into ReO for modeling qualities of reagents (primarily planned/specified qualities) such as primer length, and to model how reagents are linked to data they are used to generate", "waiting for CARO to resolve modeling of multicellular organism cell, and gross anatomical part, in order to decide how to procede in ReO"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "precedes"@en; "OBO_REL:0000018"; "relationship", "ro_bfo_bridge"; rdfs:domain . a owl:AnnotationProperty; rdfs:label "reo_developer_action_item"; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "reo_developer_question"; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_developer_insight"; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "reo_behaving_badly"; "FLAG for classes where there is unexpected or undesirable behavior upon reasoning, or known problematic/inconsistent/unprincipled modeling that might be fixed at some point (and a place to record/desribe this behavior)."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "has associated axiom(nl)"@en; "An axiom associated with a term expressed using natural language"@en; "Person:Alan Ruttenberg"@en; "Person:Alan Ruttenberg"@en; "has associated axiom(nl)"@en . a owl:AnnotationProperty; rdfs:label "has associated axiom(fol)"@en; "An axiom expressed in first order logic using CLIF syntax"@en; "Person:Alan Ruttenberg"@en; "Person:Alan Ruttenberg"@en; "has associated axiom(fol)"@en . a owl:AnnotationProperty; rdfs:label "is allocated id range"@en; "Add as annotation triples in the granting ontology"@en, "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\""@en; "PERSON:Alan Ruttenberg"@en; "is allocated id range"@en . a owl:AnnotationProperty; rdfs:label "reo_annotations_to_depracate"; "temp place holder for collecting all reo annotation properties that i will eventually delete (since there is no ObsoleteAnnotation property)"; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty; rdfs:label "elucidation"@en; "Person:Barry Smith"@en; "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en; "elucidation"@en; "person:Alan Ruttenberg"@en . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "derived_into"@en; "OBO_REL:0000016"; "relationship", "ro_bfo_bridge"; rdfs:domain . a owl:AnnotationProperty; rdfs:label "particular class example"; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "has_participant"@en; rdfs:comment "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."; "OBO_REL:0000019"; "ro_bfo_bridge", "relationship"; rdfs:domain ; _:2dc679 . _:2dc679 a ; rdfs:label "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t"@en; _:2dc689 . _:2dc689 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:AnnotationProperty; rdfs:label "has ID prefix"@en; "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created."; "Person:Alan Ruttenberg"; """Ontology: Annotations: 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" 'has ID digit count' : 7, rdfs:label \"RO id policy\" 'has ID policy for': \"RO\"""" . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty; rdfs:label "location_of"@en; "ro_bfo_bridge", "relationship"; "OBO_REL:0000009"; rdfs:domain . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "obo_foundry_definition"; """An annotation used to record a more general, end-user readable definition of a class, phrased in more user-readable structure (ie does not need to be Aristotelian) and more general language (ie avoiding use of ontology-specific terms). Intention is to promote better end-user understanding of a term and facilitate its re-use in other ontologies, by removing ontology-specific connotations and complexity from the definition."""; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "reo_obsolete_annotation"; "an annotation property intended to store annotations that are outdated, where developers with to maintain a record for possible referecne in the future. This property should live in a documentation/developer layer not presented to end-users."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "ReO aristotelian definition"@en; "records an alternate, ReO-preferred derfinition for classes imported from external ontologies, that makes no changes other than altering the genus to confer appropriate aristotelian format for the current ontology, and possible altering use of other terms in the differential to be consistent with terminology used in the current ontology."; rdfs:subPropertyOf . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "reo_is_placeholder_for"@en; "FLAG used to indicate that a class is temporary or out of scope for the core ontology being developed, and will be modified or replaced by a class imported from an appropriate ontology."; rdfs:subPropertyOf . a owl:AnnotationProperty; rdfs:label "ReO annotations"@en; "ReO development and documentation annotation"; """grouping class subsuming all annotation properties to be used during development for developer documentation, or to record documentation inforamtion to be stored in separate layer for public use. Records ReO design and implementation issues, decisions, and action items, and make it easy for developers to find and address open issues by displaying all usages of a given developer annotation property. """ . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:isDefinedBy . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty . a owl:AnnotationProperty; rdfs:label "located_in"@en; rdfs:comment "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"; "relationship", "ro_bfo_bridge"; "OBO_REL:0000008"; rdfs:domain ; _:2dc699 . _:2dc699 a ; rdfs:label "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)"@en; _:2dc6a9 . _:2dc6a9 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:AnnotationProperty; rdfs:label "reo_comment"; rdfs:subPropertyOf . a owl:ObjectProperty, owl:FunctionalProperty; rdfs:label "inheres in"@en; rdfs:comment "This property is functional because it is defined as a relation that holds between instances, not classes. At an instance level, a dependent continuant inheres_in only one individual. Thus, at an instance level, if some quality or role or function is asserted to inhere in more than one thing, then it should be the case that these things are equivalent", "This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on"; "RO-proposed"; "A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation."; "This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant."; "inheres_in"@en; ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "is bearer of"@en; "bearer of"@en, "bearer_of"@en; owl:inverseOf ; ; rdfs:range ; rdfs:domain ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "is realized by"@en; "executed_during (from old OBI:is_realized_by property)"@en, "realized by"@en; ; rdfs:subPropertyOf owl:topObjectProperty; owl:propertyChainAxiom _:2dc6b9 . _:2dc6b9 rdf:first ; rdf:rest _:2dc6c9 . _:2dc6c9 rdf:first ; rdf:rest rdf:nil . _:2dc6d9 a owl:Axiom; """not sure this is correct I think this is used so that reagent roles that are realized through biological processes that are part_of techniques can still be said to be realized by some technique (as required by the definition of reagent role? . . .but the reagent role def says that they can be realized by (part_of some technique . . . so maybe not) (e.g. the reagent role; inhering in expression constructs)"""; owl:annotatedSource ; owl:annotatedProperty owl:propertyChainAxiom; owl:annotatedTarget _:2dc6e9 . _:2dc6e9 rdf:first ; rdf:rest _:2dc6f9 . _:2dc6f9 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "realizes"@en; "RO-proposed"; """OBI uses the realizes relation for two distinct and different purposes, one of which is wrong. In ReO, we create a new relation (achieves specification) to replace the incorrect usage. 1. 'realizes' is used correctly to relate a process to a realizable entity such as a role or function 2. OBI uses realizes incorrectly to describe the relation between a planned process and a quality>information carrier where the process executes the specified actions described by the directive information content - see OBI:study intervention for example:iiis part of' some ('study design execution' and (realizes some (concretizes some 'intervention design'))) this is a different type of 'realization' than in case #1. the realization in case #1 applied here would describe the process of physically implementing the 'pattern' represented by information bearer dependent continuant by writing it down, or typing it in a computer. Importantly, the key difference here is that this process is independent of the directive information content of this information bearer (ie it refers to the physical recording for some directive specification, not the execution of the processes outlined in this specification.) - presumably there is an implied 'information carrier' in this axiom that concretizes the intervention design. ( 'is part of' some ('study design execution' and (realizes some ('information carrier' and concretizes some intervention design))) - however, an information carrier is a quality in OBI, and the realizes relation holds between a realizable entity and a process. this is a problem . . . if it is the information carrier that is being realized, this type of information carrier needs to be a realizable entity, or a different type of realization is occurring (ie different than the idea of a pattern which would be describe by #1) that requires a new relation Proposed solution: - relate a process to a directive info entity>plan specification such as study design>intervention design using a achieves_specification property (such as that implemented in ReO as a parent of the current OBI property 'achieves planned objective' (aka achieves objective specification' in ReO)"""; rdfs:comment "The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. NOTE: there appears to be some consistency in usage as to whether processes or continuants realize"; "Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation"; owl:inverseOf ; ; rdfs:range ; rdfs:domain ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "concretization of"@en; "BFO2: this term has the label 'concretization of', but it should be called 'is concretized as', since this is a relation between a generically dep continuant and a specificially dep continuant which it is concretized as."; "Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter."; "concretization_of"@en; "is concretized as"; ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "concretizes"@en; "Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter."; "is concretization of"; ; rdfs:range ; rdfs:domain ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "occurs in"@en; "unfolds in"@en; ; rdfs:range ; rdfs:domain ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "is function of"@en; "A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function"; "RO-proposed"; "function of"@en, "function_of"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "is quality of"@en; "RO-proposed"; "A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality"; "quality of"@en, "quality_of"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "is role of"@en; "RO-proposed"; "A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role"; "role of"@en, "role_of"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "has function"@en; "has_function"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "has quality"@en; "has_quality"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "has role"@en; "has_role"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "model_of"; "Disease or condition for which the organism presents some or all defining characteristics."; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "Transgenic mice are often models for a specific disease."; rdfs:comment "here we need to have a more clear definition in dependence of the model", """Shortcut relation expanding to one of : (1) 'has role' some ('reagent role' and ('is realized by' some ((assay or investigation) and (has_specified_output some ('data item' and ('is about' some disease)))))) (2) is_specified_input_of some ((assay or investigation) and (achieves_objective_specification some ('objective specification' and ('is about' some disease)))) (3) is_specified_input_of some ((assay or investigation) and (reallizes some ('objective specification' and ('is about' some disease))))"""; "model of"; "a relation between a biological system such as a cell line or model organism and some disease or condition of which it exhibits features, allowing it to serve as a proxy for study of the disease or condition."; """ERO - fix property domain definition so that cell lines can be models. Also, consider renaming this property to distinguish from a relation between a model that is an information artifact and a biological system that it represents. (physical model of? functional model of?) Also, property that should ultimately live in RO(dev) or ERO or OBI, and be imported into ReO and CLO and other ontologies as needed). CLO currently uses an 'is_model_for' relation from http://www.ebi.ac.uk/cellline, which has the same meaning as ReO:model_of """; rdfs:range ; ; ; rdfs:subPropertyOf owl:topObjectProperty; rdfs:domain _:2dc709 . _:2dc709 a owl:Class; owl:unionOf _:2dc719 . _:2dc719 rdf:first ; rdf:rest _:2dc729 . _:2dc729 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "has_documentation"; "An antibody has documentation describing attributes of the antibody."; "Document that contains relevant resource information."; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "has documentation"; ; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "related_technique"; "Flow cytometry is a related technique for a flow cytometer instrument."; "Method in which the resource can be used."; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "related technique"; "has_related_technique"; ; ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty, owl:FunctionalProperty; rdfs:label "has measurement unit label"@en; rdfs:domain ; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "is about"@en; "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en; "This document is about information artifacts and their representations"@en; "is_about is a (currently) primitive relation that relates an information artifact to an entity."@en; "person:Alan Ruttenberg"@en; rdfs:domain ; ; ; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "mentions"@en; "7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)"@en, "7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation \"mentions\" in it's (logical) definition"@en; "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E"@en; "PERSON: Jonathan Rees"@en, "Person: Alan Ruttenberg"@en; ; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "denotes"@en; "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named."@en; "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan"@en; "denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically"@en; "person:Alan Ruttenberg"@en; rdfs:domain ; rdfs:subPropertyOf ; ; rdfs:range ; rdfs:comment _:2dc739, _:2dc749 . a owl:ObjectProperty; rdfs:label "is quality measurement of"@en; "the length of a PCR product as measured by running against a standard DNA ladder is a measurement datum that 'is quality measurement of' the 'lenght' quality inehreing in the PCR product."; "a relation between a measurement datum and a quality of a material entity that this datum measures."; "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later"@en; "Alan Ruttenberg"@en; rdfs:domain ; rdfs:subPropertyOf ; ; rdfs:range . a owl:ObjectProperty; rdfs:label "is duration of"@en; "Person:Alan Ruttenberg"@en; "relates a process to a time-measurement-datum that represents the duration of the process"@en; ; rdfs:subPropertyOf ; ; rdfs:range . a owl:ObjectProperty; rdfs:label "is quality measured as"@en; "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en; "Person:Alan Ruttenberg"@en; "inverse of the relation of is quality measurement of"@en; rdfs:range ; ; owl:inverseOf ; rdfs:subPropertyOf ; ; rdfs:domain . a owl:ObjectProperty; rdfs:label "is quality specification of"@en; "IAO/OBI - provide the example here for them, if it fits"; "Person:Alan Ruttenberg"@en, "Person:Bjoern Peters"@en; "a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality."@en; "the specified length of a PCR product indicated in a protocol to amplify a span of DNA calculated to be 2 kilobases, according to sequence analysis and primer design, is an objective specification that 'is quality specification of' the 'length' quality inhering in the desired PCR product."; rdfs:domain ; ; rdfs:subPropertyOf ; ; rdfs:range . a owl:ObjectProperty, owl:FunctionalProperty; rdfs:label "has time stamp"@en; "Alan Ruttenberg"@en; "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken"@en; ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "has measurement datum"@en; "Alan Ruttenberg"@en; "relates a time stamped measurement datum to the measurement datum that was measured"@en; ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "obsolete_is_concretization_of"@en; "Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter."; "PERSON: Alan Ruttenburg", "PERSON: Barry Smith"; "is_concretization_of"; "replaced by: http://purl.obolibrary.org/obo/BFO_0000059"; "obsolete_is_concretization_of"; "replaced by BFO2:0000059 concretizes"; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is_specified_input_of"@en; "PERSON:Bjoern Peters", "Alan Ruttenberg"@en; "is_specified_input_of"; "A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of."@en; "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay"@en; owl:inverseOf ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "obsolete_is_concretized_as"@en; "Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter."; "PERSON: Alan Ruttenberg", "PERSON: Barry Smith"; "is_concretized_as"; "replaced by: http://purl.obolibrary.org/obo/BFO_0000058"; "obsolete_is_concretized_as"; "replaced by BFO2:0000058 is concretization of (note here that this property should read is concretized as . . . . feedback to BFO2)"; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "obsolete_is_realized_by"@en; "GROUP:OBI:", "PERSON: Chris Mungall"; "Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]"; "executed_during", "has_realization", "is_realized_as"; "is_realized_by"; "replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by'"; "obsolete_is_realized_by"; "replaced by BFO2 'is realized by' BFO_0000054"; ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is_manufactured_by"@en; "OBI - ask aobut cases that would necessitate a parent such as ReO:created_by, such as 'creation' of a blood sample through collection from an organism. This sample is intentionally created and thus a processed material, but is it 'manufactured'?"; rdfs:comment "Note that this is a more precise subclass of has_producer/creator relation, as manufacturing is a more precise type of material proceesssing than production/creation (ie manufacturing implies an output created de novo to bear some function, while a creation process can include simple contextual relocations such as creating a blood sample from an organism."; "Alan Ruttenberg"@en, "Liju Fan"@en; "c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the \"Manufacturer Role\", and those people/and or machines were members or of directed by the organization to do this."@en; "has_make"@en, "has_manufacturer"@en; "http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)"@en; "is_manufactured_by"@en; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "is_specified_output_of"@en; "PERSON:Bjoern Peters", "Alan Ruttenberg"@en; "is_specified_output_of"; "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en; owl:inverseOf ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "achieves_planned_objective"; "A cell sorting process achieves the objective specification 'material separation objective'"; "BP, AR, PPPB branch"; "PPPB branch derived"; "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process."; "achieves_planned_objective", "achieves_objective_specification"; "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch"; rdfs:range ; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "has grain"; "PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349"; "has grain"; "the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car."; "has granular part"; "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form"@en; "a non-transitive, irreflexive parthood relation between an entity and some indeterminate grainular part, such that removal of such a part does not necessarily damage or diminish the whole."; "OBI (they have imported BFO's has granular part, but still h av eand use this has grain property)"; "PERSON: Alan Ruttenberg"@en; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is grain of"@en; "is grain of"; rdfs:comment "replace with BFO2:'is granular part of'?"; "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349"@en; "PERSON: Alan Ruttenberg"@en; owl:inverseOf ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "objective_achieved_by"; "This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process."; "definition needs clean up to indicate directionality"; "objective_achieved_by"; "objective_specification_achieved_by"; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "transforms"@en; rdfs:comment "a relation that holds between a process and a participant that is physically transformed/modified in the process. The participant thereby emerges as a modified version of the input entity (ie identity is retained across the process - so the participant is both input and output)"; rdfs:domain ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "used_to_study"@en; rdfs:comment """Shortcut relation expanding to one of : (1) 'has role' some ('reagent role' and ('is realized by' some ((assay or investigation) and (has_specified_output some ('data item' and ('is about' some biological_process)))))) (2) is_specified_input_of some ((assay or investigation) and (achieves_objective_specification some ('objective specification' and ('is about' some biological_process)))) (3) is_specified_input_of some ((assay or investigation) and (reallizes some ('objective specification' and ('is about' some biological_process))))""", "a relation holding between a continuant (e.g. a reagent) and a biological process it is used to investigate"; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty; rdfs:domain _:2dc759 . _:2dc759 a owl:Class; owl:unionOf _:2dc769 . _:2dc769 rdf:first ; rdf:rest _:2dc779 . _:2dc779 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "obsolete_model_of"; "property that should ultimately live in RO(dev) or ERO or OBI, and be imported into ReO and CLO and other ontologies as needed). CLO currently uses an 'is_model_for' relation from http://www.ebi.ac.uk/cellline, which has the same meaning as ReO:model_of "; "realtion holding between an organism or reagent and a disease which its inherent properties make it suitable to study."; "ERO model_of? (or EFO is_model_for?)"; rdfs:comment "shortcut relation expanding to something resembling : is_specified_input_of some ( (technique or research project) and (reallizes some (OBI:objective specification and is_about some disease)))"; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "capable_of"@en; "Example: osteoclast capable_of bone resorption."; "BFO_0000053 some (BFO_0000054 only ?Y)"; "A relation between a material entity (such as a cell) and a process in which some realizable entity inhereing in the material entity is realized."; "RO:capable_of"; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty; owl:propertyChainAxiom _:2dc789 . _:2dc789 rdf:first ; rdf:rest _:2dc799 . _:2dc799 rdf:first ; rdf:rest rdf:nil . _:2dc7a9 a owl:Axiom; "Note that this property chain is necessary for 'RNA interference plasmid' to infer as a type of 'expression construct'"; owl:annotatedSource ; owl:annotatedProperty owl:propertyChainAxiom; owl:annotatedTarget _:2dc7b9 . _:2dc7b9 rdf:first ; rdf:rest _:2dc7c9 . _:2dc7c9 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "used_to_generate"@en; rdfs:comment "shortcut relation that expands to ' is _specified_input_of some (technique and (has_specified_output some (reagent or organism)) '"; "a relation that holds between a reagent and a organism, construct, cell culture, or antibody that the reagent is used to generate"; rdfs:domain ; rdfs:subPropertyOf owl:topObjectProperty; rdfs:range _:2dc7d9 . _:2dc7d9 a owl:Class; owl:unionOf _:2dc7e9 . _:2dc7e9 rdf:first ; rdf:rest _:2dc7f9 . _:2dc7f9 rdf:first ; rdf:rest _:2dc809 . _:2dc809 rdf:first ; rdf:rest _:2dc819 . _:2dc819 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "contains_process"@en; "a cell contains_process gene expression, becasue the cell does not particpate in gene expression (proteins and DNA and RNA and nucleotides are the actual participants), but contains each of the participants in the process"; "A relation between a continuant and a process that occurs within the continuant, but in which the continuant is not a participant. The continuant stands in a 'contains' relation to each of the participants in the process."; rdfs:comment "could be a shortcut for 'contains some (participates_in)'"; owl:inverseOf ; ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "obsolete_descends_from"@en; rdfs:comment "used in axiom defining clonal cell culture and clonal cell line, becasue derives_from no work with this axiom (due to transitivity?)"; "replaced with originates_from"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "originates_from"@en; rdfs:comment """A non-transitive child of develops_from, that can be used to express cardinality constraints on a derivation or transformation relation. (similar to the use of has_component when needing to express cardinality constraints on the has_part relation) This property is often used in a complex/nested class expression asserting that the material entity A originates from material entity B, which is an input into some process or event that is responsible for the change in identity marking the origination of entity A. For example, the class expression: 'clonal cell line' is a 'cell line' and (originates_from exactly 1 cell and (is_specified_input_of some 'cell culture expansion')). Here, entity A (a clonal cell line) originates from entity B (a cell) through the process of this cell being input into a cell culture expansion process. This execution of this process marks the point in time when the clional cell line comes into existance."""; """A non-transitive relation between two material entities, indicating that entity 'A' (and all its parts) can be traced back to one and only one seperate entity 'B', such that at a specific point in time, entity A came into existence through a single derivation or transformation event from entity B. In such a case, entity A can be said to originate_from entity B. Because 'originates_from' is non-transitive, entity A can be said to develop_from but not originate_from any material entity that gave rise to entity B through some previous derivation or transformation process. For example, a clonal cell line can originate_from only one single cell, whose division into two cells represents the derivation event marking the origin of the clonal cell line. However, becasue the derives_from relation is transitive, this cell line can be said to derive_from not only this single cell, but previous cells from which this cell was derived through earlier cell divisions. Thus, a given entity A can originate_from only one other material entity, ie the entity from which the original instance of A came into existance through some derivation or transformation event. """; "PERSON: Matthew Brush"; "consider clarifying the meaning of 'coming into existance'. It is clear that a new entity comes into existance from a derivation event, but does an entity come into existance from a transformation? Transformations change the type of an entity, but not its identity . . . so it is unclear if this change in type represence a 'coming into existance'. If it does not, then 'originates_from' should be made a non-transitive child of 'derives_from', and used only in cases of derivation where a non-transitive property is needed for use with a cardinality restriction."; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is component part of"@en; "RO-proposed"; rdfs:comment "Inverse of has_component, for use in recording part_of with a cardinality constraint."; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "gained_through"; "a relation holding between a realizable entity and some process through which the role begins to inhere in an independent continuant bearer"; rdfs:domain ; rdfs:range . a owl:ObjectProperty; rdfs:label "specifies"; rdfs:comment """relation between some action specification and entities it specifies. These entities can include material entities whose participation or intentional application/use is specified, or processes whose occurrence or intentional execution is specified."""; rdfs:domain ; rdfs:subPropertyOf ; rdfs:range . a owl:ObjectProperty; rdfs:label "specifies_use_of"; rdfs:comment """relation between some action specification and some processed material bearing some function or role that is realized in the execution of the specified action Ex: the action specifications outlined in an immunization protocol would specify the participation of some T cell or B cell, but specifies the use of some syringe and some immunogenic material."""; rdfs:domain ; rdfs:subPropertyOf ; rdfs:range . a owl:ObjectProperty; rdfs:label "specifies_execution_of"; rdfs:comment """relation between some action specification an a planned process whose intentional execution it specifies. For ex, the action specification part of an immunization protocol could specify the occurrence of some adaptive immune response in the host organism, an specify the execution of some injection of immunogenic material into the host organism, and specify the result of some GO:immunoglobulin biosynthetic process. This class is analogous to the specifies_use_of property for material entity outputs of specified processes.""", "is this property (and its children) a shortcut relation, expanding to specifies_occurrence_of some (has_participant some . . .)"; "specifies_planned_process"; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "confers"; "a relation holding between a process and a realizable entity that begins to inhere in some independent continuant as a result of this process"; owl:inverseOf ; rdfs:range ; rdfs:domain . a owl:ObjectProperty; rdfs:label "confers_role"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is_subject_of"; """a relation holding between an entity and an information artifact that is about that entity (ie specifies, describes, denotes, mentions that entity). Used as inverse property of 'is about'."""; rdfs:range ; owl:inverseOf ; ; rdfs:domain . a owl:ObjectProperty; rdfs:label "is_specified_by"; rdfs:comment "a relation holding between an entity and a directive information entity that prescribes a use, application, or occurrence of the entity)"; rdfs:range ; owl:inverseOf ; rdfs:subPropertyOf ; rdfs:domain . a owl:ObjectProperty; rdfs:label "is_denoted_by"; rdfs:comment "a relation holding between an entity and an information artifact that references this entity (but does not prescribe a use, application, or occurrence of the entity)"; rdfs:range ; owl:inverseOf ; rdfs:subPropertyOf ; rdfs:domain . a owl:ObjectProperty; rdfs:label "execution_specified_by"; "a relation holding between a planned process and a directive information entity that specifies the performance of this process by some agent"; rdfs:range ; rdfs:domain ; owl:inverseOf ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "use_specified_by"; "a relation holding between an independent continuant and a directive information entity that specifies the application of this independent continuant in some process "; owl:inverseOf ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "achieves_specification"; """OBI (OBI has a relation 'achieves planned objective', but ReO needs analogous relations linking planned processes to other directive information entities (plan and action specifications) that they achieve (OBI prefers to use the realizes relation to link processes to plan specifications they achieve (realizes some (concretizes some protocol)). I dont agree here, and created the 'achieves_plan_specification' property for this need, under this more generic 'achieves specification' property. In addition, we have similarly expanded analogous modeling around the inverse property 'objective achieved by'. So this property could be useful in addressing the perceived problem regarding the use of the realizes relation between a planned process and a information carrier that concretizes a directive information entity. (see note on realizes relation for more)""", "OBI? if they wish to implement thisclass/ heirarchy"; rdfs:range ; rdfs:domain . a owl:ObjectProperty; rdfs:label "achieves_action_specification"; rdfs:range ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "achieves_plan_specification"; rdfs:comment "According to OBI, this could be a shortcut relation for 'realizes some (concretizes some 'plan specification'). But as noted in feedback annotaitn, I have concerns about the use of the 'realizes' relation in this way."; """OBI prefers to use the realizes relation to link processes to plan specifications they achieve (realizes some (concretizes some protocol)). I dont agree here, and created the 'achieves_plan_specification' property for this need, under this more generic 'achieves specification' property. So this property could be useful in addressing the perceived problem regarding the use of the realizes relation between a planned process and a information carrier that concretizes a directive information entity. (see note on realizes relation for more)"""; rdfs:range ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "specification_achieved_by"; rdfs:domain ; rdfs:range . a owl:ObjectProperty; rdfs:label "obsolete_objective_achieved_by"; "objective_specification_achieved_by", "obsolete_objective_achieved_by"; "replaced by OBI:objective_achieved_by"; "OBI:'objective_achieved_by"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "plan_specification_achieved_by"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "action_specification_achieved_by"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is quality specified as"; "OBI (discuss distinction I am making (with unit labels and with value specification vs measurement data ICEs and with related object properties as well) between measured and specified data)"; owl:inverseOf ; rdfs:range ; ; rdfs:subPropertyOf ; rdfs:domain . a owl:ObjectProperty; rdfs:label "has_immunogen" . a owl:ObjectProperty; rdfs:label "recognizes"; "a type of targeting relation reserved to describe the relation between an adaptive immune receptor complex and its antigenic target, as antibodies are generated with the function of targeting a specific antigen. For example, antibody x 'recognizes' antigen y if x interacts with an epitope part of y (above some threshhold affinity), and thereby realizes the binding function of the antibody."; """'recognizes' may be treated as a shortcut relation for: 'is bearer of' some ('antigen binding function' and ('is realized by' some ('epitope binding an adaptive immune receptor' and (realizes some 'disposition to be bound by an adaptive immune receptor' and ('inheres in' some (epitope and (part_of some antigen))))))) OR 'is agent in' some ('epitope binding an adaptive immune receptor' and ('has participant' some (antigen and ('has role' some 'molecular target role')))) . . . assuming the 'agent in' relation is resolved to have compatible meaning here""", """Note that we make the 'recognizes' relation transitive across the part_of relation (as indicated in the property chain below), such that if an antibody recognizes some epitope then it also recognizes the antigen of which it is a part, and a larger material entity of which the antigen may be a part (e.g. in cases where the experimental target is some cell or tissue), the antibody can also be said to 'recognize' this larger material entity. Similarly, if an antigenic material has_part some antigen that is recognized by an antibody, then that antibody can be said to recognize the antigenic material. Note also that the recognizes relation could be replaced by the pattern: antibody and 'is agent in' some 'chemical interaction'"""; rdfs:domain ; rdfs:subPropertyOf ; owl:propertyChainAxiom _:2dc829 . _:2dc829 rdf:first ; rdf:rest _:2dc839 . _:2dc839 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "towards"; "http://purl.org/obo/owl/OBO_REL#towards? Not yet in BFO2 or RO, but may be under discussion here according to some threads in OBI tracker"; "a relation between a relational dependent continuant and an independent continuant, that distinguishes the main bearers of the relational dependent continuant from additional dependents."; rdfs:domain . a owl:ObjectProperty; rdfs:label "congener_of"; """a synthetic peptide is a congener_of a protein (they represent the same type of entitiy, but the former is synthetically manufactured and the latter is prodiced via ribosomal synthesis). used in ReO to indicate that calsses indicated to be 'biological' (e.g. biomacromolecule) need not actually derive from some organism, but must represent a natural type that is endogneously produced by an organism"""; "a relation holding between entities that are of the same type (ie same genus), but may differ in origin"; "same_type_as"; . a owl:ObjectProperty; rdfs:label "has unit label"; rdfs:domain ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "specifies_occurrence_of"; rdfs:comment "relation between some action specification an a processual entitiy whose occurrence it specifies."; rdfs:domain ; rdfs:subPropertyOf ; rdfs:range . a owl:ObjectProperty; rdfs:label "specifies_participation_of"; rdfs:comment """relation between some action specification and a material entity whose participation is specified. Ex: the action specifications outlined in an immunization protocol would specify the participation of some T cell or B cell, but specifies the use of some syringe and some immunogenic material."""; rdfs:domain ; rdfs:subPropertyOf ; rdfs:range . a owl:ObjectProperty; rdfs:label "occurrence_specified_by"; "a relation holding between a process and a directive information entity that specifies the occurrence of this process"; rdfs:range ; rdfs:subPropertyOf ; owl:inverseOf ; rdfs:domain . a owl:ObjectProperty; rdfs:label "participation_specified_by"; "a relation holding between an independent continuant and a directive information entity that specifies the participation of this independent continuant in some process"; rdfs:range ; rdfs:subPropertyOf ; owl:inverseOf ; rdfs:domain . a owl:ObjectProperty; rdfs:label "specifies_creation_of"; rdfs:comment """relation between some action specification and some material entity that is produced/output as a result fo the specified action Ex: the action specifications outlined in an antibody production protocol would specify the participation of some T cell or B cell,specifies the use of some syringe and some immunogenic material, and specifiy the ouput of some antibody reagent. NOTE that the action specified need not be a material processing technique, as in some cases such as a reagent creation objective, reagents can be 'created' through purely cognitive/intention actions whereby some agent decides to apply some material as a reagent in a technique."""; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "specifies_result_of"; "specifies_resulting_process"; rdfs:comment """relation between some action specification an a planned process whose occurrence marks a desired end result of the specification. For ex, the action specification part of an immunization protocol could specify the occurrence of some adaptive immune response in the host organism, an specify the execution of some injection of immunogenic material into the host organism, and specify the result of some GO:immunoglobulin biosynthetic process This class is analogous to the specifies_creation_of property for material entity outputs of specified processes."""; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "exploits"; rdfs:comment """could be a shortcut relation, expanding to: inheres_in some (bearer_of some ...)""", """relation between a dependent continuant and a more fundamental dependent continuant (dispositions being most fundamental, followed by functions, followed by roles), where the more fundamental dependent continuant must inheres in some independent continuant in order for it to bear the more complex dependent continuant. Ex: the 'molecular target role' exploits a more fundamental 'molecular binding function', as a bearer of the role must also bear the function. Ex: a 'drug role' played by cycloheximde in some experimental context exploits a more fundamental 'protein synthesis inhibitor function' with which this molecule is synthesized in some bacteria, which in turn exploits a more fundamental ‘molecular binding disposition', which in turn exploits some 'charged' quality of the molecule. Ex: a reagent role exploits a more fundamental disposition to participate in a chemical reaction/interaction."""; . a owl:ObjectProperty; rdfs:label "is_recognized_by"; "property should live in external ontology - RO, or some ontology of molecular events/entities"; owl:inverseOf ; owl:propertyChainAxiom _:2dc849 . _:2dc849 rdf:first ; rdf:rest _:2dc859 . _:2dc859 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "results_in"; "results_in process is in OBI, but no invers (process_results_in) is currently implemented." . a owl:ObjectProperty; rdfs:label "created_by"; "a relation between some agent and a processed material that is produced by the agent through some planned process."; rdfs:comment "can include manufacturing of new entities with a specified function, or simply a contextual relocation of some portion of material, such as a blood sample being created by a flobotamist. So here, 'creation' does not require 'de novo' production."; rdfs:domain ; rdfs:range . a owl:ObjectProperty; rdfs:label "obsolete_manufactured_by"; "OBI or ERO class?"; "has_manufacturer"; "replaced by OBI:is_manufacture_by"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is_realized_during"; rdfs:comment """temporaty/test property - if is_realized_by is not interpreted as transitive across the part of relation, if could be useful to have this property which is. For ex, to say that an experimental antibody target is a research material, because it has part that a role that is realized by some biological process that is part of a technique. so if we say that research material is any material that participates_in some technique or has_role that is realized_during some technique, then experimental antibody target will qualify."""; owl:propertyChainAxiom _:2dc869 . _:2dc869 rdf:first ; rdf:rest _:2dc879 . _:2dc879 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "bears_concretization_of"; "has this been created elsewhere? vet with IAO/OBI?"; rdfs:comment "a shorcut relation for : bearer_of some (concretizes some generically dependent continuant)"; "a relation between a material information bearer or material genetic sequence bearer and generically dependent continuant that carries information or sequence content that the bearer encodes"; ; rdfs:range ; rdfs:domain ; owl:propertyChainAxiom _:2dc889 . _:2dc889 rdf:first ; rdf:rest _:2dc899 . _:2dc899 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "obsolete_encodes_genetic_sequence_from"; """too out there - not particularlty useful - but see 'encodes_genomic_sequence_from_organism (or whatever we decide to name this relation) - which does have some practical utility in allowing us to relate a recombinant protein to the organism in whose genome its sequence is specified. For now, just use bears_concretization_of - which can also relate a material bearer of some GDC to the GDC it bears"""; rdfs:comment "Note here that the range of this property is any known sequence content, including a naturally occurring genetic locus that can be traced to the genotype of an organism (ie a gene or allele, some intergenic region, etc), or an artifactually generated sequences with no corresponding natural genetic locus"; "a relation between a material genetic sequence bearer and a genertic sequence region whose sequence information the bearer encodes"; , ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "exists_during"; "from old RO-proposed "; "c exists_during p iff exists(t) & c exists-at t & start_of(p) <= t & t <= end_of(p)" . a owl:ObjectProperty; rdfs:label "has_disposition"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "arises_from"; "A relation between two continuants, C and D. C develops_from D if C derived_from D or C transformation_of D. On the class level: C develops from D if and only if, for any x and any time t, the following holds: if x instantiates C at time t, then 1. either for some time t1, x instantiates D at t1 and t1 precedes t, and there is no time interval t2 such that x instantiates C at t2 and x instantiates D at t2 ; 2. or for some time t1 , there is some y such that y instantiates D at t1 and x derived_from y. On the instance level: x develops_from y is indistinguishable from x derives_from y"; "RO-proposed.owl"; "RO(dev) property?" . a owl:ObjectProperty; rdfs:label "is quality described by"; rdfs:range ; ; owl:inverseOf ; rdfs:domain . a owl:ObjectProperty; rdfs:label "has specified unit label"; "OBI (discuss distinction I am making (with unit labels and with value specification vs measurement data ICEs and with related object properties as well) between measured and specified data)"; rdfs:domain ; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "is quality information about"; "a relation between an information content entity (a measurement datum or an objective specification) and a quality of a material entity that this information content entity either measures or specifies."; rdfs:domain ; rdfs:subPropertyOf ; rdfs:range . a owl:ObjectProperty; rdfs:label "encoded_in_material_bearer"; """a shorcut relation linking an information content entity or genetic sequence region to a material information bearer or informatioon macromolecule, respectively. is shortcut for: 'is concretized as' some ('inheres in' some (material information bearer' or 'information macromolecule')"""; owl:inverseOf ; , ; rdfs:domain . a owl:ObjectProperty; rdfs:label "has aggregate part"; "a non-transitive, irreflexive has_part relation between a collection or object aggregate and an object that is an individual, separable part of the collection"; "has member part"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "aggregate part of"; "member part of"; "RNAO:'member of', or possibly BFO:'is granular part of' or BFO:'is aggregate of'"; "relationship between an object and a collection of which it is a separable part"; owl:inverseOf ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "encodes_genomic_sequence_from_organism"; rdfs:comment """Naturally produced proteins can be related to an organism directly by using the derived_from relation. This is not the case for synthetic or recombinant proteins, because there is no inheritance of physical material from the organism (which is required for a derivation). Rather, there is inheritance of the sequence information content from the genome of the organism. This shortcut relation captures this notion, allowing us to relate a recombinant or synthetic protein to the organism in whose genome its sequence is specified. Note that this property can also be used to relate a natural protein to an organism (where derives_from would also be acceptible)"""; """a shortcut relation between an information macromolecule and the organism in whose genome its sequence is specified. Expands to: bears_concretization_of some ('genetic sequence region' and ('proper part of' some (genome and (encoded_in_material_bearer some organism))))"""; rdfs:range ; , . a owl:ObjectProperty; rdfs:label "has_sequence_alteration"; rdfs:comment """shortcut relation, expands to: has_part some ('nucleic acid' and (bears_concretization_of some sequence_alteration"""; "ERO - see if ReO should house such shortcut relations and ERO import them back, or if ERO should house them and ReO import them and then provide expansions/translations into full logical version"; "realtion between a mutant nucleic acid or protein, or a cell or organism that carries such a mutant macromolecule, and a sequence variation that deviates from some canonical or reference sequence."; ; rdfs:range . a owl:ObjectProperty; rdfs:label "targets"; """In an interaction between an antibody and an antigen, the antibody targets the antigen because this reflect a function which the antibody was created to perform. In an interaction between a DNA probe and a chromosome, the probe targets the chromosome because some intentional agent is using the probe for the specified purpose of detecting the chromosome (ie it has a intentionally defined role as a moelcular label)"""; rdfs:comment """this relation reflects a potential to target and bind some entity, not that such an interaction has actually taken place (as in OBI:bound_to). As a shortcut relation, it could expand to: has_function some ('molecular binding function' and (is_realized_by some ('chemical interaction' and (has_participant some (has_role some 'molecular target role'))))) OR 'is agent in' some ('chemical interaction' and ('has participant' some ('molecular entity' and ('has role' some 'molecular target role')))) (assuming the 'agent in' relation is resolved to have compatible meaning here)""", "In a given molecular interaction, the participant that 'targets' the other is considered causative in initiating the interaction. From a strictly physical perspective, however, any molecular interaction is intentionally and casuatively symmetric (ie x and y both contribute equally to the interaction). It is only when a function or role of the participants is considered that one can be said to act as an agent and 'target' the other."; "a relation between molecular entities, whereby molecular entity x 'targets' molecular entity y if x interacts with y (above some threshhold affinity), and x bears some function or role realized in this interaction that is is created or applied to facilitate. Thus, x has evolved to, been engineered to, or is applied and perceived by some agent to play an 'active' role in facilitating the interaction."; rdfs:domain _:2dc8a9 . _:2dc8a9 a owl:Class; owl:unionOf _:2dc8b9 . _:2dc8b9 rdf:first ; rdf:rest _:2dc8c9 . _:2dc8c9 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "genetically_derives_from"; "expressed from"; rdfs:comment """Note that this is a relation between material entities, not sequence GDCs. We use this relation to link a protein with either a DNA molecule or an RNA molecule from which it is physically transcribed/translated, or an mRNA to a DNA molecule froom which it is transcribed. As this relation applies at the physical level, it does not link a synthetic oligopeptide to a DNA molecule (in this case however, it could be accurate to say that the synthetic peptide 'sequence_derives_from' some RNA or DNA sequence, where the peptide sequence would be transcribable/translatable from the DNA sequence). Note also that this relation is transitive, so it links protein to both RNA and DNA.""", """shortcut relation for: For the link between protein and RNA: is_output_of (translation and (realizes some ('information template role' and ('inheres in' some RNA)))) For the link between protein and DNA: is_output_of (translation and (realizes some ('information template role' and ('inheres in' some (RNA and (is_output_of some (transcription and (realizes some ('information template role' and ('inheres in' some DNA)))))))))) For the link between mRNA and DNA: is_output_of (transcription and (realizes some ('information template role' and ('inheres in' some DNA))))"""; "This is the 'material' counterpart of the 'sequence_derives_from' relation that holds between the 'informational' content of RNA and DNA sequences, amino acid and RNA sequences, or amino acid and DNA sequences"; "a relation between sequence molecules (DNA, RNA, protein) wherein one serves as a template for the transmission of genetic information through the processes of transcription and translation (specifically, DNA or RNA to RNA or protein)."; ; rdfs:range _:2dc8d9; rdfs:domain _:2dc909 . _:2dc8d9 a owl:Class; owl:unionOf _:2dc8e9 . _:2dc8e9 rdf:first ; rdf:rest _:2dc8f9 . _:2dc8f9 rdf:first ; rdf:rest rdf:nil . _:2dc909 a owl:Class; owl:unionOf _:2dc919 . _:2dc919 rdf:first ; rdf:rest _:2dc929 . _:2dc929 rdf:first ; rdf:rest _:2dc939 . _:2dc939 rdf:first ; rdf:rest _:2dc949 . _:2dc949 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "developed_by"; "ERO:developed_by"; rdfs:domain ; rdfs:range . a owl:ObjectProperty; rdfs:label "translated_from"; rdfs:comment """shortcut relation for: is_output_of (translation and (realizes some ('information template role' and ('inheres in' some RNA))))"""; rdfs:domain ; rdfs:subPropertyOf ; rdfs:range _:2dc959 . _:2dc959 a owl:Class; owl:unionOf _:2dc969 . _:2dc969 rdf:first ; rdf:rest _:2dc979 . _:2dc979 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "transcribed_from"; rdfs:comment """shortcut relation for: is_output_of (transcription and (realizes some ('information template role' and ('inheres in' some DNA))))"""; "transcript_expressed_from"; rdfs:range ; rdfs:domain ; rdfs:subPropertyOf . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "sequence_derives_from"; """relation holding between the amino acid sequence of the SHH protein and the DNA sequence of the SHH gene, or the RNA sequence of the SHH mRNA. Furthermore, this relation could hold between a synthetic peptide and a RNA or DNA sequence, where the peptide sequence would be transcribable/translatable from the DNA sequence."""; "generically_expressed_from", "sequence_expressed_from", "generically_derives_from"; "This is the 'informational' counterpart of the 'genetically_derives_from' relation that holds between the material manifestations of DNA, RNA, and protein macromolecules."; "relation between two genetic sequence regions (GDCs) that describes the 'mapping' of genetic sequence information from RNA sequence to DNA sequence, amino acid sequence to RNA sequence, or amino acid sequence ot DNA sequence"; ; rdfs:range ; rdfs:domain _:2dc989 . _:2dc989 a owl:Class; owl:unionOf _:2dc999 . _:2dc999 rdf:first ; rdf:rest _:2dc9a9 . _:2dc9a9 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "has_principal_part"; "in a nucleic acid extract, nucleic acids represent principal parts, while any buffers or stabilizing chemicals represent secondary, non-principal parts"; rdfs:comment "a non-transitive, irreflexive has_part relation between some material entity and a component or granular part that represents a specified element of high import, and wherein all other grains or components serve some secondary function in support of this principal part"; rdfs:subPropertyOf . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "genetically_derived_into"; "a relation between a nucleic acid or mRNA molecule and an RNA or protein molecule for which it serves as a template for transmission of genetic information through the processes of transcription and translation."; "expresses_gene_product", "expresses"; "This is the 'material' counterpart of the 'sequence_derives_into' relation that holds between the 'informational' content of DNA and RNA sequences, RNA and amino acid sequences, or DNA and amino acid sequence"; rdfs:comment "Note that this is a relation between material entiteis, not sequences (GDCs). We use this relation to link a nucleic acid with an RNA or protein which is generated through its transcription and/or translation. As this relation applies at the physical level, it does not link a DNA molecule to a synthetic peptide (rather, the sequence_derives_into relation could be used to link a DNA sequence to a synthetic peptide sequence that would be transcribed/translated from the DNA sequence).", """shortcut relation for: For the link between RNA and protein: is_input_of some (translation and (has_output some protein) or 'has role' some ('information template role' and ('is realized by' some (translation and (has_output some protein)))) For the link between DNA and protein: is_input_of some (transcription and (has_output some (RNA and (is_input_of some (translation and (has_output some protein)))))) or 'has role' some ('information template role' and ('is realized by' some (transcription and (has_output some (RNA and ('has role' some ('information template role' and ('is realized by' some (translation and (has_output some protein)))))))))) For the link between DNA and mRNA: is_input_of some (transcription and (has_output some mRNA) or 'has role' some ('information template role' and ('is realized by' some (transcription and (has_output some mRNA))))"""; owl:inverseOf ; rdfs:range _:2dc9b9; rdfs:domain _:2dca09 . _:2dc9b9 a owl:Class; owl:unionOf _:2dc9c9 . _:2dc9c9 rdf:first ; rdf:rest _:2dc9d9 . _:2dc9d9 rdf:first ; rdf:rest _:2dc9e9 . _:2dc9e9 rdf:first ; rdf:rest _:2dc9f9 . _:2dc9f9 rdf:first ; rdf:rest rdf:nil . _:2dca09 a owl:Class; owl:unionOf _:2dca19 . _:2dca19 rdf:first ; rdf:rest _:2dca29 . _:2dca29 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "sequence_derives_into"; "generically_derives_into", "generically_expresses"; "relation between two genetic sequence regions (GDCs) that describes the 'mapping' of genetic sequence information from DNA sequence to RNA sequence, RNA sequence to amino acid sequence, or DNA to amino acid sequence"; "This is the 'informational' counterpart of the 'genetically_derives_into' relation that holds between the material manifestations of DNA, RNA, and protein macromolecules."; """relation holding between the DNA sequence of the SHH gene and corresponding RNA sequence of the SHH mRNA and the corresponding amio acid sequence from the SHH protein. Furthermore, this relation could hold between a DNA or RNA sequence and a synthetic peptide that would be transcribed/translated from the DNA or RNA sequence."""; rdfs:domain ; owl:inverseOf ; rdfs:range _:2dca39 . _:2dca39 a owl:Class; owl:unionOf _:2dca49 . _:2dca49 rdf:first ; rdf:rest _:2dca59 . _:2dca59 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "has_monomeric_unit"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is_monomeric_unit_of"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "has_owner"; rdfs:range _:2dca69 . _:2dca69 a owl:Class; owl:unionOf _:2dca79 . _:2dca79 rdf:first ; rdf:rest _:2dca89 . _:2dca89 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "validated_for_technique"; "has_validated_technique"; "a stronger relation than simple has_related_technique, in that this implies prior successful use in a given technique, and that some level of testing or validation has been performed for a given reagent (not just that the reagent could potentially be applied in some technique)"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "transcribed_into"; "expresses_transcript"; owl:inverseOf ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "translated_into"; "expresses_protein"; owl:inverseOf ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "has_original_part"; """original parts of A are no longer parts of A but were parts of A when they came into existence. Example: Apples harvested from an apple tree, tissue samples in a lab. """; "taken from BioTop:has_original_part - consider import if this property is kept/useful"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "original_part_of"; """original parts of A are no longer parts of A but were parts of A when they came into existence. Example: Apples harvested from an apple tree, tissue samples in a lab. """; "taken from BioTop:original_part_of - consider import if this property is kept/useful"; owl:inverseOf ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "is_variant_of"; rdfs:comment """Possibly useful proeprty from SIO: is variant of: a relationship indicating that two entities are different (by some measure), but either achieve the same objectives in different ways or are permutations of one another (temporal, logical or otherwise)"""; "SIO:is variant of?" . a owl:ObjectProperty, owl:ReflexiveProperty; rdfs:label "has cardinal part"; rdfs:comment "a has_part property that is reflexive but not transitive, and relates an entity to its core components at the level of granularity at which the whole entity itself exists (similar to has direct part in this way). Thus, a cell can be said to 'have cardinal part' itself (because the property is reflexive), or a nucleus or other organelle (because these exist at same level of granularity as the cell), but not a DNA molecule or potassium ion (because these are not components at the same level of granularity as the cell)"; "Used in cases where we want to place cardinality restrictions on a parthood relation that allows for the bearer of the relation to be part of itself. See examples of usage for where/how this is useful."; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "has_direct_part"; "a non-transitive, irreflexive relation that specifies a part at a particular level of granularity (ie. that at which the whole exists) (from SIO)"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "has component"@en; "Can be used in recording has_part with a cardinality constraint (because this property is not transitive)"; "Beisswanger, E., Schulz, S., Stenzhorn, H., Hahn, U.: BioTop: An upper domain ontology for the life sciences. Applied Ontology 3(4), 205–212 (2008)"; "MIREOT from RO", ; "has component part"; "a non-transitive, irreflexive relation between a material entiy and its constituent components based upon a non-overlapping and exhaustive partition, like a protein chain is related to its constituent amino acid monomers. The sortal identity of a compound changes as soon as a single component is added or removed (e.g., when we remove an amino acid from the peptide chain of a protein this might change the over-all nature of the protein)."; "PERSON:Matthew Brush"; rdfs:comment "For use in recording has_part with a cardinality constraint."@en, "The non-transitive relation hasComponentPart (inverse: componentPartOf) relates components with a compound. Components strictly partition the compound, and the compound is the mereological sum of its components. A loss of some component affects the integrity of the compound, and possibly the type it instantiates, e.g. a complete vs. a defective organism. (source: BioTop:has granular part)"@en; ; owl:inverseOf ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "gene product of"@en; "This RO relation seems to link a material gene product (an independent continuant) to its gene (seqeunce GDC) . . . so this property would be complemented by ReO:genetically derives_from which operates purely on the physical level to link a material gene product to the material gene from which it was transcribed and/or translated, and ReO:sequence_derives_from which operates purely on the sequence/GDC level to link a gene product sequence (GDC) to its corresponding gene GDC"; "Chris Mungall"@en; "definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\""; ; owl:inverseOf ; ; rdfs:range ; rdfs:domain ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "has gene product"@en; "This RO relation seems to link a gene (seqeunce GDC) to its material gene product (an independent continuant) . . . so this property would be complemented by ReO:genetically derives_into which operates purely on the physical level to link a material gene to its material product, and ReO:sequence_derives_into which operates purely on the sequence/GDC level to link gene sequence info to the sequence info of its possible products,"; "Chris Mungall"@en; "every HOTAIR lncRNA is the gene product of some HOXC gene", "every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene"; "x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y"; ; ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "has input"@en; ; ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "has output"@en; ; ; owl:inverseOf ; rdfs:domain ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "produces"@en; "Melissa Haendel"; rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue."; "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix."; ; owl:inverseOf ; ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "produced by"@en; "Melissa Haendel"; ; ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "genome_of"; "SO - no definition or domain/range or usage of this proeprty, but I use it here to link a genome to the species of organism from which derives the cell in which the genome is encoded, or the virus species in which the genome is encoded (as opposed to the particular cell or virion in which it is encoded)"; rdfs:range ; rdfs:domain ; ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "transcribed_from"; rdfs:comment "Example: primary_transcript transcribed_from gene."; "X is transcribed_from Y if X is synthesized from template Y."; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "transcribed_to"; rdfs:comment "Example: gene transcribed_to primary_transcript."; "Inverse of transcribed_from."; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "translates_to"; rdfs:comment "Example: codon translates_to amino_acid."; "Inverse of translation _of."; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "translation_of"; rdfs:comment "Example: Polypeptide translation_of CDS."; "X is translation of Y if X is translated by ribosome to create Y."; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "has functional parent"; "MHB: by my understanding, it seems that for a molecule X that has_functional_parent Y, the derivation of x from Y must be physically/chemically possible, but a particular molecule does not have to have actually been derived from its functional parent to come into existence"; "http://www.ebi.ac.uk/chebi/userManualForward.do#has%20functional%20parent"; """Used to denote the relationship between two molecular entities (or classes of entities), one of which possesses one or more chacteristic groups from which the other CAN be derived by functional modification. Definition: A has_functional_parent B if and only if given any a, a instantiates A , has molecular graph ag and a obo:has_part some functional group fg, then there is some b such that b instantiates B, has molecular graph bg and has functional group fg’ such that bg is the result of a graph transformation process on ag resulting in the conversion of fg into fg’."""; "16α-hydroxyprogesterone (CHEBI:15826) can be derived by functional modification (i.e. 16α-hydroxylation) of progesterone (CHEBI:17026)."; rdfs:subPropertyOf ; . a owl:ObjectProperty; rdfs:label "is substituent group from"; """Indicates the relationship between a substituent group (or atom) and its parent molecular entity, from which it is formed by loss of one or more protons or simple groups such as hydroxy groups. E.g. Definition: A is_substituent_group_from B if and only if A is a group and B is a molecular entity; given any a that instantiates A, a has molecular graph ag and specified attachment point agap, and there is some b that instantiates B and has molecular graph bg, then it is the case that bg is the result of a graph transformation process on ag resulting in the replacement of agap by some group bgg (which may be a hydrogen atom or a more complex group)."""; "http://www.ebi.ac.uk/chebi/userManualForward.do#is%20substituent%20group%20from"; "The L-valino group (CHEBI:32854) is derived by a proton loss from the N atom of L-valine (CHEBI:16414)"; ; rdfs:subPropertyOf owl:topObjectProperty . a owl:ObjectProperty; rdfs:label "output_of"; "is_output_of"; ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a owl:ObjectProperty; "obsolete_bearer_of"; rdfs:subPropertyOf ; _:2dca99; _:2dcab9, _:2dcac9 . _:2dca99 _:2dcaa9 . a owl:ObjectProperty; """RO-proposed no longer to be used, and this term no equivalent term found in BFO2 relaitons or new RO(dev), so created in REO (but will ultimately like to see this in RO and import back into REO) (note that RO(dev) devleops_from is similar?"""; "arises_from"; "obsolete_develops_from"; rdfs:subPropertyOf ; _:2dcad9 . _:2dcad9 _:2dcae9 . a owl:ObjectProperty; "obsolete_exists_during"; "RO-proposed no longer to be used, and this term no found in BFO2 relaitons or new RO(dev), so created in REO (but will ultimately like to see this in RO and import back into REO)"; rdfs:subPropertyOf ; _:2dcaf9; _:2dcb09 . a owl:ObjectProperty; "obsolete_has_disposition"; "RO-proposed no longer to be used, and this term no found in BFO2 relaitons or new RO(dev), so created in REO (but will ultimately like to see this in RO and import back into REO)"; rdfs:subPropertyOf ; _:2dcb19 . a owl:ObjectProperty; "obsolete_has_function"; rdfs:subPropertyOf ; _:2dcb29 . _:2dcb29 _:2dcb39 . a owl:ObjectProperty; "obsolete_has_input"; rdfs:subPropertyOf . a owl:ObjectProperty; "obsolete_has_output"; rdfs:subPropertyOf ; _:2dcb49 . _:2dcb49 _:2dcb59 . a owl:ObjectProperty; "obsolete_has_quality"; rdfs:subPropertyOf ; _:2dcb69 . _:2dcb69 _:2dcb79 . a owl:ObjectProperty; "obsolete_has_role"; rdfs:subPropertyOf ; _:2dcb89 . _:2dcb89 _:2dcb99 . a owl:ObjectProperty; "obsolete_inheres_in"; rdfs:subPropertyOf ; _:2dcba9; _:2dcbb9 . _:2dcbb9 _:2dcbc9 . a owl:ObjectProperty; "obsolete_realizes"; rdfs:subPropertyOf ; _:2dcbd9; _:2dcbf9, _:2dcc19; _:2dcc09, _:2dcc29 . _:2dcbd9 _:2dcbe9 . a owl:ObjectProperty; "obsolete_unfolds_in"; rdfs:subPropertyOf ; rdfs:range ; rdfs:domain ; _:2dcc39 . _:2dcc39 _:2dcc49 . a owl:ObjectProperty; rdfs:label "obsolete_output_of"@en; rdfs:comment "submit to RO prooposed?"; "obsolete_is_output_of"; "replaced with updated version of uberon output_of"; ; rdfs:subPropertyOf . a owl:ObjectProperty . a owl:ObjectProperty; rdfs:label "oblolete_hasPart"; "oblolete_hasPart"; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "adjacent_to"@en; rdfs:comment "Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum"; "OBO_REL:0000012"; "relationship"; rdfs:subPropertyOf owl:topObjectProperty; _:2dcc59 . _:2dcc59 a ; rdfs:label "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity"@en; _:2dcc69 . _:2dcc69 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty; rdfs:label "agent_in"@en; "relationship", "ro_bfo_bridge"; "OBO_REL:0000022"; rdfs:range ; rdfs:subPropertyOf . a owl:ObjectProperty; rdfs:label "contained_in"@en; rdfs:comment "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):"; "relationship"; "OBO_REL:0000010"; rdfs:range ; rdfs:domain ; owl:inverseOf ; _:2dcc79 . _:2dcc79 a ; rdfs:label "C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)"@en; _:2dcc89 . _:2dcc89 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty; rdfs:label "contains"@en; "relationship"; rdfs:comment "The contains relation is different from has_part in that contains implies that the 'contained entity' is either at a different level of granularity than the 'containing entity', or that the contained entity is not a necessary structural component of the containing entity (as is often the case when the containing entity has a function to hold some other material). For example, we would use 'contains' to describe the relationship between a cell and a protein it expresses, or the relation between a tube and a sample it holds."; "OBO_REL:0000011" . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "derived_into"@en; "OBO_REL:0000016"; "relationship", "ro_bfo_bridge"; rdfs:range . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "derives_from"@en; rdfs:comment "Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant."; """OBO/BFO? derives_from is used in many different ways: 1. Something large deriving from something smaller which contributes material to it (cell line derives from some cell) . . . i would say this is akin to an 'originates_from' relation 2. Something small deriving from larger entity of which it was a part . . . would be akin to a 'was_once_part_of' relation (biological specimen derives from some organism, monoclonal antiody derives from some hybridoma) 3. derivation at similar scale (eg a modified cell derives from an unmodified cell. mRNA deriving from pre-mRNA. a protein complex derives from an individual protein) . . . many of these are arguable transformations And in ReO I have an example of both #1 and #2 in the same axiom, which really highlights the issue : monoclonal antibody: derives_from some ('hybridoma cell line' and (derives_from some ('B cell' and (part_of some organism)))) NOTE THAT THE ABOVE IS NOT QUITE RIGHT, BUT SMITH ET ALL CAME UP SIMILARLY WITH THREE TYPES OF DERIVATION IN FIGURE 3 OF THEIR 2005 GENOME BIOLOGY PAPER (Relations in Biomedical Ontologies, 2005, Genome Biology 3A: 1 from 1 DERIVATION - blastula deriveing from zygote) 3B: 1 from many derivation - zygote deriving from sperm and egg) 3C: many from 1 derivation - promyleocytes deriving from a precursor myeloblast)"""; "ro_bfo_bridge", "relationship"; "OBO_REL:0000015"; rdfs:subPropertyOf ; rdfs:range ; owl:inverseOf ; owl:propertyChainAxiom _:2dcc99, _:2dccb9; _:2dccd9; _:2dccf9 . _:2dcc99 rdf:first ; rdf:rest _:2dcca9 . _:2dcca9 rdf:first ; rdf:rest rdf:nil . _:2dccb9 rdf:first ; rdf:rest _:2dccc9 . _:2dccc9 rdf:first ; rdf:rest rdf:nil . _:2dccd9 a ; rdfs:label "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'."@en; _:2dcce9 . _:2dcce9 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . _:2dccf9 a ; rdfs:label "derived_from"@en . a owl:ObjectProperty; rdfs:label "has_agent"@en; "OBO_REL:0000021"; "ro_bfo_bridge", "relationship"; rdfs:range ; owl:inverseOf ; rdfs:subPropertyOf ; _:2dcd09 . _:2dcd09 a ; rdfs:label "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process"@en; _:2dcd19 . _:2dcd19 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "has_improper_part"@en; rdfs:comment "See reasons for obsoletion of improper_part_of"; "relationship"; """RO - this class has two parents - should only have obsoleteClass as a parent since it was obsoleted (see reasons for obsoleting improper_part_of : OBSOLETE. The definition is \"As for part_of, with the additional constraint that subject and object may be identical\". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as \"improper_part_of is part_of but not proper_part_of\",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]) Ultimately, will replace RO with BFO2 relations, so may not be an issue for us."""; "OBO_REL:0000024"; rdfs:subPropertyOf , . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "has_integral_part"@en; "relationship"; "OBO_REL:0000005"; rdfs:subPropertyOf . a owl:ObjectProperty, owl:ReflexiveProperty, owl:TransitiveProperty; rdfs:label "has_part"@en; "Note that we have made has_part (and its invers part_of) REFLEXIVE in ReO. The sub-property has_proper_part is to be used when parthood is not reflexive (ie when the parthood relation does not allow for the whole to be part of itself)"; "relationship"; "OBO_REL:0000003"; rdfs:comment "This relation can hold across granularities, such that entities existing at finer levels can be considered (e.g. a cell or organism can have part a protein, small molecule, or atom)"; owl:inverseOf ; owl:propertyChainAxiom _:2dcd29, _:2dcd49 . _:2dcd29 rdf:first ; rdf:rest _:2dcd39 . _:2dcd39 rdf:first ; rdf:rest rdf:nil . _:2dcd49 rdf:first ; rdf:rest _:2dcd59 . _:2dcd59 rdf:first ; rdf:rest rdf:nil . a owl:ObjectProperty; rdfs:label "has_participant"@en; rdfs:comment "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."; "OBO_REL:0000019"; "ro_bfo_bridge", "relationship"; rdfs:range ; owl:propertyChainAxiom _:2dcd69; _:2dcd89 . _:2dcd69 rdf:first ; rdf:rest _:2dcd79 . _:2dcd79 rdf:first ; rdf:rest rdf:nil . _:2dcd89 a ; rdfs:label "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t"@en; _:2dcd99 . _:2dcd99 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "has_proper_part"@en; "relationship"; "OBO_REL:0000007"; """1. Note that we have made has_part (and its invers part_of) REFLEXIVE in ReO. The sub-property has_proper_part is to be used ANY TIME parthood is NOT REFLEXIVE (ie when the parthood relation does not allow for the whole to be part of itself). 2. Note also that all children here are irreflexive and non-transitive"""; rdfs:comment "This relation can hold across granularities, such that entities existing at finer levels can be considered (e.g. a cell or organism can have proper part a protein, small molecule, or atom)"; "a has_part relation that is transitive but not reflexive (such that no entity can be a proper_part_of itself)"; rdfs:subPropertyOf ; owl:inverseOf . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "improper_part_of"@en; rdfs:comment "OBSOLETE. The definition is \"As for part_of, with the additional constraint that subject and object may be identical\". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as \"improper_part_of is part_of but not proper_part_of\",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]"; "relationship"; "OBO_REL:0000025"; """RO - this class has two parents - should only have obsoleteClass as a parent since it was obsoleted (see reasons for obsoleting improper_part_of : OBSOLETE. The definition is \"As for part_of, with the additional constraint that subject and object may be identical\". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as \"improper_part_of is part_of but not proper_part_of\",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]) Ultimately, will replace RO with BFO2 relations, so may not be an issue for us."""; rdfs:subPropertyOf , ; owl:inverseOf ; _:2dcda9 . _:2dcda9 a ; rdfs:label "As for part_of, with the additional constraint that subject and object may be identical"@en; _:2dcdb9 . _:2dcdb9 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "integral_part_of"@en; "OBO_REL:0000004"; "relationship"; owl:inverseOf ; rdfs:subPropertyOf ; _:2dcdc9 . _:2dcdc9 a ; rdfs:label "C integral_part_of C' if and only if: C part_of C' AND C' has_part C"@en; _:2dcdd9 . _:2dcdd9 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "located_in"@en; rdfs:comment "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"; "relationship", "ro_bfo_bridge"; "OBO_REL:0000008"; rdfs:range ; _:2dcde9 . _:2dcde9 a ; rdfs:label "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)"@en; _:2dcdf9 . _:2dcdf9 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "location_of"@en; "ro_bfo_bridge", "relationship"; "OBO_REL:0000009"; rdfs:range ; owl:inverseOf . a owl:ObjectProperty, owl:ReflexiveProperty, owl:TransitiveProperty; rdfs:label "part_of"@en; rdfs:comment "Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell."; "relationship"; "OBO_REL:0000002"; _:2dce09 . _:2dce09 a ; rdfs:label "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)"@en; _:2dce19 . _:2dce19 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty; rdfs:label "participates_in"@en; "relationship", "ro_bfo_bridge"; "OBO_REL:0000020"; rdfs:range ; owl:inverseOf . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "preceded_by"@en; rdfs:comment "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other."; "ro_bfo_bridge", "relationship"; "OBO_REL:0000017"; rdfs:range ; owl:inverseOf ; _:2dce29 . _:2dce29 a ; rdfs:label "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. "@en; _:2dce39 . _:2dce39 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "precedes"@en; "OBO_REL:0000018"; "relationship", "ro_bfo_bridge"; rdfs:range . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "proper_part_of"@en; "OBO_REL:0000006"; "relationship"; rdfs:subPropertyOf ; _:2dce49 . _:2dce49 a ; rdfs:label "As for part_of, with the additional constraint that subject and object are distinct"@en; _:2dce59 . _:2dce59 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty; rdfs:label "relationship"@en; rdfs:comment "this relation was superfluous, so it has been obsoleted"; "obsolete_relationship"; "relationship"; rdfs:subPropertyOf ; _:2dce69 . _:2dce69 a ; rdfs:label "A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances."@en; _:2dce79 . _:2dce79 a ; rdfs:label "GOC:cjm"; "http://purl.org/obo/owl/GOC#GOC_cjm"^^xsd:anyURI . a owl:ObjectProperty, owl:TransitiveProperty; rdfs:label "transformation_of"@en; rdfs:comment "When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes."; "ro_bfo_bridge", "relationship"; "OBO_REL:0000013"; rdfs:subPropertyOf ; rdfs:range ; _:2dce89 . _:2dce89 a ; rdfs:label "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2."@en; _:2dce99 . _:2dce99 a ; rdfs:label "PMID:15892874"; "http://purl.org/obo/owl/PMID#PMID_15892874"^^xsd:anyURI . a owl:ObjectProperty; rdfs:label "transformed_into"@en; rdfs:comment "Obsoleted"; "relationship", "ro_bfo_bridge"; "OBO_REL:0000014"; "obsolete_transformed_into"; rdfs:subPropertyOf ; rdfs:range . a owl:DatatypeProperty; rdfs:label "has_inventory_number"; "An example inventory number can be in the form: 12345"; "Inventory identifier for the resource."; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; rdfs:subPropertyOf ; . a owl:DatatypeProperty, owl:FunctionalProperty; rdfs:label "has_entrez_gene_id"; "A unique identifier assigned to each record in the Entrez Gene database."; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "The entrez gene ID of mouse CD34 is 12490."; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_CAS_number"; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "The CAS number for NaOH."; "Unique numerical identifier for a chemical as defined by the Chemical Abstracts Service (CAS)."; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_IUPAC_name"; "International Union of Pure and Applied Chemistry (IUPAC) name of the chemical."; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "The IUPAC name for NaOH."; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_uniPROT_ID"; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "The UniPROT ID for Mad4 protein."; "Unique numerical identifier for a chemical as defined by the UniProt database."; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_gene_symbol"; "CD4."; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky"; "The official symbol for the gene."; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_InChI_key"; "PERSON: Melissa Haendel"; "PERSON: Melissa Haendel"; "The InChi key number for NaOH."; "Unique numerical identifier for a chemical as defined by the InChI Key database."; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_antibody_registry_ID"; "AB12345."; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky"; "The unique ID number assigned to an antibody in the Neurosicence Information Framework (NIF) antibody registry. "; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_clone_ID"; "Clone identification number assigned to a monoclonal antibody."; "N-262."; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky"; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_lot_number"; "4521"; "PERSON: Nicole Vasilevsky"; "The identification number assigned to a particular quantity or lot of material from a single manufacturer."; "http://www.answers.com/topic/lot-number"; rdfs:subPropertyOf ; . a owl:DatatypeProperty; rdfs:label "has_catalog_number"; "Catalog number of a commercially manufactured reagent."; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky"; "SC-1234"; rdfs:subPropertyOf ; . a owl:DatatypeProperty, owl:FunctionalProperty; rdfs:label "has measurement value"@en; rdfs:domain ; rdfs:subPropertyOf ; ; rdfs:range xsd:float . a owl:DatatypeProperty; rdfs:label "has_entrez_gene_id"@en; rdfs:comment """?shortcut relation for?: For a nucleic acid reagent: has_part some (nucleic acid and (bears_concretization_of some (part_of some gene))) For a protein reagent: has_part some (polypeptide and (genetically_derives_from some (nucleic acid and (bears_concretization_of some (part_of some gene))))) or has_part some (polypeptide and (bears_concretization_of some ('protein region' and (generically_derives_from some (part_of some gene)))) For a synthetic oligopeptide (note here there is no physical link from the peptide to the gene - so we cannot use the first approach above that works for protein reagents - we can only use the second design pattern): has_part some (polypeptide and (bears_concretization_of some ('protein region' and (generically_derives_from some (part_of some gene))))""", "Note that the information macromolecule need not contain the entire sequence held in the entrez gene record, but only a significant portion of it."; "relates an amino acid chain or nucleic acid or SO:region to an entrez_gene record that describes a sequence that is represented in the sequence of the amino acid chain, nucleic acid, or region. "; rdfs:range xsd:string; rdfs:subPropertyOf owl:topDataProperty; rdfs:domain _:2dcea9 . _:2dcea9 a owl:Class; owl:unionOf _:2dceb9 . _:2dceb9 rdf:first ; rdf:rest _:2dcec9 . _:2dcec9 rdf:first ; rdf:rest _:2dced9 . _:2dced9 rdf:first ; rdf:rest _:2dcee9 . _:2dcee9 rdf:first ; rdf:rest _:2dcef9 . _:2dcef9 rdf:first ; rdf:rest _:2dcf09 . _:2dcf09 rdf:first ; rdf:rest rdf:nil . a owl:DatatypeProperty; rdfs:label "has_entrez_gene_symbol"@en; rdfs:comment "relates an amino acid chain or nucleic acid or SO:region to an entrez_gene record that describes a sequence that is represented in the sequence of the amino acid chain, nucleic acid, or region. ", "Note that the information macromolecule need not contain the entire sequence held in the entrez gene record, but only a significant portion of it."; rdfs:range xsd:string; rdfs:subPropertyOf owl:topDataProperty; rdfs:domain _:2dcf19 . _:2dcf19 a owl:Class; owl:unionOf _:2dcf29 . _:2dcf29 rdf:first ; rdf:rest _:2dcf39 . _:2dcf39 rdf:first ; rdf:rest _:2dcf49 . _:2dcf49 rdf:first ; rdf:rest _:2dcf59 . _:2dcf59 rdf:first ; rdf:rest _:2dcf69 . _:2dcf69 rdf:first ; rdf:rest _:2dcf79 . _:2dcf79 rdf:first ; rdf:rest rdf:nil . a owl:DatatypeProperty; rdfs:label "has specification value"; ; rdfs:subPropertyOf . a owl:DatatypeProperty; rdfs:label "has numeric value"; rdfs:domain ; ; rdfs:range xsd:float . a owl:DatatypeProperty; rdfs:label "has sequence length"; rdfs:comment """test shortcut relation to conenct a sequence macromolecule to its length as measured by number of monomers it contains (or number of base pairs in dsDNA) Would expand to : 'has quality' some (length and ('is quality valued as' some (('scalar measurement datum' or 'length value specification) and ('has unit label' value 'amino acids' or nucleotides or 'base pairs'') and ('has numeric value' exactly 1 Literal))))"""; rdfs:domain ; ; rdfs:subPropertyOf ; rdfs:range xsd:string . a owl:DatatypeProperty; rdfs:label "has quality value"; rdfs:comment "range is a string so that units can be recorded as part of a numeric value"; rdfs:domain ; rdfs:range xsd:string . a owl:DatatypeProperty; rdfs:label "has_identifier"; "relation" . a owl:Class; rdfs:label "anatomical structure"; rdfs:subClassOf ; "Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome."; rdfs:comment "replace with CARO2 definition/class when available"; , . a owl:Class; rdfs:label "portion of organism substance"; rdfs:subClassOf ; "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body."; , . a owl:Class; rdfs:label "material anatomical entity"; owl:equivalentClass _:2dcf89; rdfs:subClassOf , _:2dcfc9, _:2dcfd9; "Anatomical entity that has mass."; """CARO2: If ReO wants to consider things like tissue specimens to be subtypes of anatomical entity>…tissue, then we cannot use CARO anatomical entities because these are necessarily part of an organism!! but would be nice to have some hierarchical link between tissue specimen and tissue . . . may need to be a derives from link if we use CARO anatomical entities I would prefer that CARO relax its requirement that anatomical entities need to be part of or located in an organism, and rather say that they are part of or derive from an organism in a way that retains their internal structure (ie a liver removed from a mouse is an anatomical entity> liver, but not once it is homogenized . . . that is, contextual processings retain anatomical identity, but physical processing/experimental modification. how can we state this logically in owl? (ie that an anatomical entity is located in an organism or derived from an organism through some contextual modification process? . . . .perhaps : is specified output of some contextual processing and has specified input some (part_of some organism) ? Note that if CARO wants to use CL cell as they suggest in a editor note, then they cannot have this req because CL cell includes cells in vitro If they do not relax this requirement, I can still use CARO but not be able to assert any specimens as children - rather, would related to CARO classes using a derives from relation. Or I can create a reo label for CARO classes that is 'native ___' , and have the more general parent sit outside the CARO anatomical entity hierarchy (for ex, like I did with LC cell and native cell), but this seems like overkill and not needed for ReO."""; . _:2dcf89 a owl:Class; owl:intersectionOf _:2dcf99 . _:2dcf99 rdf:first ; rdf:rest _:2dcfb9 . _:2dcfb9 rdf:first _:2dcfa9; rdf:rest rdf:nil . _:2dcfa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dcfc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dcfd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "anatomical system"; rdfs:subClassOf ; "Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity."; , . a owl:Class; rdfs:label "multi-cellular organism"; owl:equivalentClass _:2dcfe9; rdfs:subClassOf , , _:2dd029; "Anatomical structure that is an individual member of a species and consists of more than one cell."; "organism that is an individual member of a species and, at some point in its life-cycle, consists of more than one cell."; "multicellular organism"; . _:2dcfe9 a owl:Class; owl:intersectionOf _:2dcff9 . _:2dcff9 rdf:first ; rdf:rest _:2dd019 . _:2dd019 rdf:first _:2dd009; rdf:rest rdf:nil . _:2dd009 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2dd029 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "cell"; rdfs:subClassOf ; "Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane."; "obsolete_cell"; "replaced with CL:cell"; , . a owl:Class; rdfs:label "cell component"; rdfs:subClassOf ; "Anatomical structure that is a direct part of the cell."; , . a owl:Class; rdfs:label "compound organ component"; rdfs:subClassOf ; "Multi-tissue structure that is part of a compound organ."; , . a owl:Class; rdfs:label "simple organ"; rdfs:subClassOf ; "Multi-tissue structure that is not part of a compound organ."; , . a owl:Class; rdfs:label "compound organ"; rdfs:subClassOf ; "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types."; , . a owl:Class; rdfs:label "male organism"; rdfs:subClassOf ; "Gonochoristic organism that can produce male gametes."; , . a owl:Class; rdfs:label "female organism"; rdfs:subClassOf ; "Gonochoristic organism that can produce female gametes."; , . a owl:Class; rdfs:label "hermaphroditic organism"; rdfs:subClassOf ; "Multi-cellular organism that can produce both male and female gametes."; , . a owl:Class; rdfs:label "asexual organism"; rdfs:subClassOf ; "Multi-cellular organism that does not produce gametes."; , . a owl:Class; rdfs:label "organism subdivision"; rdfs:subClassOf ; "Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism."; , . a owl:Class; rdfs:label "acellular anatomical structure"; rdfs:subClassOf ; "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue."; , . a owl:Class; rdfs:label "anatomical cluster"; rdfs:subClassOf ; "Anatomical group that has its parts adjacent to one another."; , . a owl:Class; rdfs:label "extraembryonic structure"; rdfs:subClassOf ; "Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo."; , . a owl:Class; rdfs:label "portion of tissue"; rdfs:subClassOf ; "Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships."; , . a owl:Class; rdfs:label "sequential hermaphroditic organism"; rdfs:subClassOf ; "Hermaphroditic organism that produces gametes first of one sex, and then later of the other sex."; , . a owl:Class; rdfs:label "synchronous hermaphroditic organism"; rdfs:subClassOf ; "Hermaphroditic organism that produces both male and female gametes at the same time."; , . a owl:Class; rdfs:label "gonochoristic organism"; rdfs:subClassOf ; "Multi-cellular organism that has male and female sexes."; , . a owl:Class; rdfs:label "protandrous hermaphroditic organism"; rdfs:subClassOf ; "Sequential hermaphroditic organism that produces\\ngametes first of the male sex, and then later of the\\nfemale sex."; , . a owl:Class; rdfs:label "protogynous hermaphroditic organism"; rdfs:subClassOf ; "Sequential hermaphroditic organism that produces\\ngametes first of the female sex, and then later of the\\nmale sex."; , . a owl:Class; rdfs:label "anatomical group"; rdfs:subClassOf ; "Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue."; , . a owl:Class; rdfs:label "multi-tissue structure"; rdfs:subClassOf ; "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types."; , . a owl:Class; rdfs:label "portion of cell substance"; rdfs:subClassOf ; "Portion of organism substance located within a cell."; , . a owl:Class; rdfs:label "single cell organism"; owl:equivalentClass _:2dd039; rdfs:subClassOf , , , _:2dd079, _:2dd089; owl:disjointWith ; "Cell that is an individual member of a species."; "unicellular organism"; "monocellular organism", "single cell organism"; "re-import new class from CARO2 - should be modeled similarly as here, and maybe even have 'unicellular organism' as label."; """Guidelines and Conventions for 'Cell' Classes: Asserted Class Hierarchies: 'unicellular organism in environment', 'unicellular organism ex environment' Equivalent Class Hierarchies : 'experimentally modified unicellular organism' Logical Modeling Conventions:"""; ; , . _:2dd039 a owl:Class; owl:intersectionOf _:2dd049 . _:2dd049 rdf:first ; rdf:rest _:2dd069 . _:2dd069 rdf:first _:2dd059; rdf:rest rdf:nil . _:2dd059 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2dd079 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2dd089 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "basal lamina"; rdfs:subClassOf ; "Acellular anatomical structure that consists of a thin sheet of fibrous proteins that underlie and support the cells of an epithelium. It separates the cells of an epithelium from any underlying tissue."; , . a owl:Class; rdfs:label "epithelium"; rdfs:subClassOf ; "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina."; , . a owl:Class; rdfs:label "simple cuboidal epithelium"; rdfs:subClassOf ; "Unilaminar epithelium that consists of a single layer of cuboidal cells."; , . a owl:Class; rdfs:label "simple columnar epithlium"; rdfs:subClassOf ; "Unilaminar epithelium that consists of a single layer of columnar cells."; , . a owl:Class; rdfs:label "multilaminar epithelium"; rdfs:subClassOf ; "Epithelium that consists of more than one layer of epithelial cells."; , . a owl:Class; rdfs:label "simple squamous epithelium"; rdfs:subClassOf ; "Unilaminar epithelium that consists of a single layer of squamous cells."; , . a owl:Class; rdfs:label "atypical epithelium"; rdfs:subClassOf ; "Epithelium that consists of epithelial cells not arranged in one ore more layers."; , . a owl:Class; rdfs:label "cavitated compound organ"; rdfs:subClassOf ; "Compound organ that contains one or more macroscopic anatomical spaces."; , . a owl:Class; rdfs:label "unilaminar epithelium"; rdfs:subClassOf ; "Epithelium that consists of a single layer of epithelial cells."; , . a owl:Class; rdfs:label "solid compound organ"; rdfs:subClassOf ; "Compound organ that does not contain macroscopic anatomical spaces."; , . a owl:Class; rdfs:label "epithelial cell"; rdfs:subClassOf ; "Cell which has as its part a cytoskeleton that allows for tight cell to cell contact and which has apical-basal cell polarity."; "replaced by CL:epithelial cell"; "obsolete_epithelial cell"; , . a owl:Class; rdfs:label "multi-cell-component structure"; rdfs:subClassOf ; "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part."; , . a owl:Class; rdfs:label "neuron projection bundle"; rdfs:subClassOf ; "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses."; "nerve fiber bundle"; , . a owl:Class; rdfs:label "XTP"; rdfs:subClassOf ; "The xanthosine 5'-phosphate in which the 5'-phosphate is a triphosphate group."; "XTP", "xanthosine 5'-(tetrahydrogen triphosphate)"; . a owl:Class; rdfs:label "ATP"; rdfs:subClassOf ; "A purine ribonucleoside 5'-triphosphate that has formula C10H16N5O13P3."; "ATP", "adenosine 5'-(tetrahydrogen triphosphate)"; . a owl:Class; rdfs:label "glycine"; rdfs:subClassOf ; "GLYCINE", "Glycine", "aminoacetic acid", "glycine"; "The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain."; . a owl:Class; rdfs:label "L-leucine"; rdfs:subClassOf ; "L-Leucine", "L-leucine"; "The L-enantiomer of leucine."; . a owl:Class; rdfs:label "UTP"; rdfs:subClassOf ; "A pyrimidine ribonucleoside 5'-triphosphate having uracil as the nucleobase."; "UTP", "uridine 5'-(tetrahydrogen triphosphate)"; . a owl:Class; rdfs:label "biotin"; rdfs:subClassOf , , _:2dd099; "5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid", "BIOTIN", "Biotin"; "An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins."; ; ; , . _:2dd099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-histidine"; rdfs:subClassOf ; "(2S)-2-amino-3-(1H-imidazol-4-yl)propanoic acid", "L-Histidine", "L-histidine"; "The L-enantiomer of the amino acid histidine."; . a owl:Class; rdfs:label "GTP"; rdfs:subClassOf ; "A purine ribonucleoside 5'-triphosphate that has formula C10H16N5O14P3."; "GTP", "guanosine 5'-(tetrahydrogen triphosphate)"; . a owl:Class; rdfs:label "L-glutamic acid"; rdfs:subClassOf ; "(2S)-2-aminopentanedioic acid", "L-Glutamic acid", "L-glutamic acid"; "An optically active form of glutamic acid having L-configuration."; . a owl:Class; rdfs:label "ITP"; rdfs:subClassOf ; "ITP", "inosine 5'-(tetrahydrogen triphosphate)"; "The inosine phosphate that has a triphosphate group at the 5'-position."; . a owl:Class; rdfs:label "L-methionine residue"; rdfs:subClassOf , _:2dd0a9; "L-methionine residue"; . _:2dd0a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dATP"; rdfs:subClassOf ; "2'-deoxyadenosine 5'-(tetrahydrogen triphosphate)", "dATP"; "A purine 2'-deoxyribonucleoside 5'-triphosphate having adenine as the nucleobase."; . a owl:Class; rdfs:label "dCTP"; rdfs:subClassOf ; "2'-deoxycytidine 5'-(tetrahydrogen triphosphate)", "dCTP"; "A 2'-deoxycytidine phosphate having cytosine as the nucleobase."; . a owl:Class; rdfs:label "L-valine"; rdfs:subClassOf ; "L-Valine", "L-valine"; "The L-enantiomer of valine."; . a owl:Class; rdfs:label "L-arginine"; rdfs:subClassOf ; "An L-alpha-amino acid that is the L-isomer of arginine."; "L-Arginine", "L-arginine"; . a owl:Class; rdfs:label "dGTP"; rdfs:subClassOf ; "2'-deoxyguanosine 5'-(tetrahydrogen triphosphate)", "dGTP"; "A purine 2'-deoxyribonucleoside 5'-triphosphate having guanine as the nucleobase."; . a owl:Class; rdfs:label "2'-deoxyribonucleoside triphosphate"; rdfs:subClassOf ; "2'-Deoxyribonucleoside triphosphate", "2'-deoxyribonucleoside triphosphate"; "deoxyribonucleoside triphosphate"; . a owl:Class; rdfs:label "L-selenocysteine"; rdfs:subClassOf ; "(2R)-2-amino-3-selanylpropanoic acid", "L-Selenocysteine"; "A selenocysteine that has formula C3H7NO2Se."; . a owl:Class; rdfs:label "L-methionine"; rdfs:subClassOf ; "L-Methionine", "L-methionine"; "The L-enantiomer of methionine."; . a owl:Class; rdfs:label "carbohydrate"; owl:equivalentClass _:2dd0b9; rdfs:subClassOf , , _:2dd0e9, _:2dd129; "The generic term 'carbohydrate' includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates."; "carbohydrate", "carbohydrates"; . _:2dd0b9 a owl:Class; owl:unionOf _:2dd0c9 . _:2dd0c9 rdf:first ; rdf:rest _:2dd0d9 . _:2dd0d9 rdf:first ; rdf:rest rdf:nil . _:2dd0e9 a owl:Class; owl:complementOf _:2dd0f9 . _:2dd0f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd109 . _:2dd109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd119 . _:2dd119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-tryptophan"; rdfs:subClassOf ; "L-Tryptophan", "L-tryptophan"; "The L-enantiomer of tryptophan."; . a owl:Class; rdfs:label "L-threonine"; rdfs:subClassOf ; "An optically active form of threonine having L-configuration."; "L-Threonine", "L-threonine"; . a owl:Class; rdfs:label "nucleoside diphosphate"; rdfs:subClassOf ; "Nucleoside diphosphate"; . a owl:Class; rdfs:label "L-alanine"; rdfs:subClassOf ; "L-Alanine", "L-alanine"; "The L-enantiomer of alanine."; . a owl:Class; rdfs:label "deoxyribonucleic acid"; rdfs:subClassOf ; "Deoxyribonucleic acid", "deoxyribonucleic acids"; "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms."; ; , . a owl:Class; rdfs:label "L-aspartic acid"; rdfs:subClassOf ; "(2S)-2-aminobutanedioic acid", "L-Aspartic acid", "L-aspartic acid"; "The L-enantiomer of aspartic acid."; . a owl:Class; rdfs:label "L-serine"; rdfs:subClassOf ; "L-Serine", "L-serine"; "The L-enantiomer of serine."; . a owl:Class; rdfs:label "nucleoside monophosphate"; rdfs:subClassOf ; "Nucleoside monophosphate", "nucleoside monophosphate"; . a owl:Class; rdfs:label "L-isoleucine"; rdfs:subClassOf ; "L-Isoleucine", "L-isoleucine"; "The L-enantiomer of isoleucine."; . a owl:Class; rdfs:label "L-asparagine"; rdfs:subClassOf ; "An optically active form of asparagine having L-configuration."; "L-Asparagine", "L-asparagine"; . a owl:Class; rdfs:label "L-proline"; rdfs:subClassOf ; "L-Proline", "L-proline"; "Pyrrolidine in which the pro-S hydrogen at position 2 is substituted by a carboxylic acid group. L-Proline is the only one of the twenty DNA-encoded amino acids which has a secondary amino group alpha to the carboxyl group. It is an essential component of collagen and is important for proper functioning of joints and tendons. It also helps maintain and strengthen heart muscles."; . a owl:Class; rdfs:label "glucose"; rdfs:subClassOf ; "Glucose", "gluco-hexose", "glucose"; "monosaccharide sugar that is an important energy source in living organisms and is a component of many carbohydrates"; ; . a owl:Class; rdfs:label "L-phenylalanine"; rdfs:subClassOf ; "(2S)-2-amino-3-phenylpropanoic acid", "L-Phenylalanine", "L-phenylalanine"; "The L-enantiomer of phenylalanine."; . a owl:Class; rdfs:label "nucleoside triphosphate"; rdfs:subClassOf ; "Nucleoside triphosphate"; rdfs:comment "Natural nucleoside triphosphates include adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), 5-methyluridine triphosphate (m5UTP), and uridine triphosphate (UTP). These terms refer to those nucleoside triphosphates that contain ribose. The nucleoside triphosphates containing deoxyribose take prefix deoxy- in their names and small d- in their abbreviations: deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate (dCTP), deoxythymidine triphosphate (dTTP) and deoxyuridine triphosphate"; "http://en.wikipedia.org/wiki/Nucleoside_triphosphate"; "a nucleoside phosphate containing three phosphate groups bound to its sugar ring"; . a owl:Class; rdfs:label "L-cysteine"; rdfs:subClassOf ; "An optically active form of cysteine having L-configuration."; "L-Cysteine", "L-cysteine"; . a owl:Class; rdfs:label "cytidine"; rdfs:subClassOf ; "A pyrimidine nucleoside in which cytosine is attached to ribofuranose via a beta-N(1)-glycosidic bond."; "Cytidine", "cytidine"; ; . a owl:Class; rdfs:label "dUTP"; rdfs:subClassOf ; "2'-deoxyuridine 5'-(tetrahydrogen triphosphate)", "dUTP"; "A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C9H15N2O14P3."; . a owl:Class; rdfs:label "CTP"; rdfs:subClassOf ; "A pyrimidine ribonucleoside 5'-triphosphate that has formula C9H16N3O14P3."; "CTP", "cytidine 5'-(tetrahydrogen triphosphate)"; . a owl:Class; rdfs:label "transfer RNA"; rdfs:subClassOf ; "A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis."; "transfer RNA"; . a owl:Class; rdfs:label "L-tyrosine"; rdfs:subClassOf ; "An optically active form of tyrosine having L-configuration."; "L-Tyrosine", "L-tyrosine"; . a owl:Class; rdfs:label "ribonucleoside triphosphate"; rdfs:subClassOf ; "Ribonucleoside triphosphate", "ribonucleoside triphosphate"; . a owl:Class; rdfs:label "L-lysine"; rdfs:subClassOf ; "(2S)-2,6-diaminohexanoic acid", "L-Lysine", "L-lysine"; "An L-alpha-amino acid; the L-isomer of lysine."; . a owl:Class; rdfs:label "L-glutamine"; rdfs:subClassOf ; "An optically active form of glutamine having L-configuration."; "L-Glutamine", "L-glutamine"; . a owl:Class; rdfs:label "lipid"; owl:equivalentClass _:2dd139; rdfs:subClassOf , , _:2dd1b9, _:2dd1c9, _:2dd1d9, _:2dd229, _:2dd239; "'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids."; "Lipid", "lipid", "lipids", "biological lipid"; "an organic small molecule of biological origin that is soluble in nonpolar solvents, and is comprised primarily of carbon and hydrogen atoms. Lipids include saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. "; "http://goldbook.iupac.org/L03571.html"; rdfs:comment """Opinions and authorities vary as to whether some lipids can be considered to be macromolecules. Here, we consider lipids to be small molecules, despite the fact that many can be quite large, since they are not true macromolecules in the sense that they are not comprised of repeating monomeric subunits. The term 'lipid' covers a wide range of substances which contain moieties belonging chemically to hydrocarbons, alcohols, aldehydes, acids, amines or glucides. Accordingly, lipids cannot be defined structurally, but are rather defined by their chemical proeprties (ie their solubility in non-polar solvents). The majority of lipid molecules are waxes, triacylglycerols, phospholipids and glycolipids. Other substances are also considered as lipids while belonging to other classes of molecules, e.g. fat soluble vitamins (A, D, E and K), coenzymes (ubiquinones), pigments (carotenoids), terpenes, phenolics and sterols. (http://www.cyberlipid.org/cyberlip/home0001.htm)"""; . _:2dd139 a owl:Class; owl:intersectionOf _:2dd149 . _:2dd149 rdf:first ; rdf:rest _:2dd169 . _:2dd169 rdf:first _:2dd159; rdf:rest rdf:nil . _:2dd159 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd179 . _:2dd179 a owl:Class; owl:intersectionOf _:2dd189 . _:2dd189 rdf:first ; rdf:rest _:2dd1a9 . _:2dd1a9 rdf:first _:2dd199; rdf:rest rdf:nil . _:2dd199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd1b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd1c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd1d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd1e9 . _:2dd1e9 a owl:Class; owl:intersectionOf _:2dd1f9 . _:2dd1f9 rdf:first ; rdf:rest _:2dd219 . _:2dd219 rdf:first _:2dd209; rdf:rest rdf:nil . _:2dd209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd229 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd239 a owl:Class; owl:complementOf _:2dd249 . _:2dd249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd259 . _:2dd259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd269 . _:2dd269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dTTP"; rdfs:subClassOf ; "A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H17N2O14P3."; "dTTP", "thymidine 5'-(tetrahydrogen triphosphate)"; . a owl:Class; rdfs:label "ribosomal RNA"; rdfs:subClassOf ; "RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis."; "Ribosomal RNA", "ribosomal RNA"; . a owl:Class; rdfs:label "polysaccharide"; rdfs:subClassOf , , _:2dd279, _:2dd289, _:2dd2c9; "A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues."; "Polysaccharide", "polysaccharide", "polysaccharides"; """A macromolecule consisting of (typically) large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues, but here we include even di- or tri-saccharides as polysaccharides so as not to have to enforce some arbitrary cutoff."""; "ChEBI - clarify if our interpretation here that even di- or tri-saccharides qualify is in agreement with their definition . . . pretty sure it is not, as they have the class 'oligosaccharide' to account for shorter carbohydrate macromolecules wehre the number of monomers is known."; . _:2dd279 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dd289 a owl:Class; owl:complementOf _:2dd299 . _:2dd299 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd2a9 . _:2dd2a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd2b9 . _:2dd2b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd2c9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "nucleobase"; rdfs:subClassOf ; """Nucleobases are a group of nitrogen-based molecules that are required to form nucleotides, the basic building blocks of DNA and RNA. Nucleobases provide the molecular structure necessary for the hydrogen bonding of complementary DNA and RNA strands, and are key components in the formation of stable DNA and RNA molecules. Nucleobases (or nucleotide bases/nitrogenous bases/aglycones) provide the nucleotide structure necessary to form base pairs. The primary nucleobases are cytosine, guanine, adenine (DNA and RNA), thymine (DNA) and uracil (RNA), abbreviated as C, G, A, T, and U, respectively. """; "http://en.wikipedia.org/wiki/Nucleobase"; . a owl:Class; rdfs:label "5-azacytidine"; rdfs:subClassOf , , , , _:2dd2d9, _:2dd2f9, _:2dd309; "4-amino-1-beta-D-ribofuranosyl-1,3,5-triazin-2(1H)-one", "5-Azacytidine", "5-azacytidine"; "A N-glycosyl-1,3,5-triazine that has formula C8H12N4O5."; ; . _:2dd2d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd2e9 . _:2dd2e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd2f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd319 . _:2dd319 a owl:Class; owl:intersectionOf _:2dd329 . _:2dd329 rdf:first ; rdf:rest _:2dd349 . _:2dd349 rdf:first _:2dd339; rdf:rest rdf:nil . _:2dd339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-pyrrolysine"; rdfs:subClassOf ; "An L-lysine derivative having a (2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarboxy group at the N(6)-position."; "N(6)-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine"; . a owl:Class; rdfs:label "bromine atom"; rdfs:subClassOf ; "A halogen that has formula Br."; "bromine"; . a owl:Class; rdfs:label "chlorine atom"; rdfs:subClassOf ; "A halogen that has formula Cl."; "chlorine"; . a owl:Class; rdfs:label "molecular entity"; rdfs:subClassOf ; "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity."; "molecular entity"; """A primary axis of classification under molecular entity is 'organic' vs 'inorganic'. A primary axis of classification under organic moelcular entity is 'macromolecule' vs 'small molecule'. Along the way in each of these hierarchies, it is important to indicate whether members of these classes bear concretizations of genetic sequence information. This is because this criteria is important for distinguishing 'chemical reagents' (which do not bear such information) from 'protein reagents' and 'nucleic acid reagents' (which do bear such information). For this reason, many of the classes below contain an axiom such as 'not (has_part some (bearer_of some (is_concretization_of some 'genetic sequence region')))' """; , . a owl:Class; rdfs:label "cyclic nucleotide"; rdfs:subClassOf ; . a owl:Class; rdfs:label "fluorine atom"; rdfs:subClassOf ; "A halogen that has formula F."; "fluorine"; . a owl:Class; rdfs:label "chemical entity"; rdfs:subClassOf ; "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances."; . a owl:Class; rdfs:label "group"; rdfs:subClassOf , _:2dd359; "A defined linked collection of atoms or a single atom within a molecular entity."; "group", "submolecule", "contiguous chemical group"; "chemical group"; "My reading of the term 'linked' in the definition of ChEBI:chemical group is that this group must be a contiguous, self-connected entity, and not spatially separated across different parts of a molecular entity"; . _:2dd359 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "halogen"; rdfs:subClassOf ; "halogen", "halogens"; . a owl:Class; rdfs:label "inorganic molecular entity"; rdfs:subClassOf , _:2dd369; "A molecular entity that contains no carbon."; rdfs:comment "from eagle-i :a chemical consisting of a well-defined number of atoms covalently bonded together, and containing metal atoms. Inorganic compounds do not contain chemical moities consisting of carbon and hydrogen bonded together. Examples of inorganic compounds are: Salts: sodium chloride (NaCl), magnesium sulfate (MgSO4), Oxides: carbon dioxide (CO2), silicon dioxide (SiO2) and Iron (II, III) oxide (Fe3O4), Acids: hydrogen chloride (HCl) and sulfuric acid (H2SO4), Bases: sodium hydroxide (NaOH)."; . _:2dd369 a owl:Class; owl:complementOf _:2dd379 . _:2dd379 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd389 . _:2dd389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd399 . _:2dd399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd3a9 a owl:Axiom; "axiom here (and on other non-information molecular entities) is necessary to classify molecular reagents accordingly as chemical reagents vs nucleic acid or protein reagents."; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2dd3b9 . _:2dd3b9 a owl:Class; owl:complementOf _:2dd3c9 . _:2dd3c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd3d9 . _:2dd3d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd3e9 . _:2dd3e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "inorganic salt"; rdfs:subClassOf ; . a owl:Class; rdfs:label "iodine atom"; rdfs:subClassOf ; "Chemical element with atomic number 53."; "iodine"; . a owl:Class; rdfs:label "modified amino acid"; owl:equivalentClass _:2dd3f9; rdfs:subClassOf , _:2dd439; "Examples include any naturally-occurring or artificial modifications of amino acids that result in structures not represented in the set of canonical amino acids, such as O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine."; "a non-canonical amino acid that is functionally derived from (ie a variant of) some other amino acid"; "amino acid derivative"; rdfs:comment """Note that here the notion of 'modified' is distinct from our notion of 'experimentally modified' (where the latter holds that there is some experimental modification process that takes as input some unmodified material entity and outputs a modified variant of this same material entity). Being 'modified' merely reflects some physical variation with respect to some reference object or structure- so modified amino acids can be synthesized de novo, such that there is not necessarily some experimental modification process that takes as input some unmodified amino acid and outputs a modified variant. For now we have only claimed the 'reference' set of unmodified amino acids to contain the set of canonical amino acid structures. As canonical amino acids are defined strictly by their molecular structures, any modifications will result in a modified, non-canonical amino acid (e.g. even a natural modification such as a phosphorylation)."""; "This class includes all amino acids, natural or unnatural, that are functional derivatives of / variants of some as of yet undefiend set of foundational, 'unmodified' amino acids (which includes at minimum the set of canonical amino acids). We acknowledge this definition is vague and imprecise, and are working with ChEBI and others to address this. However, we implement this class now with the expectation that users will apply common sense to determine if a given amino acid is modified or not. As a point of reference, see the Sigma catalog entries for 'amino acids' (http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16181993) vs 'modified amino acids' (http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16360557) "; . _:2dd3f9 a owl:Class; owl:intersectionOf _:2dd409 . _:2dd409 rdf:first ; rdf:rest _:2dd429 . _:2dd429 rdf:first _:2dd419; rdf:rest rdf:nil . _:2dd419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd449 a owl:Axiom; "not yet clear if the has functional parent relation is appropriate here, or if we should use the is_variant_of property"; owl:annotatedSource ; owl:annotatedProperty owl:equivalentClass; owl:annotatedTarget _:2dd459 . _:2dd459 a owl:Class; owl:intersectionOf _:2dd469 . _:2dd469 rdf:first ; rdf:rest _:2dd489 . _:2dd489 rdf:first _:2dd479; rdf:rest rdf:nil . _:2dd479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "elemental molecule"; rdfs:subClassOf ; "A molecule all atoms of which have the same atomic number."; rdfs:comment "elemental molecules contain more than one atom of the same type bonded together, whereas atomic moelcular entities represent single, independently existing atoms "; . a owl:Class; rdfs:label "nitrogen atom"; rdfs:subClassOf ; "nitrogen"; . a owl:Class; rdfs:label "nonmetal atom"; rdfs:subClassOf ; "nonmetal"; . a owl:Class; rdfs:label "nucleoside phosphate"; rdfs:subClassOf ; "a nucleoside-containing small molecule that contains at least one phosphate group bound to its sugar ring"; . a owl:Class; rdfs:label "oxygen atom"; rdfs:subClassOf ; "A chalcogen that has formula O."; "oxygen"; . a owl:Class; rdfs:label "sodium chloride"; rdfs:subClassOf ; "An inorganic chloride salt having sodium(1+) as the counterion."; "sodium chloride"; . a owl:Class; rdfs:label "sulfur atom"; rdfs:subClassOf ; "A chalcogen that has formula S."; "sulfur"; . a owl:Class; rdfs:label "boron atom"; rdfs:subClassOf ; "A boron group element atom that has formula B."; "boron"; . a owl:Class; rdfs:label "selenium atom"; rdfs:subClassOf ; "A chalcogen that has formula Se."; "selenium"; . a owl:Class; rdfs:label "silicon atom"; rdfs:subClassOf ; "A carbon group element atom that has formula Si."; "silicon"; . a owl:Class; rdfs:label "carbon atom"; rdfs:subClassOf ; "A carbon group element atom that has formula C."; "carbon"; . a owl:Class; rdfs:label "phosphorus atom"; rdfs:subClassOf ; "A pnictogen that has formula P."; "phosphorus"; . a owl:Class; rdfs:label "dITP"; rdfs:subClassOf ; "2'-deoxyinosine 5'-(tetrahydrogen triphosphate)"; "A deoxyinosine phosphate compound having a triphosphate group at the 5'-position."; . a owl:Class; rdfs:label "mononucleotide"; rdfs:subClassOf ; "Mononucleotide", "mononucleotide"; . a owl:Class; rdfs:label "protium atom"; rdfs:subClassOf ; "The stable isotope of hydrogen with relative atomic mass 1.007825 and a natural abundance of 99.9885 atom percent (from Greek pirhoomegatauomicronsigma, first)."; "protium"; . a owl:Class; rdfs:label "deuterium atom"; rdfs:subClassOf ; "The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second)."; "deuterium"; . a owl:Class; rdfs:label "tritium atom"; rdfs:subClassOf , _:2dd499; "The radioactive isotope of hydrogen with relative atomic mass 3.016049 and half-life of 12.33 years (from Greek taurhoiotatauomicronsigma, third)."; "tritium"; . _:2dd499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "glycine residue"; rdfs:subClassOf , _:2dd4a9; "glycine residue"; . _:2dd4a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-cysteine residue"; rdfs:subClassOf , _:2dd4b9; "L-cysteine residue"; . _:2dd4b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-arginine residue"; rdfs:subClassOf , _:2dd4c9; "L-arginine residue"; . _:2dd4c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-tryptophan residue"; rdfs:subClassOf , _:2dd4d9; "L-tryptophan residue"; . _:2dd4d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-aspartic acid residue"; rdfs:subClassOf , _:2dd4e9; "L-aspartic acid residue"; . _:2dd4e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-lysine residue"; rdfs:subClassOf , _:2dd4f9; "L-lysine residue"; . _:2dd4f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-glutamic acid residue"; rdfs:subClassOf , _:2dd509; "L-glutamic acid residue"; . _:2dd509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-histidine residue"; rdfs:subClassOf , _:2dd519; "L-histidine residue"; . _:2dd519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-phenylalanine residue"; rdfs:subClassOf , _:2dd529; "L-phenylalanine residue"; . _:2dd529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-serine residue"; rdfs:subClassOf , _:2dd539; "L-serine residue"; . _:2dd539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-selenocysteine residue"; rdfs:subClassOf , _:2dd549; "L-selenocysteine residue"; . _:2dd549 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-leucine residue"; rdfs:subClassOf , _:2dd559; "L-leucine residue"; . _:2dd559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-isoleucine residue"; rdfs:subClassOf , _:2dd569; "L-isoleucine residue"; . _:2dd569 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-glutamine residue"; rdfs:subClassOf , _:2dd579; "L-glutamine residue"; . _:2dd579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-threonine residue"; rdfs:subClassOf , _:2dd589; "L-threonine residue"; . _:2dd589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-valine residue"; rdfs:subClassOf , _:2dd599; "L-valine residue"; . _:2dd599 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "helium atom"; rdfs:subClassOf ; "A s-block element atom that has formula He."; "helium"; . a owl:Class; rdfs:label "helium-3 atom"; rdfs:subClassOf ; "The stable isotope of helium with relative atomic mass 3.016029. The least abundant (0.000137 atom percent) isotope of naturally occurring helium."; "helium-3"; . a owl:Class; rdfs:label "helium-4 atom"; rdfs:subClassOf ; "The stable isotope of helium with relative atomic mass 4.002603. The most abundant (99.99 atom percent) isotope of naturally occurring helium."; "helium-4"; . a owl:Class; rdfs:label "astatine atom"; rdfs:subClassOf ; "A halogen that has formula At."; "astatine"; . a owl:Class; rdfs:label "germanium atom"; rdfs:subClassOf ; "A carbon group element atom that has formula Ge."; "germanium"; . a owl:Class; rdfs:label "monoatomic entity"; rdfs:subClassOf ; "A monoatomic entity is a molecular entity consisting of a single atom."; rdfs:comment "atomic moelcular entities represent single, independently existing atoms, whereas ChEBI:atoms represent any atom, including those that are part of larger molecules"; "atomic molecular entity"; . a owl:Class; rdfs:label "inorganic group"; rdfs:subClassOf ; "Any substituent group which does not contain carbon."; "inorganic chemical group"; . a owl:Class; rdfs:label "organic group"; rdfs:subClassOf ; "Any substituent group or skeleton containing carbon."; "organic chemical group"; . a owl:Class; rdfs:label "atom"; rdfs:subClassOf ; "A chemical entity constituting the smallest component of an element having the chemical properties of the element."; "atom"; "clarify why this is not a chemical group (which is defined as a defined linked collection of atoms or a single atom within a molecular entity.)"; . a owl:Class; rdfs:label "elemental molecular entity"; rdfs:subClassOf ; "A molecular entity all atoms of which have the same atomic number."; rdfs:comment "elemental molecular entities include stand-alone atoms (atomic molecular entities) and molecules comprised of only one type of atom (elemental molecules)"; . a owl:Class; rdfs:label "noble gas atom"; rdfs:subClassOf ; "noble gas", "noble gases"; . a owl:Class; rdfs:label "neon atom"; rdfs:subClassOf ; "A noble gas atom that has formula Ne."; "neon"; . a owl:Class; rdfs:label "radon atom"; rdfs:subClassOf ; "A noble gas atom that has formula Rn."; "radon"; . a owl:Class; rdfs:label "radon-220 atom"; rdfs:subClassOf ; "A radon atom that has formula Rn."; "radon-220"; . a owl:Class; rdfs:label "radon-222 atom"; rdfs:subClassOf ; "A radon atom that has formula Rn."; "radon-222"; . a owl:Class; rdfs:label "radon-219 atom"; rdfs:subClassOf ; "A radon atom that has formula Rn."; "radon-219"; . a owl:Class; rdfs:label "metal atom"; rdfs:subClassOf ; "metal"; . a owl:Class; rdfs:label "biomacromolecule"; rdfs:subClassOf ; "A macromolecule formed by a living organism."; "biopolymer"; "not needed after implementation of new info vs non-info molecular entity split in org molecular entity hierarchy"; "obsolete_biomacromolecule"; , . a owl:Class; rdfs:label "nucleic acid"; rdfs:subClassOf , , _:2dd5a9, _:2dd5b9, _:2dd5f9, _:2dd609; "A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid."; "nucleic acids"; "A polynucleotide comprised of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid."; "Need to ask ChEBI if polynucleotides containing one or more analog residues qualify as nucleic acids, or if they are limited to polynucleotides containing only natural, canonical nucleotides."; , . _:2dd5a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd5b9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2dd5c9 . _:2dd5c9 a owl:Class; owl:unionOf _:2dd5d9 . _:2dd5d9 rdf:first ; rdf:rest _:2dd5e9 . _:2dd5e9 rdf:first ; rdf:rest rdf:nil . _:2dd5f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd609 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "ribonucleic acid"; rdfs:subClassOf ; "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins."; "ribonucleic acid", "ribonucleic acids"; """MHB: defined in ChEBI as 'naturally occuring\". Imolications of this definition for modeling synthetic/processed material RNA reagents as children? Note that DNA is not defined using this language of being 'naturally ocurring'."""; ; , . a owl:Class; rdfs:label "messenger RNA"; rdfs:subClassOf ; "An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation."; "messenger RNA"; . a owl:Class; rdfs:label "canonical amino-acid residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "alpha-amino acid"; rdfs:subClassOf ; "alpha-amino acid"; "obsolete_alpha-amino acid"; . a owl:Class; rdfs:label "amino-acid residue"; rdfs:subClassOf , , _:2dd619, _:2dd629, _:2dd639; "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue."; "amino-acid residue"; . _:2dd619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd639 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "amino acid"; rdfs:subClassOf ; "A carboxylic acid containing one or more amino groups."; "an orgnaic small molecule containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen"; "natural amino acid"; rdfs:comment "Note that this class is defined loosely enough such that unnatural small molecules that meet the enumerated structural requirements can qualify as aas"; . a owl:Class; rdfs:label "oxygen-18 atom"; rdfs:subClassOf ; "The stable isotope of oxygen with relative atomic mass 17.999160 and 0.205 atom percent natural abundance."; "oxygen-18"; . a owl:Class; rdfs:label "oxygen-16 atom"; rdfs:subClassOf ; "The stable isotope of oxygen with relative atomic mass 15.994914. The most abundant (99.76 atom percent) isotope of naturally occurring oxygen."; "oxygen-16"; . a owl:Class; rdfs:label "oxygen-17 atom"; rdfs:subClassOf ; "The stable isotope of oxygen with relative atomic mass 16.999131. The least abundant (0.038 atom percent) isotope of naturally occurring oxygen."; "oxygen-17"; . a owl:Class; rdfs:label "nucleoside"; rdfs:subClassOf ; "Nucleoside", "nucleoside", "nucleosides"; "Nucleosides are ribosyl or deoxyribosyl derivatives of the pyrimidine or purine bases adenine, guanine, xanthine, thymine, cytosine, and uracil."; . a owl:Class; rdfs:label "macromolecule"; rdfs:subClassOf ; "A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass."; "macromolecule"; "obsolete_macromolecule"; "was incompatible with design decision to use organic/inorganic as primary axis of classificaiton for chemical/molecular entities (as macromolecules could be either, and didnt want to make this into an equivalent class to allow its continued use). "; , . a owl:Class; rdfs:label "monosaccharide"; rdfs:subClassOf , , , _:2dd649; "Monosaccharide", "monosaccharide", "monosaccharides"; "Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group."; . _:2dd649 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "protein"; rdfs:subClassOf ; "A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome."; "proteins"; "obsolete_protein"; "replaced with PRO:amino acid chain > protein"; , . a owl:Class; rdfs:label "carbon-14 atom"; rdfs:subClassOf , _:2dd659; "A carbon atom that has formula C."; "carbon-14"; . _:2dd659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "carbon-13 atom"; rdfs:subClassOf ; "A carbon atom that has formula C."; "carbon-13", "carbon-13 atom"; . a owl:Class; rdfs:label "carbon-11 atom"; rdfs:subClassOf ; "A carbon atom that has formula C."; "carbon-11"; . a owl:Class; rdfs:label "carbon-10 atom"; rdfs:subClassOf ; "A carbon atom that has formula C."; "carbon-10"; . a owl:Class; rdfs:label "carbon-12 atom"; rdfs:subClassOf ; "A carbon atom that has formula C."; "carbon-12"; . a owl:Class; rdfs:label "oxygen-15 atom"; rdfs:subClassOf ; "The radioactive isotope of oxygen with relative atomic mass 15.003065. The longest-lived oxygen radionuclide with half-life of 122.2 s."; "oxygen-15"; . a owl:Class; rdfs:label "oxygen-19 atom"; rdfs:subClassOf ; "An oxygen atom that has formula O."; "oxygen-19"; . a owl:Class; rdfs:label "nitrogen-15 atom"; rdfs:subClassOf ; "The stable isotope of nitrogen with relative atomic mass 15.000109. The least abundant (0.368 atom percent) isotope of naturally occurring nitrogen."; "nitrogen-15"; . a owl:Class; rdfs:label "nitrogen-13 atom"; rdfs:subClassOf ; "The radioactive isotope of nitrogen with relative atomic mass 13.0057386. The longest-lived nitrogen radionuclide with half-life of 9.965 min."; "nitrogen-13"; . a owl:Class; rdfs:label "nitrogen-16 atom"; rdfs:subClassOf ; "nitrogen-16"; . a owl:Class; rdfs:label "nitrogen-17 atom"; rdfs:subClassOf ; "nitrogen-17"; . a owl:Class; rdfs:label "nitrogen-14 atom"; rdfs:subClassOf ; "The stable isotope of nitrogen with relative atomic mass 14.003074. The most abundant (99.63 atom percent) isotope of naturally occurring nitrogen."; "nitrogen-14"; . a owl:Class; rdfs:label "fluorine-18 atom"; rdfs:subClassOf ; "The radioactive isotope of fluorine with relative atomic mass 18.000938. The longest-lived fluorine radionuclide with half-life of 109.77 min."; "fluorine-18"; . a owl:Class; rdfs:label "fluorine-19 atom"; rdfs:subClassOf ; "The stable isotope of fluorine with relative atomic mass 18.998403 and nuclear spin (1)/2."; "fluorine-19"; . a owl:Class; rdfs:label "nucleotide"; rdfs:subClassOf ; "A nucleotide is a nucleoside phosphate. It is composed of a nucleobase, a sugar moiety and one to three phosphate groups."; "Nucleotide"; . a owl:Class; rdfs:label "helium-6 atom"; rdfs:subClassOf ; "The radioactive isotope of helium with relative atomic mass 6.01889 and half-life of 806.7 ms."; "helium-6"; . a owl:Class; rdfs:label "helium-8 atom"; rdfs:subClassOf ; "The radioactive isotope of helium with relative atomic mass 8.03392 and half-life of 119.0 ms."; "helium-8"; . a owl:Class; rdfs:label "nucleoside tetraphosphate"; rdfs:subClassOf ; . a owl:Class; rdfs:label "nucleoside pentaphosphate"; rdfs:subClassOf ; . a owl:Class; rdfs:label "sodium phosphate"; rdfs:subClassOf , _:2dd669; "sodium phosphate"; . _:2dd669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "phosphorus-31 atom"; rdfs:subClassOf ; "The stable isotope of phosphorus with relative atomic mass 30.973762 and nuclear spin (1)/2."; "phosphorus-31"; . a owl:Class; rdfs:label "phosphorus-32 atom"; rdfs:subClassOf , _:2dd679; "The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days."; "phosphorus-32"; . _:2dd679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "phosphorus-33 atom"; rdfs:subClassOf , _:2dd689; "The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2."; "phosphorus-33"; . _:2dd689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "silicon-29 atom"; rdfs:subClassOf ; "The stable isotope of silicon with relative atomic mass 28.9764947, 4.683 atom percent natural abundancy, and nuclear spin (1)/2."; "silicon-29"; . a owl:Class; rdfs:label "silicon-28 atom"; rdfs:subClassOf ; "The stable isotope of silicon with relative atomic mass 27.9769265. The most abundant (92.23 atom percent) isotope of naturally occurring silicon."; "silicon-28"; . a owl:Class; rdfs:label "silicon-30 atom"; rdfs:subClassOf ; "The stable isotope of silicon with relative atomic mass 29.9737702. The least abundant (3.09 atom percent) isotope of naturally occurring silicon."; "silicon-30"; . a owl:Class; rdfs:label "silicon-31 atom"; rdfs:subClassOf ; "The radioactive isotope of silicon with relative atomic mass 30.975363, half-life of 2.62 hours and nuclear spin (3)/2."; "silicon-31"; . a owl:Class; rdfs:label "silicon-32 atom"; rdfs:subClassOf ; "The radioactive isotope of silicon with relative atomic mass 31.974148. The longest-lived silicon radionuclide with half-life of 172 years."; "silicon-32"; . a owl:Class; rdfs:label "sulfur-32 atom"; rdfs:subClassOf ; "The stable isotope of sulfur with relative atomic mass 31.972071. The most abundant (95.02 atom percent) isotope of naturally occurring sulfur."; "sulfur-32"; . a owl:Class; rdfs:label "sulfur-33 atom"; rdfs:subClassOf ; "The stable isotope of sulfur with relative atomic mass 32.9714585, 0.75 atom percent natural abundance, and nuclear spin (3)/2."; "sulfur-33"; . a owl:Class; rdfs:label "sulfur-34 atom"; rdfs:subClassOf ; "The stable isotope of sulfur with relative atomic mass 33.9678668 and 4.21 atom percent natural abundance."; "sulfur-34"; . a owl:Class; rdfs:label "sulfur-36 atom"; rdfs:subClassOf ; "The stable isotope of sulfur with relative atomic mass 35.9670809. The least abundant (0.02 atom percent) isotope of naturally occurring sulfur."; "sulfur-36"; . a owl:Class; rdfs:label "sulfur-35 atom"; rdfs:subClassOf , _:2dd699; "The radioactive isotope of sulfur with relative atomic mass 34.9690322 and nuclear spin (3)/2. The longest-lived sulfur radionuclide with half-life of 87.5 days."; "sulfur-35"; . _:2dd699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "sulfur-37 atom"; rdfs:subClassOf ; "The radioactive isotope of sulfur with relative atomic mass 36.9711257 and half-life of 5.05 min."; "sulfur-37"; . a owl:Class; rdfs:label "sulfur-38 atom"; rdfs:subClassOf ; "The radioactive isotope of sulfur with relative atomic mass 37.97116 and half-life of 170.3 min."; "sulfur-38"; . a owl:Class; rdfs:label "digoxigenin"; rdfs:subClassOf , , _:2dd6a9; "3beta,12beta,14-trihydroxy-5beta-card-20(22)-enolide"; "A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta,- 12beta- and 14beta-positions."; ; , . _:2dd6a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-alanine residue"; rdfs:subClassOf , _:2dd6b9; "L-alanine residue"; . _:2dd6b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "UMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "L-tyrosine residue"; rdfs:subClassOf , _:2dd6c9; "L-tyrosine residue"; . _:2dd6c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "zebularine"; rdfs:subClassOf , , , , _:2dd6d9, _:2dd729, _:2dd739; "1-beta-D-ribofuranosylpyrimidin-2(1H)-one", "Zebularine"; "A pyrimidine ribonucleoside that has formula C9H12N2O5."; "http://www.caymanchem.com/app/template/Product.vm/catalog/10975"; "a cytidine analog that acts as a DNA methylation inhibitor by forming a covalent complex with DNA methyltransferases (DNMTs) By stabilizing the binding of DNMTs to DNA, zebularine hinders methylation and decreases dissociation, trapping DNMT and preventing its turnover"; ; . _:2dd6d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd6e9 . _:2dd6e9 a owl:Class; owl:intersectionOf _:2dd6f9 . _:2dd6f9 rdf:first ; rdf:rest _:2dd719 . _:2dd719 rdf:first _:2dd709; rdf:rest rdf:nil . _:2dd709 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd749 . _:2dd749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "double-stranded DNA"; rdfs:subClassOf , _:2dd759; "Double-stranded DNA"; ; . _:2dd759 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd769 . _:2dd769 a owl:Class; owl:intersectionOf _:2dd779 . _:2dd779 rdf:first ; rdf:rest _:2dd799 . _:2dd799 rdf:first _:2dd789; rdf:rest rdf:nil . _:2dd789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd7a9 . _:2dd7a9 a owl:Class; owl:intersectionOf _:2dd7b9 . _:2dd7b9 rdf:first ; rdf:rest _:2dd7d9 . _:2dd7d9 rdf:first _:2dd7c9; rdf:rest _:2dd7f9 . _:2dd7c9 a owl:Restriction; owl:onProperty ; owl:hasValue . _:2dd7f9 rdf:first _:2dd7e9; rdf:rest rdf:nil . _:2dd7e9 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . _:2dd809 a owl:Axiom; ""; "exploratory axiom - will have to be refined to align with OBI model when it is finished"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2dd819 . _:2dd819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd829 . _:2dd829 a owl:Class; owl:intersectionOf _:2dd839 . _:2dd839 rdf:first ; rdf:rest _:2dd859 . _:2dd859 rdf:first _:2dd849; rdf:rest rdf:nil . _:2dd849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd869 . _:2dd869 a owl:Class; owl:intersectionOf _:2dd879 . _:2dd879 rdf:first ; rdf:rest _:2dd899 . _:2dd899 rdf:first _:2dd889; rdf:rest _:2dd8b9 . _:2dd889 a owl:Restriction; owl:onProperty ; owl:hasValue . _:2dd8b9 rdf:first _:2dd8a9; rdf:rest rdf:nil . _:2dd8a9 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "locked nucleic acid"; rdfs:subClassOf , _:2dd8c9, _:2dd8d9 . _:2dd8c9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2dd8d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . "Nucleic acid polymers where the residues contain 'locked' deoxyribose units and are linked by phosphodiester bonds. The deoxyribose unit conformation is 'locked' by a 2'-C,4'-C-oxymethylene link."; "locked nucleic acid", "LNA"; rdfs:comment "LNA oligomers are synthesized chemically. The locked ribose conformation enhances base stacking and backbone pre-organization. This significantly increases the hybridization properties (melting temperature) of oligonucleotides"; . a owl:Class; rdfs:label "peptide nucleic acid"; rdfs:subClassOf , _:2dd8e9, _:2dd8f9; "Nucleic acids where the sugar-phosphate backbone has been replaced by a neutral polyamide backbone such as N-(2-aminoethyl)glycine units."; "peptide nucleic acid"; rdfs:comment """these are nucleic acid analogs where the ribose-sugar backbone of DNA and RNA is replaced by a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The various purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. The name is somewhat of a misnomer as PNA is not an acid. Synthetic peptide nucleic acid oligomers have been used in recent years in molecular biology procedures, diagnostic assays and antisense therapies. Due to their higher binding strength it is not necessary to design long PNA oligomers for use in these roles, which usually require oligonucleotide probes of 20–25 bases"""; . _:2dd8e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dd8f9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "argon atom"; rdfs:subClassOf ; "A noble gas atom that has formula Ar."; "argon"; . a owl:Class; rdfs:label "hydrogen atom"; rdfs:subClassOf ; "A s-block element atom that has formula H."; "hydrogen"; . a owl:Class; rdfs:label "krypton atom"; rdfs:subClassOf ; "A noble gas atom that has formula Kr."; "krypton"; . a owl:Class; rdfs:label "xenon atom"; rdfs:subClassOf ; "A noble gas atom that has formula Xe."; "xenon"; . a owl:Class; rdfs:label "canonical nucleotide residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "canonical deoxyribonucleotide residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "canonical ribonucleotide residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "dTMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "AMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "CMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "nucleotide residue"; rdfs:subClassOf , , _:2dd909, _:2dd919, _:2dd929; . _:2dd909 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd929 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dCMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "dGMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "dAMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "GMP residue"; rdfs:subClassOf ; . a owl:Class; rdfs:label "L-proline residue"; rdfs:subClassOf , _:2dd939; "L-proline residue"; . _:2dd939 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-asparagine residue"; rdfs:subClassOf , _:2dd949; "L-asparagine residue"; . _:2dd949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organic molecular entity"; rdfs:subClassOf ; "Any molecular entity that contains carbon."; "Talk here about choice to model at top level the dichotomy between infor and non-info macromolecules - see INTRODUCTION on ChEBI 2008 NAR paper for support here."; rdfs:comment "From eagle-i : A chemical substance comprised of two or more elements combined bonded in a fixed ratio and containing carbon and hydrogen atoms. The following elements can also be found in organic compounds: Nitrogen (N); oxygen (O), Fluor (F), phosphorous (P), sulfur (S), chlorine (Cl), selenium (Se), bromine (Br), iodine (I). Organic compounds do not contain metals. Examples of organic compounds are: methane (CH4), pyrrole (C4H5N), Methionine (C3H7NO2S), Selenocysteine (C3H7NO2Se), Phenoxymethylpenicillin (C16H18N2O5S) and Adenosine triphosphate (C10H16N5O13P3)."; , . a owl:Class; rdfs:label "DAPI"; rdfs:subClassOf , , , _:2dd959, _:2dd969, _:2dd979; "2-(4-carbamimidoylphenyl)-1H-indole-6-carboximidamide"; "An indole that has formula C16H15N5."; ; . _:2dd959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dd979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Alexa Fluor 546"; rdfs:subClassOf ; "An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3."; "sodium 6-(2-carboxy-3,4,6-trichloro-5-{[2-({6-[(2,5-dioxopyrrolidin-1-yl)oxy]-6-oxohexyl}amino)-2-oxoethyl]thio}phenyl)-2,2,4,8,10,10-hexamethyl-3,4,5a,8,9,10,11,12a-octahydro-2H-pyrano[3,2-g:5,6-g']diquinolin-1-ium-12,14-disulfonate"; ; . a owl:Class; rdfs:label "dextran"; rdfs:subClassOf ; "A (1->6)-alpha-D-glucan which has extra branching consisting of (1->2), (1->3) or (1->4) linkages."; "http://en.wikipedia.org/wiki/Dextran"; "a polysachharide that is a complex, branched glucan made of many glucose molecules, composed of chains of varying lengths (from 3 to 2000 kilodaltons)."; ; . a owl:Class; rdfs:label "boron-11"; rdfs:subClassOf ; "The stable isotope of boron with relative atomic mass 11.009306, 80.1 atom percent natural abundance and nuclear spin 3/2."; "boron-11"; . a owl:Class; rdfs:label "xenon-129 atom"; rdfs:subClassOf ; "The stable isotope of xenon with relative atomic mass 128.904780, 26.4 atom percent natural abundance and nuclear spin 1/2."; "xenon-129"; . a owl:Class; rdfs:label "selenium-77 atom"; rdfs:subClassOf ; "The stable isotope of selenium with relative atomic mass 76.919915, 7.60 atom percent natural abundance and nuclear spin 1/2."; "selenium-77"; . a owl:Class; rdfs:label "iodine-127 atom"; rdfs:subClassOf ; "The stable isotope of iodine with relative atomic mass 126.904468, 100 atom percent natural abundance and nuclear spin 5/2."; "iodine-127"; . a owl:Class; rdfs:label "iodine-129 atom"; rdfs:subClassOf ; "The isotope of iodine with relative atomic mass 128.904988, and nuclear spin 7/2."; "iodine-129"; . a owl:Class; rdfs:label "Alexa Fluor 488"; rdfs:subClassOf ; "A fluorescent dye of absorption wavelength 495 nm and emission wavelength 519 nm, derived from a 3,6-diaminoxanthenium-4,5-disulfate."; ; . a owl:Class; rdfs:label "Alexa Fluor 555"; rdfs:subClassOf ; "4-(6-amino-3-imino-4,5-disulfo-3H-xanthen-9-yl)benzene-1,3-dicarboxylic acid"; "A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate."; ; . a owl:Class; rdfs:label "bromine-79 atom"; rdfs:subClassOf ; "The stable isotope of bromine with relative atomic mass 78.918338, 50.69 atom percent natural abundance and nuclear spin 3/2."; . a owl:Class; rdfs:label "germanium-73 atom"; rdfs:subClassOf ; "The stable isotope of germanium with relative atomic mass 72.923459, 7.73 atom percent natural abundance and nuclear spin 9/2."; . a owl:Class; rdfs:label "chemical substance"; rdfs:subClassOf ; "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types."; . a owl:Class; rdfs:label "pure substance"; rdfs:subClassOf ; "A pure substance is a chemical substance composed of multiple molecules, which are all of the same kind."; "pure chemical substance"; . a owl:Class; rdfs:label "mixture"; rdfs:subClassOf ; "A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind."; "chemical mixture"; . a owl:Class; rdfs:label "nucleobase-containing molecular entity"; rdfs:subClassOf ; "Any compound that has a nucleobase as a part."; "obsolete_ nucleobase containing molecular entity"; "replaced with nucleosidic small molecule (because the chebi class here includes polynucleotides)"; . a owl:Class; rdfs:label "carbohydrate derivative"; rdfs:subClassOf , _:2dd989; "Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds."; . _:2dd989 a owl:Class; owl:complementOf _:2dd999 . _:2dd999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd9a9 . _:2dd9a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd9b9 . _:2dd9b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "TTP"; rdfs:subClassOf ; "5-methyluridine 5'-(tetrahydrogen triphosphate)"; "A pyrimidine ribonucleoside 5'-triphosphate in which the pyrimidine element is 5-methyluracil."; . a owl:Class; rdfs:label "single-stranded DNA"; rdfs:subClassOf , _:2dd9c9; "Single-stranded DNA"; ; , . _:2dd9c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dd9d9 . _:2dd9d9 a owl:Class; owl:intersectionOf _:2dd9e9 . _:2dd9e9 rdf:first ; rdf:rest _:2dda09 . _:2dda09 rdf:first _:2dd9f9; rdf:rest rdf:nil . _:2dd9f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dda19 . _:2dda19 a owl:Class; owl:intersectionOf _:2dda29 . _:2dda29 rdf:first ; rdf:rest _:2dda49 . _:2dda49 rdf:first _:2dda39; rdf:rest _:2dda69 . _:2dda39 a owl:Restriction; owl:onProperty ; owl:hasValue . _:2dda69 rdf:first _:2dda59; rdf:rest rdf:nil . _:2dda59 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "cell line culturing"; rdfs:subClassOf , , _:2dda79, _:2dda89, _:2dda99, _:2ddaa9; "a processual entity that is the collection of all processes directly involved in maintenance of an active cell culture, following its initial establishment "; "cell culture maintenance"; "OBI:maintaining cell culture"; "PERSON: Matthew Brush"; rdfs:comment "OBO:maintaining cell culture definition - a protocol application in which cells are kept alive in a defined environment outside of an organism."; "CLO, OBI (confirm that CLO would consider this and child terms general enough to cover cell culture maintenance (ie not just cell line maintenance) - I modeled it here using this approach, as it seems more useful to use these classes in this way. Note too that this makes the CLO class have same semantics as the OBI:maintaining cell culture class . . if the CLO class is not intended to cover cultures, then I should import the OBI class here"; . _:2dda79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dda89 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dda99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddaa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_cell line"; rdfs:subClassOf ; "adapted from definitions from EFO:cell line and OBI:cell line culture"; "PERSON:Matthew Brush"; "the primary axis of classification for the cell line hierarchy is based on the distinction between permanent vs primary cell lines, as these represent mutually exclusive categories under which all cell line classes can be asserted. Accordingly, classes representing established, named cell lines (eg HeLa, PC-12, NIH-3T3) are asserted as children of 'permanent cell line' or 'primary cell line'. A number of additional equivalent classes (e.g. clonal cell line, expression cell line, disease-model cell line) have also been created and logically defined, such that asserted classes representing named cell lines can be classified into multiple categories based on the axioms describing their respective attributes. Similarly, instances of cell lines described in databases or catalogs using this model can be similarly classified in along multiple dimensions."; "A cell culture that is descended through one or more subcultures from a single primary cell culture. The cell population is homogenous but not neccessarily clonal. Cell lines are established upon the first subculture of a primary cell culture, whereby a subset of cells from the primary culture are separated into fresh media for continued propagation."; "CLO: Note that the ReO-preferred meaning of cell line is fundamentally different the CLO definition below, which defines cell lines as having the ability to proliferate indefinitely. By contrast, ReO:cell lines can be either permanent (proliferate indefinitely) or primary (do not proliferate indefinately). This term should live in CLO, but we need to come to agreement on its definition. "; "OBI_0100062 cell line culture"; "obsoleted when implemented new cell culture hierarchy . . . but ultimately need to consult CLO and see what the intended coverage of this class is so we can import it back to replace one of our placeholder classes (likely 'multicellular organism cell culture')" . a owl:Class; rdfs:label "suspension cell line culturing"; rdfs:subClassOf , _:2ddab9; "a cell culturing technique where cells do not require a surface for growth and differentiation. This method is appropriate for cells that are adapted to suspension culture or cells that are non-adhesive (e.g. hematopoietic cells)", "suspension cell line culturing is a cell line culturing method where cells do not require a surface for growth and differentiation. This method is appropriate for cells that are adapted to suspension culture or cells that are non-adhesive (e.g. hematopoietic cells)"; . _:2ddab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ddac9 . _:2ddac9 a owl:Class; owl:intersectionOf _:2ddad9 . _:2ddad9 rdf:first ; rdf:rest _:2ddaf9 . _:2ddaf9 rdf:first _:2ddae9; rdf:rest rdf:nil . _:2ddae9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "adherent cell line culturing"; rdfs:subClassOf , _:2ddb09; "a cell line culturing technique where cells require a surface for growth and differentiation.", "adherent cell line culturing is a cell line culturing method where cells require a surface for growth and differentiation."; . _:2ddb09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ddb19 . _:2ddb19 a owl:Class; owl:intersectionOf _:2ddb29 . _:2ddb29 rdf:first ; rdf:rest _:2ddb49 . _:2ddb49 rdf:first _:2ddb39; rdf:rest rdf:nil . _:2ddb39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; owl:equivalentClass _:2ddb59; rdfs:subClassOf , _:2ddb99, _:2ddba9; owl:disjointWith ; """Class Naming Conventions: 1. The term 'primary' is avoided in the preferred label as it has different meanings in different communities (can mean 'not yet passaged' or 'no immortalized'). In communities where this is the case, users can choose to apply the term 'primary' in their applications as they desire. However, in ReO we avoid the use of 'primary' due to its ambiguity (we do however make 'primary cell culture' an alternative term for 'unpassaged cell culture', since there is no dispute that such a culture qualifies as primary). 2. The term 'line' is also subject to varied interpretation (can refer to a culture that is immortalized, or a culture that has been passaged). Here, we use 'line' only in cases where the culture has been immortalized, and use 'culture' in labels of classes that are not immortal."""; "All particular multicellular organism cell culture classes (eg HeLa, 3T3, HEK293, etc) should be asserted under the immortal cell line or mortal cell culture branches, and axioms added to allow classification under appropriate equivalent classes. "; "a multicellular organism cell culture that is not immortalized and thus not capable of indefinite proliferation in vitro. A mortal cell culture divides a limited number of times before undergoing senescence."; "OBI and CLO: clarify intended meaning of the classes 'primary cell culture' in OBI and 'primary cell line' and CLO, to see which can be re-used or xrefed here. E.g OBI:primary cell culture may be a xref here, assuming OBI intendes this class to refer to cell cultures that are not immortalized"; "PERSON: Matthew Brush"; "mortal cell culture"; "primary MEF cell cultures, primary neuron cultures"; . _:2ddb59 a owl:Class; owl:intersectionOf _:2ddb69 . _:2ddb69 rdf:first ; rdf:rest _:2ddb89 . _:2ddb89 rdf:first _:2ddb79; rdf:rest rdf:nil . _:2ddb79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddb99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddba9 a owl:Class; owl:complementOf _:2ddbb9 . _:2ddbb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell line", "permanent cell line"; owl:equivalentClass _:2ddbc9; rdfs:subClassOf , , _:2ddc09, _:2ddc19, _:2ddc69; rdfs:comment "A cell line is a cell factor which describes a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism. The cells of such a population share common characteristics.", "Immortal cell lines can result from several different processes : (1) an intentional in vitro immortalization process whereby specific genetic alterations known to confer immortality are introduced, or cells are treated with a mutagen and immortalized cells selected based on their continued proliferation, or through hybridoma technology whereby an immortal cancer cells are fused with mortal cells to generate a new immortal cell line; (2) isolation and culturing of cells from a malignant cancer that underwent immortlaizing transformation events in vivo to enable continuous growth in culture. (3) spontaneous immortalizing mutations that occur in culture."; "Atwood et al (2000) OED of Biochemistry and Molecular Biology, Oxford University Press.", "MO_562"; "James Malone", "Jie Zheng", "Tomasz Adamusiak", "PERSON: Matthew Brush"; "OBI (is this eq to OBI: immortalized cell line culture - yes, assuming that this is meant to cover all immortal lines, and not just those immortalized through some in vitro immortalization process . . . need to follow up with them on this point - already posted a tracker item but not yet resolved)"; "PERSON: Matthew Brush"; "permanent cell line", "established cell line", "cell line", "'continuous cell line'"; "HeLa cell line, CHO cell line, immortalized MEF cell lines"; "immortal cell line"; "Note also that the term 'line' is subject to varied interpretation (can refer to a culture that is immortalized, or a culture that has been passaged). Here, we use 'line' only in cases where the culture has been immortalized, and use 'culture' in labels of classes that are not immortal. Thus, all children of 'immortal cell line' are called lines (and 'immortal' is not included in their labels)."; "a cell line that can be passaged in an infinite number of generations (i.e., immortalized)."; "http://en.wikipedia.org/wiki/Immortalised_cell_line"; "a multicellular organism cell culture that is able to proliferate indefinitely if given sufficient space and nutrients."; ; . _:2ddbc9 a owl:Class; owl:intersectionOf _:2ddbd9 . _:2ddbd9 rdf:first ; rdf:rest _:2ddbf9 . _:2ddbf9 rdf:first _:2ddbe9; rdf:rest rdf:nil . _:2ddbe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddc09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddc19 a owl:Class; owl:unionOf _:2ddc39 . _:2ddc39 rdf:first _:2ddc29; rdf:rest _:2ddc59 . _:2ddc29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddc59 rdf:first _:2ddc49; rdf:rest rdf:nil . _:2ddc49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddc69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddc79 a owl:Axiom; "There are no 'passaged' or 'unpassaged' immortal cell line subclasses here (as there are for mortal cell cultures), as it is presumed that passaging is part of the immortalization process. However, if we say that immortal cell lines can be created through culturing of a cell or cell population that has been immortalized 'naturally' through an in vivo malignant transformation, then it would be possible to have a unpassaged immortal cell line. This, however, we believe to be a very rare outlier, as all such cell lines are typically passaged multiple times before their use in an experiment to 'establish' the line and define its growth conditions. Thus, we include an axiom that all immortal cell lines are output of some cell passaging. As a result, immortal cell lines derived from cancer cells are not considered here unless they have been passaged."; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2ddc89 . _:2ddc89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "mixed adherent and suspension cell line culturing"; rdfs:subClassOf ; . a owl:Class; rdfs:label "HeLa"; rdfs:subClassOf , , , , _:2ddc99, _:2ddca9, _:2ddcb9, _:2ddd89; rdfs:comment "example particular cell line, axiomatized such that it will be subsumed by several defined cell line classes to illustrate reasoning/inferfence that can be done within the cell culture hierarchy"; ; . _:2ddc99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddcb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ddcc9 . _:2ddcc9 a owl:Class; owl:intersectionOf _:2ddcd9 . _:2ddcd9 rdf:first ; rdf:rest _:2ddcf9 . _:2ddcf9 rdf:first _:2ddce9; rdf:rest rdf:nil . _:2ddce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ddd09 . _:2ddd09 a owl:Class; owl:intersectionOf _:2ddd19 . _:2ddd19 rdf:first ; rdf:rest _:2ddd39 . _:2ddd39 rdf:first _:2ddd29; rdf:rest rdf:nil . _:2ddd29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ddd49 . _:2ddd49 a owl:Class; owl:intersectionOf _:2ddd59 . _:2ddd59 rdf:first ; rdf:rest _:2ddd79 . _:2ddd79 rdf:first _:2ddd69; rdf:rest rdf:nil . _:2ddd69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddd89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "MEF-1"; rdfs:subClassOf , , , , , , _:2ddd99, _:2ddde9, _:2dddf9, _:2ddec9; "CLO (discuss design pattern for defining derivation/origin of cell line. CLO approach for this class is suspect as it states the cell line derives form cells that are part of an embryo that is part of a mouse. Here, we replace with our ReO axiom. This issue is relevant to how we will define equivalent classes based on life cycle stage of organism from which a cell line is generated (embryonic cell line is such an example class in ReO) )"; "The MEF-1 cell line was initiated in 1993 by transfection of mouse embryo fibroblasts with an SV40 coding plasmid. The cells are wild-type for the low density lipoprotein receptor related protein (LRP). This cell line along with the PEA 10 (see ATCC CRL-2215) and PEA 13 (see ATCC CRL-2216) cell lines constitute a genetically defined system to study the endocytosis of ligands by the LRP. The above cell lines are the only available experimental system to study the effect of LRP deficiency because LRP deficient mouse embryos die in utero. "; "http://www.biocompare.com/ProductDetails/1837919/MEF-1.html"; rdfs:comment "disease: SV40 transformed"; "example particular cell line, axiomatized such that it will be subsumed by several defined cell line classes to illustrate reasoning/inferfence that can be done within the cell culture hierarchy"; ; . _:2ddd99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ddda9 . _:2ddda9 a owl:Class; owl:intersectionOf _:2dddb9 . _:2dddb9 rdf:first ; rdf:rest _:2dddd9 . _:2dddd9 rdf:first _:2dddc9; rdf:rest rdf:nil . _:2dddc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddde9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dddf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dde09 . _:2dde09 a owl:Class; owl:intersectionOf _:2dde19 . _:2dde19 rdf:first ; rdf:rest _:2dde39 . _:2dde39 rdf:first _:2dde29; rdf:rest rdf:nil . _:2dde29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dde49 . _:2dde49 a owl:Class; owl:intersectionOf _:2dde59 . _:2dde59 rdf:first ; rdf:rest _:2dde79 . _:2dde79 rdf:first _:2dde69; rdf:rest rdf:nil . _:2dde69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dde89 . _:2dde89 a owl:Class; owl:intersectionOf _:2dde99 . _:2dde99 rdf:first ; rdf:rest _:2ddeb9 . _:2ddeb9 rdf:first _:2ddea9; rdf:rest rdf:nil . _:2ddea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell"; owl:equivalentClass _:2dded9; rdfs:subClassOf , _:2ddf39, _:2ddf49, _:2ddf59, _:2ddf69; "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane."; rdfs:comment "The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one)."; """Axiomatization Conventions for 'Cell' Classes: Use the axiomatization recommendations below to achieve inferred classification under appropriate equivalent class hierarchies. Parthood : declaring if members of the cell class is part of an organism (in case of multicellular organism cells), part of an environment (in case of unicellular organisms), or 'grain of' some type of cell culture, will allow inferred classification under the 'cell in vitro' hierarchy. Participation : declaring a type of planned process from which members of a cell class may be output from (in particular, any cell modification techniques) will enable inferred classification in 'experimentally modified cell' hierarchy. For example, see the recently created (8-20-12) 'experimentally transformed cell line cell' class - which is asserted as a type of multicellular organism cell and given the axioms'(is_specified_output_of some 'cell culture cell transformation')' and ''is grain of' some 'immortal cell line' ' to allow proper classification as a type of 'immortal cell line cell'."""; """Classification Axes for the Cell Hierarchy: Asserted Class Hierarchies: primary asserted classification is based on a split between 'multicellular organism cell' and 'unicellular organism' (note that unicellular organism 'cells' are asserted as organisms in the organism branch, and inferred to be cells). Equivalent Class Hierarchies : alternate classification is basd on experimental context of the cell, and include a 'cell in vitro' vs 'native cell' split, and also 'experimentally modified cell' and 'cell antibody target'. Further subclassing below this first level is done based on the in vivo/environment vs ex vivo/ex environment distinction. A third level is then based on experimental modification (unmodified cells vs experimentally modified cells)"""; "unclear from the definition of cell in CARO and CL whether their being an anatomical structure requires that they are part of an organism. until this resolved, will use a REO:cell class as placeholder to subsume both cell in vivo and cell ex vivo"; . _:2dded9 a owl:Class; owl:intersectionOf _:2ddee9 . _:2ddee9 rdf:first ; rdf:rest _:2ddf09 . _:2ddf09 rdf:first _:2ddef9; rdf:rest _:2ddf29 . _:2ddef9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ddf29 rdf:first _:2ddf19; rdf:rest rdf:nil . _:2ddf19 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2ddf39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ddf49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddf59 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2ddf69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddf79 a owl:Axiom; "Note that this is likely true even for enucleatd cells such as RBCs, as these will have mitochondriawhich themselves have genomes"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2ddf89 . _:2ddf89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "primary cell culture cell"; owl:equivalentClass _:2ddf99; rdfs:subClassOf , _:2ddfd9, _:2ddfe9; "A cell culture cell that is part of a cell culture that does not have the capacity to proliferate indefinitely."; "mortal cell culture cell", "primary cell culture cell"; """We recommend avoiding use of the term 'primary', as to some this means 'yet to be passaged' and for others it means 'not immortalized'. Thus we recommend the label 'mortal cell culture cell' rather than ‘primary cell line cell’. Note also that in ReO we view the term 'culture' as more general than 'line', where culture covers all types of cultures (mortal and immortal), while ‘line’ is used in labels only for cell cultures that are immortalized. This is because, as with the term ‘primary’, there is varied use of the term ‘line’. To some it means ‘any cell culture that has been passaged’, and to others it means ‘any cell culture that can be propagated long term (ie immortalized)’. So, while there may be disagreement that a passaged but mortal culture is a cell line, all would agree that an immortalized culture is a cell line. Thus our use of the labels ‘mortal cell culture cell’ and ‘immortal cell line cell’."""; "mortal cell culture cell"; . _:2ddf99 a owl:Class; owl:intersectionOf _:2ddfa9 . _:2ddfa9 rdf:first ; rdf:rest _:2ddfc9 . _:2ddfc9 rdf:first _:2ddfb9; rdf:rest rdf:nil . _:2ddfb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddfd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ddfe9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "permanent cell line cell"; owl:equivalentClass _:2ddff9; rdfs:subClassOf , _:2de039, _:2de089; "A cell culture cell that is part of a cell line having the capacity to proliferate indefinitely if given appropriate space and nutrients."; "immortal cell line cell", "permanent cell culture cell"; "Note that we use the preferred label 'immortal cell line cell', as 'immortalized' implies generation through some directed experimental immortalization, when some immortal cell line cells originate 'naturally' from tumor cells having undergone in vivo transformation "; "immortal cell line cell"; . _:2ddff9 a owl:Class; owl:intersectionOf _:2de009 . _:2de009 rdf:first ; rdf:rest _:2de029 . _:2de029 rdf:first _:2de019; rdf:rest rdf:nil . _:2de019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de039 a owl:Class; owl:unionOf _:2de059 . _:2de059 rdf:first _:2de049; rdf:rest _:2de079 . _:2de049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de079 rdf:first _:2de069; rdf:rest rdf:nil . _:2de069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "native cell"; owl:equivalentClass _:2de099; rdfs:subClassOf , ; owl:disjointWith ; "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)."; rdfs:comment "To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).", "Note that 'native' here bears significance only in relation to the location of a cell as part of an environment or organism, and not to the internal state of the cell. Thus, native cells can display altered physical structure or internal biochemical processes/metabolism, as a result of some experimental modification."; "A cell that is found in a natural setting, and not re-located by some intentional agent to a controlled artificial setting for use in some investigation or study. Covers multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)."; ; . _:2de099 a owl:Class; owl:unionOf _:2de0b9 . _:2de0b9 rdf:first _:2de0a9; rdf:rest _:2de109 . _:2de0a9 a owl:Class; owl:intersectionOf _:2de0c9 . _:2de0c9 rdf:first ; rdf:rest _:2de0e9 . _:2de0e9 rdf:first _:2de0d9; rdf:rest rdf:nil . _:2de0d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de109 rdf:first _:2de0f9; rdf:rest rdf:nil . _:2de0f9 a owl:Class; owl:intersectionOf _:2de119 . _:2de119 rdf:first ; rdf:rest _:2de139 . _:2de139 rdf:first _:2de129; rdf:rest rdf:nil . _:2de129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "fibroblast neural crest derived"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neuronal receptor cell (sensu Animalia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "cell culture cell"; owl:equivalentClass _:2de149; rdfs:subClassOf , , _:2de189, _:2de1d9, _:2de1e9, _:2de239; owl:disjointWith ; "A cell in vitro that is propagated as part of a cell culture."; rdfs:comment "The class has been re-labeled to 'culture' instead of 'line', as this class intends to cover cultured cells of multicellular and unicellular organisms, and both immortal and mortal cultured cells. 'Cell line' has different meanings to different people, in some cases referring to a culture that has been passaged, and in others referring to cultures that are immortal. 'Cell line cell' is included, however, as a narrow synonym.", "while cultured multicellular organism cells are considered to be experimentally modfied, they are not considered to be cells ex vivo, as 'ex vivo' is conceived of as 'having once been part of an organism', and a given cell culture cell has not at any point in its existence been a part of some organism. Thus, cultured cells stand outside the in vivo/ex vivo split, and are inferred to be experimentally modified cells."; "a multicellular organism cell that is maintained (propagated or held metabolically active) in vitro as part of a cell culture"; "CL: not clear whether this CL class is intended to refer to only cultured multicellular organism cells, or ALL cultured cells. So unclear if the CL:cell culture cell should be importer here as 'cultured mulcticellular organism cell', as we have done, or if it should be imported to replace 'cell culture cell'. We assume it is meant only to refer to cultured multicelllular organism cells, but need to confirm with CL - and if this is correct, they should change their definition to clarify this."; "cultured multicellular organism cell"; . _:2de149 a owl:Class; owl:intersectionOf _:2de159 . _:2de159 rdf:first ; rdf:rest _:2de179 . _:2de179 rdf:first _:2de169; rdf:rest rdf:nil . _:2de169 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de199 . _:2de199 a owl:Class; owl:intersectionOf _:2de1a9 . _:2de1a9 rdf:first ; rdf:rest _:2de1c9 . _:2de1c9 rdf:first _:2de1b9; rdf:rest rdf:nil . _:2de1b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de1d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de1e9 a owl:Class; owl:complementOf _:2de1f9 . _:2de1f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de209 . _:2de209 a owl:Class; owl:unionOf _:2de219 . _:2de219 rdf:first ; rdf:rest _:2de229 . _:2de229 rdf:first ; rdf:rest rdf:nil . _:2de239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "germ line stem cell"; rdfs:subClassOf ; "germline stem cell"; . a owl:Class; rdfs:label "smooth muscle cell neural crest derived"; rdfs:subClassOf ; . a owl:Class; rdfs:label "CNS neuron (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neuron neural crest derived"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neuroblast"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stem cell"; owl:equivalentClass _:2de249; rdfs:subClassOf , _:2de289; "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells."; . _:2de249 a owl:Class; owl:intersectionOf _:2de259 . _:2de259 rdf:first ; rdf:rest _:2de279 . _:2de279 rdf:first _:2de269; rdf:rest rdf:nil . _:2de269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "single fate stem cell"; rdfs:subClassOf ; "A stem cell that self-renews as well as give rise to a single mature cell type."; "unipotent stem cell", "unipotential stem cell"; . a owl:Class; rdfs:label "epithelial fate stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "hematopoietic stem cell"; rdfs:subClassOf ; "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119."; "HSC", "blood forming stem cell", "hemopoietic stem cell"; rdfs:comment "Markers differ between species, and two sets of markers have been described for mice."; . a owl:Class; rdfs:label "erythroid progenitor cell"; rdfs:subClassOf ; "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative)."; . a owl:Class; rdfs:label "monoblast"; rdfs:subClassOf ; "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus."; rdfs:comment "Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid."; . a owl:Class; rdfs:label "mature eosinophil"; rdfs:subClassOf ; "A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive."; rdfs:comment "Eosinophils are CD125-positive (IL-5R), GM-CSFR-positive, IL-3R-positive, VLA4-positive. They can also express MHC Class I & II, CD4, CD9, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD17, CD18, CD24, CD25,CD28, CD29, CD32, CD33, CD35, CD37, CD39, CD43, CD44, CD45, CD45RB, CD45RO, CD46, CD47, CD48, CD49d, CD49f, CD50, CD52, CD53, CD54, CD55, CD58, CD59, CD62L, CD63, CD65, CD66, CD69, CD71, CD76, CD80, CD81, CD82, CD86, CD87, CD88, CD89, CD92, CD95, CD97, CD98, CD99, CD100, CD101, CD116, CD117, CD119, CD120, CD123, CD124, CD125, CD131, CD137, CD139, CD148, CD149, CD151, CD153, CD156, CD162, CD161, CD162, CD165, CD174, CD182, CD183, CD191, CD192, CD193, CD196, CD213, IL9R, ad integrin, beta-7 integrin, FceRI, IL13Ra1, TGFbR, PAFR, LTB4R, C3aR, CystLT1R, CystLT2R, fMLPR, CRTH2 (PGD2 receptor), histamine 4R, IDO, KYN, PAR-2, Siglec-8, Siglec-10, LIR1, LIR2, LIR3, LIR7, TLR7, TLR8, and VLA-4. Eosinophils can also secrete CXCL1, eotaxin-1, GM-CSF, IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-16, IL-18, IFN-gamma, LTC4, MIP-1alpha, NGF, PAF, RANTES, substance P, TGF-alpha, TGF-beta, TNF-alpha, and VIP."; "mature eosinocyte", "mature eosinophil leucocyte", "mature eosinophil leukocyte"; . a owl:Class; rdfs:label "neutrophilic myeloblast"; rdfs:subClassOf ; "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor."; rdfs:comment "These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction."; . a owl:Class; rdfs:label "mature basophil"; rdfs:subClassOf ; "A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation."; rdfs:comment "Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4."; "mature basophil leucocyte", "mature basophil leukocyte"; . a owl:Class; rdfs:label "neuronal stem cell"; rdfs:subClassOf ; "NSC", "neural stem cell"; "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors."; . a owl:Class; rdfs:label "multi fate stem cell"; rdfs:subClassOf ; "A stem cell that can give rise to multiple lineages of cells."; "multi-fate stem cell", "multifate stem cell", "multipotent cell", "multipotent stem cell"; . a owl:Class; rdfs:label "common myeloid progenitor"; rdfs:subClassOf ; "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata-1, Gata2, C/EBPa, and Pu.1."; "CMP", "common myeloid precursor"; rdfs:comment "CMP are reportedly CD38-positive, CD45RA-negative, and CD123-positive."; . a owl:Class; rdfs:label "megakaryocyte-erythroid progenitor cell"; rdfs:subClassOf ; "A progenitor cell committed to the megakaryocyte and erythroid lineages."; "CFU-EM", "MEP", "colony forming unit erythroid megakaryocyte", "megakaryocyte/erythroid progenitor cell"; . a owl:Class; rdfs:label "common lymphoid progenitor"; rdfs:subClassOf ; "A oligopotent progenitor cell committed to the lymphoid lineage."; "CLP", "common lymphocyte precursor", "common lymphocyte progenitor", "common lymphoid precursor"; rdfs:comment "CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative."; . a owl:Class; rdfs:label "totipotent stem cell"; rdfs:subClassOf ; "A stem cell from which all cells of the body can form."; "totipotential stem cell"; . a owl:Class; rdfs:label "fibroblast"; rdfs:subClassOf ; "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped."; rdfs:comment "These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative."; . a owl:Class; rdfs:label "chondroblast"; rdfs:subClassOf ; "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell."; "chrondoplast"; . a owl:Class; rdfs:label "ameloblast"; rdfs:subClassOf ; "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell."; "amelocyte", "enamel secreting cell"; rdfs:comment "non-encoded relationship from VSAO produces VSAO:0000066 ! pre-enamel. Legacy definition: A cylindrical epithelial cell in the innermost layer of the enamel organ. Their functions include contribution to the development of the dentinoenamel junction by the deposition of a layer of the matrix, thus producing the foundation for the prisms (the structural units of the dental enamel), and production of the matrix for the enamel prisms and interprismatic substance. (From Jablonski's Dictionary of Dentistry, 1992)."; . a owl:Class; rdfs:label "odontoblast"; rdfs:subClassOf ; "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell."; rdfs:comment "legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin."; . a owl:Class; rdfs:label "cementoblast"; rdfs:subClassOf ; rdfs:comment "Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth."; "Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell."; "cementum secreting cell"; . a owl:Class; rdfs:label "osteoblast"; rdfs:subClassOf ; "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell."; rdfs:comment "non-encoded relationships from VSAO - capable_of_producing VSAO:0000020"; . a owl:Class; rdfs:label "ependymal cell"; rdfs:subClassOf ; "A neurectoderm derived cell that lines the neural lumen."; "ependymocyte"; . a owl:Class; rdfs:label "epithelial cell"; rdfs:subClassOf ; "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina."; "epitheliocyte"; . a owl:Class; rdfs:label "ciliated epithelial cell"; rdfs:subClassOf ; "An epithelial cell that has a cillia."; . a owl:Class; rdfs:label "duct epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "branched duct epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "blood vessel endothelial cell"; rdfs:subClassOf ; "An endothelial cell that lines the vasculature."; "cuboidal endothelial cell of vascular tree"; . a owl:Class; rdfs:label "non-branched duct epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "barrier epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "columnar/cuboidal epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "squamous epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "mesothelial cell"; rdfs:subClassOf ; "A flattened epithelial cell of mesenchymal origin that lines the serous cavity."; "mesotheliocyte"; . a owl:Class; rdfs:label "peridermal cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stratified epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "blood cell"; rdfs:subClassOf ; "A cell found predominately in the blood."; . a owl:Class; rdfs:label "epithelial cell of lung"; rdfs:subClassOf ; . a owl:Class; rdfs:label "epithelial cell of pancreas"; rdfs:subClassOf ; "An epithelial cell of the pancreas."; . a owl:Class; rdfs:label "T cell"; rdfs:subClassOf ; "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex."; "T lymphocyte", "T-cell", "T-lymphocyte"; . a owl:Class; rdfs:label "Kupffer cell"; rdfs:subClassOf ; "A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system."; rdfs:comment "Markers: Mouse: F4/80+, CD11b-low, CD68+, sialoadhesin+, CD163/SRCR+; role or process: immune, antigen-presentation, clearance of senescent erythrocytes, iron metabolism. Kupffer cells are also reportedly C3aR-positive, CD14-low, CD54-positive, CD88-positive, and CD284-positive. They are also capable of producing IL-1, IL-6, TNF-alpha, nitric oxide, PGD2, PGE2, PGF2alpha, and TXA2."; "hepatic macrophage", "littoral cell of hepatic sinusoid", "liver macrophage", "macrophagocytus stellatus", "stellate cell of von Kupffer", "von Kupffer cell"; . a owl:Class; rdfs:label "osteoclast"; rdfs:subClassOf ; "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive."; rdfs:comment "Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid."; . a owl:Class; rdfs:label "granulocyte"; rdfs:subClassOf ; "A leukocyte with abundant granules in the cytoplasm."; "granular leucocyte", "granular leukocyte", "polymorphonuclear leukocyte"; . a owl:Class; rdfs:label "neuron associated cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "mature neutrophil"; rdfs:subClassOf ; "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/ day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive .\""; rdfs:comment "Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils.\\nNeutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A))."; "PMN", "mature neutrocyte", "mature neutrophil leucocyte", "mature neutrophil leukocyte", "mature neutrophilic leucocyte", "mature neutrophilic leukocyte", "polymorphonuclear neutrophil", "polynuclear neutrophilic leucocyte", "polynuclear neutrophilic leukocyte"; . a owl:Class; rdfs:label "mast cell"; rdfs:subClassOf ; "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development."; rdfs:comment "Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5."; "histaminocyte", "labrocyte", "mastocyte"; . a owl:Class; rdfs:label "interneuron"; rdfs:subClassOf ; "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions."; . a owl:Class; rdfs:label "motor neuron"; rdfs:subClassOf ; "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement."; "anterior horn cell", "motoneuron"; . a owl:Class; rdfs:label "sensory neuron"; rdfs:subClassOf ; "Any neuron having a sensory function; an afferent neuron conveying sensory impulses."; . a owl:Class; rdfs:label "polymodal neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "bipolar neuron"; rdfs:subClassOf ; "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body."; . a owl:Class; rdfs:label "multipolar neuron"; rdfs:subClassOf ; "Neuron with an axon and two or more dendrites."; . a owl:Class; rdfs:label "pseudounipolar neuron"; rdfs:subClassOf ; "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma."; . a owl:Class; rdfs:label "unipolar neuron"; rdfs:subClassOf ; "Neuron with an axon and no dendrites."; . a owl:Class; rdfs:label "autonomic neuron"; rdfs:subClassOf ; "A neruon whose cell body is within an autonomic ganglion."; . a owl:Class; rdfs:label "cholinergic neuron"; rdfs:subClassOf ; "A neuron that uses acetylcholine as a vesicular neurotransmitter."; . a owl:Class; rdfs:label "adrenergic neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "peptidergic neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "peripheral neuron"; rdfs:subClassOf ; "A neuron that is part of nerve found outside the central nervous system."; . a owl:Class; rdfs:label "columnar neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "mononuclear phagocyte"; rdfs:subClassOf ; "A vertebrate phagocyte with a single nucleus."; . a owl:Class; rdfs:label "endothelial cell"; rdfs:subClassOf ; "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm."; rdfs:comment "From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]."; "endotheliocyte"; . a owl:Class; rdfs:label "pioneer neuron"; rdfs:subClassOf ; "Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance."; . a owl:Class; rdfs:label "CNS neuron (sensu Vertebrata)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "basket cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Golgi cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "granule cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Purkinje cell"; rdfs:subClassOf ; "Purkinje neuron", "Purkinje's cell"; "The output neuron of the cerebellar cortex."; . a owl:Class; rdfs:label "stellate cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neuron associated cell (sensu Vertebrata)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "glial cell (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "glial cell"; rdfs:subClassOf ; "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons."; "neuroglial cell"; . a owl:Class; rdfs:label "macroglial cell"; rdfs:subClassOf ; "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together."; "macrogliocyte"; . a owl:Class; rdfs:label "astrocyte"; rdfs:subClassOf ; "A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury."; rdfs:comment "Astrocytes are reportedly CD68-negative, CD121a-positive, CD184-positive, CD192-positive, CRF-positive, EGFR-positive, GFAP-positive, GLUT1-positive, MBP-negative, and NGFR-positive."; "astrocytic glia"; . a owl:Class; rdfs:label "oligodendrocyte"; rdfs:subClassOf ; "A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system."; . a owl:Class; rdfs:label "microglial cell"; rdfs:subClassOf ; "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive."; rdfs:comment "Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD19-negative, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive."; "brain-resident macrophage", "hortega cells", "microglia", "microgliocyte"; . a owl:Class; rdfs:label "neuron associated cell (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "gut endothelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "corneal endothelial cell"; rdfs:subClassOf ; "Cell of the single layer of large flattened cells covering the surface of the cornea."; . a owl:Class; rdfs:label "fibrocyte"; rdfs:subClassOf ; "An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes."; rdfs:comment "Cultured human fibrocytes are MHCI-positive, MHCII-positive, CD1a-negative, CD3-negative, CD4-negative, CD8-negative, CD10-negative, CD11b-positive, CD13-positive, CD14-negative, CD16-negative, CD18-positive, CD19-negative, CD25-negative, CD29-positive, CD32-positive, CD33-negative, CD34-positive, CD38-negative, CD40-positive, CD44-negative, CD45RO-positive, CD49a-positive, CD49b-positive, CD49c-negative, CD49d-negative, CD49e-positive, CD49f-negative, CD56-negative, CD58-positive, CD61-positive, CD64-positive, CD70-negative, CD71-positive, CD80-positive, CD83-negative, CD86-positive, CD103-negative, CD105-positive, CD181-positive, CD182-negative, CD183-positive, CD184-positive, CD185-negative, CD186-negative, CD191-positive, CD192-negative, CD193-positive, CD194-positive, CD195-positive, CD196-negative, CD197-positive, CD199-positive, desmin-negative, F4/80-positive, Gr1-positive, LSP-1-positive, MHCI-positive, MHCII-positive, alpha-SMA-negative, TCRab-negative, TCRgd-negative, and vimentin-positive. Fibrocytes are also capable of secreting angiogenin, bFGF, CCL2, CCL3, CCL4, CCL8, CXCL1, type I collagen, type III collagen, CTGF, fibronectin, GM-CSF, IL-1a, IL-6, IL-8, IL-10, M-CSF, MMP-9, PDGF-A, TGF-alpha, TGF-beta1, TNF-alpha, VEGF-A, and type I collagen."; . a owl:Class; rdfs:label "fat cell"; rdfs:subClassOf ; "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides."; "adipocyte", "adipose cell"; . a owl:Class; rdfs:label "osteocyte"; rdfs:subClassOf ; "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi."; rdfs:comment "VSAO relationship simplified OBO_REL:integral_part_of VSAO:0000118"; . a owl:Class; rdfs:label "chondrocyte"; rdfs:subClassOf ; "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell."; "cartilage cell"; . a owl:Class; rdfs:label "cementocyte"; rdfs:subClassOf ; "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth."; rdfs:comment "CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def)."; . a owl:Class; rdfs:label "hyalocyte"; rdfs:subClassOf ; "A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen."; . a owl:Class; rdfs:label "guidepost cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "simple columnar epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "melanocyte"; rdfs:subClassOf ; "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance."; . a owl:Class; rdfs:label "glandular epithelial cell"; rdfs:subClassOf ; "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules."; . a owl:Class; rdfs:label "GAG secreting cell"; rdfs:subClassOf ; "A cell that secretes glycosaminoglycans."; "hyaluronic acid secreting cell"; . a owl:Class; rdfs:label "peptic cell"; rdfs:subClassOf ; "A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen."; "chief cell of stomach", "gastric chief cell", "pepsinogen secreting cell", "zymogenic cell"; . a owl:Class; rdfs:label "Clara cell"; rdfs:subClassOf ; "Clara cell of bronchiole", "bronchiolar non-ciliated "; "Epithelial progenitor cell of the lung. Clara cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Clara cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium."; . a owl:Class; rdfs:label "parietal cell"; rdfs:subClassOf ; "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl."; "oxyntic cell"; . a owl:Class; rdfs:label "chromaffin cell"; rdfs:subClassOf ; "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system."; "phaeochromocyte"; . a owl:Class; rdfs:label "hepatocyte"; rdfs:subClassOf ; "The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated."; . a owl:Class; rdfs:label "myoepithelial cell"; rdfs:subClassOf ; "Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament."; "basket epithelial cell", "myoepitheliocyte"; . a owl:Class; rdfs:label "myofibroblast cell"; rdfs:subClassOf ; "An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell."; "MFB"; rdfs:comment "Myofibroblasts are alpha-SMA-positive, CD34-negative, CD45-negative. They are reportedly capable of secreting IL-1beta, IL-6, and TNF-alpha."; . a owl:Class; rdfs:label "muscle cell"; rdfs:subClassOf ; "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns."; "muscle fiber", "myocyte"; . a owl:Class; rdfs:label "skeletal muscle cell"; rdfs:subClassOf ; "A somatic cell located in skeletal muscle."; . a owl:Class; rdfs:label "slow muscle cell"; rdfs:subClassOf ; "A muscle cell that develops tension more slowly than a fast-twitch fiber."; "slow muscle fiber"; . a owl:Class; rdfs:label "fast muscle cell"; rdfs:subClassOf ; "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron ."; "glycolytic muscle fiber"; . a owl:Class; rdfs:label "smooth muscle cell"; rdfs:subClassOf ; "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)."; "SMCs", "myocytes, smooth muscle", "non-striated muscle cell", "smooth muscle fiber"; . a owl:Class; rdfs:label "cardiac muscle cell (sensu Arthopoda)"; rdfs:subClassOf ; "A striated muscle cell found in the heart. They develop from cardiac myoblasts."; . a owl:Class; rdfs:label "flight muscle cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "pain receptor cell"; rdfs:subClassOf ; "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings."; "nociceptor", "nocireceptor"; . a owl:Class; rdfs:label "mechanoreceptor cell"; rdfs:subClassOf ; "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system."; . a owl:Class; rdfs:label "touch receptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "auditory hair cell"; rdfs:subClassOf ; "A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system."; rdfs:comment "In mammals these cells are located in the organ of Corti."; "auditory receptor cell", "cochlear hair cell", "inner ear hair cell", "inner ear receptor cell"; . a owl:Class; rdfs:label "gravity sensitive cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "acceleration receptive cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "thermoreceptor cell"; rdfs:subClassOf ; "A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain."; . a owl:Class; rdfs:label "chemoreceptor cell"; rdfs:subClassOf ; "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood."; . a owl:Class; rdfs:label "olfactory receptor cell"; rdfs:subClassOf ; "Schultze's cell", "olfactory receptor neuron", "olfactory sensory neuron"; . a owl:Class; rdfs:label "pH receptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "taste receptor cell"; rdfs:subClassOf ; "A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste."; "taste bud cell"; . a owl:Class; rdfs:label "photoreceptor cell"; rdfs:subClassOf ; "A cell specialized to detect and transduce light."; . a owl:Class; rdfs:label "synovial cell"; rdfs:subClassOf ; "A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid."; "hyaluronic acid secreting cell", "synoviocyte"; . a owl:Class; rdfs:label "myelinating Schwann cell"; rdfs:subClassOf ; "A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons."; "neurilemmal cell"; . a owl:Class; rdfs:label "erythrocyte"; rdfs:subClassOf ; "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen."; "RBC", "red blood cell"; . a owl:Class; rdfs:label "platelet"; rdfs:subClassOf ; "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation."; rdfs:comment "Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF."; "anucleate thrombocyte", "blood platelet", "enucleate thrombocyte"; . a owl:Class; rdfs:label "macrophage"; rdfs:subClassOf ; "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells."; rdfs:comment "Morphology: Diameter 30_M-80 _M, abundant cytoplasm, low N/C ratio, eccentric nucleus. Irregular shape with pseudopods, highly adhesive. Contain vacuoles and phagosomes, may contain azurophilic granules; markers: Mouse & Human: CD68, in most cases CD11b. Mouse: in most cases F4/80+; role or process: immune, antigen presentation, & tissue remodelling; lineage: hematopoietic, myeloid."; "histiocyte"; . a owl:Class; rdfs:label "B cell"; rdfs:subClassOf ; "A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity."; "B lymphocyte", "B-cell", "B-lymphocyte"; . a owl:Class; rdfs:label "keratinizing barrier epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "non keratinizing barrier epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "brush border epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stratified squamous epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stratified cuboidal epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Merkel cell"; rdfs:subClassOf ; "A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber."; "Merkel's cell"; . a owl:Class; rdfs:label "glial cell (sensu Vertebrata)"; rdfs:subClassOf ; "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear."; . a owl:Class; rdfs:label "transitional epithelial cell"; rdfs:subClassOf ; "A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium."; . a owl:Class; rdfs:label "Mauthner neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Rohon-Beard neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "extramedullary cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "eurydendroid cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "guard mother cell"; rdfs:subClassOf ; "Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells."; rdfs:comment "replaced_by: PO:0000351"; . a owl:Class; rdfs:label "trichome"; rdfs:subClassOf ; "Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata."; rdfs:comment "replaced_by: PO:0000282"; . a owl:Class; rdfs:label "eye photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "guard cell"; rdfs:subClassOf ; "Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor."; rdfs:comment "replaced_by: PO:0000293"; "stomatal guard cell"; . a owl:Class; rdfs:label "socket cell"; rdfs:subClassOf ; "Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome."; rdfs:comment "replaced_by: PO:0000115"; . a owl:Class; rdfs:label "tracheal epithelial cell"; rdfs:subClassOf ; "An epithelial cell found in the trachea."; "tracheocyte"; . a owl:Class; rdfs:label "keratinocyte"; rdfs:subClassOf ; "An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell."; rdfs:comment "Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive."; "keratinized cell of epidermis", "malpighian cell"; . a owl:Class; rdfs:label "pneumocyte"; rdfs:subClassOf ; "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."; "alveolar epithelial cell", "pneumonocyte"; . a owl:Class; rdfs:label "metanephric mesenchyme stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "extracellular matrix secreting cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "adrenal medulla chromaffin cell"; rdfs:subClassOf ; "A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation."; "medullary chromaffin cell of adrenal gland"; . a owl:Class; rdfs:label "neuroblast (sensu Vertebrata)"; rdfs:subClassOf ; "An embryonic cell that develops into a nerve cell or neuron."; . a owl:Class; rdfs:label "neuroblast (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "glioblast (sensu Vertebrata)"; rdfs:subClassOf ; "An early neural cell developing from the early ependymal cell of the neural tube."; "spongioblast"; . a owl:Class; rdfs:label "glioblast (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "extraembryonic cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "amnioserosal cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "trophoblast cell"; rdfs:subClassOf ; "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface."; "trophoblastic cell"; . a owl:Class; rdfs:label "epiblast cell"; rdfs:subClassOf ; "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation."; . a owl:Class; rdfs:label "blastemal cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "muscle stem cell"; rdfs:subClassOf ; "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types. Distinct cell type from satellite cell."; . a owl:Class; rdfs:label "hair matrix stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stratified epithelial stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "sphincter associated smooth muscle cell"; rdfs:subClassOf ; "A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning."; . a owl:Class; rdfs:label "vascular associated smooth muscle cell"; rdfs:subClassOf ; "A smooth muscle cell assocatiated with the vasculature."; "VSMC", "vascular smooth muscle cell"; . a owl:Class; rdfs:label "epidermal cell"; rdfs:subClassOf ; "An epithelial cell of the integument (the outer layer of an organism)."; "cell of epidermis"; . a owl:Class; rdfs:label "sheath cell (sensu Nematoda)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "histoblast"; rdfs:subClassOf ; . a owl:Class; rdfs:label "osteoprogenitor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "humidity receptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "tracheoblast"; rdfs:subClassOf ; . a owl:Class; rdfs:label "sensory processing neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neurosecretory neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "nephrogenic mesenchyme stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "prohemocyte (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "socket cell (sensu Nematoda)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "blood cell (sensu Nematoda and Protostomia)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "ganglion interneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "pavement cell"; rdfs:subClassOf ; "Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina."; rdfs:comment "replaced_by: PO:0000332"; . a owl:Class; rdfs:label "CNS interneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neuroepidermoblast"; rdfs:subClassOf ; . a owl:Class; rdfs:label "CNS short range interneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "scolopidial sheath cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "CNS long range interneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "hypodermal cell"; rdfs:subClassOf ; "An epithelial cell of the hypodermis of flatworms."; . a owl:Class; rdfs:label "arcade cell"; rdfs:subClassOf ; "An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding."; . a owl:Class; rdfs:label "seam cell"; rdfs:subClassOf ; "An epithelial fate stem cell found in flatworms."; . a owl:Class; rdfs:label "syncytial epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "pore cell"; rdfs:subClassOf ; "Forms the terminal part of the cuticle-lined excretory duct of C. elegans."; . a owl:Class; rdfs:label "GLR cell"; rdfs:subClassOf ; "A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role."; . a owl:Class; rdfs:label "yolk cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "imaginal disc cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "reticular cell"; rdfs:subClassOf ; "Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum."; "reticulum cell"; . a owl:Class; rdfs:label "gonadtroph"; rdfs:subClassOf ; "A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH)."; "delta basophil", "follicle stimulating hormone secreting cell", "gonadotrope", "gonadotrope cell", "gonadotroph", "pituitary delta cell"; . a owl:Class; rdfs:label "follicle stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "obliquely striated muscle cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "chief cell of parathyroid gland"; rdfs:subClassOf ; "An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone."; "parathyroid chief cell", "parathyroid gland chief cell", "parathyroid hormone secreting cell", "principal cell of parathyroid gland"; . a owl:Class; rdfs:label "white fat cell"; rdfs:subClassOf ; "Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole."; "white adipose cell", "white fat cell"; . a owl:Class; rdfs:label "brown fat cell"; rdfs:subClassOf ; "A cell from the thermogenic form of adipose tissue found in newborns of many species, including humans, and in hibernating mammals. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation."; "brown adipocyte", "brown adipose cell"; . a owl:Class; rdfs:label "dendritic cell"; rdfs:subClassOf ; "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)."; . a owl:Class; rdfs:label "Langerhans cell"; rdfs:subClassOf ; "LC", "Langerhans' cell"; "Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000021 )(PMID: 19243617). These cells are also CD1a-high, CD14-negative, CD207-positive (langerin), CD324-positive (E-cadherin), and DCIR-positive. They reside in the epidermis."; . a owl:Class; rdfs:label "adepithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "epidermal cell (sensu arthropoda)"; rdfs:subClassOf ; "An epidermal cell that secretes chitinous cuticle from its apical side."; rdfs:comment "While insect epidermis is generally columnar/cuboidal, there are certainly well studied cases where it is not (e.g.- Rhodnius prolixus when starved). So it would be safer to add this as a differentium for particular species where this is known. -DSJ."; . a owl:Class; rdfs:label "epidermoblast"; rdfs:subClassOf ; "An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions."; . a owl:Class; rdfs:label "neuroglioblast"; rdfs:subClassOf ; . a owl:Class; rdfs:label "ganglion mother cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "thyrotroph"; rdfs:subClassOf ; "A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center."; "beta-basophil", "thyroid stimulating hormone secreting cell", "thyrotrope"; . a owl:Class; rdfs:label "follicle cell"; rdfs:subClassOf ; rdfs:comment "Editors note: check this. Currently used in goxp"; "ovarian follicle cell"; . a owl:Class; rdfs:label "connective tissue type mast cell"; rdfs:subClassOf ; "MC(TC)", "MCTC", "TC mast cells"; "Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent."; rdfs:comment "They are CD88-positive. The cytoplasmic granules contain high levels of histamine and heparin (mouse) or major neutral proteases, tryptase, chymase, carboxypeptidase A, and cathepsin G (humans). Reportedly, they cannot produce leukotrienes (LTC4) and IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype."; . a owl:Class; rdfs:label "mucosal type mast cell"; rdfs:subClassOf ; "MC(T)", "MCT", "T mast cells"; "Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype."; rdfs:comment "They are CD88-negative. The cytoplasmic granules contain low levels of histamine and high levels of chondroitin sulfate (mouse) or major neutral proteases and tryptase (humans). Additionally, they can produce leukotrienes (LTC4), IL-5, IL-6, and low levels of IL-4. They are reportedly very heterogeneous depending upon location and can convert to the MC(T) phenotype."; . a owl:Class; rdfs:label "visible light photoreceptor cell"; rdfs:subClassOf ; "A photoreceptor cell that detects visible light."; . a owl:Class; rdfs:label "scotopic photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "photopic photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "CD4-positive helper T cell"; rdfs:subClassOf ; "A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions."; "CD4-positive T-helper cell", "CD4-positive helper T lymphocyte", "CD4-positive helper T-cell", "CD4-positive helper T-lymphocyte"; . a owl:Class; rdfs:label "UV sensitive photoreceptor cell"; rdfs:subClassOf ; "A photoreceptor cell that detects ultraviolet light."; . a owl:Class; rdfs:label "blue sensitive photoreceptor cell"; rdfs:subClassOf ; "A photoreceptor cell that is sensitive to blue light."; . a owl:Class; rdfs:label "green sensitive photoreceptor cell"; rdfs:subClassOf ; "A photoreceptor cell that is sensitive to green light."; . a owl:Class; rdfs:label "red sensitive photoreceptor cell"; rdfs:subClassOf ; "A photoreceptor cell that is sensitive to red light."; . a owl:Class; rdfs:label "inhibitory interneuron"; rdfs:subClassOf ; "An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS)."; . a owl:Class; rdfs:label "stromal cell"; rdfs:subClassOf ; "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere."; . a owl:Class; rdfs:label "follicular epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "granulosa cell"; rdfs:subClassOf ; "A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors."; "granulosa cell of ovary"; . a owl:Class; rdfs:label "theca cell"; rdfs:subClassOf ; "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells."; . a owl:Class; rdfs:label "paneth cell"; rdfs:subClassOf ; "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix."; . a owl:Class; rdfs:label "perineuronal satellite cell"; rdfs:subClassOf ; "A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia."; "perineural satellite cell", "perineuronal satellite oligodendroglial cell", "satellite oligodendrocyte"; . a owl:Class; rdfs:label "phagocyte (sensu Vertebrata)"; rdfs:subClassOf ; "A phagocyte in vertebrates that is able to phagocytosis."; . a owl:Class; rdfs:label "mononuclear cytotrophoblast cell"; rdfs:subClassOf ; "A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast."; "Langhans' cell"; . a owl:Class; rdfs:label "syncytiotrophoblast cell"; rdfs:subClassOf ; "A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo. It It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy."; "plasmidotrophoblast", "syncytial trophoblast", "syntrophoblast"; . a owl:Class; rdfs:label "afferent neuron"; rdfs:subClassOf ; "A neuron which conveys sensory information centrally from the periphery."; "input neuron"; . a owl:Class; rdfs:label "efferent neuron"; rdfs:subClassOf ; "A neuron which sends impulses peripherally to activate muscles or secretory cells."; "output neuron"; . a owl:Class; rdfs:label "nitrergic neuron"; rdfs:subClassOf ; "A nerve cell where transmission is mediated by nitric oxide."; . a owl:Class; rdfs:label "pigmented epithelial cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "primary neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "primary sensory neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "CAP motoneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "primary motor neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "primary interneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "secondary neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "secondary motor neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neuron"; rdfs:subClassOf ; "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system."; rdfs:comment "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma."; "nerve cell"; . a owl:Class; rdfs:label "melanoblast"; rdfs:subClassOf ; "A cell that originates from the neural crest and differentiates into a pigment cell."; rdfs:comment "Derived from UBERON:0002342 neural crest."; . a owl:Class; rdfs:label "lymphocyte"; rdfs:subClassOf ; "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin."; rdfs:comment "Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)"; . a owl:Class; rdfs:label "slowly adapting mechanoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "T-helper 1 cell"; rdfs:subClassOf ; "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma."; "Th1 T cell", "Th1 T lymphocyte", "Th1 T-cell", "Th1 T-lymphocyte", "Th1 cell", "helper T cell type 1"; . a owl:Class; rdfs:label "T-helper 2 cell"; rdfs:subClassOf ; "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4."; "Th2 T cell", "Th2 T lymphocyte", "Th2 T-cell", "Th2 T-lymphocyte", "Th2 cell", "helper T cell type 2"; . a owl:Class; rdfs:label "proerythroblast"; rdfs:subClassOf ; "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers."; "rubriblast"; . a owl:Class; rdfs:label "basophilic erythroblast"; rdfs:subClassOf ; "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers."; "basophilic normoblast", "early erythroblast", "early normoblast", "prorubricyte"; . a owl:Class; rdfs:label "polychromatophilic erythroblast"; rdfs:subClassOf ; "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers."; "intermediate erythroblast", "intermediate normoblast", "polychromatic erythroblast", "polychromatic normoblast", "polychromatophilic normoblast", "rubricyte"; . a owl:Class; rdfs:label "unimodal nocireceptor"; rdfs:subClassOf ; . a owl:Class; rdfs:label "orthochromatic erythroblast"; rdfs:subClassOf ; "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated."; "acidophilic erythroblast", "eosinophilic erythroblast", "late erythoblast", "orthochromatic normoblast", "pyknotic eto enrythroblast"; . a owl:Class; rdfs:label "megakaryocyte progenitor cell"; rdfs:subClassOf ; "CFU-Meg", "Meg-CFC", "colony-forming unit-megakaryocyte", "megacaryoblast", "megacaryocyte progenitor cell", "megakaryoblast", "megakaryocytic progenitor cell"; rdfs:comment "Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative."; "The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative)."; . a owl:Class; rdfs:label "neuronal brush cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "megakaryocyte"; rdfs:subClassOf ; "A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm."; rdfs:comment "Megakaryocytes are reportedly CD181-positive and CD182-positive."; "megacaryocyte", "megalocaryocyte", "megalokaryocyte"; . a owl:Class; rdfs:label "granulocyte monocyte progenitor cell"; rdfs:subClassOf ; "A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata-1, Gata2 but do express C/EBPa, and Pu.1."; "CFU-GM", "GMP", "colony forming unit granulocyte macrophage", "granulocyte-macrophage progenitor"; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID: 19243617). GMPs are reportedly CD34-positive, CD38-positive, CD45RA-positive, and CD123-positive."; . a owl:Class; rdfs:label "reticulocyte"; rdfs:subClassOf ; "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds."; . a owl:Class; rdfs:label "promonocyte"; rdfs:subClassOf ; "A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules."; rdfs:comment "Morphology: Mononuclear cell, diameter 14-18 _M, fine azurophilic granules; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; Fetal: Liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid."; . a owl:Class; rdfs:label "band form neutrophil"; rdfs:subClassOf ; "A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative."; rdfs:comment "They are found in the Band 1 fraction."; "rod neutrophil"; . a owl:Class; rdfs:label "amacrine cell"; rdfs:subClassOf ; "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons."; rdfs:comment "Not clear if this term overlaps with retinal bipolar neuron (CL:0000748)."; "amacrine neuron"; . a owl:Class; rdfs:label "nucleate erythrocyte"; rdfs:subClassOf ; "An erythrocyte having a nucleus."; . a owl:Class; rdfs:label "neutrophilic promyelocyte"; rdfs:subClassOf ; "A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression."; rdfs:comment "These cells are CD11b-negative, CD15-positive, CD16-negative, CD49d-positive, CD68-positive, CD35-negative, and fMLP receptor-negative. They are found in the Band 3 fraction."; "neutrophilic premyelocyte", "neutrophilic progranulocyte"; . a owl:Class; rdfs:label "angioblastic mesenchymal cell"; rdfs:subClassOf ; "A mesenchymal stem cell capable of developing into blood vessel endothelium."; rdfs:comment "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive."; "angioblast", "chondroplast"; . a owl:Class; rdfs:label "polymodal nocireceptor"; rdfs:subClassOf ; . a owl:Class; rdfs:label "parafollicular cell"; rdfs:subClassOf ; "A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secrets calcitonin, 5-hydroxytryptamine and dopamine."; "C cell"; . a owl:Class; rdfs:label "retinal cone cell"; rdfs:subClassOf ; "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision."; . a owl:Class; rdfs:label "corneal epithelial cell"; rdfs:subClassOf ; "An epithelial cell of the cornea."; "epithelial cell of cornea"; . a owl:Class; rdfs:label "monocyte"; rdfs:subClassOf ; rdfs:comment "Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid."; "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells."; . a owl:Class; rdfs:label "type EC enteroendocrine cell"; rdfs:subClassOf ; "A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain)."; "Kulchitsky cell", "argentaffin cell", "enterochromaffin cell"; . a owl:Class; rdfs:label "experimentally modified cell in vitro"; owl:equivalentClass _:2de299; rdfs:subClassOf , , _:2de2d9; owl:disjointWith ; "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure."; rdfs:comment "This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this.experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells . There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12"; "an experimentally modified cell that is the specified output of an experimental modification technique that introduces physical changes to the cell (ie changes in composition and/or internal structural arrangement)", "a cell that was at some point the specified output from an experimental modification technique in which specified physical changes (ie structural or compositional changes) are made to the cell (e.g. a cell labeling technique, fixation, or culturing) "; "Primary axis of classification below experimentally modified cell is taxonoic cell type (exp modified multicellular organsim cells vs ex mod unicellular organisms). Additional equivalent classes defined based on technique are also created (sectioned cell, chemically fixed cell, cell culture cell), which group cells of either multicellular organism or unicellular organism origin according to experimental techniques applied to modify them."; "To get experimentally modified cell hierarchy to classify correctly, all material processing techniques that have a modified cell as specified output should have an axiom asserting that it achieves an 'experimental modification objective' and 'have as output some 'cell' or (has_grain some 'cell')'"; . _:2de299 a owl:Class; owl:intersectionOf _:2de2a9 . _:2de2a9 rdf:first ; rdf:rest _:2de2c9 . _:2de2c9 rdf:first _:2de2b9; rdf:rest rdf:nil . _:2de2b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de2d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "border follicle cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neutrophilic myelocyte"; rdfs:subClassOf ; "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive."; rdfs:comment "These cells are also CD15-positive, CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction."; . a owl:Class; rdfs:label "peritoneal macrophage"; rdfs:subClassOf ; "A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive."; rdfs:comment "Markers: Mouse: F4/80-high, CD11b-high, CD68+, SIGNR1+, Dectin-1+."; . a owl:Class; rdfs:label "neutrophilic metamyelocyte"; rdfs:subClassOf ; "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin."; rdfs:comment "These cells are also CD35-negative, CD49d-positive, and fMLP receptor-negative. They are found in the Band 2 fraction."; "juvenile neutrophil"; . a owl:Class; rdfs:label "alveolar macrophage"; rdfs:subClassOf ; "A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative."; rdfs:comment "Markers: Mouse: F4/80mid, CD11b-/low, CD11c+, CD68+, sialoadhesin+, dectin-1+, MR+, CX3CR1-."; "dust cell"; . a owl:Class; rdfs:label "enterocyte"; rdfs:subClassOf ; "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen."; . a owl:Class; rdfs:label "cold sensing thermoreceptor cell"; rdfs:subClassOf ; "A thermoreceptor cell that detects reduced temperatures."; . a owl:Class; rdfs:label "odontoclast"; rdfs:subClassOf ; "A specialized osteoclast associated with the absorption and removal of cementum."; . a owl:Class; rdfs:label "cochlear inner hair cell"; rdfs:subClassOf ; "A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated."; . a owl:Class; rdfs:label "warmth sensing thermoreceptor cell"; rdfs:subClassOf ; "A thermoreceptor cell that detects reduced temperatures."; . a owl:Class; rdfs:label "enucleate erythrocyte"; rdfs:subClassOf ; "An erythrocyte lacking a nucleus."; . a owl:Class; rdfs:label "pyramidal cell"; rdfs:subClassOf ; "A projection neuron in the cerebral cortex and the hippocampus. Pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their cortical region."; "projection neuron", "pyramidal neuron"; . a owl:Class; rdfs:label "outer hair cell"; rdfs:subClassOf ; "A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea."; "cochlear outer hair cell"; . a owl:Class; rdfs:label "pressoreceptor cell"; rdfs:subClassOf ; "A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls."; . a owl:Class; rdfs:label "retinal rod cell"; rdfs:subClassOf ; "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision."; . a owl:Class; rdfs:label "vestibular hair cell"; rdfs:subClassOf ; "A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem."; "vestibular receptor cell"; . a owl:Class; rdfs:label "eosinophil progenitor cell"; rdfs:subClassOf ; "EoP"; rdfs:comment "These cells are CD34-positive, CD45RA-negative, CD71-negative, and lineage-negative (CD2, CD3 epsilon, CD4, CD5, CD8a, CD14, CD19, CD20, integrin alpha-M, NCAM-1, SCA-1, Ly6G, Ly76)."; . a owl:Class; rdfs:label "eosinophilic myelocyte"; rdfs:subClassOf ; "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive."; . a owl:Class; rdfs:label "basophil progenitor cell"; rdfs:subClassOf ; "A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa."; "BaP"; rdfs:comment "BaP are also CD13-low and integrin beta-7-low. They are lin-negative (CD2, CD3e, CD4, CD5, CD8, CD11b, CD14, CD19, CD20, ly6g, ly76, and NCAM-1). They also lack expression of mast cell protease 1 (MCP-1) and microphthalmia-associated transcription factor (mitf)."; . a owl:Class; rdfs:label "basophilic myelocyte"; rdfs:subClassOf ; "A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive."; . a owl:Class; rdfs:label "GABAergic neuron"; rdfs:subClassOf ; "A neuron that uses GABA as a vesicular neurotransmitter"; "GABA-ergic neuron"; . a owl:Class; rdfs:label "sheath cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "support cell (sensu Nematoda)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "natural killer cell"; rdfs:subClassOf ; "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells."; "NK cell"; . a owl:Class; rdfs:label "CD4-positive, alpha-beta T cell"; rdfs:subClassOf ; "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor."; "CD4-positive, alpha-beta T lymphocyte", "CD4-positive, alpha-beta T-cell", "CD4-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "CD8-positive, alpha-beta T cell"; rdfs:subClassOf ; "A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor."; "CD8-positive, alpha-beta T lymphocyte", "CD8-positive, alpha-beta T-cell", "CD8-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "olfactory granule cell"; rdfs:subClassOf ; "Granule cell that is part of the olfactory bulb."; . a owl:Class; rdfs:label "hepatic stellate cell"; rdfs:subClassOf ; "A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver."; rdfs:comment "Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen."; "Ito cell", "hepatic perisinusoidal cell", "perisinusoidal cell"; . a owl:Class; rdfs:label "Hensen cell"; rdfs:subClassOf ; "A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti."; "Hensen's cell", "cell of Hensen", "external limiting cell of organ of Corti"; . a owl:Class; rdfs:label "Claudius cell"; rdfs:subClassOf ; "A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti."; "cell of Claudius", "external supporting cell of Claudius", "external supporting cell of vestibular epithelium"; . a owl:Class; rdfs:label "Deiter's cell"; rdfs:subClassOf ; "Deiters cell", "outer phalangeal cell"; "The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression."; . a owl:Class; rdfs:label "Mueller cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "chromophil cell of anterior pituitary gland"; rdfs:subClassOf ; "A cell that stains readily in the anterior pituitary gland."; . a owl:Class; rdfs:label "acidophil cell of pars distalis of adenohypophysis"; rdfs:subClassOf ; "An acidophilic chromophil cell that of the anterior pituitary gland."; "acidophil cell of pars anterior of adenohypophysis", "acidophil of pars anterior of adenohypophysis", "acidophil of pars distalis of adenohypophysis", "pituitary alpha cell"; . a owl:Class; rdfs:label "basophil cell of pars distalis of adenohypophysis"; rdfs:subClassOf ; "A basophillic chromophil cell that of the anterior pituitary gland."; "basophil cell of anterior lobe of hypophysis"; . a owl:Class; rdfs:label "Bergmann glial cell"; rdfs:subClassOf ; "Bergmann astrocyte", "Bergmann glial cell of cerebellum"; "Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses."; . a owl:Class; rdfs:label "pituicyte"; rdfs:subClassOf ; "A cell with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment."; . a owl:Class; rdfs:label "basal cell"; rdfs:subClassOf ; "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament."; . a owl:Class; rdfs:label "multinucleated giant cell"; rdfs:subClassOf ; "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes."; "Langerhans giant cell", "foreign body giant cell", "macrophage polykaryon", "multinucleate giant cell", "syncytial giant cell"; rdfs:comment "Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this."; . a owl:Class; rdfs:label "kidney granular cell"; rdfs:subClassOf ; "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation."; "JG cell", "renin secreting cell"; . a owl:Class; rdfs:label "prickle cell"; rdfs:subClassOf ; "A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer. A function of this cell is to generate keratin."; "prickle cell of epidermis"; . a owl:Class; rdfs:label "pinealocyte"; rdfs:subClassOf ; "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation."; . a owl:Class; rdfs:label "glomerular visceral epithelial cell"; rdfs:subClassOf ; "A glomerular visceral epithelial cell is a specialized kidney epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells."; rdfs:comment "GO has podocyte as a related synonym due to concern this may refer to more than one cell type. However, this did not turn up in my search. If podocyte does refer to more than one cell type, then we should classify the synonym to 'related'."; "podocyte"; . a owl:Class; rdfs:label "cuticle secreting cell"; rdfs:subClassOf ; "An epithelial cell that secretes cuticle."; . a owl:Class; rdfs:label "eggshell secreting cell"; rdfs:subClassOf ; "An extracellular matrix secreting cell that secretes eggshell."; . a owl:Class; rdfs:label "glycocalyx secreting cell"; rdfs:subClassOf ; "An extracellular matrix secreting cell that secretes glycocalyx."; . a owl:Class; rdfs:label "neuroglioblast (sensu Nematoda)"; rdfs:subClassOf ; . a owl:Class; rdfs:label "closable valve cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "fenestrated cell"; rdfs:subClassOf ; "window cell"; . a owl:Class; rdfs:label "collagen secreting cell"; rdfs:subClassOf ; "An extracellular matrix secreting cell that secretes collagen."; . a owl:Class; rdfs:label "centripetally migrating follicle cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Kenyon cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "interfollicle cell"; rdfs:subClassOf ; "fly stalk cell"; . a owl:Class; rdfs:label "glutamatergic neuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "muscle precursor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "radial glial cell"; rdfs:subClassOf ; "A transient cell present only in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration."; . a owl:Class; rdfs:label "M cell"; rdfs:subClassOf ; "An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes."; "M-cell", "microfold cell"; . a owl:Class; rdfs:label "ependymoglial cell"; rdfs:subClassOf ; "A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space."; "ependymal astrocyte"; . a owl:Class; rdfs:label "littoral cell of liver"; rdfs:subClassOf ; . a owl:Class; rdfs:label "cerebrospinal fluid secreting cell"; rdfs:subClassOf ; "A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid."; . a owl:Class; rdfs:label "R1 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "perijunctional fibroblast"; rdfs:subClassOf ; "A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina."; . a owl:Class; rdfs:label "R2 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stellate interneuron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "terminal Schwann cell"; rdfs:subClassOf ; "A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse."; . a owl:Class; rdfs:label "neuroglioform cell"; rdfs:subClassOf ; "A stellate interneuron having 7-10 dendrites that may branch."; "spiderweb cell"; . a owl:Class; rdfs:label "R3 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Cajal-Retzius cell"; rdfs:subClassOf ; "One of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene."; . a owl:Class; rdfs:label "R4 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "dopaminergic neuron"; rdfs:subClassOf ; "A neuron that releases dopamine as a neurotransmitter."; "dopaminergic cell"; . a owl:Class; rdfs:label "R5 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "endothelial tip cell"; rdfs:subClassOf ; "A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels."; . a owl:Class; rdfs:label "R6 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "choroid plexus epithelial cell"; rdfs:subClassOf ; "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord."; "epithelial cell of choroid plexus"; . a owl:Class; rdfs:label "R7 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "leptomeningeal cell"; rdfs:subClassOf ; "Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus."; . a owl:Class; rdfs:label "R8 photoreceptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "neurecto-epithelial cell"; rdfs:subClassOf ; "Epithelial cells derived from neural plate and neural crest."; rdfs:comment "The term \"neuroepithelial cell\" is used to describe both this cell type and sensory epithelial cell (CL:0000098)."; . a owl:Class; rdfs:label "stratum granulosum cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "fusimotor neuron"; rdfs:subClassOf ; "A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons."; . a owl:Class; rdfs:label "somatic stem cell"; rdfs:subClassOf , , _:2de2e9; "A stem cell that can give rise to cell types of the body other than those of the germ-line."; . _:2de2e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "leading edge cell"; rdfs:subClassOf ; "A cell at the front of a migrating epithelial sheet."; . a owl:Class; rdfs:label "urothelial cell"; rdfs:subClassOf ; "A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria."; . a owl:Class; rdfs:label "striated muscle cell"; rdfs:subClassOf ; "Muscle cell which has as its direct parts myofilaments organized into sarcomeres."; . a owl:Class; rdfs:label "leukocyte"; rdfs:subClassOf ; "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue."; "immune cell", "leucocyte", "white blood cell"; . a owl:Class; rdfs:label "retinal ganglion cell"; rdfs:subClassOf ; "RGC", "gangliocyte", "ganglion cell of retina"; "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve."; . a owl:Class; rdfs:label "spinal accessory motor neuron"; rdfs:subClassOf ; "A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord."; "SACMN"; . a owl:Class; rdfs:label "periarticular chondrocyte"; rdfs:subClassOf ; "A round chondrocyte that first differentiates in the late embryonic growth plate of bone."; . a owl:Class; rdfs:label "hypertrophic chondrocyte"; rdfs:subClassOf ; "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)."; rdfs:comment "is hypertrophic pathological or normal? and can it be described using a pato term?"; . a owl:Class; rdfs:label "columnar chondrocyte"; rdfs:subClassOf ; "A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate."; . a owl:Class; rdfs:label "horizontal cell"; rdfs:subClassOf ; "A neuron that laterally connects other neurons in the inner nuclear layer of the retina."; . a owl:Class; rdfs:label "cardiac muscle cell"; rdfs:subClassOf ; "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei."; "cardiac muscle fiber", "cardiac myocyte", "cardiomyocyte", "heart muscle cell"; . a owl:Class; rdfs:label "retinal bipolar neuron"; rdfs:subClassOf ; "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer."; . a owl:Class; rdfs:label "ON-bipolar cell"; rdfs:subClassOf ; "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors."; . a owl:Class; rdfs:label "OFF-bipolar cell"; rdfs:subClassOf ; "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells hyperpolarize in response to light stimulation of their corresponding photoreceptors."; . a owl:Class; rdfs:label "rod bipolar cell"; rdfs:subClassOf ; "A bipolar neuron found in the retina and having connections with rod photoreceptor cells and neurons in the inner plexiform layer."; . a owl:Class; rdfs:label "cone retinal bipolar cell"; rdfs:subClassOf ; "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer."; . a owl:Class; rdfs:label "type 1 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities."; "DB1 cone bipolar cell"; . a owl:Class; rdfs:label "type 2 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1."; "FMB cone bipolar cell"; . a owl:Class; rdfs:label "type 3 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer."; "DB2 cone bipolar cell"; . a owl:Class; rdfs:label "type 4 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer."; "DB3 cone bipolar cell"; . a owl:Class; rdfs:label "type 5 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches."; "DB4 cone bipolar cell"; . a owl:Class; rdfs:label "type 6 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4."; "DB5 cone bipolar cell"; . a owl:Class; rdfs:label "type 7 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer."; "IMB cone bipolar cell"; . a owl:Class; rdfs:label "type 8 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer."; "DB6 cone bipolar cell"; . a owl:Class; rdfs:label "type 9 cone bipolar cell (sensu Mus)"; rdfs:subClassOf ; "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer."; "BB cone bipolar cell"; . a owl:Class; rdfs:label "nucleated thrombocyte"; rdfs:subClassOf ; "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates."; rdfs:comment "Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals."; . a owl:Class; rdfs:label "myeloid cell"; rdfs:subClassOf ; "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage."; . a owl:Class; rdfs:label "erythroid lineage cell"; rdfs:subClassOf ; "A immature or mature cell in the lineage leading to and including erythrocytes."; rdfs:comment "Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes."; "erythropoietic cell"; . a owl:Class; rdfs:label "erythroblast"; rdfs:subClassOf ; "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers."; "normoblast"; . a owl:Class; rdfs:label "myeloid leukocyte"; rdfs:subClassOf ; "A cell of the monocyte, granulocyte, or mast cell lineage."; . a owl:Class; rdfs:label "basophil"; rdfs:subClassOf ; "Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive."; rdfs:comment "Matures in the bone marrow and account for <1% of leukocytes in the peripheral blood, spleen, and bone marrow. Basophils are described as being CD11a-positive, CD11b-positive, CD13-positive, CD15-positive, CD18-positive, CD21-positive, CD25-positive, CD29-positive, CD35-positive, CD40-positive, CD40L-positive, CD44-positive, CD45R-negative, CD46-positive, CD49a-positive, CD49b-positive, CD49d-positive, CD55-positive, CD59-positive, CD62L-positive, CD63-positive, CD69-positive, CD90-negative, CD116-positive, CD117-negative, CD124-positive, CD125-positive, CD131-positive, CD161-positive, CD184-positive, CD191-positive, CD192-positive, CD197-positive, CD200R3-positive, CD218-positive, CD282-positive, CD284-positive, CD289-positive, CD290-positive, CD294-positive, natural killer cell receptor 2B4-positive, smad1-positive, CD3-negative, CD4-negative, CD7-negative, CD8-negative, CD14-negative, CD15-negative, CD16-negative, CD19-negative, CD20-negative, CD34-negative, CD36-negative, CD45R-negative, CD56-negative, CD57-negative, CD235a-negative, and GR1-negative. Transcription factors- GATA1-positive, PU.1-positive."; "basophilic leucocyte", "basophilic leukocyte"; . a owl:Class; rdfs:label "immature basophil"; rdfs:subClassOf ; "Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking."; "immature basophilic leucocyte", "immature basophilic leukocyte"; . a owl:Class; rdfs:label "basophilic metamyelocyte"; rdfs:subClassOf ; "A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive."; . a owl:Class; rdfs:label "band form basophil"; rdfs:subClassOf ; "A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil."; . a owl:Class; rdfs:label "eosinophil"; rdfs:subClassOf ; "Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive."; rdfs:comment "Eosinophils are also CD14-negative, CD32-positive, CD44-positive, CD48-positive, CD69-positive, CD192-negative, MBP1-positive, MBP2-positive, TLR2-negative, TLR4-negative, and lineage-negative (B220, CD2, CD14, CD19, CD56, CD71, CD117, CD123, CD235a (glycophorin A), and TER119). The cytokines IL-3, IL-5, and GM-CSF are involved in their development and differentiation. Usually considered CD16-negative, CD16 is observed on eosinophilic metamyelocyte."; "eosinocyte", "eosinophilic granulocyte", "eosinophilic leucocyte", "eosinophilic leukocyte"; . a owl:Class; rdfs:label "immature eosinophil"; rdfs:subClassOf ; "Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking."; "immature eosinocyte", "immature eosinophilic leucocyte", "immature eosinophilic leukocyte"; . a owl:Class; rdfs:label "eosinophilic metamyelocyte"; rdfs:subClassOf ; "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative."; . a owl:Class; rdfs:label "band form eosinophil"; rdfs:subClassOf ; "A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil."; . a owl:Class; rdfs:label "neutrophil"; rdfs:subClassOf ; "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes."; "neutrocyte", "neutrophil leucocyte", "neutrophil leukocyte", "neutrophilic leucocyte", "neutrophilic leukocyte"; . a owl:Class; rdfs:label "immature neutrophil"; rdfs:subClassOf ; "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking."; "immatuer neutrophilic leukocyte", "immature neutrocyte", "immature neutrophil leucocyte", "immature neutrophil leukocyte", "immature neutrophilic leucocyte"; . a owl:Class; rdfs:label "mesangial phagocyte"; rdfs:subClassOf ; "A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling."; . a owl:Class; rdfs:label "mononuclear osteoclast"; rdfs:subClassOf ; "A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts."; rdfs:comment "Morphology: mononuclear, highly vesicular."; . a owl:Class; rdfs:label "multinuclear osteoclast"; rdfs:subClassOf ; "A specialized multinuclear osteoclast associated with the absorption and removal of bone."; rdfs:comment "Morphology: multinucleated, highly vesicular."; "multinucleated osteoclast"; . a owl:Class; rdfs:label "multinuclear odontoclast"; rdfs:subClassOf ; "A specialized multinuclear osteoclast associated with the absorption and removal of cementum."; rdfs:comment "Morphology: multinucleated, highly vesicular; location: roots of deciduous (milk) teeth."; "multinucleated odontoclast"; . a owl:Class; rdfs:label "mononuclear odontoclast"; rdfs:subClassOf ; "A specialized mononuclear osteoclast associated with the absorption and removal of cementum."; rdfs:comment "Morphology: Mononuclear, highly vesicular; location: roots of deciduous (milk) teeth."; . a owl:Class; rdfs:label "myeloid dendritic cell"; rdfs:subClassOf ; "A dendritic cell of the myeloid lineage."; "CD11c+CD123- DC", "mDC"; rdfs:comment "These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8)."; . a owl:Class; rdfs:label "multinucleated phagocyte"; rdfs:subClassOf ; "A phagocyte formed by the fusion of mononuclear phagocytes."; . a owl:Class; rdfs:label "plasmacytoid dendritic cell"; rdfs:subClassOf ; "A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection."; "DC2", "IPC", "T-associated plasma cell", "interferon-producing cell", "lymphoid dendritic cell", "pDC", "plasmacytoid T cell", "plasmacytoid monocyte", "type 2 DC"; . a owl:Class; rdfs:label "mature B cell"; rdfs:subClassOf ; "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen."; "mature B lymphocyte", "mature B-cell", "mature B-lymphocyte"; . a owl:Class; rdfs:label "plasma cell"; rdfs:subClassOf ; "A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin."; "plasmacyte"; . a owl:Class; rdfs:label "memory B cell"; rdfs:subClassOf ; "A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative."; "memory B lymphocyte", "memory B-cell", "memory B-lymphocyte"; . a owl:Class; rdfs:label "naive B cell"; rdfs:subClassOf ; "A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD27-negative and that has not yet been activated by antigen in the periphery."; "naive B lymphocyte", "naive B-cell", "naive B-lymphocyte"; . a owl:Class; rdfs:label "alpha-beta T cell"; rdfs:subClassOf ; "A T cell that expresses an alpha-beta T cell receptor complex."; "alpha-beta T lymphocyte", "alpha-beta T-cell", "alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "immature alpha-beta T cell"; rdfs:subClassOf ; "An alpha-beta T cell that has an immature phenotype and has not completed T cell selection."; "immature alpha-beta T lymphocyte", "immature alpha-beta T-cell", "immature alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "mature alpha-beta T cell"; rdfs:subClassOf ; "A alpha-beta T cell that has a mature phenotype."; "mature alpha-beta T lymphocyte", "mature alpha-beta T-cell", "mature alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "CD4-positive, CD25-positive, alpha-beta regulatory T cell"; rdfs:subClassOf ; "A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release."; "CD4-positive, CD25-positive, alpha-beta regulatory T lymphocyte", "CD4-positive, CD25-positive, alpha-beta regulatory T-cell", "CD4-positive, CD25-positive, alpha-beta regulatory T-lymphocyte"; . a owl:Class; rdfs:label "CD4-positive, alpha-beta intraepithelial T cell"; rdfs:subClassOf ; "A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract."; "CD4-positive, alpha-beta intraepithelial T lymphocyte", "CD4-positive, alpha-beta intraepithelial T-cell", "CD4-positive, alpha-beta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "CD8-positive, alpha-beta cytotoxic T cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive."; "CD8-positive, alpha-beta cytotoxic T lymphocyte", "CD8-positive, alpha-beta cytotoxic T-cell", "CD8-positive, alpha-beta cytotoxic T-lymphocyte"; rdfs:comment "Note that while T cells of this subset are loosely referred to 'cytotoxic T cells,' as many other T cell types, including CD4-positive, alpha-beta T cells and gamma-delta T cells exhibit cytotoxicity in vitro and in vivo."; . a owl:Class; rdfs:label "CD8-positive, alpha-beta regulatory T cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release."; "CD8-positive, alpha-beta regulatory T lymphocyte", "CD8-positive, alpha-beta regulatory T-cell", "CD8-positive, alpha-beta regulatory T-lymphocyte"; . a owl:Class; rdfs:label "CD8-alpha-beta-positive, alpha-beta intraepithelial T cell"; rdfs:subClassOf ; "A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements."; "CD8-positive, alpha-beta intraepithelial T lymphocyte", "CD8-positive, alpha-beta intraepithelial T-cell", "CD8-positive, alpha-beta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "alpha-beta intraepithelial T cell"; rdfs:subClassOf ; "A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements."; "alpha-beta intraepithelial T lymphocyte", "alpha-beta intraepithelial T-cell", "alpha-beta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "gamma-delta T cell"; rdfs:subClassOf ; "A T cell that expresses a gamma-delta T cell receptor complex."; rdfs:comment "Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways."; "gamma-delta T lymphocyte", "gamma-delta T-cell", "gamma-delta T-lymphocyte", "gammadelta T cell"; . a owl:Class; rdfs:label "immature gamma-delta T cell"; rdfs:subClassOf ; "A gamma-delta T cell that has an immature phenotype."; rdfs:comment "Note that gamma-delta T cells have both thymic and extrathymic differentiation pathways."; "immature gamma-delta T lymphocyte", "immature gamma-delta T-cell", "immature gamma-delta T-lymphocyte"; . a owl:Class; rdfs:label "mature gamma-delta T cell"; rdfs:subClassOf ; "A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location."; "mature gamma-delta T lymphocyte", "mature gamma-delta T-cell", "mature gamma-delta T-lymphocyte"; . a owl:Class; rdfs:label "gamma-delta intraepithelial T cell"; rdfs:subClassOf ; "A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses."; "gamma-delta intraepithelial T lymphocyte", "gamma-delta intraepithelial T-cell", "gamma-delta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "CD8-alpha alpha positive, gamma-delta intraepithelial T cell"; rdfs:subClassOf ; "A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive."; "CD8-positive, gamma-delta intraepithelial T lymphocyte", "CD8-positive, gamma-delta intraepithelial T-cell", "CD8-positive, gamma-delta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "CD4-negative CD8-negative gamma-delta intraepithelial T cell"; rdfs:subClassOf ; "A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative."; "CD4-positive, gamma-delta intraepithelial T lymphocyte", "CD4-positive, gamma-delta intraepithelial T-cell", "CD4-positive, gamma-delta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "immature single positive thymocyte"; rdfs:subClassOf ; "A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive."; "ISP", "T.ISP.th", "immature single positive T cell", "immature single positive T lymphocyte", "immature single positive T-lymphocyte"; rdfs:comment "Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and rearranging the T cell receptor alpha chain and expressing the CD8 coreceptor. This stage comes between the DN4 and DP stages."; . a owl:Class; rdfs:label "DN2 thymocyte"; rdfs:subClassOf ; "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive."; "DN2 alpha-beta immature T lymphocyte", "DN2 alpha-beta immature T-cell", "DN2 alpha-beta immature T-lymphocyte", "DN2 cell", "DN2 immature T cell", "TN2 cell", "TN2 thymocyte", "double negative 2", "preT.DN2.Th"; rdfs:comment "Note that this type of thymocyte is at the earliest stage of T cell receptor rearrangement of the beta, gamma, and delta T cell receptor chains."; . a owl:Class; rdfs:label "DN3 thymocyte"; rdfs:subClassOf ; "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain."; "DN3 alpha-beta immature T lymphocyte", "DN3 alpha-beta immature T-cell", "DN3 alpha-beta immature T-lymphocyte", "DN3 cell", "DN3 immature T cell", "TN3 cell", "TN3 thymocyte", "double negative 3", "preT.DN3.Th"; . a owl:Class; rdfs:label "DN4 thymocyte"; rdfs:subClassOf ; "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive."; "DN4 alpha-beta immature T lymphocyte", "DN4 alpha-beta immature T-lymphocyte", "DN4 cell", "DN4 immature T cell", "DN4 immature T-cell", "T.DN4.th", "double negative 4"; rdfs:comment "Note that this type of thymocyte has passed the beta-selection checkpoint and is rapidly proliferating and beginning to rearrange the T cell receptor alpha chain."; . a owl:Class; rdfs:label "double-positive, alpha-beta thymocyte"; rdfs:subClassOf ; "A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors."; "DP cell", "DP thymocyte", "double-positive, alpha-beta immature T lymphocyte"; rdfs:comment "Thymocytes of this stage are undergoing positive and negative selection."; . a owl:Class; rdfs:label "CD4-positive, alpha-beta thymocyte"; rdfs:subClassOf ; "An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative."; "CD4-positive, alpha-beta immature T lymphocyte", "CD4-positive, alpha-beta immature T-cell", "CD4-positive, alpha-beta immature T-lymphocyte", "SP CD4 cell"; . a owl:Class; rdfs:label "CD8-positive, alpha-beta thymocyte"; rdfs:subClassOf ; "An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative."; "CD8-positive, alpha-beta immature T lymphocyte", "CD8-positive, alpha-beta immature T-cell", "CD8-positive, alpha-beta immature T-lymphocyte", "SP CD8 cell"; . a owl:Class; rdfs:label "memory T cell"; rdfs:subClassOf ; "A distinctly differentiated long-lived T cell that has the phenotype CD45RO-positive and CD127-positive."; "memory T lymphocyte", "memory T-cell", "memory T-lymphocyte"; . a owl:Class; rdfs:label "mature NK T cell"; rdfs:subClassOf ; "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response."; "mature NK T lymphocyte", "mature NK T-cell", "mature NK T-lymphocyte", "mature NKT cell", "mature natural killer T cell", "mature natural killer T lymphocyte", "mature natural killer T-cell", "mature natural killer T-lymphocyte"; . a owl:Class; rdfs:label "regulatory T cell"; rdfs:subClassOf ; "A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release."; rdfs:comment "This cell type may express FoxP3 and CD25 and secretes IL-10 and TGF-beta."; "regulatory T lymphocyte", "regulatory T-cell", "regulatory T-lymphocyte"; . a owl:Class; rdfs:label "immature B cell"; rdfs:subClassOf ; "An immature B cell is a precursor B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation."; "immature B lymphocyte", "immature B-cell", "immature B-lymphocyte", "newly formed B Cell"; . a owl:Class; rdfs:label "precursor B cell"; rdfs:subClassOf ; "A precursor B cell is a B cell with the phenotype CD10-positive."; "pre-B cell"; . a owl:Class; rdfs:label "transitional stage B cell"; rdfs:subClassOf ; "An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen."; "transitional stage B lymphocyte", "transitional stage B-cell", "transitional stage B-lymphocyte"; . a owl:Class; rdfs:label "B-1 B cell"; rdfs:subClassOf ; "A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive."; "B-1 B lymphocyte", "B-1 B-cell", "B-1 B-lymphocyte"; . a owl:Class; rdfs:label "B-1a B cell"; rdfs:subClassOf ; "A B-1 B cell that has the phenotype CD5-positive."; "B-1a B lymphocyte", "B-1a B-cell", "B-1a B-lymphocyte", "B1a B cell"; . a owl:Class; rdfs:label "B-1b B cell"; rdfs:subClassOf ; "A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell."; "B-1b B lymphocyte", "B-1b B-cell", "B-1b B-lymphocyte"; . a owl:Class; rdfs:label "B-2 B cell"; rdfs:subClassOf ; "A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative."; "B-2 B lymphocyte", "B-2 B-cell", "B-2 B-lymphocyte"; . a owl:Class; rdfs:label "immature natural killer cell"; rdfs:subClassOf ; "A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR)."; rdfs:comment "In mouse the NKR are Ly49 molecules and in human these cells express KIR molecules."; "immature NK cell"; . a owl:Class; rdfs:label "mature natural killer cell"; rdfs:subClassOf ; "A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules."; "mature NK cell"; . a owl:Class; rdfs:label "pro-NK cell"; rdfs:subClassOf ; "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative."; rdfs:comment "Most markers only described for human pro NK cells."; "NKP", "natural killer cell progenitor", "pro-natural killer cell"; . a owl:Class; rdfs:label "pro-B cell"; rdfs:subClassOf ; "A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs."; "pro-B lymphocyte", "pro-B-cell", "pro-B-lymphocyte", "progenitor B cell"; . a owl:Class; rdfs:label "pro-T cell"; rdfs:subClassOf ; "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage."; "pro-T lymphocyte", "progenitor T cell"; . a owl:Class; rdfs:label "thromboblast"; rdfs:subClassOf ; "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates."; rdfs:comment "Note that this is a non-mammalian cell type."; . a owl:Class; rdfs:label "basophilic myeloblast"; rdfs:subClassOf ; "A myeloblast committed to the basophil lineage."; . a owl:Class; rdfs:label "basophilic promyelocyte"; rdfs:subClassOf ; "A promyelocyte committed to the basophil lineage."; . a owl:Class; rdfs:label "mast cell progenitor"; rdfs:subClassOf ; "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative."; "MCP"; rdfs:comment "MCP are CD16-positive, CD32-positive, CD34-positive, CD45-positive, integrin beta-7-positive, and lin-negative (CD2, CD3e, CD4, CD5, CD8a, CD14, CD19, CD20, CD27, integrin alpha-M, ly6c, ly6g, NCAM-1, and ter119). These cells also express the transcription factors GATA-1, GATA-2, and MITF, but not C/EBPa."; . a owl:Class; rdfs:label "eosinophilic myeloblast"; rdfs:subClassOf ; "A myeloblast committed to the eosinophil lineage."; . a owl:Class; rdfs:label "eosinophilic promyelocyte"; rdfs:subClassOf ; "A promyelocyte committed to the eosinophil lineage."; . a owl:Class; rdfs:label "neutrophil progenitor cell"; rdfs:subClassOf ; "A progenitor cell of the neutrophil lineage."; . a owl:Class; rdfs:label "myeloblast"; rdfs:subClassOf ; "The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow."; . a owl:Class; rdfs:label "promyelocyte"; rdfs:subClassOf ; "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative."; . a owl:Class; rdfs:label "hematopoietic multipotent progenitor cell"; rdfs:subClassOf ; "A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans."; "MPP", "hemopoietic progenitor cell"; rdfs:comment "Markers differ between mouse and human."; . a owl:Class; rdfs:label "lymphoid lineage restricted progenitor cell"; rdfs:subClassOf ; "A progenitor cell restricted to the lymphoid lineage."; rdfs:comment "Note that this is a class of cell types, not an identified single cell type."; . a owl:Class; rdfs:label "myeloid lineage restricted progenitor cell"; rdfs:subClassOf ; "A progenitor cell restricted to the myeloid lineage."; rdfs:comment "Note that this is a class of cell types, not an identified single cell type."; . a owl:Class; rdfs:label "immature conventional dendritic cell"; rdfs:subClassOf ; "An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low."; . a owl:Class; rdfs:label "mature conventional dendritic cell"; rdfs:subClassOf ; "A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node."; . a owl:Class; rdfs:label "mononuclear cell"; rdfs:subClassOf ; "A leukocyte with a single non-segmented nucleus in the mature form."; . a owl:Class; rdfs:label "follicular B cell"; rdfs:subClassOf ; "A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative."; "Fo B cell"; . a owl:Class; rdfs:label "germinal center B cell"; rdfs:subClassOf ; "A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation."; . a owl:Class; rdfs:label "marginal zone B cell"; rdfs:subClassOf ; "A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD23-negative, CD21/35-high."; . a owl:Class; rdfs:label "vestibular dark cell"; rdfs:subClassOf ; "An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings."; . a owl:Class; rdfs:label "ciliated olfactory receptor neuron"; rdfs:subClassOf ; "An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob."; "ciliated olfactory sensory neuron", "ciliated sensory neuron"; . a owl:Class; rdfs:label "microvillous olfactory receptor neuron"; rdfs:subClassOf ; "An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli."; "microvillous olfactory sensory neuron"; . a owl:Class; rdfs:label "crypt olfactory receptor neuron"; rdfs:subClassOf ; "An olfactory receptor cell with short cilia growing in an invagination bordered by microvilli."; "crypt cell", "crypt olfactory sensory neuron", "crypt sensory neuron"; . a owl:Class; rdfs:label "serotonergic neuron"; rdfs:subClassOf ; "5-HT neuron", "5-hydroxytryptamine neuron"; "A neuron that releases serotonin as a neurotransmitter."; . a owl:Class; rdfs:label "olfactory epithelial support cell"; rdfs:subClassOf ; "Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons."; "olfactory sustentacular cell", "supporting cell of olfactory epithelium", "sustentaculocyte of olfactory epithelium"; . a owl:Class; rdfs:label "sensory hair cell"; rdfs:subClassOf ; "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system."; . a owl:Class; rdfs:label "neuromast hair cell"; rdfs:subClassOf ; "Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface."; . a owl:Class; rdfs:label "classical monocyte"; rdfs:subClassOf ; "A type of monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors. This cell type is characterized by high expression of CCR2 in both rodents and humans, and of being larger size than non-classical monocytes."; rdfs:comment "Markers: CCR2+CXCCR1 (human, mouse, rat)."; "inflammatory monocyte"; . a owl:Class; rdfs:label "elicited macrophage"; rdfs:subClassOf ; "A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive."; rdfs:comment "Markers: CD11b+, CD68+; Mouse: F4/80+; role or process: immune, inflammation (inflammatory response)."; "free macrophage", "wandering histiocyte"; . a owl:Class; rdfs:label "suppressor macrophage"; rdfs:subClassOf ; "A macrophage that suppresses immune responses."; rdfs:comment "Markers: May express: IL10, TGFbeta."; . a owl:Class; rdfs:label "inflammatory macrophage"; rdfs:subClassOf ; "An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity."; rdfs:comment "Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reactive oxygen species, nitric oxide; role or process: immune, inflammation (inflammatory response)."; "classically activated macrophage"; . a owl:Class; rdfs:label "tissue-resident macrophage"; rdfs:subClassOf ; "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells."; "fixed macrophage", "resting histiocyte"; . a owl:Class; rdfs:label "gastrointestinal tract (lamina propria) macrophage"; rdfs:subClassOf ; "A gut-associated lymphoid tissue macrophage found in lamina propria of the gut."; . a owl:Class; rdfs:label "thymic macrophage"; rdfs:subClassOf ; "A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes."; rdfs:comment "Role or process: immune, clearance of apoptotic thymocytes, antigen-presentation."; . a owl:Class; rdfs:label "secondary lymphoid organ macrophage"; rdfs:subClassOf ; "A tissue-resident macrophage found in a secondary lymphoid organ."; . a owl:Class; rdfs:label "lymph node macrophage"; rdfs:subClassOf ; "A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high."; "MF.LN"; rdfs:comment "Marker was observed on rat cells."; . a owl:Class; rdfs:label "tonsillar macrophage"; rdfs:subClassOf ; "A gut-associated lymphoid tissue macrophage found in tonsils."; . a owl:Class; rdfs:label "Peyer's patch macrophage"; rdfs:subClassOf ; "A gut-associated lymphoid tissue macrophage found in the Peyer's patches."; . a owl:Class; rdfs:label "splenic macrophage"; rdfs:subClassOf ; "A secondary lymphoid organ macrophage found in the spleen."; rdfs:comment "Role or process: immune, clearance of apoptotic and senescent cells."; . a owl:Class; rdfs:label "splenic marginal zone macrophage"; rdfs:subClassOf ; "A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive."; rdfs:comment "Markers: Mouse: F4/80-, MARCO+, SR-A+, SIGN-R1+, Dectin2+."; . a owl:Class; rdfs:label "splenic metallophillic macrophage"; rdfs:subClassOf ; "A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive."; rdfs:comment "Markers: Mouse: F4/80-, Dectin2-low, sialoadhesin+."; . a owl:Class; rdfs:label "splenic red pulp macrophage"; rdfs:subClassOf ; "A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low."; rdfs:comment "Markers: Mouse: F4/80+, CD68+, MR+, Dectin2+, macrosialin+, sialoadhesin-low; role or process: immune, clearance of senescent erythrocytes."; . a owl:Class; rdfs:label "non-classical monocyte"; rdfs:subClassOf ; rdfs:comment "Markers: CCR2-CX3CCR1+ (human, mouse, rat); human: CD16+, CCR5+, CD32/FcgRII-high, MHCII+, CD86+; mouse: CD62L-Ly6C-."; "Subset of monocytes characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, but increased co-stimulatory activity. May also play a role in tissue repair."; "patrolling monocyte", "resident monocyte"; . a owl:Class; rdfs:label "splenic white pulp macrophage"; rdfs:subClassOf ; "A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive."; rdfs:comment "Markers: Mouse: F4/80-, CD68+, macrosialin+."; . a owl:Class; rdfs:label "splenic tingible body macrophage"; rdfs:subClassOf ; "A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive."; . a owl:Class; rdfs:label "central nervous system macrophage"; rdfs:subClassOf ; "A tissue-resident macrophage found in the central nervous system."; "CNS macrophage"; . a owl:Class; rdfs:label "meningeal macrophage"; rdfs:subClassOf ; "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors."; . a owl:Class; rdfs:label "choroid-plexus macrophage"; rdfs:subClassOf ; "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors."; . a owl:Class; rdfs:label "perivascular macrophage"; rdfs:subClassOf ; "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+."; rdfs:comment "Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+."; . a owl:Class; rdfs:label "thymic medullary macrophage"; rdfs:subClassOf ; "A thymic macrophage found in the thymic medulla."; . a owl:Class; rdfs:label "thymic cortical macrophage"; rdfs:subClassOf ; "A thymic macrophage found in the thymic cortex."; . a owl:Class; rdfs:label "mucosa-associated lymphoid tissue macrophage"; rdfs:subClassOf ; "A tissue-resident macrophage found in the mucosa associated lymphoid tissue."; . a owl:Class; rdfs:label "gut-associated lymphoid tissue macrophage"; rdfs:subClassOf ; "A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut."; . a owl:Class; rdfs:label "nasal and broncial associated lymphoid tissue macrophage"; rdfs:subClassOf ; "A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues."; . a owl:Class; rdfs:label "lymph node subcapsular sinus macrophage"; rdfs:subClassOf ; "A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive."; . a owl:Class; rdfs:label "lymph node tingible body macrophage"; rdfs:subClassOf ; "A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers."; . a owl:Class; rdfs:label "myeloid suppressor cell"; rdfs:subClassOf ; "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive."; rdfs:comment "Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis."; . a owl:Class; rdfs:label "alternatively activated macrophage"; rdfs:subClassOf ; "An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling."; rdfs:comment "Role or process: tissue remodeling."; . a owl:Class; rdfs:label "thymocyte"; rdfs:subClassOf ; "An immature T cell located in the thymus."; "thymic lymphocyte"; . a owl:Class; rdfs:label "DN1 thymic pro-T cell"; rdfs:subClassOf ; "A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative."; "DN1 thymic pro-T lymphocyte", "DN1 thymic pro-T-cell", "DN1 thymic pro-T-lymphocyte", "DN1 thymic progenitor T cell", "DN1 thymocyte", "double negative 1", "preT.DN1.Th"; . a owl:Class; rdfs:label "naive thymus-derived CD4-positive, alpha-beta T cell"; rdfs:subClassOf ; "An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low."; "T.4Nve.Sp", "Th0", "naive thymus-derived CD4-positive, alpha-beta T lymphocyte", "naive thymus-derived CD4-positive, alpha-beta T-cell", "naive thymus-derived CD4-positive, alpha-beta T-lymphocyte"; rdfs:comment "These cells have not been exposed to antigen following thymic T-cell selection; found in blood and secondary lymphoid organs."; . a owl:Class; rdfs:label "activated CD4-positive, alpha-beta T cell"; rdfs:subClassOf ; "A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive."; "activated CD4-positive, alpha-beta T lymphocyte", "activated CD4-positive, alpha-beta T-cell", "activated CD4-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "CD4-positive, alpha-beta memory T cell"; rdfs:subClassOf ; "CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122- high."; "CD4-positive, alpha-beta memory T lymphocyte", "CD4-positive, alpha-beta memory T-cell", "CD4-positive, alpha-beta memory T-lymphocyte"; . a owl:Class; rdfs:label "naive T cell"; rdfs:subClassOf ; "Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low."; "naive T lymphocyte", "naive T-cell", "naive T-lymphocyte"; . a owl:Class; rdfs:label "T-helper 17 cell"; rdfs:subClassOf ; "CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive that produces IL-17."; "Th17 T cell", "Th17 T lymphocyte", "Th17 T-cell", "Th17 T-lymphocyte", "Th17 cell", "helper T cell type 17"; . a owl:Class; rdfs:label "naive thymus-derived CD8-positive, alpha-beta T cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low."; rdfs:comment "Additional markers in human are CD45RA. This cell traffics in secondary lymphoid organs and blood."; "naive thymus-dervied CD8-positive, alpha-beta T lymphocyte", "naive thymus-dervied CD8-positive, alpha-beta T-cell", "naive thymus-dervied CD8-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "Tr1 cell"; rdfs:subClassOf ; "CD4-positive alpha-beta T cell with regulatory function that produces IL-10."; "T-regulatory T cell type 1", "Tr1 T cell", "Tr1 T lymphocyte", "Tr1 T-cell", "Tr1 T-lymphocyte"; . a owl:Class; rdfs:label "induced T-regulatory cell"; rdfs:subClassOf ; "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function."; "iTreg", "induced Treg", "induced regulatory T cell", "induced regulatory T lymphocyte", "induced regulatory T-cell", "induced regulatory T-lymphocyte"; . a owl:Class; rdfs:label "natural T-regulatory cell"; rdfs:subClassOf ; "CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function."; "nTreg", "natural Treg", "natural regulatory T cell", "natural regulatory T lymphocyte", "natural regulatory T-cell", "natural regulatory T-lymphocyte"; . a owl:Class; rdfs:label "central memory CD4-positive, alpha-beta T cell"; rdfs:subClassOf ; "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RO-positive, and CD25-negative."; "central CD4-positive, alpha-beta memory T cell", "central CD4-positive, alpha-beta memory T lymphocyte", "central CD4-positive, alpha-beta memory T-cell", "central CD4-positive, alpha-beta memory T-lymphocyte", "central memory CD4-positive, alpha-beta T lymphocyte", "central memory CD4-positive, alpha-beta T-cell", "central memory CD4-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "effector memory CD4-positive, alpha-beta T cell"; rdfs:subClassOf ; "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RO-positive, and CD25-negative."; "effector CD4-positive, alpha-beta memory T cell", "effector CD4-positive, alpha-beta memory T lymphocyte", "effector CD4-positive, alpha-beta memory T-cell", "effector CD4-positive, alpha-beta memory T-lymphocyte", "effector memory CD4-positive, alpha-beta T lymphocyte", "effector memory CD4-positive, alpha-beta T-cell", "effector memory CD4-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "activated CD8-positive, alpha-beta T cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative."; "activated CD8-positive, alpha-beta T lymphocyte", "activated CD8-positive, alpha-beta T-cell", "activated CD8-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "central memory CD8 positive, alpha-beta T cell"; rdfs:subClassOf ; "A CD8-positive, alpha beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RO-positive, and CD25-negative."; "central CD8-positive, alpha-beta memory T cell", "central CD8-positive, alpha-beta memory T lymphocyte", "central CD8-positive, alpha-beta memory T-cell", "central CD8-positive, alpha-beta memory T-lymphocyte", "central memory CD8-positive, alpha-beta T lymphocyte", "central memory CD8-positive, alpha-beta T-cell", "central memory CD8-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "CD8-positive, alpha-beta cytokine secreting effector T cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines."; "CD8-positive, alpha-beta cytokine secreting effector T lymphocyte", "CD8-positive, alpha-beta cytokine secreting effector T-cell", "CD8-positive, alpha-beta cytokine secreting effector T-lymphocyte"; . a owl:Class; rdfs:label "CD8-positive, alpha-beta memory T cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122- high."; "CD8-positive, alpha-beta memory T lymphocyte", "CD8-positive, alpha-beta memory T-cell", "CD8-positive, alpha-beta memory T-lymphocyte", "T.8Mem.Sp"; . a owl:Class; rdfs:label "cytotoxic T cell"; rdfs:subClassOf ; "A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive."; "cytotoxic T lymphocyte", "cytotoxic T-cell", "cytotoxic T-lymphocyte"; . a owl:Class; rdfs:label "effector T cell"; rdfs:subClassOf ; "A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response."; "effector T lymphocyte", "effector T-cell", "effector T-lymphocyte"; . a owl:Class; rdfs:label "helper T cell"; rdfs:subClassOf ; "A effector T cell that provides help in the form of secreted cytokines to other immune cells."; "T-helper cell", "helper T lymphocyte", "helper T-cell", "helper T-lymphocyte"; . a owl:Class; rdfs:label "effector memory CD8-positive, alpha-beta T cell"; rdfs:subClassOf ; "A CD8-positive, alpha beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RO-positive, and CD25-negative."; "effector CD8-positive, alpha-beta memory T cell", "effector CD8-positive, alpha-beta memory T lymphocyte", "effector CD8-positive, alpha-beta memory T-cell", "effector CD8-positive, alpha-beta memory T-lymphocyte", "effector memory CD8-positive, alpha-beta T lymphocyte", "effector memory CD8-positive, alpha-beta T-cell", "effector memory CD8-positive, alpha-beta T-lymphocyte"; . a owl:Class; rdfs:label "immature NK T cell"; rdfs:subClassOf ; "An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers."; "immature NK T lymphocyte", "immature NK T-cell", "immature NK T-lymphocyte", "immature NKT cell"; . a owl:Class; rdfs:label "CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell"; rdfs:subClassOf ; "An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative."; "CD8-alpha-alpha-positive, alpha-beta intraepithelial T lymphocyte", "CD8-alpha-alpha-positive, alpha-beta intraepithelial T-cell", "CD8-alpha-alpha-positive, alpha-beta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "dendritic epidermal T cell"; rdfs:subClassOf ; "A mature gamma-delta T cell located in the epidermis that regulates wound healing."; "DETC", "dendritic epidermal T lymphocyte", "dendritic epidermal T-cell", "dendritic epidermal T-lymphocyte"; rdfs:comment "In mice, DETC have an invariant T cell receptor."; . a owl:Class; rdfs:label "Tc1 cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta positive T cell expressing T-bet and eomesodermin and secreting interferon-gamma."; "T-cytotoxic T cell type 1", "Tc1 T cell", "Tc1 T lymphocyte", "Tc1 T-cell", "Tc1 T-lymphocyte"; . a owl:Class; rdfs:label "Tc2 cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4."; "T-cytotoxic T cell type 2", "Tc2 T cell", "Tc2 T lymphocyte", "Tc2 T-cell", "Tc2 T-lymphocyte"; . a owl:Class; rdfs:label "CD8-positive, CD25-positive, alpha-beta regulatory T cell"; rdfs:subClassOf ; "A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function."; "CD8-positive, CD25-positive, alpha-beta regulatory T lymphocyte", "CD8-positive, CD25-positive, alpha-beta regulatory T-cell", "CD8-positive, CD25-positive, alpha-beta regulatory T-lymphocyte"; . a owl:Class; rdfs:label "CD8-positive, CD28-negative, alpha-beta regulatory T cell"; rdfs:subClassOf ; "CD8-positive, CD28-negative, alpha-beta regulatory T lymphocyte", "CD8-positive, CD28-negative, alpha-beta regulatory T-cell", "CD8-positive, CD28-negative, alpha-beta regulatory T-lymphocyte"; "CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive."; . a owl:Class; rdfs:label "type I NK T cell"; rdfs:subClassOf ; "An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d."; rdfs:comment "In mouse the canonical TCR is V-alpha-14, and in humans it is V-alpha 24."; "classical NK T cell", "type I NK T lymphocyte", "type I NK T-cell", "type I NK T-lymphocyte", "type I NKT cell"; . a owl:Class; rdfs:label "type II NK T cell"; rdfs:subClassOf ; "An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d."; "type II NK T lymphocyte", "type II NK T-cell", "type II NK T-lymphocyte", "type II NKT cell"; . a owl:Class; rdfs:label "CD4-positive type I NK T cell"; rdfs:subClassOf ; "A type I NK T cell that has the phenotype CD4-positive."; "CD4-positive type I NK T lymphocyte", "CD4-positive type I NK T-cell", "CD4-positive type I NK T-lymphocyte", "CD4-positive type I NKT cell"; . a owl:Class; rdfs:label "CD4-negative, CD8-negative type I NK T cell"; rdfs:subClassOf ; "A type I NK T cell that has the phenotype CD4-negative and CD8-negative."; "CD4-negative, CD8-negative type I NK T lymphocyte", "CD4-negative, CD8-negative type I NK T-cell", "CD4-negative, CD8-negative type I NK T-lymphocyte", "CD4-negative, CD8-negative type I NKT cell"; . a owl:Class; rdfs:label "activated CD4-positive type I NK T cell"; rdfs:subClassOf ; "A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers."; "activated CD4-positive type I NK T lymphocyte", "activated CD4-positive type I NK T-cell", "activated CD4-positive type I NK T-lymphocyte", "activated CD4-positive type I NKT cell"; . a owl:Class; rdfs:label "CD4-positive type I NK T cell secreting interferon-gamma"; rdfs:subClassOf ; "A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses."; "CD4-positive type I NK T cell secreting IFN-gamma", "CD4-positive type I NK T lymphocyte secreting interferon-gamma", "CD4-positive type I NK T-cell secreting interferon-gamma", "CD4-positive type I NK T-lymphocyte secreting interferon-gamma", "CD4-positive type I NKT cell secreting interferon-gamma"; . a owl:Class; rdfs:label "CD4-positive type I NK T cell secreting interleukin-4"; rdfs:subClassOf ; "A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses."; "CD4-positive type I NK T cell secreting IL-4", "CD4-positive type I NK T lymphocyte secreting interleukin-4", "CD4-positive type I NK T-cell secreting interleukin-4", "CD4-positive type I NK T-lymphocyte secreting interleukin-4", "CD4-positive type I NKT cell secreting interleukin-4"; . a owl:Class; rdfs:label "activated CD4-negative, CD8-negative type I NK T cell"; rdfs:subClassOf ; "A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers."; "activated CD4-negative, CD8-negative type I NK T lymphocyte", "activated CD4-negative, CD8-negative type I NK T-cell", "activated CD4-negative, CD8-negative type I NK T-lymphocyte", "activated CD4-negative, CD8-negative type I NKT cell"; . a owl:Class; rdfs:label "CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"; rdfs:subClassOf ; "A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses."; "CD4-negative, CD8-negative type I NK T cell secreting IFN-gamma", "CD4-negative, CD8-negative type I NK T lymphocyte secreting interferon-gamma", "CD4-negative, CD8-negative type I NK T-cell secreting interferon-gamma", "CD4-negative, CD8-negative type I NK T-lymphocyte secreting interferon-gamma", "CD4-negative, CD8-negative type I NKT cell secreting interferon-gamma"; . a owl:Class; rdfs:label "CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"; rdfs:subClassOf ; "A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses."; "CD4-negative, CD8-negative type I NK T cell secreting IL-4", "CD4-negative, CD8-negative type I NK T lymphocyte secreting interleukin-4", "CD4-negative, CD8-negative type I NK T-cell secreting interleukin-4", "CD4-negative, CD8-negative type I NK T-lymphocyte secreting interleukin-4", "CD4-negative, CD8-negative type I NKT cell secreting interleukin-4"; . a owl:Class; rdfs:label "activated type II NK T cell"; rdfs:subClassOf ; "A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers."; "activated type II NK T lymphocyte", "activated type II NK T-cell", "activated type II NK T-lymphocyte", "activated type II NKT cell"; . a owl:Class; rdfs:label "type II NK T cell secreting interferon-gamma"; rdfs:subClassOf ; "A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers."; "type II NK T cell secreting IFN-gamma", "type II NK T lymphocyte secreting interferon-gamma", "type II NK T-cell secreting interferon-gamma", "type II NK T-lymphocyte secreting interferon-gamma", "type II NKT cell secreting interferon-gamma"; . a owl:Class; rdfs:label "type II NK T cell secreting interleukin-4"; rdfs:subClassOf ; "A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers."; "type II NK T cell secreting IL-4", "type II NK T lymphocyte secreting interleukin-4", "type II NK T-cell secreting interleukin-4", "type II NK T-lymphocyte secreting interleukin-4", "type II NKT cell secreting interleukin-4"; . a owl:Class; rdfs:label "CD4-positive, alpha-beta cytotoxic T cell"; rdfs:subClassOf ; "A CD4-positive, alpha-beta T cell that has cytotoxic function."; "CD4-positive, alpha-beta cytotoxic T lymphocyte", "CD4-positive, alpha-beta cytotoxic T-cell", "CD4-positive, alpha-beta cytotoxic T-lymphocyte"; . a owl:Class; rdfs:label "CD4-negative, CD8-negative, alpha-beta intraepithelial T cell"; rdfs:subClassOf ; "A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract."; "CD4-negative, CD8-negative, alpha-beta intraepithelial T lymphocyte", "CD4-negative, CD8-negative, alpha-beta intraepithelial T-cell", "CD4-negative, CD8-negative, alpha-beta intraepithelial T-lymphocyte"; . a owl:Class; rdfs:label "early lymphoid progenitor"; rdfs:subClassOf ; "A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative."; "ELP", "LMPP", "lymphoid-primed multipotent progenitor"; rdfs:comment "Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative."; . a owl:Class; rdfs:label "pre-natural killer cell"; rdfs:subClassOf ; "Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins."; rdfs:comment "These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive, alpha-4-beta-7 integrin-high."; "pre-NK cell"; . a owl:Class; rdfs:label "CD56-bright cytokine secreting natural killer cell"; rdfs:subClassOf ; "CD56-bright cytokine secreting NK cell"; rdfs:comment "Markers are associated with human cell types."; "NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic."; . a owl:Class; rdfs:label "cytotoxic CD56-dim natural killer cell"; rdfs:subClassOf ; "A mature natural killer cell that has the phenotype CD56-low and CD16-positive and is capable of cytotoxic function and cytokine production."; rdfs:comment "This population is mainly found in human."; "cytotoxic CD56-dim NK cell"; . a owl:Class; rdfs:label "mucosal invariant T cell"; rdfs:subClassOf ; "An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule."; "mucosal invariant T lymphocyte", "mucosal invariant T-cell", "mucosal invariant T-lymphocyte"; . a owl:Class; rdfs:label "thymic conventional dendritic cell"; rdfs:subClassOf ; "A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative."; rdfs:comment "In the mouse this cell expresses CD8-alpha-alpha."; . a owl:Class; rdfs:label "thymic plasmacytoid dendritic cell"; rdfs:subClassOf ; "A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive."; . a owl:Class; rdfs:label "Be1 Cell"; rdfs:subClassOf ; "A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma."; . a owl:Class; rdfs:label "Be2 cell"; rdfs:subClassOf ; "A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6."; . a owl:Class; rdfs:label "lymphocyte of B lineage"; rdfs:subClassOf ; "A lymphocyte of B lineage is a lymphocyte that expresses CD19 on the cell surface. An additional defining characteristic is the commitment to express an immunoglobulin complex."; rdfs:comment "Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells)."; . a owl:Class; rdfs:label "antibody secreting cell"; rdfs:subClassOf ; "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin."; . a owl:Class; rdfs:label "IgE plasma cell"; rdfs:subClassOf ; "A long lived plasma cell that secretes IgE."; . a owl:Class; rdfs:label "IgE memory B cell"; rdfs:subClassOf ; "A class switched memory B cell that expresses IgE on the cell surface."; . a owl:Class; rdfs:label "IgD plasmablast"; rdfs:subClassOf ; "A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult."; . a owl:Class; rdfs:label "IgE plasmablast"; rdfs:subClassOf ; "A plasmablast that secretes IgE."; . a owl:Class; rdfs:label "IgE short lived plasma cell"; rdfs:subClassOf ; "A short lived plasma cell that secretes IgE."; . a owl:Class; rdfs:label "preBCR-positive large pre-B-II cell"; rdfs:subClassOf ; "An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface."; . a owl:Class; rdfs:label "preBCR-negative large pre-B-II cell"; rdfs:subClassOf ; "A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes."; . a owl:Class; rdfs:label "small pre-B-II cell"; rdfs:subClassOf ; "A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes."; . a owl:Class; rdfs:label "pre-B-II cell"; rdfs:subClassOf ; "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain."; "pre-B-lymphocyte"; . a owl:Class; rdfs:label "pre-B-I cell"; rdfs:subClassOf ; "A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein."; . a owl:Class; rdfs:label "large pre-B-II cell"; rdfs:subClassOf ; "A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative."; . a owl:Class; rdfs:label "T1 B cell"; rdfs:subClassOf ; "A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative."; "transitional stage 1 B cell"; . a owl:Class; rdfs:label "T2 B cell"; rdfs:subClassOf ; "A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive."; "transitional stage 2 B cell"; . a owl:Class; rdfs:label "T3 B cell"; rdfs:subClassOf ; "A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM)."; "An1 B cell", "transitional stage 3 B cell"; . a owl:Class; rdfs:label "Bm1 B cell"; rdfs:subClassOf ; "A follicular B cell that expresses IgD, but not CD23 or CD38. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells."; . a owl:Class; rdfs:label "Bm2 B cell"; rdfs:subClassOf ; "A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells."; . a owl:Class; rdfs:label "Bm3-delta B cell"; rdfs:subClassOf ; "A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive."; . a owl:Class; rdfs:label "Bm2' B cell"; rdfs:subClassOf ; "A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative."; "Bm2-prime B cell"; . a owl:Class; rdfs:label "Bm3 B cell"; rdfs:subClassOf ; "A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type."; . a owl:Class; rdfs:label "Bm4 B cell"; rdfs:subClassOf ; "A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor."; . a owl:Class; rdfs:label "Bm5 B cell"; rdfs:subClassOf ; "A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes."; . a owl:Class; rdfs:label "Be cell"; rdfs:subClassOf ; "A mature B cell that produces cytokines that can influence CD4 T cell differentiation."; "B effector cell", "effector B cell"; . a owl:Class; rdfs:label "regulatory B cell"; rdfs:subClassOf ; "A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses."; . a owl:Class; rdfs:label "unswitched memory B cell"; rdfs:subClassOf ; "An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive and/or IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative."; . a owl:Class; rdfs:label "IgM memory B cell"; rdfs:subClassOf ; "An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative."; . a owl:Class; rdfs:label "class switched memory B cell"; rdfs:subClassOf ; "A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are usually CD27-positive and have either IgG, IgE, or IgA on the cell surface."; . a owl:Class; rdfs:label "IgA memory B cell"; rdfs:subClassOf ; "A class switched memory B cell that expresses IgA."; . a owl:Class; rdfs:label "long lived plasma cell"; rdfs:subClassOf ; "A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow."; . a owl:Class; rdfs:label "short lived plasma cell"; rdfs:subClassOf ; "A fully differentiated plasma cell that lives for months."; . a owl:Class; rdfs:label "IgA short lived plasma cell"; rdfs:subClassOf ; "A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system."; . a owl:Class; rdfs:label "IgG short lived plasma cell"; rdfs:subClassOf ; "A short lived plasma cell that secretes IgG."; . a owl:Class; rdfs:label "IgM short lived plasma cell"; rdfs:subClassOf ; "A short lived plasma cell that secretes IgM."; . a owl:Class; rdfs:label "IgG memory B cell"; rdfs:subClassOf ; "An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface."; . a owl:Class; rdfs:label "plasmablast"; rdfs:subClassOf ; "An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative."; . a owl:Class; rdfs:label "double negative memory B cell"; rdfs:subClassOf ; "A memory B cell with the phenotype IgD-negative and CD27-negative."; . a owl:Class; rdfs:label "IgG plasmablast"; rdfs:subClassOf ; "A plasmablast that secretes IgG."; . a owl:Class; rdfs:label "IgM plasmablast"; rdfs:subClassOf ; "A plasmablast that secretes IgM."; . a owl:Class; rdfs:label "IgA plasmablast"; rdfs:subClassOf ; "A plasmablast that secretes IgA."; . a owl:Class; rdfs:label "IgG plasma cell"; rdfs:subClassOf ; "A fully differentiated plasma cell that secretes IgG."; . a owl:Class; rdfs:label "IgM plasma cell"; rdfs:subClassOf ; "A fully differentiated plasma cell that secretes IgM."; . a owl:Class; rdfs:label "IgA plasma cell"; rdfs:subClassOf ; "A fully differentiated plasma cell that secretes IgA."; . a owl:Class; rdfs:label "hematopoietic cell"; rdfs:subClassOf ; "A cell of a hematopoietic lineage."; "haematopoietic cell", "haemopoietic cell", "hemopoietic cell"; . a owl:Class; rdfs:label "CD11c-low plasmacytoid dendritic cell"; rdfs:subClassOf ; "CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000001 )(PMID: 19243617). These cells are CD281-positive (TLR1), CD282-positive (TLR2), CD285-positive (TLR5), CD286-positive (TLR6), and CD288-positive (TLR8)."; . a owl:Class; rdfs:label "conventional dendritic cell"; rdfs:subClassOf ; "Conventional dendritic cell is a dendritic cell that is CD11c-high."; "DC1", "cDC", "dendritic reticular cell", "type 1 DC"; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL: 0000003)(PMID: 19243617) These cells are also CD20-negative, MHCII-positive."; . a owl:Class; rdfs:label "CD11c-negative plasmacytoid dendritic cell"; rdfs:subClassOf ; "CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive."; "CD303-positive dendritic cell"; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000004 )(PMID: 19243617). These cells are CD281-positive (TLR1), CD286-positive (TLR6), and CD290-positive (TLR10)."; . a owl:Class; rdfs:label "immature CD11c-low plasmacytoid dendritic cell"; rdfs:subClassOf ; "Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL: 0000006)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD11c-low plasmacytoid dendritic cell"; rdfs:subClassOf ; "Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000007 )(PMID: 19243617)."; . a owl:Class; rdfs:label "immature CD11c-negative plasmacytoid dendritic cell"; rdfs:subClassOf ; "Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000008 )(PMID: 19243617)."; . a owl:Class; rdfs:label "CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor"; rdfs:subClassOf ; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:1100000 )(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD11c-negative plasmacytoid dendritic cell"; rdfs:subClassOf ; "Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000009 )(PMID: 19243617)."; . a owl:Class; rdfs:label "immature CD8_alpha-negative CD11b-positive dendritic cell"; rdfs:subClassOf ; "Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000010 )(PMID: 19243617)."; . a owl:Class; rdfs:label "CD8_alpha-negative CD11b-negative dendritic cell"; rdfs:subClassOf ; "CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells."; "DC.8-4-11b-", "triple negative dendritic cell"; rdfs:comment "These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL: 0000011)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD4-positive CD11b-positive dendritic cell"; rdfs:subClassOf ; "CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative."; "DC.4+"; rdfs:comment "Defined as having a disposition to secreting anti-inflammatory cytokines.\\nThese markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL: 0000012)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD8_alpha-positive CD11b-negative dendritic cell"; rdfs:subClassOf ; "CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive."; rdfs:comment "Cells are defined as having a disposition to secreting inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000013)(PMID: 19243617)."; "DC.8+"; . a owl:Class; rdfs:label "immature CD8_alpha-negative CD11b-negative dendritic cell"; rdfs:subClassOf ; "Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:DC_CL:0000014)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD8_alpha-negative CD11b-negative dendritic cell"; rdfs:subClassOf ; "Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "These markers are associated with mouse cells. Defined as having a disposition to secretion of anti-inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000015)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD8_alpha-negative CD11b-positive dendritic cell"; rdfs:subClassOf ; "Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000016)(PMID: 19243617)."; . a owl:Class; rdfs:label "immature CD8_alpha-positive CD11b-negative dendritic cell"; rdfs:subClassOf ; "Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000017)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD8_alpha-positive CD11b-negative dendritic cell"; rdfs:subClassOf ; "Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000018)(PMID: 19243617)."; . a owl:Class; rdfs:label "dermal dendritic cell"; rdfs:subClassOf ; "Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000019)(PMID: 19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD288-positive (TLR8), and CD289-positive (TLR9)."; . a owl:Class; rdfs:label "interstitial dendritic cell"; rdfs:subClassOf ; "Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000020)(PMID: 19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10)."; . a owl:Class; rdfs:label "Kit and Sca1-positive hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative."; rdfs:comment "Cell markers are associated with mouse hematopoietic stem cell. Originally described in the dendritic cell ontology (DC_CL:0000043)(PMID: 19243617)."; "LSK stem cell", "Sca1-positive hematopoietic stem cell"; . a owl:Class; rdfs:label "immature dermal dendritic cell"; rdfs:subClassOf ; "Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000022)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature dermal dendritic cell"; rdfs:subClassOf ; "Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000023)(PMID: 19243617)."; . a owl:Class; rdfs:label "immature interstitial dendritic cell"; rdfs:subClassOf ; "Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000024)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor"; rdfs:subClassOf ; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:1110000)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature interstitial dendritic cell"; rdfs:subClassOf ; "Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000025)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD1a-positive Langerhans cell"; rdfs:subClassOf ; "CD1a-LC"; "CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive."; rdfs:comment "These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000026)(PMID: 19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD286-positive (TLR6), CD287-positive (TLR7), and CD290-positive (TLR10). When activated, these cells are capable of producing IL-6, IL-8, and IL-15."; . a owl:Class; rdfs:label "CD8_alpha-low Langerhans cell"; rdfs:subClassOf ; "CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low."; rdfs:comment "These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000027)(PMID: 19243617). They are also CD205-high, CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD285-positive (TLR5), CD286-positive (TLR6), and CD289-positive (TLR9)."; . a owl:Class; rdfs:label "immature CD1a-positive Langerhans cell"; rdfs:subClassOf ; "Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000028)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD1a-positive Langerhans cell"; rdfs:subClassOf ; "Mature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000029)(PMID: 19243617). When activated, these cells produce IL-6, IL-8, and IL-15."; . a owl:Class; rdfs:label "immature CD8_alpha-low Langerhans cell"; rdfs:subClassOf ; "Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low."; rdfs:comment "These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000030)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD115-positive monocyte OR common dendritic progenitor"; rdfs:subClassOf ; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:1111000)(PMID: 19243617)."; . a owl:Class; rdfs:label "mature CD8_alpha-low Langerhans cell"; rdfs:subClassOf ; "Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive."; rdfs:comment "These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000031)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD34-positive, CD38-positive common lymphoid progenitor"; rdfs:subClassOf ; "A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive."; "CD10-positive common lymphocyte precursor", "CD10-positive common lymphocyte progenitor", "CD10-positive common lymphoid precursor"; rdfs:comment "These markers are associated with human common lymphoid progenitors. Originally described in the dendritic cell ontology (DC_CL:0000032)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD115-positive monocyte"; rdfs:subClassOf ; "CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive."; rdfs:comment "These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000033)(PMID: 19243617)."; . a owl:Class; rdfs:label "Kit-positive, CD34-positive common myeloid progenitor"; rdfs:subClassOf ; "A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low."; rdfs:comment "Markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000034)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD34-positive, CD38-negative hematopoietic stem cell"; rdfs:subClassOf ; "CD133-positive hematopoietic stem cell"; "CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive."; rdfs:comment "Cell markers are associated with human hematopoietic stem cells. Originally described in the dendritic cell ontology (DC_CL:0000035)(PMID: 19243617)."; . a owl:Class; rdfs:label "Kit-positive, Sca1-positive common lymphoid progenitor"; rdfs:subClassOf ; "A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low."; "CD217-positive common lymphocyte precursor", "CD217-positive common lymphocyte progenitor", "CD217-positive common lymphoid precursor"; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "CD34-positive, CD38-positive common myeloid progenitor"; rdfs:subClassOf ; "A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative."; rdfs:comment "Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD7-negative lymphoid progenitor cell"; rdfs:subClassOf ; "CD7-negative lymphoid precursor"; "CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative."; rdfs:comment "These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000039)(PMID: 19243617)."; . a owl:Class; rdfs:label "CD7-positive lymphoid progenitor cell"; rdfs:subClassOf ; "CD7-positive lymphoid precursor"; "CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative."; rdfs:comment "These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID: 19243617)."; . a owl:Class; rdfs:label "common dendritic progenitor"; rdfs:subClassOf ; "CDP", "common dendritic precursor", "pro-DCs"; "Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers."; rdfs:comment "Surface markers are for mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000041) CDP are reportedly CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD11c-positive, CD14-negative, CD19-negative, CD20-negative, CD56-negative, B220-negative, Ly6g-negative, MHCII-positive, and Ter119-negative. (PMID: 19243617)."; . a owl:Class; rdfs:label "CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor"; rdfs:subClassOf ; rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:1111100)(PMID: 19243617)."; . a owl:Class; rdfs:label "cerebellar granule cell"; rdfs:subClassOf ; "Granule cell that is part of the cerebellum."; . a owl:Class; rdfs:label "cortical granule cell"; rdfs:subClassOf ; "Granule cell that is part of the cerebral cortex."; . a owl:Class; rdfs:label "hippocampal granule cell"; rdfs:subClassOf ; "Granule cell that is part of the hippocampus."; . a owl:Class; rdfs:label "cell in vitro"; owl:equivalentClass _:2de2f9; rdfs:subClassOf , , _:2de379; rdfs:comment "'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. This term is intended to contrast with 'native', which refers to cells or other biological entities that are found in a natural setting."; "A cell that has been removed from a natural environment, and placed in a controlled artificial environment for use in some investigation. Includes multicellular organism cells removed from an organism, and unicellular organisms removed from a natural environment."; "http://dictionary.reference.com/browse/in+vitro"; ; . _:2de2f9 a owl:Class; owl:intersectionOf _:2de309 . _:2de309 rdf:first ; rdf:rest _:2de329 . _:2de329 rdf:first _:2de319; rdf:rest rdf:nil . _:2de319 a owl:Class; owl:complementOf _:2de339 . _:2de339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de349 . _:2de349 a owl:Class; owl:unionOf _:2de359 . _:2de359 rdf:first ; rdf:rest _:2de369 . _:2de369 rdf:first ; rdf:rest rdf:nil . _:2de379 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Kit-positive erythroid progenitor cell"; rdfs:subClassOf ; "An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative."; rdfs:comment "Markers found on mouse cells."; . a owl:Class; rdfs:label "CD34-positive, CD38-positive granulocyte monocyte progenitor"; rdfs:subClassOf ; "A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative."; rdfs:comment "Markers are for human cells. According to different research groups, CD45RA is present or absent on this cell population."; . a owl:Class; rdfs:label "Kit-positive granulocyte monocyte progenitor"; rdfs:subClassOf ; "A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative."; rdfs:comment "Markers are found on mouse cells."; . a owl:Class; rdfs:label "CD34-positive, GlyA-negative erythroid progenitor cell"; rdfs:subClassOf ; "An erythroid progenitor cell that is CD34-positive and is GlyA-negative."; rdfs:comment "Cell markers associated with human cells."; . a owl:Class; rdfs:label "CD34-negative, GlyA-negative proerythroblast"; rdfs:subClassOf ; "A proerythoblast that is CD34-negative and GlyA-negative."; rdfs:comment "Cell surface markers are associated with human cells."; . a owl:Class; rdfs:label "CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell"; rdfs:subClassOf ; "A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative."; rdfs:comment "Markers are associated with human cell type."; . a owl:Class; rdfs:label "Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell"; rdfs:subClassOf ; "A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "Kit-low, CD34-positive eosinophil progenitor cell"; rdfs:subClassOf ; "A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell."; rdfs:comment "Markers are found on mouse cells."; . a owl:Class; rdfs:label "CD34-positive, CD38-positive eosinophil progenitor cell"; rdfs:subClassOf ; "A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell."; rdfs:comment "Markers are associated with human cells."; . a owl:Class; rdfs:label "macrophage dendritic cell progenitor"; rdfs:subClassOf ; "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages."; "MDP"; . a owl:Class; rdfs:label "pre-conventional dendritic cell"; rdfs:subClassOf ; "A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha."; . a owl:Class; rdfs:label "Kit-positive macrophage dendritic cell progenitor"; rdfs:subClassOf ; "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative."; rdfs:comment "Markers are associated with mouse cells."; "murine MDP"; . a owl:Class; rdfs:label "Kit-low proerythroblast"; rdfs:subClassOf ; "A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "GlyA-positive basophillic erythroblast"; rdfs:subClassOf ; "A basophilic erythroblast that is GlyA-positive."; rdfs:comment "Markers are associated with human cells."; . a owl:Class; rdfs:label "Kit-negative, Ly-76 high basophilic erythroblast"; rdfs:subClassOf ; "A basophilic erythroblast that is Lyg 76-high and is Kit-negative."; rdfs:comment "Cell surface markers are associated with mouse cells."; . a owl:Class; rdfs:label "Kit-negative, Ly-76 high polychromatophilic erythroblast"; rdfs:subClassOf ; "A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative."; . a owl:Class; rdfs:label "CD71-low, GlyA-positive polychromatic erythroblast"; rdfs:subClassOf ; "A polychromatiic erythroblast that is Gly-A-positive and CD71-low."; rdfs:comment "Cell surface markers are associated with human cells."; . a owl:Class; rdfs:label "Kit-negative, Ly-76 high orthochromatophilic erythroblasts"; rdfs:subClassOf ; "An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative."; rdfs:comment "Cell surface markers associated with mouse cells."; . a owl:Class; rdfs:label "CD71-negative, GlyA-positive orthochromatic erythroblast"; rdfs:subClassOf ; "An erythroblast that is GlyA-positive and CD71-negative."; rdfs:comment "Markers associated with human cells."; . a owl:Class; rdfs:label "Ly-76 high reticulocyte"; rdfs:subClassOf ; "A reticulocyte that is Ly76-high and is Kit-negative."; rdfs:comment "Marker associated with mouse cells."; . a owl:Class; rdfs:label "GlyA-positive reticulocytes"; rdfs:subClassOf ; "A reticulocyte that is GlyA-positive."; rdfs:comment "Markers is associated with human cells."; . a owl:Class; rdfs:label "GlyA-positive erythrocyte"; rdfs:subClassOf ; "An enucleate erythrocyte that is GlyA-positive."; rdfs:comment "Marker is associated with human cell types."; . a owl:Class; rdfs:label "Ly-76 high positive erythrocyte"; rdfs:subClassOf ; "An enucleate erythrocyte that is Lyg-76-high."; rdfs:comment "Marker is associated with mouse cell types."; . a owl:Class; rdfs:label "CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell"; rdfs:subClassOf ; "A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface."; rdfs:comment "Markers are associated with human cell type."; . a owl:Class; rdfs:label "Kit-positive megakaryocyte progenitor cell"; rdfs:subClassOf ; "A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell"; rdfs:subClassOf ; "A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative."; rdfs:comment "Markers are commonly associated with human cells."; . a owl:Class; rdfs:label "CD34-negative, CD41-positive, CD42-positive megakaryocyte cell"; rdfs:subClassOf ; "A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive."; rdfs:comment "Markers are commonly associated with human cells."; . a owl:Class; rdfs:label "CD9-positive, CD41-positive megakaryocyte cell"; rdfs:subClassOf ; "A megakaryocyte cell with is CD9-positive and CD41-positive."; rdfs:comment "Markers are commonly associated with mouse cells."; . a owl:Class; rdfs:label "basophil mast progenitor cell"; rdfs:subClassOf ; "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa"; "BMCP"; rdfs:comment "There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low."; . a owl:Class; rdfs:label "Fc-epsilon RIalpha-low mast cell progenitor"; rdfs:subClassOf ; "A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low."; . a owl:Class; rdfs:label "Fc-epsilon RIalpha-high basophil progenitor cell"; rdfs:subClassOf ; "A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "hematopoietic lineage restricted progenitor cell"; rdfs:subClassOf ; "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells."; . a owl:Class; rdfs:label "hematopoietic oligopotent progenitor cell"; rdfs:subClassOf ; "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers."; . a owl:Class; rdfs:label "short term hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Spa-1-positive, CD34-positive, CD150-positive, and is Flt3-negative."; rdfs:comment "Markers are associated with mouse cells."; "ST stem cell"; . a owl:Class; rdfs:label "long term hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Spa-1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative."; "LT stem cell"; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "Slamf1-negative multipotent progenitor cell"; rdfs:subClassOf ; "A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "Slamf1-positive multipotent progenitor cell"; rdfs:subClassOf ; "A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive."; "KSL cell"; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "CD2-positive, CD5-positive, CD44-positive alpha-beta intraepithelial T cell"; rdfs:subClassOf ; "Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive."; "memory alpha beta IEL"; . a owl:Class; rdfs:label "T follicular helper cell"; rdfs:subClassOf ; "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that expresses is BCL-6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production."; "T(FH)", "Tfh"; . a owl:Class; rdfs:label "immature NK T cell stage I"; rdfs:subClassOf ; "A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell."; . a owl:Class; rdfs:label "immature NK T cell stage II"; rdfs:subClassOf ; "A CD24-low, CD44-negative, NK1.1-negative NK T cell."; "NKT.44-NK1.1-.Th"; rdfs:comment "NKT.44-NK1.1-.Th was assigned as an exact synonym based on sorting strategy displayed at immgene.org."; . a owl:Class; rdfs:label "immature NK T cell stage III"; rdfs:subClassOf ; "A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell."; . a owl:Class; rdfs:label "immature NK T cell stage IV"; rdfs:subClassOf ; "A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell."; . a owl:Class; rdfs:label "CD34-positive, CD38-negative multipotent progenitor cell"; rdfs:subClassOf ; "A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative."; rdfs:comment "Cell markers are associated with human hematopoietic multipotent progenitor cells."; . a owl:Class; rdfs:label "Kit-positive, integrin beta7-high basophil mast progenitor cell"; rdfs:subClassOf ; "A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "Fraction A pre-pro B cell"; rdfs:subClassOf ; "A pro-B cell that CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive."; rdfs:comment "Markers associated with mouse cells."; "fraction A"; . a owl:Class; rdfs:label "early pro-B cell"; rdfs:subClassOf ; "A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and has TdT activity. Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage."; rdfs:comment "Markers are commonly associated with human cells."; . a owl:Class; rdfs:label "Fraction B precursor B cell"; rdfs:subClassOf ; "A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative."; "Fr. B", "Fraction B"; rdfs:comment "Markers are commonly associated with mouse cells."; . a owl:Class; rdfs:label "late pro-B cell"; rdfs:subClassOf ; "A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive."; . a owl:Class; rdfs:label "Fraction C precursor B cell"; rdfs:subClassOf ; "A precursor B cell is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain."; . a owl:Class; rdfs:label "Fraction C' precursor B cell"; rdfs:subClassOf ; "A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive."; "Fr. C'", "Fraction C-prime"; . a owl:Class; rdfs:label "CD38-high pre-BCR positive cell"; rdfs:subClassOf ; "A pre-BCR positive T cell that is CD38-high."; rdfs:comment "Markers are associated with human cells."; . a owl:Class; rdfs:label "Fraction D precursor B cell"; rdfs:subClassOf ; "A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive."; "Fr. D", "Fraction D pre-B cell"; . a owl:Class; rdfs:label "CD22-positive, CD38-low small pre-B cell"; rdfs:subClassOf ; "A small pre-B cell that is CD22-positive and CD38-low."; rdfs:comment "Markers are associated with human cell. RAG expression maybe diminishing."; "small pre-B cell"; . a owl:Class; rdfs:label "Fraction E immature B cell"; rdfs:subClassOf ; "An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive."; rdfs:comment "Markers associated with mouse cells."; . a owl:Class; rdfs:label "CD38-negative immature B cell"; rdfs:subClassOf ; "An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high."; rdfs:comment "Markers are associated with human cell type."; . a owl:Class; rdfs:label "Fraction F mature B cell"; rdfs:subClassOf ; "A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative."; . a owl:Class; rdfs:label "CD14-positive, CD16-negative classical monocyte"; rdfs:subClassOf ; "A monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive,"; rdfs:comment "Markers are associated with human monocytes."; . a owl:Class; rdfs:label "Gr1-low non-classical monocyte"; rdfs:subClassOf ; "A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive."; rdfs:comment "Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product. Also, this cell-type is sometimes described as being Gr1-negative."; . a owl:Class; rdfs:label "CD8alpha-positive thymic conventional dendritic cell"; rdfs:subClassOf ; "A conventional thymic dendritic cell that is CD8alpha-positive."; "CD8alpha-alpha-positive thymic conventional dendritic cell", "DC.8+.Th"; . a owl:Class; rdfs:label "melanophage"; rdfs:subClassOf ; "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes."; . a owl:Class; rdfs:label "T-helper 9 cell"; rdfs:subClassOf ; "A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and interleukin 4. TH2 cytokine production is surpressed."; "Th9"; . a owl:Class; rdfs:label "type I pneumocyte"; rdfs:subClassOf ; "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange."; "AT1", "ATI", "lung type 1 cells", "membranous pneumocytes", "pulmonary alveolar type I cell", "small alveolar cells", "squamous alveolar cell", "squamous alveolar lining cell", "type 1 alveolar epithelial cells", "type 1 pneumocyte", "type I alveolar epithelial cells"; . a owl:Class; rdfs:label "type II pneumocyte"; rdfs:subClassOf ; "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli."; "AT2", "ATII", "TII", "cuboidal type II cell", "granular pneumocyte", "great alveolar cell", "lung type 2 cell", "type 2 alveolar epithelial cell", "type 2 alveolocyte", "type 2 pneumocyte", "type II alveolar epithelial cell", "type II alveolocyte"; . a owl:Class; rdfs:label "pancreatic acinar cell"; rdfs:subClassOf ; "A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules."; "acinar cell of pancreas"; . a owl:Class; rdfs:label "Purkinje myocyte"; rdfs:subClassOf ; "Purkinje cell fiber", "Purkinje muscle cell", "myocytus conducens cardiacus"; "Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter."; . a owl:Class; rdfs:label "type II vestibular sensory cell"; rdfs:subClassOf ; "Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices."; "type 2 vestibular hair cell", "type 2 vestibular sensory cell", "type II hair cell"; . a owl:Class; rdfs:label "type I vestibular sensory cell"; rdfs:subClassOf ; "Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending."; "type 1 vestibular hair cell", "type 1 vestibular sensory cell", "type I hair cell"; . a owl:Class; rdfs:label "enterocyte of epithelium of large intestine"; rdfs:subClassOf ; "Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type."; "columnar cell", "columnar cell of the colon", "vacuolar absorptive cell"; . a owl:Class; rdfs:label "nodal myocyte"; rdfs:subClassOf ; "A specialized cardiac myocyte in the sinuatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery."; "P cell", "myocytus nodalis", "pacemaker cell"; . a owl:Class; rdfs:label "transitional myocyte"; rdfs:subClassOf ; "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes."; . a owl:Class; rdfs:label "myocardial endocrine cell"; rdfs:subClassOf ; "The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides)."; . a owl:Class; rdfs:label "brush cell of trachebronchial tree"; rdfs:subClassOf ; "Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known."; . a owl:Class; rdfs:label "endo-epithelial cell"; rdfs:subClassOf ; "An epithelial cell derived from endoderm."; . a owl:Class; rdfs:label "ecto-epithelial cell"; rdfs:subClassOf ; "An epithelial cell derived from ectoderm."; . a owl:Class; rdfs:label "meso-epithelial cell"; rdfs:subClassOf ; "Epithelial cell derived from mesoderm or mesenchyme."; "epithelial mesenchymal cell"; . a owl:Class; rdfs:label "pancreatic ductal cell"; rdfs:subClassOf ; "Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH."; . a owl:Class; rdfs:label "pancreatic centro-acinar cell"; rdfs:subClassOf ; "A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types."; "centroacinar cell of Langerhans", "pancreatic centroacinar cell"; . a owl:Class; rdfs:label "type II cell of adrenal medulla"; rdfs:subClassOf ; "A chromaffin cell of the adrenal medulla that produces epinephrine."; "adremergic chromaffin cell", "adrenal secreting cell of the adrenal medulla", "epiniphrine secreting cell of the adrenal medulla"; . a owl:Class; rdfs:label "type I cell of adrenal medulla"; rdfs:subClassOf ; "A chromaffin cell of the adrenal medulla that produces norepinephrine."; "noradrenergic chromaffin cell"; . a owl:Class; rdfs:label "Boettcher cell"; rdfs:subClassOf ; "A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport."; "Boettcher's cell", "Bottcher cell", "Bottcher's cell"; . a owl:Class; rdfs:label "tanycyte"; rdfs:subClassOf ; "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle."; "stretch cell"; . a owl:Class; rdfs:label "specialized cardiac myocyte"; rdfs:subClassOf ; "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart."; . a owl:Class; rdfs:label "nongranular leukocyte"; rdfs:subClassOf ; "A leukocyte that lacks granules."; "agranular leukocyte"; . a owl:Class; rdfs:label "interstitial cell of Cajal"; rdfs:subClassOf ; "ICC"; rdfs:comment "Some argue this cell type is of mesenchymal origin."; "This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise."; . a owl:Class; rdfs:label "nuocyte"; rdfs:subClassOf ; "A leukocyte cell capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive."; . a owl:Class; rdfs:label "bone marrow cell"; rdfs:subClassOf ; "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells."; rdfs:comment "MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense."; . a owl:Class; rdfs:label "interstitial cell of ovary"; rdfs:subClassOf ; "A cell that makes up the loose connective tissue of the ovary."; . a owl:Class; rdfs:label "internodal tract myocyte"; rdfs:subClassOf ; "A specialised myocyte that lies between the sinuatrial node and the atrioventricular node and is involved in the conduction of electrical signals."; . a owl:Class; rdfs:label "cortical cell of adrenal gland"; rdfs:subClassOf ; "A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol."; "adrenal cortex cell", "adrenocortical cell"; . a owl:Class; rdfs:label "regular cardiac myocyte"; rdfs:subClassOf ; "A cardiac myocyte that is connected together by transverse intercalated discs at a regular interval."; "regular cardiac muscle cell", "regular cardiac muscle fiber"; . a owl:Class; rdfs:label "type I cell of adrenal cortex"; rdfs:subClassOf ; "A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids."; "epithelial cell of zona glomerulosa of adrenal gland"; . a owl:Class; rdfs:label "regular interventricular cardiac myocyte"; rdfs:subClassOf ; "A regular cardiac myocyte of the interventricular region of the heart."; . a owl:Class; rdfs:label "CD38-positive naive B cell"; rdfs:subClassOf ; "A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery."; . a owl:Class; rdfs:label "CD38-negative naive B cell"; rdfs:subClassOf ; "A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery."; . a owl:Class; rdfs:label "IgG-positive double negative memory B cell"; rdfs:subClassOf ; "An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative."; . a owl:Class; rdfs:label "IgG-negative double negative memory B cell"; rdfs:subClassOf ; "An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative."; . a owl:Class; rdfs:label "CD38-positive IgG memory B cell"; rdfs:subClassOf ; "A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive."; . a owl:Class; rdfs:label "IgD-positive CD38-positive IgG memory B cell"; rdfs:subClassOf ; "An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive."; . a owl:Class; rdfs:label "IgD-negative CD38-positive IgG memory B cell"; rdfs:subClassOf ; "An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive."; . a owl:Class; rdfs:label "CD38-negative IgG memory B cell"; rdfs:subClassOf ; "A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive."; . a owl:Class; rdfs:label "B220-positive CD38-positive naive B cell"; rdfs:subClassOf ; "A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery."; . a owl:Class; rdfs:label "B220-low CD38-positive naive B cell"; rdfs:subClassOf ; "A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery."; . a owl:Class; rdfs:label "CD38-negative unswitched memory B cell"; rdfs:subClassOf ; "An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative."; . a owl:Class; rdfs:label "B220-positive CD38-negative unswitched memory B cell"; rdfs:subClassOf ; "A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative."; . a owl:Class; rdfs:label "B220-low CD38-negative unswitched memory B cell"; rdfs:subClassOf ; "A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative."; . a owl:Class; rdfs:label "CD38-positive unswitched memory B cell"; rdfs:subClassOf ; "A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative."; . a owl:Class; rdfs:label "B220-positive CD38-positive unswitched memory B cell"; rdfs:subClassOf ; "A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative."; . a owl:Class; rdfs:label "B220-low CD38-positive unswitched memory B cell"; rdfs:subClassOf ; "A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative."; . a owl:Class; rdfs:label "IgG-negative class switched memory B cell"; rdfs:subClassOf ; "A class switched memory B cell that lacks IgG on the cell surface."; . a owl:Class; rdfs:label "CD38-negative IgG-negative class switched memory B cell"; rdfs:subClassOf ; "A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative."; . a owl:Class; rdfs:label "CD38-positive IgG-negative class switched memory B cell"; rdfs:subClassOf ; "A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative."; . a owl:Class; rdfs:label "CD24-positive CD38-negative IgG-negative class switched memory B cell"; rdfs:subClassOf ; "An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative."; . a owl:Class; rdfs:label "CD24-negative CD38-negative IgG-negative class switched memory B cell"; rdfs:subClassOf ; "A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative."; . a owl:Class; rdfs:label "B220-positive CD38-positive IgG-negative class switched memory B cell"; rdfs:subClassOf ; "A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative."; . a owl:Class; rdfs:label "B220-low CD38-positive IgG-negative class switched memory B cell"; rdfs:subClassOf ; "A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive."; . a owl:Class; rdfs:label "CD27-positive gamma-delta T cell"; rdfs:subClassOf ; "A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma."; "gammadelta27-positive", "gd27-positive"; . a owl:Class; rdfs:label "CD27-negative gamma-delta T cell"; rdfs:subClassOf ; "A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL17 secretion."; . a owl:Class; rdfs:label "CD25-positive, CD27-positive immature gamma-delta T cell"; rdfs:subClassOf ; "A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low)."; . a owl:Class; rdfs:label "innate effector T cell"; rdfs:subClassOf ; "A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation."; . a owl:Class; rdfs:label "Tc17 cell"; rdfs:subClassOf ; "A CD8-positive, alpha-beta positive T cell with the phenotype CCR6-positive, CCR5-high, CD45RA-negative, and secreting IL-17 and some IFNg."; rdfs:comment "Found in the CD27-positive CD28-positive or CD27-negative CD28-positive fractions with the phenotype CCR4-negative and CCR7-negative."; "Tc17 T cell", "Tc17 T lymphocyte", "Tc17 T-cell", "Tc17 T-lymphocyte"; . a owl:Class; rdfs:label "regular atrial cardiac myocyte"; rdfs:subClassOf ; "Regular cardiac myocyte of a cardiac atrium."; "atrial myocyte", "regular atrial cardiac muscle fiber", "regular cardiac muscle cell of atrium"; . a owl:Class; rdfs:label "regular interatrial cardiac myocyte"; rdfs:subClassOf ; "A cardiac myocyte of the interatrial region of the heart."; . a owl:Class; rdfs:label "regular ventricular cardiac myocyte"; rdfs:subClassOf ; "Regular cardiac myocyte of a cardiac ventricle."; "regular cardiac muscle cell of ventricle", "regular ventricular cardiac muscle fiber", "ventricular myocyte"; . a owl:Class; rdfs:label "stromal cell of ovary"; rdfs:subClassOf ; "A stomal cell of the ovary"; . a owl:Class; rdfs:label "stromal cell of ovorain cortex"; rdfs:subClassOf ; "A stromal cell of the ovarian cortex."; . a owl:Class; rdfs:label "stromal cell of ovarian medulla"; rdfs:subClassOf ; "A stromal cell of the ovarian medulla."; . a owl:Class; rdfs:label "nonkeratinized cell of epidermis"; rdfs:subClassOf ; "Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues."; . a owl:Class; rdfs:label "type II cell of adrenal cortex"; rdfs:subClassOf ; "A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol."; "type II cortical cell of adrenal gland"; . a owl:Class; rdfs:label "type III cell of adrenal cortex"; rdfs:subClassOf ; "A cell in the zona reticularis that produce sex hormones."; . a owl:Class; rdfs:label "endothelial cell of lymphatic vessel"; rdfs:subClassOf ; "A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions."; "lymphatic endothelial cell"; . a owl:Class; rdfs:label "endothelial cell of vascular tree"; rdfs:subClassOf ; "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels."; rdfs:comment "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive."; "vascular endothelial cell"; . a owl:Class; rdfs:label "active chief cell of parathyroid gland"; rdfs:subClassOf ; "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1"; . a owl:Class; rdfs:label "dark chief cell of parathyroid cell"; rdfs:subClassOf ; "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules."; . a owl:Class; rdfs:label "capillary endothelial cell"; rdfs:subClassOf ; "An endothelial cell found in capillaries."; . a owl:Class; rdfs:label "ciliated columnar cell of tracheobronchial tree"; rdfs:subClassOf ; "A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree."; . a owl:Class; rdfs:label "clear chief cell of parathyroid cell"; rdfs:subClassOf ; "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells."; . a owl:Class; rdfs:label "dental pulp cell"; rdfs:subClassOf ; "A cell found within the dental pulp."; . a owl:Class; rdfs:label "epithelial cell of uterus"; rdfs:subClassOf ; "An epithelial cell of the uterus."; . a owl:Class; rdfs:label "epithelioid macrophage"; rdfs:subClassOf ; "Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation."; "epithelioid histocyte", "epitheloid macrophage"; . a owl:Class; rdfs:label "late promyelocyte"; rdfs:subClassOf ; "A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous."; . a owl:Class; rdfs:label "columnar cell of endocervix"; rdfs:subClassOf ; "A columnar cell of the cervix uteri."; . a owl:Class; rdfs:label "early promyelocyte"; rdfs:subClassOf ; "A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages."; . a owl:Class; rdfs:label "echinocyte"; rdfs:subClassOf ; "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease."; "burr cell"; . a owl:Class; rdfs:label "endosteal cell"; rdfs:subClassOf ; "A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones."; . a owl:Class; rdfs:label "external epithelial cell of tympanic membrane"; rdfs:subClassOf ; "Epithelial cell found on the external side of the tympanic membrane"; . a owl:Class; rdfs:label "general ecto-epithelial cell"; rdfs:subClassOf ; "Epithelial cells derived from general body ectoderm and ectoderm placodes."; . a owl:Class; rdfs:label "basal external epithelial cell of tympanic membrane"; rdfs:subClassOf ; "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions."; . a owl:Class; rdfs:label "superficial external epithelial cell of tympanic membrane"; rdfs:subClassOf ; "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus."; . a owl:Class; rdfs:label "internal epithelial cell of tympanic membrane"; rdfs:subClassOf ; "An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones."; . a owl:Class; rdfs:label "internal pillar cell of cochlea"; rdfs:subClassOf ; "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells."; . a owl:Class; rdfs:label "external pillar cell of cochlea"; rdfs:subClassOf ; "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells."; . a owl:Class; rdfs:label "phalangeal cell"; rdfs:subClassOf ; "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells."; . a owl:Class; rdfs:label "epithelial cell of Malassez"; rdfs:subClassOf ; "An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth."; "epithelial cell rests of Malassez ", "epithelial debris of Malassez"; . a owl:Class; rdfs:label "olfactory epithelial cell"; rdfs:subClassOf ; "A specialized cell involved in sensory perception of smell."; . a owl:Class; rdfs:label "border cell of cochlea"; rdfs:subClassOf ; "A border cell is a slender columnar cell on the medial portion of the basilar membrane."; . a owl:Class; rdfs:label "basal cell of olfactory epithelium"; rdfs:subClassOf ; "An epithelial cell located on the basal lamina of the olfactory epithelium."; . a owl:Class; rdfs:label "keratinized cell of the oral mucosa"; rdfs:subClassOf ; "A keratinized cell located in the hard palate or gingiva."; . a owl:Class; rdfs:label "globose cell of olfactory epithelium"; rdfs:subClassOf ; "A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium."; "blastema cell of olfactory epithelium"; . a owl:Class; rdfs:label "interdental cell"; rdfs:subClassOf ; "A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph."; "interdental cell of cochlea"; . a owl:Class; rdfs:label "extraglomerular mesangial cell"; rdfs:subClassOf ; "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells."; "Goormaghtigh cell", "polar cushion cells"; . a owl:Class; rdfs:label "follicular cell of ovary"; rdfs:subClassOf ; "A cell within the follicle of an ovary."; . a owl:Class; rdfs:label "primary follicular cell of ovary"; rdfs:subClassOf ; "A cell within the primary follicle of the ovary."; . a owl:Class; rdfs:label "secondary follicular cell of ovary"; rdfs:subClassOf ; "A cell of a secondary follicile within the ovary."; . a owl:Class; rdfs:label "folliculostellate cell of pars distalis of adenohypophysis"; rdfs:subClassOf ; "A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature."; "folliculostellate cell of pars anterior of adenohypophysis"; . a owl:Class; rdfs:label "epithelial cell of stomach"; rdfs:subClassOf ; "An epithelial cell found in the lining of the stomach."; . a owl:Class; rdfs:label "foveolar cell of stomach"; rdfs:subClassOf ; "An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop ."; . a owl:Class; rdfs:label "mucous cell of stomach"; rdfs:subClassOf ; "A mucous cell in the epithelium of the stomach."; . a owl:Class; rdfs:label "mucus neck cell of gastric gland"; rdfs:subClassOf ; "A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach."; . a owl:Class; rdfs:label "surface mucosal cell of stomach"; rdfs:subClassOf ; "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall."; . a owl:Class; rdfs:label "stem cell of gastric gland"; rdfs:subClassOf ; "A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit."; . a owl:Class; rdfs:label "basal proper cell of olfactory epithelium"; rdfs:subClassOf ; "A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium."; "horizontal basal cells"; . a owl:Class; rdfs:label "basal cell of epidermis"; rdfs:subClassOf ; "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane."; . a owl:Class; rdfs:label "glomerular endothelial cell"; rdfs:subClassOf ; "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate."; . a owl:Class; rdfs:label "granular cell of epidermis"; rdfs:subClassOf ; "A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules."; . a owl:Class; rdfs:label "squamous cell of epidermis"; rdfs:subClassOf ; "A flat keratinocyte immediately below the cornified layer."; . a owl:Class; rdfs:label "granulocytopoietic cell"; rdfs:subClassOf ; "A cell involved in the formation of a granulocyte."; . a owl:Class; rdfs:label "metamyelocyte"; rdfs:subClassOf ; "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare."; . a owl:Class; rdfs:label "myelocyte"; rdfs:subClassOf ; "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses."; . a owl:Class; rdfs:label "monopoietic cell"; rdfs:subClassOf ; "A cell involved in the formation of a monocyte (monopoiesis)."; . a owl:Class; rdfs:label "hepatic stem cell"; rdfs:subClassOf ; "A stem cell that can give rise to the cells of the liver."; . a owl:Class; rdfs:label "hepatic oval stem cell"; rdfs:subClassOf ; "A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue."; "hepatic oval cell"; . a owl:Class; rdfs:label "inactive chief cell of parathyoid gland"; rdfs:subClassOf ; "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1."; . a owl:Class; rdfs:label "oncocyte"; rdfs:subClassOf ; "A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands."; "oxyphil"; . a owl:Class; rdfs:label "oxyphil cell of parathyroid gland"; rdfs:subClassOf ; "An oncocyte located in the parathyroid gland."; . a owl:Class; rdfs:label "oxyphil cell of thyroid"; rdfs:subClassOf ; "An oncocyte located in the thyroid."; "Askanazy cells", "Hurthle cells"; . a owl:Class; rdfs:label "renal beta-intercalated cell"; rdfs:subClassOf ; "A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance."; . a owl:Class; rdfs:label "epithelial cell of tracheobronchial tree"; rdfs:subClassOf ; "An epithelial cell of the tracheobronchial tree."; . a owl:Class; rdfs:label "Brush cell of epithelium proper of large intestine"; rdfs:subClassOf ; "Brush cell found in the epithelial layer of the colon."; rdfs:comment "Brush cells are a distinct cell type from brush border cell-types."; . a owl:Class; rdfs:label "brush cell"; rdfs:subClassOf ; "A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known."; "caveolated cell", "fibrillovesicular cell", "multivesicular cell", "tuft cell"; . a owl:Class; rdfs:label "brush cell of lobular bronchiole"; rdfs:subClassOf ; "A brush cell found in the epithelium of lobular bronchiole."; . a owl:Class; rdfs:label "brush cell of terminal bronchiole"; rdfs:subClassOf ; "A brush cell of the epithelium in the terminal bronchiole."; . a owl:Class; rdfs:label "brush cell of trachea"; rdfs:subClassOf ; "Brush cell of the epithelium in the trachea."; . a owl:Class; rdfs:label "brush cell of bronchus"; rdfs:subClassOf ; "A brush cell found in the epithelium of bronchus."; . a owl:Class; rdfs:label "intermediate epitheliocyte"; rdfs:subClassOf ; "An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells."; "undifferentiated columnar cell of tracheobronchial tree"; . a owl:Class; rdfs:label "red muscle cell"; rdfs:subClassOf ; "A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance."; "oxidative muscle fiber", "red muscle fiber"; . a owl:Class; rdfs:label "type I muscle cell"; rdfs:subClassOf ; "A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue."; "slow twitch fiber", "slow twitch muscle cell", "type 1 muscle cell", "type 1 muscle fiber", "type I muscle fiber"; . a owl:Class; rdfs:label "type II muscle cell"; rdfs:subClassOf ; "A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate."; "type 2 muscle cell", "type 2 muscle fiber", "type II muscle fiber"; . a owl:Class; rdfs:label "white muscle cell"; rdfs:subClassOf ; "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance."; . a owl:Class; rdfs:label "type IIa muscle cell"; rdfs:subClassOf ; "A type II muscle cell that contain large amounts of myoglobin, have many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue."; "fast twitch A", "fatigue resistant fast twitch muscle cell", "type 2a muscle cell", "type 2a muscle fiber", "type IIa muscle fiber"; . a owl:Class; rdfs:label "type IIb muscle cell"; rdfs:subClassOf ; "A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity."; "type 2b muscle cell", "type 2b muscle fiber", "type IIb muscle fiber"; . a owl:Class; rdfs:label "intermediate muscle cell"; rdfs:subClassOf ; "An intermediate muscle cell that has characteristics of both fast and slow muscle cells."; . a owl:Class; rdfs:label "intermediate trophoblast"; rdfs:subClassOf ; "A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus."; . a owl:Class; rdfs:label "immature dendritic epithelial T cell precursor"; rdfs:subClassOf ; "A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; "immature DEC precursor", "immature DETC precursor"; . a owl:Class; rdfs:label "anchoring trophoblasts"; rdfs:subClassOf ; "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua."; . a owl:Class; rdfs:label "interstitial cell of pineal gland"; rdfs:subClassOf ; "A cell located between the pinealocytes."; . a owl:Class; rdfs:label "keratinized squamous cell of esophagus"; rdfs:subClassOf ; "A squamous cell that has keratin in the esophagus."; . a owl:Class; rdfs:label "light chief cell of parathyroid gland"; rdfs:subClassOf ; "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules."; . a owl:Class; rdfs:label "epithelial cell of prostate"; rdfs:subClassOf ; "An epithelial cell of the prostate."; "prostate epithelial cell"; . a owl:Class; rdfs:label "epithelial cell of prostatic duct"; rdfs:subClassOf ; "An epithelial cell of prostatic duct."; "ductal epithelial cell of prostate"; . a owl:Class; rdfs:label "epithelial cell of prostatic acinus"; rdfs:subClassOf ; "An epithelial cell of the prostatic acinus."; "acinar epithelial cell of prostate"; . a owl:Class; rdfs:label "basal cell of prostatic acinus"; rdfs:subClassOf ; "A cell of the basal layer of the epithelium in the prostatic acinus."; "basal epithelial cell of prostatic acinus"; . a owl:Class; rdfs:label "luminal cell of prostatic acinus"; rdfs:subClassOf ; "A cell of the luminal layer of the epithelium in the prostatic acinus."; . a owl:Class; rdfs:label "basal epithelial cell of prostatic duct"; rdfs:subClassOf ; "A cell that constitutes the basal layer of epithelium in the prostatic duct."; . a owl:Class; rdfs:label "luminal epithelial cell of prostatic duct"; rdfs:subClassOf ; "A cell that constitutes the luminal layer of epithelium of prostatic duct."; . a owl:Class; rdfs:label "marrow fibroblast"; rdfs:subClassOf ; "A fibroblast in the bone marrow."; . a owl:Class; rdfs:label "pulmonary interstitial fibroblast"; rdfs:subClassOf ; "A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis."; "pulmonary myofibroblast", "pulmonary septal cell"; . a owl:Class; rdfs:label "smooth muscle cell of sphincter of pupil"; rdfs:subClassOf ; "A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells."; "smooth muscle fiber of sphincter of pupil"; . a owl:Class; rdfs:label "squamous cell of ectocervix"; rdfs:subClassOf ; "A nonstratified squamous cell located in the ectocervix."; "ectocervical squamous cell"; . a owl:Class; rdfs:label "peripheral blood stem cell"; rdfs:subClassOf ; "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells)."; "PBSC"; . a owl:Class; rdfs:label "pleural macrophage"; rdfs:subClassOf ; "A tissue macrophage that is in the pleural space."; . a owl:Class; rdfs:label "pluripotent stem cell"; rdfs:subClassOf ; "A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta."; . a owl:Class; rdfs:label "primitive cardiac myocyte"; rdfs:subClassOf ; "A stem cell that can differentiate into a cardiac myocyte."; . a owl:Class; rdfs:label "intestinal crypt stem cell"; rdfs:subClassOf ; "A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells."; "stem cell of intestinal crypt of lieberkuhn"; . a owl:Class; rdfs:label "epithelial cell of alimentary canal"; rdfs:subClassOf ; "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus."; . a owl:Class; rdfs:label "epithelial cell of esophagus"; rdfs:subClassOf ; "An epithelial cell of the esophagus."; . a owl:Class; rdfs:label "epithelial cell of large intestine"; rdfs:subClassOf ; "An epithelial cell of the large intestine."; . a owl:Class; rdfs:label "epithelial cell of small intestine"; rdfs:subClassOf ; "An epithelial cell of the small intestine."; . a owl:Class; rdfs:label "stromal cell of endometrium"; rdfs:subClassOf ; "An epithelial cell that regulates growth and differentiation of the overlying epithelium."; . a owl:Class; rdfs:label "supporting cell of carotid body"; rdfs:subClassOf ; "A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings."; "carotid body sustentacular cell"; . a owl:Class; rdfs:label "epithelial cell of thyroid gland"; rdfs:subClassOf ; "An epithelial cell of thyroid gland."; . a owl:Class; rdfs:label "thyroid follicular cell"; rdfs:subClassOf ; "A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones."; "follicular cell of thyroid gland", "principal cell of thyroid gland", "thyroid gland follicular cell"; . a owl:Class; rdfs:label "neuroepithelial stem cell"; rdfs:subClassOf ; "The stem cell from which glial precursor cell arises from."; . a owl:Class; rdfs:label "epithelial cell of parathyroid gland"; rdfs:subClassOf ; "An epithelial cell of the parathyroid gland."; . a owl:Class; rdfs:label "endothelial cell of viscerocranial mucosa"; rdfs:subClassOf ; "An endothelial cell found in the mucosa associated with the facial skeleton."; . a owl:Class; rdfs:label "endothelial cell of sinusoid"; rdfs:subClassOf ; "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver."; . a owl:Class; rdfs:label "transitional cell of parathyroid gland"; rdfs:subClassOf ; "One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage."; . a owl:Class; rdfs:label "type EC2 enteroendocrine cell"; rdfs:subClassOf ; "A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine."; . a owl:Class; rdfs:label "type EC1 enteroendocrine cell"; rdfs:subClassOf ; "A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine."; . a owl:Class; rdfs:label "type ECL enteroendocrine cell"; rdfs:subClassOf ; "A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine."; . a owl:Class; rdfs:label "ecto-epithelial cell of viscerocranial mucosa"; rdfs:subClassOf ; "An epithelial cell of the mucosa associated with facial skeleton."; . a owl:Class; rdfs:label "type III taste bud cell"; rdfs:subClassOf ; "A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM."; "type 3 taste cell"; . a owl:Class; rdfs:label "type II taste cell"; rdfs:subClassOf ; "A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities."; "type 2 taste cell"; . a owl:Class; rdfs:label "type IV taste receptor cell"; rdfs:subClassOf ; "A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally."; rdfs:comment "There is debate about the exact lineage of these cell types from this progenitor. See PMID: 15738192."; "type 4 taste cell"; . a owl:Class; rdfs:label "type V taste receptor cell"; rdfs:subClassOf ; "A cell type that forms the boundary with the surrounding epithelium."; . a owl:Class; rdfs:label "type I taste bud cell"; rdfs:subClassOf ; "A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST."; "dark tongue cell", "type I taste cell", "type taste 1 cell"; . a owl:Class; rdfs:label "type I cell of carotid body"; rdfs:subClassOf ; "A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters."; "glomus cell"; . a owl:Class; rdfs:label "epithelial cell of thymus"; rdfs:subClassOf ; "An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies."; "epithelial cell of thymus gland", "epithelial reticular cell", "epithelial reticular cell of thymus", "thymic epithelial cell"; . a owl:Class; rdfs:label "type-1 epithelial cell of thymus"; rdfs:subClassOf ; "An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule."; "subcapsular thymic epithelial cell"; . a owl:Class; rdfs:label "type-6 epithelial cell of thymus"; rdfs:subClassOf ; "A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections."; "cystic thymic epithelial cells", "large mTEC", "large medullary thymic epithelial cells"; . a owl:Class; rdfs:label "type-4 epithelial cell of thymus"; rdfs:subClassOf ; "An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus."; "dark thymic epithelial cell"; . a owl:Class; rdfs:label "type-3 epithelial cell of thymus"; rdfs:subClassOf ; "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex."; "intermediate thymic epithelial cell"; . a owl:Class; rdfs:label "type-5 epithelial cell of thymus"; rdfs:subClassOf ; "A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla."; "undifferentiated mTEC", "undifferentiated medullary thymic epithelial cell", "undifferentiated thymic epithelial cell"; . a owl:Class; rdfs:label "type-2 epithelial cell of thymus"; rdfs:subClassOf ; "An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus."; "pale thymic epithelial cell"; . a owl:Class; rdfs:label "type-7 epithelial cell of thymus"; rdfs:subClassOf ; "A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin."; "spindle shaped mTEC", "spindle shaped medullary thymic epithelial cell"; . a owl:Class; rdfs:label "type B synovial cell"; rdfs:subClassOf ; "A synovial cell type that resembles fibroblasts,has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid."; . a owl:Class; rdfs:label "type A synovial cell"; rdfs:subClassOf ; "A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum."; "type A synoviocyte"; . a owl:Class; rdfs:label "pigmented ciliary epithelial cell"; rdfs:subClassOf ; "A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells."; "PE"; . a owl:Class; rdfs:label "non-pigmented ciliary epithelial cell"; rdfs:subClassOf ; "A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells."; "NPE"; . a owl:Class; rdfs:label "epithelial cell of distal tubule"; rdfs:subClassOf ; "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH."; "kidney distal tubule epithelial cell"; . a owl:Class; rdfs:label "epithelial cell of proximal tubule"; rdfs:subClassOf ; "An epithelial cell of the proximal tubule of the kidney."; "kidney proximal tubule epithelial cell"; . a owl:Class; rdfs:label "brush border cell of the proximal tubule"; rdfs:subClassOf ; "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow."; . a owl:Class; rdfs:label "epithelial cell of skin gland"; rdfs:subClassOf ; "An epithelial cell of a skin gland."; "epithelial cell of gland of skin"; . a owl:Class; rdfs:label "corticotroph"; rdfs:subClassOf ; "A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells;"; . a owl:Class; rdfs:label "mammosomatotroph"; rdfs:subClassOf ; "An acidophil cell of the anterior pitiuatry gland that produces both prolactin and growth hormone."; . a owl:Class; rdfs:label "mammotroph"; rdfs:subClassOf ; "An acidophilic cell of the anterior pituitary that produces prolactin."; "epsilon-acidophil", "lactotrope", "lactotroph", "lactotropic cell", "mammotrope", "mammotrophic cell", "mammotropic cell"; . a owl:Class; rdfs:label "somatotroph"; rdfs:subClassOf ; "An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin."; "somatotrope", "somatotropic cell", "somatrophic cell"; . a owl:Class; rdfs:label "endocrine-paracrine cell of prostate gland"; rdfs:subClassOf ; "An ecto-epithelial cell of the prostate gland that secretes hormones."; "glandular cell of prostate", "neuro-epithelial cell of prostate gland"; . a owl:Class; rdfs:label "external supporting cell of vestibular epithelium"; rdfs:subClassOf ; "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein."; . a owl:Class; rdfs:label "supporting cell of cochlea"; rdfs:subClassOf ; "An epithelial supporting cell located in the cochlea."; . a owl:Class; rdfs:label "supporting cell of vestibular epithelium"; rdfs:subClassOf ; "A supporting cell of the vestibular epithelium."; . a owl:Class; rdfs:label "external limiting cell of vestibular epithelium"; rdfs:subClassOf ; "An external limiting cell found in the vestibular epithelium."; . a owl:Class; rdfs:label "periperhal blood mesothelial cell"; rdfs:subClassOf ; "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium."; . a owl:Class; rdfs:label "neural cell"; rdfs:subClassOf ; "A cell that is part of the nervous system."; . a owl:Class; rdfs:label "connective tissue cell"; rdfs:subClassOf ; "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone."; . a owl:Class; rdfs:label "embryonic stem cell"; rdfs:subClassOf ; "A stem cell of embryonic origin."; "ESC"; rdfs:comment "This is an in vitro cell type and may be removed in future releases. These cells are reportedly SSEA-4-positive, CD73-negative, and CD324-positive."; . a owl:Class; rdfs:label "amniocyte"; rdfs:subClassOf ; "A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface."; . a owl:Class; rdfs:label "myoepithelial cell of mammary gland"; rdfs:subClassOf ; "A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative."; . a owl:Class; rdfs:label "mammary alveolar cell"; rdfs:subClassOf ; "The milk-producing cell of the alveolar unit that emerges during pregnancy."; "epithelial cell of lactiferous gland", "luminal cell of alveolus of lactiferous gland"; . a owl:Class; rdfs:label "luminal epithelial cell of mammary gland"; rdfs:subClassOf ; "A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast."; . a owl:Class; rdfs:label "mammary epithelial cell"; rdfs:subClassOf ; "An epithelial cell of the mammary gland."; "breast epithelial cell"; . a owl:Class; rdfs:label "bronchial epithelial cell"; rdfs:subClassOf ; "An epithelial cell of the bronchus."; . a owl:Class; rdfs:label "basal epithelial cell of tracheobronchial tree"; rdfs:subClassOf ; "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury."; . a owl:Class; rdfs:label "undifferentiated cell of bronchus epithelium"; rdfs:subClassOf ; "An undifferentiated columnar cell of the bronchus epithelium"; . a owl:Class; rdfs:label "ciliated cell of the bronchus"; rdfs:subClassOf ; "A ciliated cell of the bronchus."; . a owl:Class; rdfs:label "neural crest derived fat cell"; rdfs:subClassOf ; "A fat cell derived from a neural crest cell."; . a owl:Class; rdfs:label "preadipocyte"; rdfs:subClassOf ; "An undifferentiated fibroblast that can be stimulated to form a fat cell."; . a owl:Class; rdfs:label "brown preadipocyte"; rdfs:subClassOf ; "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)."; . a owl:Class; rdfs:label "buccal mucosa cell"; rdfs:subClassOf ; "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek."; . a owl:Class; rdfs:label "keratinocyte stem cell"; rdfs:subClassOf ; "A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair."; "bulge keratinocyte"; . a owl:Class; rdfs:label "CD56-positive, CD161-positive immature natural killer cell"; rdfs:subClassOf ; "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive."; rdfs:comment "Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily)."; . a owl:Class; rdfs:label "prostate stem cell"; rdfs:subClassOf ; "A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium."; "CD133-positive prostate epithelial cell"; . a owl:Class; rdfs:label "luminal cell of prostate epithelium"; rdfs:subClassOf ; "The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival."; . a owl:Class; rdfs:label "basal cell of prostate epithelium"; rdfs:subClassOf ; "An undifferentiated cell of the prostate epithelium that lacks secretory activity."; . a owl:Class; rdfs:label "circulating endothelial cell"; rdfs:subClassOf ; "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage."; . a owl:Class; rdfs:label "decidual natural killer cell"; rdfs:subClassOf ; "A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy."; "dNK cell", "decidual NK cell"; . a owl:Class; rdfs:label "CD56-negative, CD161-positive immature natural killer cell"; rdfs:subClassOf ; "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive."; rdfs:comment "Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily)."; . a owl:Class; rdfs:label "CD27-low, CD11b-low immature natural killer cell"; rdfs:subClassOf ; "An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver."; rdfs:comment "Markers are associated with mouse cells."; . a owl:Class; rdfs:label "Dx5-negative, NK1.1-positive immature natural killer cell"; rdfs:subClassOf ; "An immature natural killer cell that is NK1.1-positive and DX-5 negative."; . a owl:Class; rdfs:label "CD27-high, CD11b-high natural killer cell"; rdfs:subClassOf ; "A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion."; . a owl:Class; rdfs:label "CD27-low, CD11b-high natural killer cell"; rdfs:subClassOf ; "A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors."; . a owl:Class; rdfs:label "CD27-high, CD11b-low natural killer cell"; rdfs:subClassOf ; "A natural killer cell that is CD27-high and CD11b-low."; . a owl:Class; rdfs:label "endocardial cell"; rdfs:subClassOf ; "An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin."; "endocardial endothelial cell", "endothelial cell of endocardium"; . a owl:Class; rdfs:label "progenitor cell of endocrine pancreas"; rdfs:subClassOf ; "A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1."; "pancreatic endocrine progenitor", "pancreatic islet progenitor cell"; . a owl:Class; rdfs:label "gestational hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem cell that exists during embryogenesis."; . a owl:Class; rdfs:label "fetal liver hematopoietic progenitor cell"; rdfs:subClassOf ; "A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative."; . a owl:Class; rdfs:label "yolk sac hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive."; "hemangioblast precursor"; . a owl:Class; rdfs:label "primitive red blood cell"; rdfs:subClassOf ; "A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation."; "primitive erythroblast", "primitive erythrocyte", "primitive erythroid cell"; . a owl:Class; rdfs:label "primitive reticulocyte"; rdfs:subClassOf ; "A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains."; "megalocyte"; . a owl:Class; rdfs:label "fetal derived definitive erythrocyte"; rdfs:subClassOf ; "A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins."; "macrocyte"; . a owl:Class; rdfs:label "pyrenocyte"; rdfs:subClassOf ; "Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte."; . a owl:Class; rdfs:label "placental hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells."; . a owl:Class; rdfs:label "AGM hematopoietic stem cell"; rdfs:subClassOf ; "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC."; . a owl:Class; rdfs:label "primitive erythroid progenitor"; rdfs:subClassOf ; "A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41."; "EryP-CFC", "inner blood island hemangioblast"; . a owl:Class; rdfs:label "granule cell precursor"; rdfs:subClassOf ; "A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive."; . a owl:Class; rdfs:label "keratocyte"; rdfs:subClassOf ; "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate."; "corneal fibroblast", "corneal keratocyte"; . a owl:Class; rdfs:label "cortical thymic epithelial cell"; rdfs:subClassOf ; "An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells."; "cTEC"; . a owl:Class; rdfs:label "medullary thymic epithelial cell"; rdfs:subClassOf ; "An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output."; "mTEC"; . a owl:Class; rdfs:label "myometrial cell"; rdfs:subClassOf ; "A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin."; "myometrium smooth muscle cell"; . a owl:Class; rdfs:label "trabecular meshwork cell"; rdfs:subClassOf ; "A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure."; "trabeculocyte"; . a owl:Class; rdfs:label "respiratory epithelial cell"; rdfs:subClassOf ; "An endo-epithelial cell of the respiratory tract."; "airway epithelial cell"; . a owl:Class; rdfs:label "respiratory goblet cell"; rdfs:subClassOf ; "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion."; . a owl:Class; rdfs:label "somatic cell"; rdfs:subClassOf ; "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)."; "a cell hierarchy from some ontology that offers a single inheritance view of all relevant cell types - FMA :Cell looks promising."; . a owl:Class; rdfs:label "ear hair cell"; rdfs:subClassOf ; "A hair cell of the ear that contains the organs of balance and hearing."; "ear receptor cell"; . a owl:Class; rdfs:label "non-myelinating Schwann cell"; rdfs:subClassOf ; "A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells."; . a owl:Class; rdfs:label "immature Schwann cell"; rdfs:subClassOf ; "A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons."; . a owl:Class; rdfs:label "immature Vgamma2-positive fetal thymocyte"; rdfs:subClassOf ; "A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive and is found in the fetal thymus."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; . a owl:Class; rdfs:label "meningothelial cell"; rdfs:subClassOf ; "A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood."; "arachnoid cap cell"; . a owl:Class; rdfs:label "intermediate monocyte"; rdfs:subClassOf ; "A monocyte that has characteristics of both patrolling and inflammatory monocytes."; . a owl:Class; rdfs:label "CD141-positive myeloid dendritic cell"; rdfs:subClassOf ; "A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta."; rdfs:comment "Markers are found in human cells. Normally they represent 3-5% of peripheral blood mDCs (human). These cells express high levels of CD283 (TLR3), are capable of producing IL-12p70 and IFN-beta upon stimulation, and inducing a TH1 response [PMCID:PMC2882828]. They are also Necl2-positive. May be human equivalent of murine CD8alpha-positive DCs."; . a owl:Class; rdfs:label "Gr1-high classical monocyte"; rdfs:subClassOf ; "A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative."; rdfs:comment "Markers are associated with mice. The Gr epitope is used to describe this cell type is found on both Ly6c and Ly6g. However, its the Ly6c that is considered the specific marker, and thus used in the cross-product."; . a owl:Class; rdfs:label "CD14-low, CD16-positive monocyte"; rdfs:subClassOf ; "A patrolling monocyte that is CD14-low and CD16-positive."; rdfs:comment "Markers are associated with human monocytes."; . a owl:Class; rdfs:label "CD14-positive, CD16-positive monocyte"; rdfs:subClassOf ; "An intermediate monocyte that is CD14-positive, CD16-positive."; rdfs:comment "Markers are associated with human cells."; . a owl:Class; rdfs:label "Gr1-positive, CD43-positive monocyte"; rdfs:subClassOf ; "An intermediate monocyte that is Gr1-positive, CD43-positive."; . a owl:Class; rdfs:label "CD1c-positive myeloid dendritic cell"; rdfs:subClassOf ; "A myeloid dendritic cell found in the blood that is CD1c-positive."; rdfs:comment "Normally represent 10-20% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10) [PMID:20204387]. Upon TLR stimulation, these cells were potent producers of CXCL8 (IL-8), while producing little TNF-alpha."; . a owl:Class; rdfs:label "Fraction B/C precursor B cell"; rdfs:subClassOf ; "A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive."; . a owl:Class; rdfs:label "mature dendritic epithelial T cell precursor"; rdfs:subClassOf ; "A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; "mature DEC precursor", "mature DETC precursor"; . a owl:Class; rdfs:label "Peyer's patch B cell"; rdfs:subClassOf ; "A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative."; "Peyers patch B cell"; . a owl:Class; rdfs:label "mature Vgamma2-positive fetal thymocyte"; rdfs:subClassOf ; "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; "fetal Vgamma2-positive"; . a owl:Class; rdfs:label "fetal thymocyte"; rdfs:subClassOf ; "A thymocyte found in the fetal thymus."; . a owl:Class; rdfs:label "gamma-delta thymocyte"; rdfs:subClassOf ; "A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative)."; "gammadelta thymocyte", "gd thymocyte"; . a owl:Class; rdfs:label "immature Vgamma2-positive thymocyte"; rdfs:subClassOf ; "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; . a owl:Class; rdfs:label "mature Vgamma2-positive thymocyte"; rdfs:subClassOf ; "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; "Vgamma2-positive"; . a owl:Class; rdfs:label "immature Vgamma2-negative thymocyte"; rdfs:subClassOf ; "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-positive."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; . a owl:Class; rdfs:label "mature Vgamma2-negative thymocyte"; rdfs:subClassOf ; "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4- negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus."; rdfs:comment "NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments."; "Vgamma2-negative"; . a owl:Class; rdfs:label "Vgamma1.1-positive, Vdelta6.3-negative thymocyte"; rdfs:subClassOf ; "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor."; "Vg1.1-positive, Vd6.3-negative T cell"; . a owl:Class; rdfs:label "Vgamma1.1-positive, Vdelta6.3-positive thymocyte"; rdfs:subClassOf ; "A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor."; "Vg1.1+Vd6.3+ T cell"; . a owl:Class; rdfs:label "mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte"; rdfs:subClassOf ; "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative."; . a owl:Class; rdfs:label "immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte"; rdfs:subClassOf ; "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive."; . a owl:Class; rdfs:label "immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte"; rdfs:subClassOf ; "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive."; "immature Vg1.1+Vd6.3+ T cell"; . a owl:Class; rdfs:label "mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte"; rdfs:subClassOf ; "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative."; "mature Vg1.1+Vd6.3+ T cell"; . a owl:Class; rdfs:label "primitive erythroid lineage cell"; rdfs:subClassOf ; "An immature or mature cell of the first erythroid lineage to arise during embryonic development."; . a owl:Class; rdfs:label "mature T cell"; rdfs:subClassOf ; "A T cell that expresses a T cell receptor complex and has completed T cell selection."; "CD3e-positive T cell", "mature T-cell"; . a owl:Class; rdfs:label "immature T cell"; rdfs:subClassOf ; "A T cell that has not completed T cell selection."; "immature T-cell"; . a owl:Class; rdfs:label "nucleated reticulocyte"; rdfs:subClassOf ; "A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles."; . a owl:Class; rdfs:label "enucleated reticulocyte"; rdfs:subClassOf ; "A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes."; . a owl:Class; rdfs:label "DN2a thymocyte"; rdfs:subClassOf ; "A DN2 thymocyte that is Kit-hi."; rdfs:comment "Observed in mice."; . a owl:Class; rdfs:label "DN2b thymocyte"; rdfs:subClassOf ; "A DN2 thymocyte that is Kit-low."; rdfs:comment "Observed in mice."; . a owl:Class; rdfs:label "early T lineage precursor"; rdfs:subClassOf ; "A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive."; "ETP", "preT.ETP.Th"; rdfs:comment "ETPs are reportedly CD1a-negative, CD4-negative, CD7-positive, CD8a-negative, CD8b-negative, CD33-low, CD34-high, CD38-low, CD45RA-positive, and CD45RO-negative."; . a owl:Class; rdfs:label "CD11b-positive, CD27-positive natural killer cell"; rdfs:subClassOf ; "A mature natural killer cell that is CD11b-positive and CD27-positive."; rdfs:comment "A natural killer cell that is NK1.1-positive, CD11b-positive, and CD27-positive."; . a owl:Class; rdfs:label "resting double-positive thymocyte"; rdfs:subClassOf ; "A double-positive, alpha-beta thymocyte that is small and not proliferating."; "T.DP.sm.Th"; . a owl:Class; rdfs:label "double-positive blast"; rdfs:subClassOf ; "A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating."; "T.DPb.Th", "activated double-positive thymocyte"; . a owl:Class; rdfs:label "CD69-positive double-positive thymocyte"; rdfs:subClassOf ; "A double-positive thymocyte that is CD69-positive and has begun positive selection."; "T.DP69+.Th"; . a owl:Class; rdfs:label "CD4-intermediate, CD8-positive double-positive thymocyte"; rdfs:subClassOf ; "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor."; "T.4int8+.Th"; . a owl:Class; rdfs:label "CD4-positive, CD8-intermediate double-positive thymocyte"; rdfs:subClassOf ; "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor."; "T.4int8+.th"; . a owl:Class; rdfs:label "CD24-positive, CD4 single-positive thymocyte"; rdfs:subClassOf ; "A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor."; "CD24-positive, CD4 single-positive semimature thymocyte", "T.4SP24int.Th"; rdfs:comment "Described in the immgene database as being CD24-intermediate."; . a owl:Class; rdfs:label "CD69-positive, CD4-positive single-positive thymocyte"; rdfs:subClassOf ; "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive."; "T.4SP69+.Th", "intermediate CD4-single-positive"; . a owl:Class; rdfs:label "CD24-positive, CD8 single-positive thymocyte"; rdfs:subClassOf ; "A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor."; "CD24-positive, CD8 single-positive semimature thymocyte", "T.8SP24int.Th"; rdfs:comment "Described in the immgene database as being CD24-intermediate."; . a owl:Class; rdfs:label "CD69-positive, CD8-positive single-positive thymocyte"; rdfs:subClassOf ; "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive."; "T.8SP69+.Th", "intermediate CD8-single-positive"; . a owl:Class; rdfs:label "mature CD4 single-positive thymocyte"; rdfs:subClassOf ; "A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor."; . a owl:Class; rdfs:label "mature CD8 single-positive thymocyte"; rdfs:subClassOf ; "A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor."; "T.8SP24-.Th"; . a owl:Class; rdfs:label "NK1.1-positive natural killer cell"; rdfs:subClassOf ; "A mature NK cell that is NK1.1-positive."; "NK.sp", "NK1.1-positive NK cell"; rdfs:comment "Note: Nk1.1 expression is restricted to C57BL strains of laboratory mice."; . a owl:Class; rdfs:label "NKGA2-positive natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is NKGA2-positive."; "NK.G2A+.SP"; . a owl:Class; rdfs:label "Ly49D-positive natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is Ly49D-positive."; "NK.49D+.Sp"; . a owl:Class; rdfs:label "CD94-positive natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is CD94-positive."; "NK.94+.Sp"; . a owl:Class; rdfs:label "CD94-negative, Ly49CI-negative natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative."; "CD94- Ly49I-negative NK cell", "NK.49Cl-94-.Sp"; . a owl:Class; rdfs:label "Ly49CI-positive natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is Ly49Cl-positive."; "Ly49I-positive NK cell", "NK.49Cl+.Sp"; . a owl:Class; rdfs:label "Ly49H-positive natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is Ly49H-positive."; "LyH49H-positive"; . a owl:Class; rdfs:label "Ly49D-negative natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is Ly49D-negative."; "NK.49D-.Sp"; . a owl:Class; rdfs:label "Ly49CI-negative natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is Ly49Cl-negative."; "Ly49I-negative NK cell", "NK.49Cl-.Sp"; . a owl:Class; rdfs:label "CD94-negative natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is CD94-negative."; "NK.94-.Sp"; . a owl:Class; rdfs:label "Ly49H-negative natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is Ly49H-negative."; "LyH49H-negative"; . a owl:Class; rdfs:label "CD94-positive Ly49CI-positive natural killer cell"; rdfs:subClassOf ; "A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive."; "NK.49Cl+94+.Sp"; . a owl:Class; rdfs:label "spinal cord interneuron"; rdfs:subClassOf ; "A CNS interneuron located in the spinal cord."; rdfs:comment "Is_a interneuron, part_of UBERON:0002240."; . a owl:Class; rdfs:label "ionocyte"; rdfs:subClassOf ; "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment."; . a owl:Class; rdfs:label "Kolmer-Agduhr neuron"; rdfs:subClassOf ; "KA cell", "KA interneuron", "KA neuron", "Kolmer-Agduhr cell"; "Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons."; . a owl:Class; rdfs:label "macular hair cell"; rdfs:subClassOf ; "An auditory hair cell located in the macula that is sensitive to auditory stimuli."; . a owl:Class; rdfs:label "renal principal cell"; rdfs:subClassOf ; "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts."; . a owl:Class; rdfs:label "renal intercalated cell"; rdfs:subClassOf ; "A cuboidal epithelial cell of the kidney that regulates acid/base balance."; "intercalated cell"; . a owl:Class; rdfs:label "renal alpha-intercalated cell"; rdfs:subClassOf ; "A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance."; . a owl:Class; rdfs:label "multi-ciliated epithelial cell"; rdfs:subClassOf ; "A ciliated epithelial cell with many cilium."; . a owl:Class; rdfs:label "single ciliated epithelial cell"; rdfs:subClassOf ; "A ciliated epithelial cell with a single cilium."; . a owl:Class; rdfs:label "auditory epithelial support cell"; rdfs:subClassOf ; "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells."; . a owl:Class; rdfs:label "inner phalangeal cell"; rdfs:subClassOf ; "An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells."; . a owl:Class; rdfs:label "stretch receptor cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stratified keratinized epithelial stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "stratified non keratinized epithelial stem cell"; rdfs:subClassOf ; . a owl:Class; rdfs:label "pillar cell"; rdfs:subClassOf ; "A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti."; "pillar cell of cochlea", "pillar cell of corti", "rod cell of Corti"; . a owl:Class; rdfs:label "trophectodermal cell"; rdfs:subClassOf ; "trophectoderm cell"; . a owl:Class; rdfs:label "cell type cancer"; rdfs:subClassOf ; "A cancer that is classified by the type of cell from which it is derived."; , . a owl:Class; rdfs:label "Huntington's disease"; rdfs:subClassOf ; "A neurodegenerative disease that has_material_basis_in expansion of CAG repeats resulting in neuron degeneration affecting muscle coordination, cognitive abilities."; "HD", "Huntington's chorea", "Huntington's chorea (disorder)", "Huntington's disease", "Huntington's disease pathway"; , . a owl:Class; rdfs:label "neurodegenerative disease"; rdfs:subClassOf ; "A central nervous system disease that results_in the progressive deterioration of tissue or organ function or structure, whether due to normal bodily wear or lifestyle choices."; "Neurodegenerative disease", "degenerative disease"; , . a owl:Class; rdfs:label "disease of cellular proliferation"; rdfs:subClassOf ; "A disease that is characterized by abnormally rapid cell division."; "cell process disease"; , . a owl:Class; rdfs:label "cancer"; rdfs:subClassOf ; "A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis."; "malignant neoplasm", "malignant tumor ", "primary cancer"; , . a owl:Class; rdfs:label "adenocarcinoma"; rdfs:subClassOf ; "A carcinoma that has_material_basis_in abnormally proliferating cells, derives_from epithelial cells, which originate in glandular tissue."; "adenocarcinoma", "adenocarcinoma NOS (morphologic abnormality)", "adenocarcinoma, no subtype (morphologic abnormality)", "adenocarcinomas"; , . a owl:Class; rdfs:label "carcinoma"; rdfs:subClassOf ; "A cell type cancer that has_material_basis_in abnormally proliferating cells derived_from epithelial cells."; "Epithelioma, malignant (morphologic abnormality)", "carcinoma", "epithelioma", "malignant Epithelioma", "malignant epithelioma"; , . a owl:Class; rdfs:label "central nervous system disease"; rdfs:subClassOf ; "A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system."; , . a owl:Class; rdfs:label "disease"; rdfs:subClassOf ; "A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."; , . a owl:Class; rdfs:label "disease of anatomical entity"; rdfs:subClassOf ; "A disease that manifests in a defined anatomical structure."; , . a owl:Class; rdfs:label "nervous system disease"; rdfs:subClassOf ; "A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system."; , . a owl:Class; rdfs:label "instrument"; rdfs:subClassOf , , _:2de389, _:2de399; "A flow cytometer."; "Material entity that is designed to have a function and play a role in scientific investigation."; "PERSON: Melissa Haendel"; rdfs:comment "See OBI listserv discussion for considerations in defining instrument. http://sourceforge.net/tracker/index.php?func=detail&aid=2894801&group_id=177891&atid=886178"; "http://en.wikipedia.org/wiki/Scientific_instrument"; "instrument"; ; . _:2de389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transgenic lambda phage"; rdfs:subClassOf ; "A lambda phage expressing a gene of interest."; "A transgenic virus derived from a lambda phage that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "PERSON: Matthew Brush"; "http://en.wikipedia.org/wiki/Vector_%28molecular_biology%29"; "lambda phage vector"; ; . a owl:Class; rdfs:label "Prokaryota"; rdfs:subClassOf , , _:2de3a9; . _:2de3a9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "adeno-associated viruses"; rdfs:subClassOf ; . a owl:Class; rdfs:label "obsolete_non viral organism"; rdfs:subClassOf ; "A unicellular or multicellular individual living system that is capable of replicating or reproducing and growth and maintenance in the right environment. Examples: animal, plant, bacteria, fungus."; "replaced with NCBI cellular organism"; "obsolete_non viral organism"; "ERO : what is difference between ERO:non viroal organism and NCBITaxon cellular organism? Should they import from NCBI?"; . a owl:Class; rdfs:label "transgenic cellular organism"; owl:equivalentClass _:2de3b9; rdfs:subClassOf , , _:2de429, _:2de479; "A non-viral organism whose genetic material has been altered using genetic engineering techniques."; . _:2de3b9 a owl:Class; owl:intersectionOf _:2de3c9 . _:2de3c9 rdf:first ; rdf:rest _:2de3e9 . _:2de3e9 rdf:first _:2de3d9; rdf:rest rdf:nil . _:2de3d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de3f9 . _:2de3f9 a owl:Class; owl:unionOf _:2de409 . _:2de409 rdf:first ; rdf:rest _:2de419 . _:2de419 rdf:first ; rdf:rest rdf:nil . _:2de429 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de439 . _:2de439 a owl:Class; owl:intersectionOf _:2de449 . _:2de449 rdf:first ; rdf:rest _:2de469 . _:2de469 rdf:first _:2de459; rdf:rest rdf:nil . _:2de459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de489 . _:2de489 a owl:Class; owl:unionOf _:2de499 . _:2de499 rdf:first ; rdf:rest _:2de4a9 . _:2de4a9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "transgenic virus"; owl:equivalentClass _:2de4b9; rdfs:subClassOf , , _:2de4f9, _:2de549, _:2de559; "A virus expressing a gene of interest."; "A virus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "PERSON: Matthew Brush"; "PERSON: Matthew Brush"; "recombinant virus"; ; . _:2de4b9 a owl:Class; owl:intersectionOf _:2de4c9 . _:2de4c9 rdf:first ; rdf:rest _:2de4e9 . _:2de4e9 rdf:first _:2de4d9; rdf:rest rdf:nil . _:2de4d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de4f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de509 . _:2de509 a owl:Class; owl:intersectionOf _:2de519 . _:2de519 rdf:first ; rdf:rest _:2de539 . _:2de539 rdf:first _:2de529; rdf:rest rdf:nil . _:2de529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de549 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transgenic baculovirus"; rdfs:subClassOf ; "A transgenic virus derived from a baculovirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "Baculovirus supernatant", "Baculovirus vector"; . a owl:Class; rdfs:label "transgenic retrovirus "; rdfs:subClassOf ; "A transgenic virus derived from a lentivirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "Retrovirus supernatant", "Retrovirus vector"; . a owl:Class; rdfs:label "transgenic adenovirus"; rdfs:subClassOf ; "A transgenic virus derived from an adenovirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "Adenovirus supernatant", "Adenovirus vector"; . a owl:Class; rdfs:label "transgenic lentivirus"; rdfs:subClassOf ; "A transgenic virus derived from a lentivirus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "Lentivirus supernatant", "Lentivirus vector"; . a owl:Class; rdfs:label "transgenic adeno-associated virus"; rdfs:subClassOf ; "A transgenic virus derived from an andeno-associated virus that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms."; "Adeno-associated virus supernatant", "Adeno-associated virus vector"; . a owl:Class; rdfs:label "nuclear chromosome"; rdfs:subClassOf ; "A chromosome found in the nucleus of a eukaryotic cell."; . a owl:Class; rdfs:label "cytoplasmic chromosome"; rdfs:subClassOf ; "A chromosome found in the cytoplasm."; . a owl:Class; rdfs:label "mitochondrial chromosome"; rdfs:subClassOf ; "A chromosome found in the mitochondrion of a eukaryotic cell."; . a owl:Class; rdfs:label "reverse transcription"; rdfs:subClassOf ; "A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis."; . a owl:Class; rdfs:label "adaptive immune response"; rdfs:subClassOf ; "An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory)."; rdfs:comment "This term was added by GO_REF:0000022."; "acquired immune response"; . a owl:Class; rdfs:label "antigen binding"; rdfs:subClassOf , _:2de569, _:2de5a9; "Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen."; "antigen binding function"; "a molecular binding function inhereing in an adaptive immune receptor complex that was produced to bind selectively and non-covalently with an antigen - any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen."; . _:2de569 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de579 . _:2de579 a owl:Class; owl:unionOf _:2de589 . _:2de589 rdf:first ; rdf:rest _:2de599 . _:2de599 rdf:first ; rdf:rest rdf:nil . _:2de5a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "catalytic activity"; rdfs:subClassOf ; "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic."; "enzyme activity"; . a owl:Class; rdfs:label "cytokine activity"; rdfs:subClassOf ; "Functions to control the survival, growth, differentiation and effector function of tissues and cells."; . a owl:Class; rdfs:label "binding"; rdfs:subClassOf , _:2de5b9; rdfs:comment "For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children."; "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule."; "molecular binding function"; "a function inhereing in some molecular entity that was generated for the purpose of selectively and non-covalently associating with some other molecular entity."; . _:2de5b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "chromosome"; rdfs:subClassOf ; "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information."; . a owl:Class; rdfs:label "DNA replication"; rdfs:subClassOf ; rdfs:comment "See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'."; "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA."; . a owl:Class; rdfs:label "transcription, DNA-dependent"; rdfs:subClassOf ; "DNA-dependent transcription", "cellular transcription, DNA-dependent"; "The cellular synthesis of RNA on a template of DNA."; . a owl:Class; rdfs:label "translation"; rdfs:subClassOf ; "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome."; "protein anabolism", "protein biosynthesis", "protein biosynthetic process", "protein formation", "protein synthesis", "protein translation"; . a owl:Class; rdfs:label "immune response"; rdfs:subClassOf , _:2de5c9, _:2de5d9; "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat."; rdfs:comment "This term was improved by GO_REF:0000022. It was redefined and moved."; . _:2de5c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de5d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de5e9 . _:2de5e9 a owl:Class; owl:unionOf _:2de5f9 . _:2de5f9 rdf:first ; rdf:rest _:2de609 . _:2de609 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "biological_process"; rdfs:subClassOf ; owl:disjointWith ; "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end."; rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this."; "biological process", "physiological process"; "biological process"; . a owl:Class; rdfs:label "plastid chromosome"; rdfs:subClassOf ; "A circular DNA molecule containing plastid encoded genes."; . a owl:Class; rdfs:label "gene expression"; rdfs:subClassOf ; "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form."; . a owl:Class; rdfs:label "RNA interference"; rdfs:subClassOf ; rdfs:comment "Note that this term refers specifically to posttranscriptional mechanisms by which small interfering RNAs down-regulate gene expression. Also consider annotating to other descendants of 'gene silencing by RNA ; GO:0031047'.", "GO preferred term is 'RNA interference', but 'gene silencing by siRNA' is used here."; "RNAi", "posttranscriptional gene silencing by siRNA", "RNA interference"; "The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes."; . a owl:Class; rdfs:label "stem cell division"; rdfs:subClassOf ; "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types."; "stem cell renewal"; . a owl:Class; rdfs:label "virion assembly"; rdfs:subClassOf ; "A late phase of viral replication during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed."; "viral assembly", "viral particle assembly", "virus assembly", "virus particle assembly"; . a owl:Class; rdfs:label "immunoglobulin complex"; rdfs:subClassOf , , _:2de619, _:2de629, _:2de639; "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph."; rdfs:comment "Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available."; . _:2de619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de639 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "B cell receptor complex"; rdfs:subClassOf ; "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins."; "B lymphocyte receptor complex", "B-cell receptor complex", "B-lymphocyte receptor complex", "BCR complex", "immunoglobulin complex, membrane bound"; rdfs:comment "Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available."; . a owl:Class; rdfs:label "neuron differentiation"; rdfs:subClassOf ; "The process in which a relatively unspecialized cell acquires specialized features of a neuron."; . a owl:Class; rdfs:label "gene silencing by RNA"; rdfs:subClassOf ; "Any process in which RNA molecules inactivate expression of target genes."; "RNA-mediated gene silencing"; . a owl:Class; rdfs:label "dsRNA fragmentation"; rdfs:subClassOf ; "Cleavage of double-stranded RNA molecules by an RNaseIII-family enzyme to produce small RNAs (generally 20-30 nucleotides, depending on species) with biological function."; "double-stranded RNA fragmentation"; . a owl:Class; rdfs:label "macromolecular complex"; rdfs:subClassOf ; "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together."; "macromolecule complex"; "obsolete_macromolecular complex"; "not needed after implementation of new info vs non-info molecular entity split in org molecular entity hierarchy"; . a owl:Class; rdfs:label "gene silencing by miRNA"; rdfs:subClassOf ; "Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression."; "gene silencing by microRNA", "miRNA-mediated gene silencing", "microRNA-mediated gene silencing"; . a owl:Class; rdfs:label "T cell receptor complex"; rdfs:subClassOf , , _:2de649; "A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains."; "T lymphocyte receptor complex", "T-cell receptor complex", "T-lymphocyte receptor complex"; . _:2de649 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "immunoglobulin complex, circulating"; rdfs:subClassOf ; "An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component."; rdfs:comment "Note that an immunoglobulin complex has the function of antigen binding if a suitable antigen is available."; "antibody"; "For now, have made the choice to assert antibody reagents as types of 'GO:Ig complex, circulating', because structurally, this is most accurate. . . . however, the def of the GO class would have to be changed to invoke only structural differentia for this to be entirely accurate, as subclasses of antibody in ReO (e.g. 'antibody reagent') are not found circulating in some organism (see feedback note on this class)."; "GO (Seems like this GO class should be defined structurally, rather than by its context/location in the body (i think BP agrees here, based on comments on discussion list). Structurally, this class of immunoglobulins lacks a signal peptide that tethers it to the cell membrane. If we use this definition, then we can say accurately that antibody reagents are of this type.)"; "GO", ; "antibody" . a owl:Class; rdfs:label "chloroplast chromosome"; rdfs:subClassOf ; "A circular DNA molecule containing chloroplast encoded genes."; . a owl:Class; rdfs:label "protein complex"; rdfs:subClassOf , , _:2de659, _:2de669; "Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules."; "protein-protein complex"; . _:2de659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "production of small RNA involved in gene silencing by RNA"; rdfs:subClassOf ; "The process in which a double-stranded RNA precursor is processed into short (20-30 nt) fragments. RNA cleavage is catalyzed by a Dicer endonuclease."; "gene silencing by RNA, production of guide RNA", "gene silencing by RNA, production of small RNA"; . a owl:Class; rdfs:label "conditional specification"@en; rdfs:subClassOf ; "OBI branch derived"@en, "OBI_0000349"@en; "PlanAndPlannedProcess Branch"@en; "a directive information entity that specifies what should happen if the trigger condition is fulfilled"@en; "conditional specification"@en; ; . a owl:Class; rdfs:label "measurement unit label"@en; owl:equivalentClass _:2de679; rdfs:subClassOf , _:2de6f9; "OBI (discuss distinction I am making (with unit labels and with value specification vs measurement data ICEs and with related object properties as well) between measured and specified data)"; "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en; "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en; "Examples of measurement unit labels are liters, inches, weight per volume."@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en; "measurement unit label"@en; ; . _:2de679 a owl:Class; owl:intersectionOf _:2de689 . _:2de689 rdf:first ; rdf:rest _:2de6a9 . _:2de6a9 rdf:first _:2de699; rdf:rest rdf:nil . _:2de699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de6b9 . _:2de6b9 a owl:Class; owl:intersectionOf _:2de6c9 . _:2de6c9 rdf:first ; rdf:rest _:2de6e9 . _:2de6e9 rdf:first _:2de6d9; rdf:rest rdf:nil . _:2de6d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de6f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de709 . _:2de709 a owl:Class; owl:intersectionOf _:2de719 . _:2de719 rdf:first ; rdf:rest _:2de739 . _:2de739 rdf:first _:2de729; rdf:rest rdf:nil . _:2de729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "objective specification"@en; rdfs:subClassOf , _:2de749; "Answers the question, why did you do this experiment?"@en; "OBI Plan and Planned Process/Roles Branch"@en, "OBI_0000217"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Barry Smith"@en, "PERSON: Bjoern Peters"@en, "PERSON: Jennifer Fostel"@en; "a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en; "objective specification"@en; "purpose of a study; support of hypothesis, discovery of new information"@en; ; . _:2de749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "narrative object"@en; rdfs:subClassOf ; "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion"@en, "agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions"@en; "A narrative object is an information content entity that is a set of propositions."@en; "Examples of narrative objects are reports, journal articles, and patents submission."@en; "OBI_0000013"@en, "group:OBI"@en; "narrative object"@en; "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "action specification"@en; rdfs:subClassOf ; "Alan Ruttenberg"@en; "OBI Plan and Planned Process branch"@en; "Pour the contents of flask 1 into flask 2"@en; "a directive information entity that describes an action the bearer will take"@en; ; . a owl:Class; rdfs:label "label"@en; rdfs:subClassOf ; "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en; "GROUP: IAO"@en; "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en; "label"@en; ; . a owl:Class; rdfs:label "software"@en; rdfs:subClassOf ; "GROUP: OBI"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Bjoern Peters"@en, "PERSON: Chris Stoeckert"@en, "PERSON: Melanie Courtot"@en; "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178"@en; "software"@en; ; . a owl:Class; rdfs:label "journal article"@en; rdfs:subClassOf ; "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number."@en; "OBI_0000159"@en, "group:OBI"@en; "a report that is published in a journal"@en; "journal article"@en; "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "information carrier"@en; owl:equivalentClass _:2de759; rdfs:subClassOf , _:2de799; "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'."@en; "A quality of an information bearer that imparts the information content"@en; "PERSON: Alan Ruttenberg"@en; "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en; "The pattern in ink on a page of a paperback novel."@en; "information carrier"@en; ; . _:2de759 a owl:Class; owl:intersectionOf _:2de769 . _:2de769 rdf:first ; rdf:rest _:2de789 . _:2de789 rdf:first _:2de779; rdf:rest rdf:nil . _:2de779 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de799 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "model number"@en; rdfs:subClassOf ; "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots."@en; "Person: Alan Ruttenberg"@en; "manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers"@en; "model number"@en; ; . a owl:Class; rdfs:label "programming language"@en; rdfs:subClassOf ; "A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it."@en; "OBI_0000058"@en, "group:OBI"@en; "R, Perl, Java"@en; "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en; "programming language"@en; ; . a owl:Class; rdfs:label "data item"@en; rdfs:subClassOf ; "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en, "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en, "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en; "Data items include counts of things, analyte concentrations, and statistical summaries."@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Chris Stoeckert"@en, "PERSON: Jonathan Rees"@en; "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en; "data"@en; "data item"@en; ; . a owl:Class; rdfs:label "symbol"@en; rdfs:subClassOf ; "20091104, MC: this needs work and will most probably change"@en; "PERSON: Jonathan Rees"@en; "a smallish, word-like datum..."@en; "symbol"@en; . a owl:Class; rdfs:label "numeral"@en; rdfs:subClassOf ; "A symbol that denotes a number."@en; "PERSON: Jonathan Rees"@en; "numeral"@en; . a owl:Class; rdfs:label "information content entity"@en; rdfs:subClassOf ; "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en; "OBI_0000142"@en; "PERSON: Chris Stoeckert"@en; "an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity"@en; "information content entity"@en; ; . a owl:Class; rdfs:label "integer numeral"@en; rdfs:subClassOf ; "PERSON: Jonathan Rees"@en; "a numeral that denotes an integer"@en; "integer numeral"@en; . a owl:Class; rdfs:label "scalar measurement datum"@en; rdfs:subClassOf ; "10 feet. 3 ml."@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en; "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them."@en; "a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en; ; . a owl:Class; rdfs:label "directive information entity"@en; rdfs:subClassOf ; "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en, "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en; "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Bjoern Peters"@en; ; . a owl:Class; rdfs:label "time trigger"@en; rdfs:subClassOf ; "OBI branch derived"@en, "OBI_0000331"@en; "PlanAndPlannedProcess Branch"@en; "revisit?"@en; "time trigger"@en; ; . a owl:Class; rdfs:label "dot plot"@en; rdfs:subClassOf ; "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions."@en; "Dot plot of SSC-H and FSC-H."@en; "OBI_0000123"@en, "group:OBI"@en; "dot plot"@en; "person:Allyson Lister"@en, "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "graph"@en; rdfs:subClassOf ; "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way."@en; "OBI_0000240"@en, "group:OBI"@en; "PERSON: Lawrence Hunter"@en, "person:Alan Ruttenberg"@en, "person:Allyson Lister"@en; "graph"@en; ; . a owl:Class; rdfs:label "rule"@en; rdfs:subClassOf ; "MSI"@en; "OBI_0500021"@en, "PRS"@en; "PRS"@en; "a rule is an executable which guides, defines, restricts actions"@en; "example to be added"@en; "rule"@en; ; . a owl:Class; rdfs:label "contour plot"@en; rdfs:subClassOf ; "Contour plot of SSC-H, FSC-H, and FL1-H."@en; "OBI_0000246"@en, "group:Flow Cytometry community"@en; "contour plot"@en; "generically_dependent_continuants"@en; "person:Allyson Lister"@en, "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "algorithm"@en; rdfs:subClassOf ; "A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en; "OBI_0000270"@en, "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"@en; "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies."@en; "Philippe Rocca-Serra"@en, "PlanAndPlannedProcess Branch"@en; "algorithm"@en; ; . a owl:Class; rdfs:label "software interpreter"@en; rdfs:subClassOf ; "A software interpreter is a software application that executes some specified input software. "@en; "Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter"@en; "OBI_0000199"@en, "group:OBI"@en; "R program, Perl interpreter, Java virtual machine"@en; "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en; "software interpreter"@en; ; . a owl:Class; rdfs:label "curation status specification"@en; owl:equivalentClass _:2de7a9; rdfs:subClassOf ; "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en; "GROUP:OBI:"@en, "OBI_0000266"@en; "PERSON:Bill Bug"@en; "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en; "curation status specification"@en; . _:2de7a9 a owl:Class; owl:oneOf _:2de7b9 . _:2de7b9 rdf:first ; rdf:rest _:2de7c9 . _:2de7c9 rdf:first ; rdf:rest _:2de7d9 . _:2de7d9 rdf:first ; rdf:rest _:2de7e9 . _:2de7e9 rdf:first ; rdf:rest _:2de7f9 . _:2de7f9 rdf:first ; rdf:rest _:2de809 . _:2de809 rdf:first ; rdf:rest _:2de819 . _:2de819 rdf:first ; rdf:rest _:2de829 . _:2de829 rdf:first ; rdf:rest _:2de839 . _:2de839 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "density plot"@en; rdfs:subClassOf ; "A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel."@en; "Density plot of SSC-H and FSC-H."@en; "OBI_0000179"@en, "group:Flow Cytometry community"@en; "density plot"@en; "person:Allyson Lister"@en, "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "report"@en; rdfs:subClassOf ; "2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so."@en, "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en, "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion"@en, "disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification"@en; "Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article."@en; "GROUP: OBI"@en, "OBI_0000099"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en, "PERSON:Chris Stoeckert"@en; "a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)"@en; "report"@en; ; . a owl:Class; rdfs:label "source code module"@en; rdfs:subClassOf ; "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en; "OBI_0000039"@en, "group:OBI"@en; "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script."@en; "person:Alan Ruttenberg"@en, "person:Chris Stoeckert"@en; "source code module"@en; ; . a owl:Class; rdfs:label "data format specification"@en; rdfs:subClassOf ; "OBI branch derived"@en, "OBI_0000187"@en; "PERSON: Alan Ruttenberg"@en, "PlanAndPlannedProcess Branch"@en; "data format specification"@en; ; . a owl:Class; rdfs:label "data set"@en; rdfs:subClassOf ; "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en; "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en; "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en; "OBI_0000042"@en, "group:OBI"@en; "data set"@en; "person:Allyson Lister"@en, "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "image"@en; rdfs:subClassOf ; "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface."@en; "OBI_0000030"@en, "group:OBI"@en; "image"@en; "person:Alan Ruttenberg"@en, "person:Allyson"@en, "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "data about an ontology part"@en; rdfs:subClassOf ; "Person:Alan Ruttenberg"; "data about an ontology part is a data item about a part of an ontology, for example a term"@en . a owl:Class; rdfs:label "plan specification"@en; rdfs:subClassOf ; "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en, "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en; "Alan Ruttenberg"@en; "OBI Plan and Planned Process branch"@en, "OBI_0000344"@en; "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en; "a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications."@en; "plan specification"@en; ; . a owl:Class; rdfs:label "measurement datum"@en; rdfs:subClassOf ; "2/2/2009 is_specified_output of some assay?"@en; "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en; "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en; "OBI_0000305"@en, "group:OBI"@en; "measurement datum"@en; "person:Chris Stoeckert"@en; ; . a owl:Class; rdfs:label "version number"@en; rdfs:subClassOf ; "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name."@en; "GROUP: IAO"@en; "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version"@en; "version number"@en; ; . a owl:Class; rdfs:label "serial number"@en; rdfs:subClassOf ; "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots."@en; "GROUP: IAO"@en; "Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)"@en; "serial number"@en; ; . a owl:Class; rdfs:label "lot number"@en; rdfs:subClassOf ; "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots."@en; "GROUP: IAO"@en; "batch number"@en; "lot number"@en; ; . a owl:Class; rdfs:label "setting datum"@en; rdfs:subClassOf ; "A settings datum is a datum that denotes some configuration of an instrument."@en; "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum."@en; ; . a owl:Class; rdfs:label "conclusion textual entity"@en; rdfs:subClassOf ; "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en, "2009/10/23 Alan Ruttenberg: We need to work on the definition still"@en; "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers."@en; "Person:Alan Ruttenberg"@en; "conclusion textual entity"@en; "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660"@en; ; . a owl:Class; rdfs:label "material information bearer"@en; owl:equivalentClass _:2de849; rdfs:subClassOf , _:2de899; "An information bearer is a material_entity in which a concretization of an information content entity inheres."@en; "GROUP: IAO"@en; "a hard drive, a piece of paper with writing on it, a brain"@en; "material information bearer"@en; ; . _:2de849 a owl:Class; owl:intersectionOf _:2de859 . _:2de859 rdf:first ; rdf:rest _:2de879 . _:2de879 rdf:first _:2de869; rdf:rest rdf:nil . _:2de869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de889 . _:2de889 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2de8a9 . _:2de8a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "histogram"@en; rdfs:subClassOf ; "GROUP:OBI"@en; "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en; "histogram"@en; ; . a owl:Class; rdfs:label "heatmap"@en; rdfs:subClassOf ; "GROUP:OBI"@en; "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en; "heatmap"@en; ; . a owl:Class; rdfs:label "Venn diagram"@en; rdfs:subClassOf ; "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en; "Venn diagram"@en; "WEB: http://en.wikipedia.org/wiki/Venn_diagram"@en; ; . a owl:Class; rdfs:label "dendrogram"@en; rdfs:subClassOf ; "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en; "WEB: http://en.wikipedia.org/wiki/Dendrogram"@en; "dendrogram"@en; ; . a owl:Class; rdfs:label "scatter plot"@en; rdfs:subClassOf ; "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis."@en; "Comparison of gene expression values in two samples can be displayed in a scatter plot"@en; "PERSON:Chris Stoeckert"@en, "PERSON:James Malone"@en, "PERSON:Melanie Courtot"@en; "WEB: http://en.wikipedia.org/wiki/Scatterplot"@en; "scatter plot"@en; "scattergraph"@en; ; . a owl:Class; rdfs:label "photograph"@en; rdfs:subClassOf ; "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc."@en; "PERSON:Alan Ruttenberg"@en, "PERSON:Joanne Luciano"@en, "PERSON:Melanie Courtot"@en; "WEB: http://en.wiktionary.org/wiki/photograph"@en; ; . a owl:Class; rdfs:label "photographic print"@en; rdfs:subClassOf ; "A photographic print is a material entity upon which a photograph generically depends."@en; "PERSON:Alan Ruttenberg"@en, "PERSON:Melanie Courtot"@en; "photographic print"@en; ; . a owl:Class; rdfs:label "obsolescence reason specification"@en; owl:equivalentClass _:2de8b9; rdfs:subClassOf ; "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en; "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en; "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en; "obsolescence reason specification"@en; . _:2de8b9 a owl:Class; owl:oneOf _:2de8c9 . _:2de8c9 rdf:first ; rdf:rest _:2de8d9 . _:2de8d9 rdf:first ; rdf:rest _:2de8e9 . _:2de8e9 rdf:first ; rdf:rest _:2de8f9 . _:2de8f9 rdf:first ; rdf:rest _:2de909 . _:2de909 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "textual entity"@en; rdfs:subClassOf ; "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en; "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc."@en, "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities."@en; "PERSON: Lawrence Hunter"@en; "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en; "text"@en; "textual entity"@en; . a owl:Class; rdfs:label "citation"@en; rdfs:subClassOf ; "PERSON: Lawrence Hunter"@en; "Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183."@en; "a textual entity intended to identify a particular publication"@en; "citation"@en; ; . a owl:Class; rdfs:label "author identification"@en; rdfs:subClassOf ; "A textual entity intended to identify a particular author"@en; "L. Hunter"@en; "PERSON: Lawrence Hunter"@en; "author identification"@en; ; . a owl:Class; rdfs:label "institutional identification"@en; rdfs:subClassOf ; "A textual entity intended to identify a particular institution"@en; "PERSON: Lawrence Hunter"@en; "University of Colorado Denver School of Medicine"@en; "institutional identification"@en; ; . a owl:Class; rdfs:label "caption"@en; rdfs:subClassOf ; "A textual entity that describes a figure"@en; "Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool."@en; "PERSON: Lawrence Hunter"@en; "caption"@en; ; . a owl:Class; rdfs:label "document title"@en; rdfs:subClassOf ; "A textual entity that names a document"@en; "PERSON: Lawrence Hunter"@en; "Textual characteristics of traditional and Open Access scientific journals are similar"@en; "document title"@en; ; . a owl:Class; rdfs:label "table"@en; rdfs:subClassOf ; "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions"@en; "PERSON: Lawrence Hunter"@en; "table"@en; ; . a owl:Class; rdfs:label "table of abbreviations"@en; rdfs:subClassOf ; "A table where the constituent texts are abbreviations and their expansions"@en; "PERSON: Lawrence Hunter"@en; "table of abbreviations"@en; ; . a owl:Class; rdfs:label "figure"@en; rdfs:subClassOf ; "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en; "Any picture, diagram or table"@en; "PERSON: Lawrence Hunter"@en; "figure"@en; ; . a owl:Class; rdfs:label "diagram"@en; rdfs:subClassOf ; "A figure that expresses one or more propositions"@en; "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space."@en; "PERSON: Lawrence Hunter"@en; "diagram"@en; ; . a owl:Class; rdfs:label "document"@en; rdfs:subClassOf ; "A collection of information content entities intended to be understood together as a whole"@en; "A journal article, patent application, laboratory notebook, or a book"@en; "PERSON: Lawrence Hunter"@en; "document"@en; ; . a owl:Class; rdfs:label "publication"@en; rdfs:subClassOf ; "A document that has been accepted by a publisher"@en; "A journal article or book"@en; "PERSON: Lawrence Hunter"@en; "publication"@en; ; . a owl:Class; rdfs:label "publication about an investigation"@en; rdfs:subClassOf ; "A publication that is about an investigation"@en; "Most scientific journal articles"@en; "PERSON: Lawrence Hunter"@en; "publication about an investigation"@en; "scientific publication"@en; ; . a owl:Class; rdfs:label "patent"@en; rdfs:subClassOf ; "A document that has been accepted by a patent authority"@en; "PERSON: Lawrence Hunter"@en; "US Patent 6,449,603"@en; "patent"@en; ; . a owl:Class; rdfs:label "document part"@en; rdfs:subClassOf ; "An abstract, introduction, method or results section."@en; "PERSON: Lawrence Hunter"@en; "an information content entity that is part of a document"@en; "document part"@en; ; . a owl:Class; rdfs:label "abstract"@en; rdfs:subClassOf ; "A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes."@en; "PERSON: Lawrence Hunter"@en; "The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data."@en; "abstract"@en; ; . a owl:Class; rdfs:label "introduction to a publication about an investigation"@en; rdfs:subClassOf ; "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)"@en; "PERSON: Lawrence Hunter"@en; "Section labelled 'introduction' of a typical scientific journal article"@en; "introduction"@en; "introduction to a publication about an investigation"@en; ; . a owl:Class; rdfs:label "methods section"@en; rdfs:subClassOf ; "A part of a publication about an investigation that is about the study design of the investigation"@en; "PERSON: Lawrence Hunter"@en; "The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article."@en; "methods section"@en; ; . a owl:Class; rdfs:label "results section"@en; rdfs:subClassOf ; "A part of a publication about an investigation that is about a study design execution"@en; "PERSON: Lawrence Hunter"@en; "The section labelled 'results' in a typical scientific journal article"@en; "results section"@en; ; . a owl:Class; rdfs:label "discussion section of a publication about an investigation"@en; rdfs:subClassOf ; "A part of a publication about an investigation that is about the study interpretation of the investigation"@en; "PERSON: Lawrence Hunter"@en; "discussion section"@en; "discussion section of a publication about an investigation"@en; ; . a owl:Class; rdfs:label "references section"@en; rdfs:subClassOf ; "A part of a document that has citations as parts"@en; "PERSON: Lawrence Hunter"@en; "The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called \"literature cited\" or \"bibliography\""@en; "references section"@en; ; . a owl:Class; rdfs:label "author list"@en; rdfs:subClassOf ; "Lawrence Hunter and Kevin Brettonel Cohen"@en; "PERSON: Lawrence Hunter"@en; "author list"@en; "part of a document that enumerates the authors of the document"@en; ; . a owl:Class; rdfs:label "institution list"@en; rdfs:subClassOf ; "PERSON: Lawrence Hunter"@en; "The University of Colorado Denver School of Medicine and the University of Colorado Boulder."@en; "institution list"@en; "part of a document that has parts that are institution identifications associated with the authors of the document"@en; ; . a owl:Class; rdfs:label "author contributions section"@en; rdfs:subClassOf ; "A part of a publication that is about the specific contributions of each author"@en; "LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript."@en; "PERSON: Lawrence Hunter"@en; "author contributions section"@en; ; . a owl:Class; rdfs:label "acknowledgements section"@en; rdfs:subClassOf ; "PERSON: Lawrence Hunter"@en; "Part of a publication that is about the contributions of people or institutions other than the authors."@en; "The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript"@en; "acknowledgements section"@en; ; . a owl:Class; rdfs:label "footnote"@en; rdfs:subClassOf ; "A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document."@en; "PERSON: Lawrence Hunter"@en; "The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text."@en; "endnote"@en; "footnote"@en; ; . a owl:Class; rdfs:label "supplementary material to a document"@en; rdfs:subClassOf ; "PERSON: Lawrence Hunter"@en; "appendix"@en, "supplementary material"@en; "part of a document that is segregated from the rest of the document due to its size"@en; "supplementary material to a document"@en; ; . a owl:Class; rdfs:label "table of contents"@en; rdfs:subClassOf ; "A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred)."@en; "PERSON: Lawrence Hunter"@en; "table of contents"@en; ; . a owl:Class; rdfs:label "table of figures"@en; rdfs:subClassOf ; "A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred)."@en; "PERSON: Lawrence Hunter"@en; "table of figures"@en; ; . a owl:Class; rdfs:label "running title"@en; rdfs:subClassOf ; "A shorter version of a document title"@en; "PERSON: Lawrence Hunter"@en; "running title"@en; ; . a owl:Class; rdfs:label "copyright section"@en; rdfs:subClassOf ; "A document part that describes legal restrictions on making or distributing copies of the document"@en; "PERSON: Lawrence Hunter"@en; "This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License."@en; "copyright section"@en; ; . a owl:Class; rdfs:label "cartesian spatial coordinate datum"@en; rdfs:subClassOf ; "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en; "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude"@en; "Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "one dimensional cartesian spatial coordinate datum"@en; rdfs:subClassOf ; rdfs:comment "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region"@en; "Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "two dimensional cartesian spatial coordinate datum"@en; rdfs:subClassOf ; rdfs:comment "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region"@en; "Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "three dimensional cartesian spatial coordinate datum"@en; rdfs:subClassOf ; rdfs:comment "A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region"@en; "Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "length measurement datum"@en; rdfs:subClassOf ; "A scalar measurement datum that is the result of measurement of length quality"@en; "Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "denotator type"; owl:equivalentClass _:2de919; rdfs:subClassOf ; "A denotator type indicates how a term should be interpreted from an ontological perspective."; "Alan Ruttenberg"; "Barry Smith, Werner Ceusters"; "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." . _:2de919 a owl:Class; owl:oneOf _:2de929 . _:2de929 rdf:first ; rdf:rest _:2de939 . _:2de939 rdf:first ; rdf:rest _:2de949 . _:2de949 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "mass measurement datum"@en; rdfs:subClassOf ; "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en; "A scalar measurement datum that is the result of measurement of mass quality"@en; "Person:Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "hypothesis textual entity"@en; rdfs:subClassOf ; "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en; "A textual entity that expresses an assertion that is intended to be tested."@en; "Person:Alan Ruttenberg"@en; "hypothesis textual entity"@en; "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660"@en; ; . a owl:Class; rdfs:label "time measurement datum"@en; rdfs:subClassOf ; "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en; "A scalar measurement datum that is the result of measuring a temporal interval"@en; "Person:Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "postal address"@en; rdfs:subClassOf ; "A textual entity that is used as directive to deliver something to a person, or organization"; "2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59"; . a owl:Class; rdfs:label "author role"@en; rdfs:subClassOf ; "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name."@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en; "author role"@en; ; . a owl:Class; rdfs:label "data item extraction from journal article"; rdfs:subClassOf ; "a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing"; "Person:Alan Ruttenberg"; ; . a owl:Class; rdfs:label "documenting"@en; rdfs:subClassOf , _:2de959, _:2de969; "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape"@en; "Bjoern Peters"@en; "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database."@en; "a planned process in which a document is created or added to by including the specified input in it."@en; "wikipedia http://en.wikipedia.org/wiki/Documenting"@en; ; . _:2de959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "line graph"@en; rdfs:subClassOf ; "GROUP:OBI"@en, "WEB: http://en.wikipedia.org/wiki/Line_chart"@en; "PERSON:Chris Stoeckert"@en, "PERSON:Melanie Courtot"@en; "line chart"@en; "line graph"@en; ; . a owl:Class; rdfs:label "assigning a centrally registered identifier"@en; rdfs:subClassOf ; "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned."@en; "Person:Alan Ruttenberg"@en, "Person:Bjoern Peters"@en, "Person:Melanie Courtot"@en; "a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity"@en; ; . a owl:Class; rdfs:label "associating information with a CRID in the CRID registry"@en; rdfs:subClassOf ; "A planned process in which a CRID registry associates an information content entity with a CRID symbol"@en; "PERSON:Alan Ruttenberg"@en; ; . a owl:Class; rdfs:label "CRID symbol"@en; rdfs:subClassOf ; "A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry."@en; "IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded."@en; "Original proposal from Bjoern, discussions at IAO calls"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en; "PMID:12345, 12345 in a database column which has header \"pubmedID\""@en; . a owl:Class; rdfs:label "CRID"@en; rdfs:subClassOf ; "An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs. "@en; "Centrally Registered IDentifier"; "Entries in a Column of which the header is \"Pubmed ID\" "@en, "PMID:12345"@en, "The following URL: \"http://www.ncbi.nlm.nih.gov/pubmed/19918065\""@en, "The following sentence contains a CRID: \"The article with Pubmed ID: 19918065\". "@en; "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered."@en; "Original proposal from Bjoern, discussions at IAO calls"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en; . a owl:Class; rdfs:label "CRID registry"@en; rdfs:subClassOf ; "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process."@en; "IAO call, 20101124: PubMed registry is an instance of CRID registry"@en; "Original proposal from Bjoern, discussions at IAO calls"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en; ; . a owl:Class; rdfs:label "looking up a CRID"@en; rdfs:subClassOf ; "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol"@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Bill Hogan"@en, "PERSON: Bjoern Peters"@en, "PERSON: Melanie Courtot"@en; ; . a owl:Class; rdfs:label "time stamped measurement datum"@en; rdfs:subClassOf ; ; . a owl:Class; rdfs:label "time sampled measurement data set"@en; rdfs:subClassOf ; "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time."@en; "Alan Ruttenberg"@en; "experimental time series"@en; "pmid:20604925 - time-lapse live cell microscopy"@en; ; . a owl:Class; rdfs:label "N-glycosylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a residue hydrogen atom on a nitrogen with a carbohydrate-like group through a glycosidic bond."; "NGlycoRes"; , . a owl:Class; rdfs:label "N-formyl-L-methionine residue"; rdfs:subClassOf ; "(2S)-2-formylamino-4-(methylsulfanyl)butanoic acid", "2-formamido-4-(methylsulfanyl)butanoic acid", "2-formylamino-4-(methylthio)butanoic acid", "2-formylazanyl-4-(methylsulfanyl)butanoic acid", "MOD_RES N-formylmethionine", "N-formyl-L-methionine", "N-formylated L-methionine", "fMet", "nformylmet"; "A protein modification that effectively converts a source amino acid residue to an N-formyl-L-methionine, a natural pretranslational modification."; , . a owl:Class; rdfs:label "L-selenocysteine residue"; rdfs:subClassOf ; "(2R)-2-amino-3-selanylpropanoic acid", "2-azanyl-3-selanylpropanoic acid", "3-selenylalanine", "L-selenocysteine", "NON_STD Selenocysteine", "SeCys", "Sec", "selenium cysteine"; "A protein modification that effectively converts a source amino acid residue to an L-selenocysteine, a natural pretranslational modification."; , . a owl:Class; rdfs:label "crosslinked residues"; rdfs:subClassOf ; "A protein modification that crosslinks two or more amino acid residues with covalent bonds."; rdfs:comment "The covalent bond is formed directly between sidechain atoms. If non-aminoacid atoms are involved in connecting two or more peptide chain residues peptide chain, the connection is classified as a multivalent binding site."; "XLNK-Res-Res"; , . a owl:Class; rdfs:label "L-cystine (cross-link)"; rdfs:subClassOf ; "(2R,2'R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)", "3,3'-disulfane-1,2-diylbis(2-azanylpropanoic acid)", "3,3'-dithiobis(2-aminopropanoic acid)", "3,3'-dithiobisalanine", "3,3'-dithiodialanine", "Cys2", "Cystine ((Cys)2)", "DISULFID", "DISULFID Interchain", "L-cystine", "XLNK-SCys-SCys", "beta,beta'-diamino-beta,beta'-dicarboxydiethyldisulfide", "beta,beta'-dithiodialanine", "bis(alpha-aminopropionic acid)-beta-disulfide", "bis(beta-amino-beta-carboxyethyl)disulfide", "dicysteine"; "A protein modification that effectively cross-links two L-cysteine residues to form L-cystine."; rdfs:comment "Cross-link 2; for formation of a disulfide bond between a peptide cysteine and a free cysteine, see MOD:00765."; , . a owl:Class; rdfs:label "L-aspartic 4-phosphoric anhydride"; rdfs:subClassOf ; "(2S)-2-amino-4-oxo-4-(phosphonooxy)butanoic acid", "2-aminobutanedioic 4-phosphoric anhydride", "2-azanyl-4-oxo-4-(phosphonooxy)butanoic acid", "4-oxo-O-phosphono-L-homoserine", "4-phosphoaspartic acid", "4-phosphorylated L-aspartatic acid", "ACT_SITE 4-aspartylphosphate intermediate", "L-aspartic 4-phosphoric anhydride", "MOD_RES 4-aspartylphosphate", "PAsp", "beta-aspartyl phosphate"; "A protein modification that effectively converts an L-aspartic acid residue to L-aspartic 4-phosphoric anhydride."; , . a owl:Class; rdfs:label "3'-phospho-L-histidine"; rdfs:subClassOf ; "(2S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid", "2-azanyl-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid", "3'-phospho-L-histidine", "ACT_SITE Pros-phosphohistidine intermediate", "MOD_RES Pros-phosphohistidine", "N(pi)-phosphohistidine", "N3-phosphonohistidine", "ND1-phosphonohistidine", "NpPHis", "Npi-phosphorylated L-histidine", "histidine-N(delta)-phosphate", "histidine-N3'-phosphate", "pros-phosphohistidine"; "A protein modification that effectively converts an L-histidine residue to pros-phospho-L-histidine (N-pi-phospho-L-histidine, 3'-phospho-L-histidine)."; , . a owl:Class; rdfs:label "O-phospho-L-serine"; rdfs:subClassOf ; "(2S)-2-amino-3-(phosphonooxy)propanoic acid", "2-amino-3-hydroxypropanoic acid 3-phosphate", "2-azanyl-3-(phosphonooxy)propanoic acid", "ACT_SITE Phosphoserine intermediate", "MOD_RES Phosphoserine", "O-phospho-L-serine", "O-phosphonoserine", "O-phosphorylated L-serine", "O3-phosphoserine", "OPSer", "Phospho Seryl", "phosphorylations", "serine phosphate ester"; "A protein modification that effectively converts an L-serine residue to O-phospho-L-serine."; , . a owl:Class; rdfs:label "O-phospho-L-threonine"; rdfs:subClassOf ; "(2S,3R)-2-amino-3-(phosphonooxy)butanoic acid", "2-amino-3-hydroxybutanoic acid 3-phosphate", "2-azanyl-3-(phosphonooxy)butanoic acid", "MOD_RES Phosphothreonine", "O-phospho-L-threonine", "O-phosphorylated L-threonine", "O3-phosphothreonine", "OPThr", "Phospho Threonyl", "phosphorylationt", "threonine phosphate ester"; "A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine."; , . a owl:Class; rdfs:label "O4'-phospho-L-tyrosine"; rdfs:subClassOf ; "(2S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid", "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate", "2-azanyl-3-(4-phosphonooxyphenyl)propanoic acid", "MOD_RES Phosphotyrosine", "O4'-phospho-L-tyrosine", "O4'-phosphorylated L-tyrosine", "O4-phosphotyrosine", "OPTyr", "Phospho Tyrosinyl", "phosphorylationy", "tyrosine phosphate"; "A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine."; , . a owl:Class; rdfs:label "N-acetyl-L-alanine"; rdfs:subClassOf ; "(2S)-2-(acetamido)propanoic acid", "2-(acetylamino)propanoic acid", "2-(acetylazanyl)propanoic acid", "AcAla", "MOD_RES N-acetylalanine", "N-acetyl-L-alanine", "N-acetylated L-alanine", "acetylalanine"; "A protein modification that effectively converts an L-alanine residue to N-acetyl-L-alanine."; , . a owl:Class; rdfs:label "N6-acetyl-L-lysine"; rdfs:subClassOf ; "(2S)-6-acetamido-2-aminohexanoic acid", "6-acetylamino-2-aminohexanoic acid", "6-acetylazanyl-2-aminohexanoic acid", "MOD_RES N6-acetyllysine", "N(zeta)-acetyllysine", "N6-acetyl-L-lysine", "N6-acetylated L-lysine", "N6AcLys", "acetylk", "epsilon-acetyllysine"; "A protein modification that effectively converts an L-lysine residue to N6-acetyl-L-lysine."; , . a owl:Class; rdfs:label "omega-N-methyl-L-arginine"; rdfs:subClassOf ; "(2S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid", "MOD_RES Omega-N-methylarginine", "MOD_RES Omega-N-methylated arginine", "NG-methylarginine", "NoMeArg", "omega-N-methyl-L-arginine", "omega-N-methylated L-arginine"; "A protein modification that effectively converts an L-arginine residue to N(omega)-methyl-L-arginine."; , . a owl:Class; rdfs:label "N6,N6,N6-trimethyl-L-lysine"; rdfs:subClassOf ; "(5S)-5-amino-5-carboxy-N,N,N-trimethylpentan-1-aminium", "2-amino-6-(trimethylammonio)hexanoic acid", "5-azanyl-5-carboxy-N,N,N-trimethylpentanazanium", "MOD_RES N6,N6,N6-trimethyllysine", "N(zeta)-trimethyllysine", "N-trimethylation (of lysine)", "N6,N6,N6-trimethyl-L-lysine", "N6,N6,N6-trimethylated L-lysine", "N6,N6,N6-trimethyllysin-N6-ium", "N6,N6,N6-trimethyllysine cation", "N6Me3+Lys", "epsilon-trimethyllysine"; "A protein modification that effectively converts an L-lysine residue to N6,N6,N6-trimethyl-L-lysine."; rdfs:comment "DeltaMass calculates the mass difference from protonated lysine rather than neutral lysine"; , . a owl:Class; rdfs:label "N6-myristoyl-L-lysine"; rdfs:subClassOf ; "(2S)-2-amino-6-(tetradecanoylamino)hexanoic acid", "2-amino-6-(tetradecanamido)hexanoic acid", "LIPID N6-myristoyl lysine", "N(zeta)-myristoyllysine", "N6-(1-oxotetradecyl)-L-lysine", "N6-(C14:0 aliphatic acyl)lysine", "N6-myristoyl-L-lysine", "N6-myristoylated L-lysine", "N6MyrLys", "epsilon-myristoyllysine", "myristoylationk"; "A protein modification that effectively converts an L-lysine residue to N6-myristoyl-L-lysine."; , . a owl:Class; rdfs:label "S-geranylgeranyl-L-cysteine"; rdfs:subClassOf ; "(2R)-2-amino-3-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanylpropanoic acid", "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid", "LIPID S-geranylgeranyl cysteine", "S-geranylgeranyl", "S-geranylgeranyl-L-cysteine", "SGergerCys", "geranylgeranylc"; "A protein modification that effectively converts an L-cysteine residue to S-geranylgeranyl-L-cysteine."; rdfs:comment "DeltaMass calculates the mass with two double bonds rather than four"; , . a owl:Class; rdfs:label "N6-lipoyl-L-lysine"; rdfs:subClassOf ; "(2S)-2-amino-6-(5-[(3R)-1,2-dithiolan-3-yl]pentanamido)hexanoic acid", "(2S)-2-amino-6-[(5-[(3R)-1,2-dithiolan-3-yl]pentanoyl)amino]hexanoic acid", "(2S,6'R)-2-amino-6-(6,8-dithiooctanamido)hexanoic acid", "2-amino-6-(5-[1,2-dithiolan-3-yl]-1-oxopentyl)aminohexanoic acid", "MOD_RES N6-lipoyllysine", "N-Lipoyl- (on Lysine)", "N6-6,8-dithiooctanoyllysine", "N6-lipoyl-L-lysine", "N6-lipoyllysine", "N6LipLys", "lipoylk"; "A protein modification that effectively converts an L-lysine residue to N6-lipoyl-L-lysine."; , . a owl:Class; rdfs:label "N6-pyridoxal phosphate-L-lysine"; rdfs:subClassOf ; "(2S)-2-amino-6-[([3-hydroxy-2-methyl-5-phosphonooxymethylpyridin-4-yl]methylidene)amino]hexanoic acid", "MOD_RES N6-(pyridoxal phosphate)lysine", "N6-pyridoxal phosphate-L-lysine", "N6PydoxLys", "Pyridoxal phosphate (Schiff Base formed to lysine)"; "A protein modification that effectively converts an L-lysine residue to N6-pyridoxal phosphate-L-lysine."; rdfs:comment "From DeltaMass: Average Mass: 231"; , . a owl:Class; rdfs:label "N4-glycosyl-L-asparagine"; rdfs:subClassOf ; "A protein modification that effectively converts an L-asparagine residue to an N4-glycosyl-L-asparagine."; "N4GlycoAsn"; , . a owl:Class; rdfs:label "chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine"; rdfs:subClassOf ; "A protein modification that effectively cross-links an L-serine residue to the polymer chondroitin sulfate by a D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl tetrasaccharide."; "chondroitin 4-sulfate (chondroitin sulfate A)", "chondroitin 6-sulfate (chondroitin sulfate C)", "chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine", "poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-6-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine"; , . a owl:Class; rdfs:label "heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine"; rdfs:subClassOf ; "A protein modification that effectively cross-links an L-serine residue to the polymer heparan sulfate by a D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl tetrasaccharide."; "heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine", "heparin", "heparitin sulfate", "poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine"; , . a owl:Class; rdfs:label "2'-alpha-mannosyl-L-tryptophan"; rdfs:subClassOf ; "(2S)-2-amino-3-(2-beta-D-mannopyranosyl-1H-indol-3-yl)propanoic acid", "2'-mannosyl-L-tryptophan", "2'-tryptophan C-mannoside", "C2'ManTrp", "CARBOHYD C-linked (Man)"; "A protein modification that effectively converts an L-tryptophan residue to 2'-alpha-mannosyl-L-tryptophan."; , . a owl:Class; rdfs:label "L-beta-methylthioaspartic acid"; rdfs:subClassOf ; "(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid", "3-(methylthio)-L-aspartic acid", "3-carboxy-S-methyl-cysteine", "3-methylthio-aspartic acid", "3MeSAsp", "MOD_RES 3-methylthioaspartic acid", "beta-Methylthio-aspartic acid", "beta-methylthio-aspartic acid", "bmethylthiold", "methythiold"; "A protein modification that effectively converts an L-aspartic acid residue to L-beta-methylthioaspartic acid."; , . a owl:Class; rdfs:label "acetylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with an acetyl group."; "AcRes", "Acetylation (N terminus, N epsilon of Lysine, O of Serine) (Ac)"; rdfs:comment "Amino hydrogens are replaced to produce amides; hydroxyl hydrogens are replaced to produce esters; and hydrosulfanyl (thiol) hydrogens are replaced to produce sulfanyl esters (thiol esters). From DeltaMass: Average Mass: 42"; , . a owl:Class; rdfs:label "O-glycosylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a residue hydrogen atom on an oxygen with a carbohydrate-like group through a glycosidic bond."; "OGlycoRes"; , . a owl:Class; rdfs:label "methylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with a methyl group."; rdfs:comment "From DeltaMass: Average Mass: 14 Average Mass Change:14 References:Methylation of Asparagine (found in phycobiliproteins) Klotz and Glazer (1987) J. Biol. Chem. 262; 17350-17355"; "MeRes", "Methylation (N terminus, N epsilon of Lysine, O of Serine, Threonine or C terminus, N of Asparagine)"; , . a owl:Class; rdfs:label "myristoylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with a myristoyl group."; "C14:0 aliphatic acylated residue", "MyrRes", "Myristoylation"; rdfs:comment "From DeltaMass: Average Mass: 210"; , . a owl:Class; rdfs:label "N-acetylaminoglucosylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with an N-acetylaminoglucose group through a glycosidic bond."; "GlcNAcRes"; , . a owl:Class; rdfs:label "glycosylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with an carbohydrate-like group through a glycosidic bond."; "GlycoRes"; , . a owl:Class; rdfs:label "phosphorylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with a phosphono group (H2PO3 or 'phosphate')."; rdfs:comment "From DeltaMass: Average Mass: 80."; "PhosRes", "Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine)"; , . a owl:Class; rdfs:label "isoprenylated residue"; rdfs:subClassOf ; "A protein modification that effectively replaces a hydrogen atom with a group derived from an isoprene polymer, such as a geranyl (C10), farnesyl (C15) or geranylgeranyl (C20) group."; "IpRes"; , . a owl:Class; rdfs:label "N-acetylated L-lysine"; rdfs:subClassOf ; "A protein modification that effectively converts an L-lysine residue to either N2-acetyl-L-lysine, or N6-acetyl-L-lysine."; "NAcLys"; , . a owl:Class; rdfs:label "dimethylated L-arginine"; rdfs:subClassOf ; "A protein modification that effectively replaces two hydrogen atoms of an L-arginine residue with two methyl groups."; "NNMe2Arg", "dimethylr"; , . a owl:Class; rdfs:label "O-(N-acetylamino)glucosyl-L-threonine"; rdfs:subClassOf ; "(2S,3R)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)butanoic acid", "CARBOHYD O-linked (GlcNAc)", "CARBOHYD O-linked (HexNAc)", "O-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-threonine", "O-(N-acetylamino)glucosyl-L-threonine", "O-(N-acetylglucosaminyl)-L-threonine", "O-glycosylthreonine", "O-threonyl-beta-N-acetylglucosaminide", "O3-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-threonine", "O3-(N-acetylglucosaminyl)threonine", "OGlcNAcThr"; "A protein modification that effectively converts an L-threonine residue to O3-(N-acetylaminoglucosyl)-L-threonine."; , . a owl:Class; rdfs:label "O-fucosyl-L-serine"; rdfs:subClassOf ; "(2S)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)propanoic acid", "CARBOHYD O-linked (Fuc)", "CARBOHYD O-linked (dHex)", "O-fucosyl-L-serine", "O-glycosylserine", "O3-fucosylserine", "OFucSer"; "A protein modification that effectively converts an L-serine residue to an O-fucosylserine."; , . a owl:Class; rdfs:label "O-fucosyl-L-threonine"; rdfs:subClassOf ; "(2S,3R)-2-amino-3-(6-deoxy-alpha-D-galactopyranosyloxy)butanoic acid", "CARBOHYD O-linked (Fuc)", "CARBOHYD O-linked (dHex)", "O-fucosyl-L-threonine", "O-glycosylthreonine", "O3-fucosylthreonine", "OFucThr"; "A protein modification that effectively converts an threonine residue to an O-fucosylthreonine."; , . a owl:Class; rdfs:label "O-xylosyl-L-serine"; rdfs:subClassOf ; "(2S)-2-amino-3-(alpha-D-xylopyranosyloxy)propanoic acid", "O-(beta-D-xylopyranosyl)-L-serine", "O-glycosylserine", "O-xylosyl-L-serine", "O3-xylosylserine", "OXylSer"; "A protein modification that effectively converts an L-serine residue to O3-xylosylserine."; rdfs:comment "One glycosylated serine with weak electron density was modeled as O3-alpha-xylosylserine, while O3-alpha-mannosyl serine and threonine were modeled at ten other positions. The authors do not discuss this exception or provide chemical evidence for it. Since an O3-xylosyl serine modification has not been reported in any other fungal proteins, the modification is probably also an O3-alpha-mannosyl serine, see MOD:00810 [JSG]."; , . a owl:Class; rdfs:label "glycosylphosphatidylinositolated residue"; rdfs:subClassOf ; "A protein modification that effectively converts a residue to a glycosylphosphatidylinositolethanolamidated."; "GPIRes"; , . a owl:Class; rdfs:label "S-(L-leucyl)-L-cysteine"; rdfs:subClassOf ; "(2R)-2-amino-3-([(2S)-2-amino-4-methylpentanoyl]sulfanyl)propanoic acid", "CROSSLNK Leucyl cysteine thioester (Cys-Leu)", "S-(2-amino-4-methylpentanoyl)cysteine", "S-(L-leucyl)-L-cysteine", "XLNK1LeuSCys", "leucine cysteine thioester"; "A protein modification that effectively crosslinks an L-leucine residue and an L-cysteine residue by a thioester bond to form S-(L-leucyl)-L-cysteine."; rdfs:comment "Cross-link 2."; , . a owl:Class; rdfs:label "2-pyrrolidone-5-carboxylic acid"; rdfs:subClassOf ; "A protein modification that effectively converts a source amino acid residue to 2-pyrrolidone-5-carboxylic acid."; rdfs:comment "From DeltaMass: Average Mass: -18 Average Mass Change: -18.01 References:The conversion of glutamic acid to pyroglutamic was reported for the beta-amiloid protein. Miller et al. Arch. Biochem. Biophy. (1993) 301, 41-52."; "PyrGlu"; , . a owl:Class; rdfs:label "ubiquitinylated lysine"; rdfs:subClassOf ; "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a ubiquitin."; , . a owl:Class; rdfs:label "sumoylated lysine"; rdfs:subClassOf ; "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a sumo (Small Ubiquitin-related MOdifier) protein."; , . a owl:Class; rdfs:label "neddylated lysine"; rdfs:subClassOf ; "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a nedd8 protein."; , . a owl:Class; rdfs:label "L-pyrrolysine residue"; rdfs:subClassOf ; "(2S)-2-amino-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]aminohexanoic acid", "2-azanyl-6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]azanylhexanoic acid", "L-pyrrolysine", "N6-(4-methyl-1,2-didehydropyrrolidine-5-carboxyl)-L-lysine", "N6-(4-methyl-delta-1-pyrroline-5-carboxyl)-L-lysine", "N6-([(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl)-L-lysine", "NON_STD Pyrrolysine", "Pyl", "monomethylamine methyltransferase cofactor lysine adduct"; "A protein modification that inserts or replaces a residue with an L-pyrrolysine residue, a natural pretranslational modification."; , . a owl:Class; rdfs:label "ubiquitination signature tetrapeptidyl lysine"; rdfs:subClassOf ; "A protein modification that crosslinks the N6-amino of a peptidyl lysine with the carboxyl of leucyl-arginyl-glycyl-glycine, the C-terminal tetrapeptide of ubiquitin."; , . a owl:Class; rdfs:label "neoplasm"; rdfs:subClassOf ; "A tumor resulting from abnormal and uncontrolled autonomous new cell growth (proliferation)that may be benign or malignant."; "tumor"; "OBO Foundry (this is a MPATH class, but given the problems with this ontology it should be considered a placeholder for a neoplasm class from a more OBO-compliant pathology or disease ontology that represents pathological material entities)"; . a owl:Class; rdfs:label "adenocarcinoma"; rdfs:subClassOf ; "Malignant neoplasm of epithelial cells in glandular or glandlike pattern. (M-8140/3)."; "adenocarcinoma tumor"; "OBO Foundry (this is a MPATH class, but given the problems with this ontology it should be considered a placeholder for a class from a more OBO-compliant pathology or disease ontology that represents pathological material entities)"; rdfs:comment "changed label from adenocarcinima to distinguish from DOID:adenocarcinoma disease"; . a owl:Class; rdfs:label "carcinoma"; rdfs:subClassOf ; "Any of various types of malignant neoplasm derived from epithelial cells, chiefly glandular (adenocarcinoma) or squamous (squamous cell carcinoma)."; "carcinoma tumor"; "OBO Foundry (this is a MPATH class, but given the problems with this ontology it should be considered a placeholder for a class from a more OBO-compliant pathology or disease ontology that represents pathological material entities)"; rdfs:comment "changed label from adenocarcinima to distinguish from DOID:adenocarcinoma disease"; . a owl:Class; rdfs:label "Dipodomys"; rdfs:subClassOf ; "kangaroo rats"; . a owl:Class; rdfs:label "Cricetulus griseus"; rdfs:subClassOf ; "Chinese hamster", "Chinese hamsters", "Cricetulus aureus"; . a owl:Class; rdfs:label "Mesocricetus auratus"; rdfs:subClassOf ; "Syrian golden hamster", "Syrian golden hamsters", "Syrian hamster", "golden hamster"; . a owl:Class; rdfs:label "Gerbillinae"; rdfs:subClassOf ; "gerbils"; . a owl:Class; rdfs:label "Mus"; rdfs:subClassOf ; "mice"; . a owl:Class; rdfs:label "Mus musculus"; rdfs:subClassOf ; "house mouse", "mouse"; . a owl:Class; rdfs:label "Rattus"; rdfs:subClassOf ; "rat", "rats"; . a owl:Class; rdfs:label "Rattus norvegicus"; rdfs:subClassOf ; "Norway rat", "Rattus sp. strain Wistar", "brown rat", "rat", "rats"; . a owl:Class; rdfs:label "Cavia porcellus"; rdfs:subClassOf ; "Domestic guinea pig", "guinea pig"; . a owl:Class; rdfs:label "Viruses"; rdfs:subClassOf , _:2de979; "virion"; "virus"; . _:2de979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Poxviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Vaccinia virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Variola virus"; rdfs:subClassOf ; "small pox virus", "smallpox", "smallpox virus"; . a owl:Class; rdfs:label "Herpesviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Human herpesvirus 2"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Suid herpesvirus 1"; rdfs:subClassOf ; "Pseudorabies virus"; . a owl:Class; rdfs:label "Hepadnaviridae"; rdfs:subClassOf ; "hepatitis B-type viruses"; . a owl:Class; rdfs:label "Hepatitis B virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Baculoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Adenoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Polyomavirus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Simian virus 40"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Cauliflower mosaic virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Reoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Flaviviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Flavivirus"; rdfs:subClassOf ; "arboviruses group B"; . a owl:Class; rdfs:label "Coronaviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Paramyxoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Cyanobacteria"; rdfs:subClassOf ; "blue-green algae", "blue-green bacteria", "cyanophytes"; . a owl:Class; rdfs:label "Measles virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Rhabdoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Rabies virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Orthomyxoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Influenza A virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Retroviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Lentivirus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Hyperotreti"; rdfs:subClassOf ; "fish", "fishes"; . a owl:Class; rdfs:label "Murine leukemia virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Avian myeloblastosis virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Rous sarcoma virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Picornaviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Hepatitis A virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Tobacco mosaic virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "unclassified phages"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Dengue virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Human immunodeficiency virus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Staphylococcus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Staphylococcus aureus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Staphylococcus epidermidis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Deinococcus radiodurans"; rdfs:subClassOf ; "Deinococcus radiidurans"; . a owl:Class; rdfs:label "Streptococcaceae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Streptococcus sanguinis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Streptococcus pneumoniae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Streptococcus pyogenes"; rdfs:subClassOf ; . a owl:Class; rdfs:label "cellular organisms"; owl:equivalentClass _:2de989; rdfs:subClassOf , _:2de9c9; "ERO : what is difference between ERO:non viral organism and NCBITaxon cellular organism? Should they import from NCBI?"; "cellular organism"; "non-viral organism"; "NCBI: cellular organism"; . _:2de989 a owl:Class; owl:intersectionOf _:2de999 . _:2de999 rdf:first ; rdf:rest _:2de9b9 . _:2de9b9 rdf:first _:2de9a9; rdf:rest rdf:nil . _:2de9a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2de9c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Streptococcus equi"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Burkholderia mallei"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Bacillus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Bacillus anthracis"; rdfs:subClassOf ; "anthrax", "anthrax bacterium"; . a owl:Class; rdfs:label "Papillomaviridae"; rdfs:subClassOf ; "Papillomavirus"; . a owl:Class; rdfs:label "Polyomaviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Emericella nidulans"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Caulimoviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Campylobacter"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Bacteria"; rdfs:subClassOf ; "eubacteria"; . a owl:Class; rdfs:label "Mycoplasma pneumoniae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Archaea"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Francisella tularensis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Dermaptera"; rdfs:subClassOf ; "earwigs"; . a owl:Class; rdfs:label "Streptococcus mitis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Human adenovirus 5"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Burkholderia pseudomallei"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Pseudomonas aeruginosa"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Archaeognatha"; rdfs:subClassOf ; "bristletails"; . a owl:Class; rdfs:label "Ephemeroptera"; rdfs:subClassOf ; "mayflies"; . a owl:Class; rdfs:label "Psocoptera"; rdfs:subClassOf ; "book lice", "booklice and barklice"; . a owl:Class; rdfs:label "Strepsiptera"; rdfs:subClassOf ; "twisted-wing parasites"; . a owl:Class; rdfs:label "Trichoptera"; rdfs:subClassOf ; "caddisflies"; . a owl:Class; rdfs:label "Thysanura"; rdfs:subClassOf ; "silverfish and firebrats"; . a owl:Class; rdfs:label "Chlorophyta"; rdfs:subClassOf ; "green algae"; . a owl:Class; rdfs:label "Squalidae"; rdfs:subClassOf ; "dogfish sharks"; . a owl:Class; rdfs:label "Chlamydomonas reinhardtii"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Sciurus carolinensis"; rdfs:subClassOf ; "eastern gray squirrel", "gray squirrel"; . a owl:Class; rdfs:label "Dipodidae"; rdfs:subClassOf ; "jerboas"; . a owl:Class; rdfs:label "Takifugu rubripes"; rdfs:subClassOf ; "tiger puffer", "torafugu"; . a owl:Class; rdfs:label "Burkholderia"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Teleostei"; rdfs:subClassOf ; "teleost fishes"; . a owl:Class; rdfs:label "Ananas nanus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Viridiplantae"; rdfs:subClassOf ; "green plants"; . a owl:Class; rdfs:label "Eremothecium gossypii"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Heteroptera"; rdfs:subClassOf ; "true bugs"; . a owl:Class; rdfs:label "Euglenozoa"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Acrobeloides ellesmerensis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Arabidopsis thaliana"; rdfs:subClassOf ; "mouse-ear cress", "thale cress", "thale-cress"; . a owl:Class; rdfs:label "Ovibos moschatus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Anolis sagrei"; rdfs:subClassOf ; "brown anole"; . a owl:Class; rdfs:label "Junonia coenia"; rdfs:subClassOf ; "buckeye", "peacock butterfly"; . a owl:Class; rdfs:label "Mammalia"; rdfs:subClassOf ; "mammals"; . a owl:Class; rdfs:label "Sigmodon hispidus"; rdfs:subClassOf ; "hispid cotton rat"; . a owl:Class; rdfs:label "Dictyostelium discoideum"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Fungi"; rdfs:subClassOf ; "fungi"; . a owl:Class; rdfs:label "Pneumocystis carinii"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Neisseria gonorrhoeae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Schizosaccharomyces pombe"; rdfs:subClassOf ; "fission yeast"; . a owl:Class; rdfs:label "Saccharomyces"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Saccharomyces cerevisiae"; rdfs:subClassOf ; "baker's yeast", "brewer's yeast", "lager beer yeast", "yeast"; . a owl:Class; rdfs:label "Aspergillus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Insecta"; rdfs:subClassOf ; "true insects"; . a owl:Class; rdfs:label "Embioptera"; rdfs:subClassOf ; "web-spinners"; . a owl:Class; rdfs:label "Neurospora crassa"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Chamaeleo"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Cryptococcus neoformans"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Eikenella corrodens"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Candida albicans"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Escherichia coli"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Leishmania"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Eleutherodactylus coqui"; rdfs:subClassOf ; "Puerto Rican coqui", "coqui"; . a owl:Class; rdfs:label "Trichomonas vaginalis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Naegleria gruberi"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Burkholderia thailandensis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Plasmodium falciparum"; rdfs:subClassOf ; "malaria parasite P. falciparum"; . a owl:Class; rdfs:label "Ciliophora"; rdfs:subClassOf ; "ciliates"; . a owl:Class; rdfs:label "Tetrahymena"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Tetrahymena thermophila"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Euplotes"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Oxytricha"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Taeniopygia guttata"; rdfs:subClassOf ; "zebra finch"; . a owl:Class; rdfs:label "Chlorocebus pygerythrus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Cnidaria"; rdfs:subClassOf ; "cnidarians", "coelenterates"; . a owl:Class; rdfs:label "Hydra"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Scyphozoa"; rdfs:subClassOf ; "jellyfishes"; . a owl:Class; rdfs:label "Trematoda"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Schistosoma mansoni"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Fasciola hepatica"; rdfs:subClassOf ; "liver fluke"; . a owl:Class; rdfs:label "Nematoda"; rdfs:subClassOf ; "nematode", "nematodes", "roundworm", "roundworms"; . a owl:Class; rdfs:label "Caenorhabditis briggsae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Caenorhabditis elegans"; rdfs:subClassOf ; "nematode"; . a owl:Class; rdfs:label "Yersinia pestis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Yersinia pseudotuberculosis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Annelida"; rdfs:subClassOf ; "annelid worms"; . a owl:Class; rdfs:label "Pheretima sieboldi"; rdfs:subClassOf ; "earthworm"; . a owl:Class; rdfs:label "Mollusca"; rdfs:subClassOf ; "molluscs", "mollusks"; . a owl:Class; rdfs:label "Gastropoda"; rdfs:subClassOf ; "gastropods"; . a owl:Class; rdfs:label "Aplysia"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Helix aspersa"; rdfs:subClassOf ; "brown garden snail"; . a owl:Class; rdfs:label "Cephalopoda"; rdfs:subClassOf ; "cephalopods"; . a owl:Class; rdfs:label "Sepiidae"; rdfs:subClassOf ; "cuttlefish", "cuttlefishes"; . a owl:Class; rdfs:label "Arthropoda"; rdfs:subClassOf ; "arthropods"; . a owl:Class; rdfs:label "Crustacea"; rdfs:subClassOf ; "crustaceans"; . a owl:Class; rdfs:label "Vibrio cholerae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "lobster"; rdfs:subClassOf ; "lobsters"; . a owl:Class; rdfs:label "Astacoidea"; rdfs:subClassOf ; "crayfish"; . a owl:Class; rdfs:label "Virgaviridae"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Callinectes"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Gasterosteus aculeatus"; rdfs:subClassOf ; "three spined stickleback", "three-spined stickleback"; . a owl:Class; rdfs:label "Orthoptera"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Acheta domesticus"; rdfs:subClassOf ; "house cricket"; . a owl:Class; rdfs:label "Locusta migratoria"; rdfs:subClassOf ; "migratory locust"; . a owl:Class; rdfs:label "Coleoptera"; rdfs:subClassOf ; "beetles"; . a owl:Class; rdfs:label "Lepidoptera"; rdfs:subClassOf ; "butterflies and moths", "moths"; . a owl:Class; rdfs:label "Bombyx mori"; rdfs:subClassOf ; "domestic silkworm", "silk moth", "silkworm"; . a owl:Class; rdfs:label "Spodoptera frugiperda"; rdfs:subClassOf ; "fall armyworm"; . a owl:Class; rdfs:label "Manduca"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Diptera"; rdfs:subClassOf ; "flies"; . a owl:Class; rdfs:label "Culicidae"; rdfs:subClassOf ; "mosquitos"; . a owl:Class; rdfs:label "Aedes aegypti"; rdfs:subClassOf ; "yellow fever mosquito"; . a owl:Class; rdfs:label "Aedes albopictus"; rdfs:subClassOf ; "Asian tiger mosquito", "forest day mosquito"; . a owl:Class; rdfs:label "Anopheles gambiae"; rdfs:subClassOf ; "African malaria mosquito", "Anopheles gambiae sensu stricto"; . a owl:Class; rdfs:label "Drosophila"; rdfs:subClassOf ; "fruit flies"; . a owl:Class; rdfs:label "Drosophila melanogaster"; rdfs:subClassOf ; "fruit fly"; . a owl:Class; rdfs:label "Musca domestica"; rdfs:subClassOf ; "house fly"; . a owl:Class; rdfs:label "Hymenoptera"; rdfs:subClassOf ; "hymenopterans"; . a owl:Class; rdfs:label "Aspergillus fumigatus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Mantodea"; rdfs:subClassOf ; "mantids"; . a owl:Class; rdfs:label "Siphonaptera"; rdfs:subClassOf ; "fleas"; . a owl:Class; rdfs:label "Neuroptera"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Hemiptera"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Dallia pectoralis"; rdfs:subClassOf ; "Alaska blackfish"; . a owl:Class; rdfs:label "Strongylocentrotus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Chordata"; rdfs:subClassOf ; "chordates"; . a owl:Class; rdfs:label "Tunicata"; rdfs:subClassOf ; "tunicates"; . a owl:Class; rdfs:label "Ascidiacea"; rdfs:subClassOf ; "sea squirts"; . a owl:Class; rdfs:label "Vertebrata"; rdfs:subClassOf ; "vertebrates"; . a owl:Class; rdfs:label "Petromyzontidae"; rdfs:subClassOf ; "lampreys"; . a owl:Class; rdfs:label "Myxine glutinosa"; rdfs:subClassOf ; "Atlantic hagfish", "common hagfish", "hagfish"; . a owl:Class; rdfs:label "Chondrichthyes"; rdfs:subClassOf ; "cartilaginous fishes", "fish", "fishes"; . a owl:Class; rdfs:label "Elasmobranchii"; rdfs:subClassOf ; "elasmobranchs"; . a owl:Class; rdfs:label "Discopyge ommata"; rdfs:subClassOf ; "electric ray", "ocellated electric ray"; . a owl:Class; rdfs:label "Torpedo"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Danio rerio"; rdfs:subClassOf ; "leopard danio", "zebra danio", "zebra fish", "zebrafish"; . a owl:Class; rdfs:label "Astyanax mexicanus"; rdfs:subClassOf ; "Mexican tetra", "blind cave fish"; . a owl:Class; rdfs:label "Electrophorus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Fundulus heteroclitus"; rdfs:subClassOf ; "Atlantic killifish", "killifish", "mummichog"; . a owl:Class; rdfs:label "Oryzias latipes"; rdfs:subClassOf ; "Japanese medaka", "Japanese rice fish", "medaka"; . a owl:Class; rdfs:label "Haplochromis burtoni"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Amphibia"; rdfs:subClassOf ; "amphibians"; . a owl:Class; rdfs:label "Caudata"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Ambystoma mexicanum"; rdfs:subClassOf ; "axolotl"; . a owl:Class; rdfs:label "Salamandridae"; rdfs:subClassOf ; "newts"; . a owl:Class; rdfs:label "Notophthalmus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Notophthalmus viridescens"; rdfs:subClassOf ; "eastern newt", "red-spotted newt"; . a owl:Class; rdfs:label "Pleurodeles"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Triturus"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Anura"; rdfs:subClassOf ; "anurans", "frogs", "frogs and toads"; . a owl:Class; rdfs:label "Xenopus borealis"; rdfs:subClassOf ; "Kenyan clawed frog", "Marasbit clawed frog"; . a owl:Class; rdfs:label "Xenopus laevis"; rdfs:subClassOf ; "African clawed frog", "clawed frog", "common platanna", "platanna"; . a owl:Class; rdfs:label "Xenopus (Silurana) tropicalis"; rdfs:subClassOf ; "western clawed frog"; . a owl:Class; rdfs:label "Lepidobatrachus laevis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Rana catesbeiana"; rdfs:subClassOf ; "bullfrog", "bullfrogs"; . a owl:Class; rdfs:label "Rana pipiens"; rdfs:subClassOf ; "northern leopard frog"; . a owl:Class; rdfs:label "Testudines"; rdfs:subClassOf ; "anapsid reptiles", "turtles"; . a owl:Class; rdfs:label "Crocodylidae"; rdfs:subClassOf ; "crocodilians"; . a owl:Class; rdfs:label "Lepidosauria"; rdfs:subClassOf ; "lepidosaurs"; . a owl:Class; rdfs:label "Blattodea"; rdfs:subClassOf ; "cockroaches"; . a owl:Class; rdfs:label "Aves"; rdfs:subClassOf ; "birds"; . a owl:Class; rdfs:label "Anatidae"; rdfs:subClassOf ; "waterfowl"; . a owl:Class; rdfs:label "Anas"; rdfs:subClassOf ; "ducks"; . a owl:Class; rdfs:label "Phasianidae gen. sp."; rdfs:subClassOf ; . a owl:Class; rdfs:label "Gallus gallus"; rdfs:subClassOf ; "bantam", "chicken", "chickens"; . a owl:Class; rdfs:label "Meleagris gallopavo"; rdfs:subClassOf ; "common turkey", "turkey", "wild turkey"; . a owl:Class; rdfs:label "Didelphidae"; rdfs:subClassOf ; "American opossums", "opossums"; . a owl:Class; rdfs:label "Coturnix japonica"; rdfs:subClassOf ; "Japanese quail"; . a owl:Class; rdfs:label "Tupaia"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Primates"; rdfs:subClassOf ; "primate"; . a owl:Class; rdfs:label "Ehrlichia chaffeensis"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Callithrix"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Lethenteron"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Aotus trivirgatus"; rdfs:subClassOf ; "douroucouli", "night monkey", "northern night monkey", "owl monkey"; . a owl:Class; rdfs:label "Cebus"; rdfs:subClassOf ; "capuchin monkeys"; . a owl:Class; rdfs:label "Cebus albifrons"; rdfs:subClassOf ; "brown pale-fronted capuchin", "pale-fronted capuchin", "white-fronted capuchin"; . a owl:Class; rdfs:label "Cebus apella"; rdfs:subClassOf ; "Tufted capuchin", "black-capped capuchin", "brown capuchin", "brown-capped capuchin"; . a owl:Class; rdfs:label "Cebus capucinus"; rdfs:subClassOf ; "white-faced capuchin", "white-faced sapajou", "white-throated capuchin"; . a owl:Class; rdfs:label "Saimiri"; rdfs:subClassOf ; "squirrel monkeys"; . a owl:Class; rdfs:label "Saimiri sciureus"; rdfs:subClassOf ; "South American squirrel monkey", "common squirrel monkey"; . a owl:Class; rdfs:label "Callicebus"; rdfs:subClassOf ; "titi monkeys"; . a owl:Class; rdfs:label "Cercopithecidae"; rdfs:subClassOf ; "Old World monkeys", "monkey", "monkeys"; . a owl:Class; rdfs:label "Chlorocebus aethiops"; rdfs:subClassOf ; "African green monkey", "African green monkeys", "green monkey", "grivet", "savanah monkey", "vervet monkey"; . a owl:Class; rdfs:label "Erythrocebus patas"; rdfs:subClassOf ; "hussar", "patas monkey", "red guenon"; . a owl:Class; rdfs:label "Macaca"; rdfs:subClassOf ; "macaques"; . a owl:Class; rdfs:label "Macaca arctoides"; rdfs:subClassOf ; "bear macaque", "stump-tailed macaque"; . a owl:Class; rdfs:label "Macaca fascicularis"; rdfs:subClassOf ; "crab eating macaque", "crab-eating macaque", "cynomolgus monkey", "cynomolgus monkeys", "long-tailed macaque"; . a owl:Class; rdfs:label "Macaca fuscata"; rdfs:subClassOf ; "Japanese macaque", "Japanese monkey"; . a owl:Class; rdfs:label "Macaca mulatta"; rdfs:subClassOf ; "Rhesus monkey", "rhesus macaque", "rhesus macaques", "rhesus monkeys"; . a owl:Class; rdfs:label "Macaca nemestrina"; rdfs:subClassOf ; "pig-tailed macaque", "pigtail macaque", "pigtail monkey"; . a owl:Class; rdfs:label "Burkholderia cenocepacia"; rdfs:subClassOf ; . a owl:Class; rdfs:label "Papio"; rdfs:subClassOf ; "baboons"; . a owl:Class; rdfs:label "Papio anubis"; rdfs:subClassOf ; "Doguera baboon", "Kenya baboon", "Olive baboon", "baboon"; . a owl:Class; rdfs:label "Pan troglodytes"; rdfs:subClassOf ; "chimpanzee"; . a owl:Class; rdfs:label "Homo sapiens"; rdfs:subClassOf ; "human", "man"; . a owl:Class; rdfs:label "Canis lupus familiaris"; rdfs:subClassOf ; "dog", "dogs"; . a owl:Class; rdfs:label "Ursus americanus"; rdfs:subClassOf ; "American black bear"; . a owl:Class; rdfs:label "Mustela lutreola"; rdfs:subClassOf ; "European mink", "mink"; . a owl:Class; rdfs:label "Mustela putorius furo"; rdfs:subClassOf ; "black ferret", "domestic ferret", "ferret"; . a owl:Class; rdfs:label "Equidae"; rdfs:subClassOf ; "horses"; . a owl:Class; rdfs:label "Equus asinus"; rdfs:subClassOf ; "African ass", "African wild ass", "Somali wild ass", "ass", "domestic ass", "donkey"; . a owl:Class; rdfs:label "Equus caballus"; rdfs:subClassOf ; "domestic horse", "equine", "horse"; . a owl:Class; rdfs:label "Lethenteron camtschaticum"; rdfs:subClassOf ; "Japanese lamprey", "arctic lamprey"; . a owl:Class; rdfs:label "Sus scrofa domesticus"; rdfs:subClassOf ; "domestic pig"; . a owl:Class; rdfs:label "Rangifer tarandus"; rdfs:subClassOf ; "caribou", "reindeer"; . a owl:Class; rdfs:label "Bos taurus"; rdfs:subClassOf ; "bovine", "cattle", "cow", "domestic cattle", "domestic cow"; . a owl:Class; rdfs:label "Capra hircus"; rdfs:subClassOf ; "domestic goat", "goat", "goats"; . a owl:Class; rdfs:label "Ovis aries"; rdfs:subClassOf ; "domestic sheep", "lambs", "sheep", "wild sheep"; . a owl:Class; rdfs:label "Oryctolagus cuniculus"; rdfs:subClassOf ; "European rabbit", "Japanese white rabbit", "domestic rabbit", "rabbit", "rabbits"; . a owl:Class; rdfs:label "Rodentia"; rdfs:subClassOf ; "rodents"; . a owl:Class; rdfs:label "Spermophilus parryii"; rdfs:subClassOf ; "Arctic ground squirrel"; . a owl:Class; rdfs:label "planned process"@en; owl:equivalentClass _:2de9d9; rdfs:subClassOf , _:2dea19; "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)"; "6/11/9: Edited at workshop. Used to include: is initiated by an agent", "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en; "Bjoern Peters"; "Injecting mice with a vaccine in order to test its efficacy"; "branch derived"; "A processual entity that realizes a plan which is the concretization of a plan specification."@en; "Note that the plan which a planned process realizes is not necessarily a part of the planned process. Thus, planned processes such as assays do not have planning as a part, while other planned processes such as experiments or investigations do contain as parts some planning process."; "planned process"@en; ; . _:2de9d9 a owl:Class; owl:intersectionOf _:2de9e9 . _:2de9e9 rdf:first ; rdf:rest _:2dea09 . _:2dea09 rdf:first _:2de9f9; rdf:rest rdf:nil . _:2de9f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dea19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biological feature identification objective"@en; rdfs:subClassOf ; "Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature."@en; "Jennifer Fostel"@en; "biological feature identification objective"@en; ; . a owl:Class; rdfs:label "processed material"@en; owl:equivalentClass _:2dea29; rdfs:subClassOf , _:2dea69, _:2dea79; "a material entity that is the output of some material processing, (representing a new entity derived from the input material, or an altered version of the input material that is transformed in during material processing)"; "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples"@en; "Is a material entity that is created or changed during material processing."@en; "PERSON: Alan Ruttenberg"@en; "processed material"@en; ; . _:2dea29 a owl:Class; owl:intersectionOf _:2dea39 . _:2dea39 rdf:first ; rdf:rest _:2dea59 . _:2dea59 rdf:first _:2dea49; rdf:rest rdf:nil . _:2dea49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dea69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dea79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "software optimization objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software."@en; "software optimization objective"@en; ; . a owl:Class; rdfs:label "investigation"@en; rdfs:subClassOf , _:2dea89, _:2dea99, _:2deaa9, _:2deaf9, _:2deb09; ""; "Could add specific objective specification"; "Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation", "Lung cancer investigation using expression profiling, a stem cell transplant investigation. Planned processes such as biobanking are not investigations, though they may be part of an investigation. Similarly, the design and production of a microarray is not an investigation, but might be part of an investigation."; "a planned process aimed at producing information of a scientific nature, to test or generate one or more hypotheses. Investigations consists of parts: planning, study design execution, documentation, and analysis, and produce conclusion(s) about the nature of reality as output. Study design execution includes processes such as assays and techniques."; "Bjoern Peters"@en; "OBI branch derived"@en; "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en; "investigation"@en; ; . _:2dea89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dea99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2deaa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2deab9 . _:2deab9 a owl:Class; owl:intersectionOf _:2deac9 . _:2deac9 rdf:first ; rdf:rest _:2deae9 . _:2deae9 rdf:first _:2dead9; rdf:rest rdf:nil . _:2dead9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2deaf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2deb09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "evaluant role"@en; rdfs:subClassOf , _:2deb19, _:2deb29; "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term."; "GROUP: Role Branch"; "OBI"; "a role that inheres in an entity that is gained through a planning process upon an agent’s intent to study the entity through some assay, and realized in the execution of an assay which generates data about the entity "; """Evaluant vs Specimen Roles Explained: Both roles are ultimately realized in a process that generates information about the bearer (ie an investigation or an assay). That is, specimens and evaluants both bear some agents intent to be studied. The key difference is that, while an evaluant role is realized only in an assay, a specimen role is realized more broadly in an investigation (or, more precisely, a technique that is part of an investigation, since all 'study design execution' steps are techniques). (Recall that investigations consist of several processual parts, and that study design execution is the part where actual techniques are performed.) So, this means that a specimen role can be realized in either an assay (like an evaluant), or in a material processing technique that occurs during an investigation - but only one that generates another specimen (as ultimately the original specimen must bear an intent to be studied in the investigation, if only in virtue of some part of it (derived through some material processing technique) being studied). So, to recap: a specimen role is_realized_by some (technique and (part_of some investigation). An evaluant role is_realized_by only assay. Not all things that bear a specimen role will end up bearing an evaluant role (only those parts / derivations of the specimen that end up being that which data is generated about in some assay (ie those that end up also bearing an evaluant role) Example scenario: If I collect an organism from an environment and intend to study it as an example of its type, it has a specimen role. This role may be realized directly in an assay about the organism, or in some material processing technique in which another specimen is generated from the original organism specimen (ie its blood is drawn form the organism as a derived/secondary specimen, intended to be studied in some assay is performed with this blood as the evaluant). So ultimately a specimen must itself play an evaluant role or some part of it/entity derived from it through a material processing technique must play an evaluant role """; "Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)"@en, "examples of features that could be described in an evaluant: quality.... e.g. \"contains 10 pg/ml IL2\", or \"no glucose detected\")"@en; "When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role."@en; "a role that inheres in an entity that is realized in an assay in which data is generated about the bearer of the evaluant role"@en; "evaluant role"@en; ; . _:2deb19 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2deb29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2deb39 . _:2deb39 a owl:Class; owl:intersectionOf _:2deb49 . _:2deb49 rdf:first ; rdf:rest _:2deb69 . _:2deb69 rdf:first _:2deb59; rdf:rest rdf:nil . _:2deb59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "assay"@en; owl:equivalentClass _:2deb79; rdfs:subClassOf , _:2debb9, _:2dec09, _:2dec19, _:2dec29, _:2decb9; "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house."; "A planned process with the objective to produce information about some evaluant"@en; "material analysis technique", "measuring"@en, "scientific observation"@en; "Developers should ASSERT all planned processes that have an assay objective (ie have output some information about a research material) to be assays. "; "a technique with the objective to produce information about some evaluant. "; """Experiment vs Assay: an assay is a self-contained planned process, which does not include planning, documentation, or analysis processes. This sets it apart from an experiment, which does include such additional steps as parts."""; "OBI branch derived"@en; "PlanAndPlannedProcess Branch"@en; "assay"@en; ; ; . _:2deb79 a owl:Class; owl:intersectionOf _:2deb89 . _:2deb89 rdf:first ; rdf:rest _:2deba9 . _:2deba9 rdf:first _:2deb99; rdf:rest rdf:nil . _:2deb99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2debb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2debc9 . _:2debc9 a owl:Class; owl:intersectionOf _:2debd9 . _:2debd9 rdf:first ; rdf:rest _:2debf9 . _:2debf9 rdf:first _:2debe9; rdf:rest rdf:nil . _:2debe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dec09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dec19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dec29 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2dec39 . _:2dec39 a owl:Class; owl:intersectionOf _:2dec49 . _:2dec49 rdf:first ; rdf:rest _:2dec69 . _:2dec69 rdf:first _:2dec59; rdf:rest rdf:nil . _:2dec59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dec79 . _:2dec79 a owl:Class; owl:intersectionOf _:2dec89 . _:2dec89 rdf:first ; rdf:rest _:2deca9 . _:2deca9 rdf:first _:2dec99; rdf:rest rdf:nil . _:2dec99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2decb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "culture medium"@en; rdfs:subClassOf , , _:2decc9, _:2decd9, _:2ded29; "a processed material that provides the needed nourishment for microorganisms or cells grown in vitro."; "culture medium"; "A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008"@en; "OBI"@en; "Person: Jennifer Fostel, Jie Zheng"@en; ; . _:2decc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2decd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dece9 . _:2dece9 a owl:Class; owl:intersectionOf _:2decf9 . _:2decf9 rdf:first ; rdf:rest _:2ded19 . _:2ded19 rdf:first _:2ded09; rdf:rest rdf:nil . _:2ded09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ded29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ded39 . _:2ded39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ded49 . _:2ded49 a owl:Class; owl:intersectionOf _:2ded59 . _:2ded59 rdf:first ; rdf:rest _:2ded79 . _:2ded79 rdf:first _:2ded69; rdf:rest rdf:nil . _:2ded69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "reagent role"@en; rdfs:subClassOf ; "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term."; "reagent"; "reagent role"; "www.answers.com/topic/reagent; November 2008"; "MIREOT from OBI"; "obsolete_reagent role"; "Buffer, dye, a catalyst, a solvating agent."@en; "GROUP: Role Branch"@en; "a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"@en; ; . a owl:Class; rdfs:label "material processing"@en; owl:equivalentClass _:2ded89; rdfs:subClassOf , _:2ded99, _:2deda9, _:2dedb9, _:2dedc9; "A cell lysis, production of a cloning vector, creating a buffer."; "PERSON: Frank Gibson", "PERSON: Jennifer Fostel", "PERSON: Melanie Courtot", "PERSON: Philippe Rocca Serra", "PERSON: Bjoern Peters"@en; "material processing"; """OBI (Clarify meaning of 'physical change' in the definition of this class: As far as I can tell, 'physical change' is considered broadly by OBI as any re-arrangement of matter in the input material, such that processes resulting in material separation, material collection, and material combination are considered material processing. Also, it is confusing to use the term 'transformation' in the logical definition, where referring to the description of the 'material transformation objective' makes it clear that 'transformation' here is not used in the same sense as in the relation of transformation (ie here it is more generally conceived to include any process with material input and material output, whereas the relation of transformation is more strictly defined to refer to a specific kind of processual change to an input material). Suggestion to change label of 'material transformation objective' to 'material processing objective'.)"""; "a planned process in which physical changes, including contextual reorganizations or structural modification, are made to some input material to generate some processed research material."; "A planned process which results in physical changes in a specified input material"@en; """For now, I have directly asserted all trivial material processing classes (ie those that are clearly to be classified as material processings) as children of material processing, so as not to have to manually attach an axiom regarding achieving a material processing objective to all classes I want to classify as a material processing. OBI seems to use a mixed approach - some classes are directly asserted as children of material processing, but the majority are inferred based on their achieves planned objective axiom. """; "OBI branch derived"@en; "material transformation"@en; ; . _:2ded89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ded99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2deda9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dedb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dedc9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "protocol testing objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols."@en; "protocol testing objective"@en; ; . a owl:Class; rdfs:label "study subject role"@en; rdfs:subClassOf , _:2dedd9; "OBI"; "study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about."; "GROUP: Role Branch"@en; "study subject role"@en; ; . _:2dedd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "specimen role"@en; rdfs:subClassOf , _:2dede9, _:2dee39, _:2dee89; "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.", "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation."; "GROUP: Role Branch"; "OBI"; "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient."; "specimen role"; "a role borne by a material entity that is gained during a specimen creation process and that can be realized by use of the specimen in an investigation"@en; "a role inhering in some material entity that is gained through a planned process in which it is identified (and typically tagged or collected) as an example of its kind, and realized through its use in a technique as part of an investigation."; ; . _:2dede9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dedf9 . _:2dedf9 a owl:Class; owl:intersectionOf _:2dee09 . _:2dee09 rdf:first ; rdf:rest _:2dee29 . _:2dee29 rdf:first _:2dee19; rdf:rest rdf:nil . _:2dee19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dee39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dee49 . _:2dee49 a owl:Class; owl:intersectionOf _:2dee59 . _:2dee59 rdf:first ; rdf:rest _:2dee79 . _:2dee79 rdf:first _:2dee69; rdf:rest rdf:nil . _:2dee69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dee89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dee99 a owl:Axiom; "maybe dont need this given reference to 'specimen creation' in the axiom above"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2deea9 . _:2deea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "sequence feature identification objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide."@en; "sequence feature identification objective"@en; ; . a owl:Class; rdfs:label "molecular feature identification objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications."@en; "molecular feature identification objective"@en; ; . a owl:Class; rdfs:label "hardware testing objective"@en; rdfs:subClassOf ; "Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner."@en; "Jennifer Fostel"@en; "hardware testing objective"@en; ; . a owl:Class; rdfs:label "protocol optimization objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol."@en; "protocol optimization objective"@en; ; . a owl:Class; rdfs:label "nutrient role"@en; rdfs:subClassOf , _:2deeb9; "19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment."; "nutrient"; "nutrient role"; "GROUP: Role branch"@en; "Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia."@en; "a biological role that inheres in a material entity and is realized in the use of that material entity by an organism or cultured biomaterial to provide nourishment and support ongoing metabolism"; "Wikipedia, feb 29, 2008"@en; "a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment."@en; ; . _:2deeb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "methodology testing objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies."@en; "methodology testing objective"@en; ; . a owl:Class; rdfs:label "cellular feature identification objective"@en; rdfs:subClassOf ; "Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation."@en; "Jennifer Fostel"@en; "cellular feature identification objective"@en; ; . a owl:Class; rdfs:label "hardware optimization objective"@en; rdfs:subClassOf ; "Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware."@en; "Jennifer Fostel"@en; "hardware optimization objective"@en; ; . a owl:Class; rdfs:label "software testing objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software."@en; "software testing objective"@en; ; . a owl:Class; rdfs:label "organization"@en; rdfs:subClassOf , , _:2deec9; "GROUP: OBI"; "PERSON: Alan Ruttenberg", "PERSON: Bjoern Peters", "PERSON: Philippe Rocca-Serra", "PERSON: Susanna Sansone"; "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en; "consider using foaf:Organization (ero and VIVO and arg use this class)"; "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en; "organization"@en; ; . _:2deec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organism feature identification objective"@en; rdfs:subClassOf ; "Jennifer Fostel"@en; "Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle."@en; "organism feature identification objective"@en; ; . a owl:Class; rdfs:label "protocol"@en; rdfs:subClassOf ; "scientific protocol", "experimental protocol", "research protocol"; "OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)"@en; "PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice."@en; "PlanAndPlannedProcess Branch"@en; "a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process."@en; "protocol"@en; ; . a owl:Class; rdfs:label "analyte role"@en; rdfs:subClassOf , _:2deed9, _:2def09; "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term."; "GROUP: Role Branch"; "Glucose in blood (measured in an assay to determine the concentration of glucose)."; "OBI"; "analyte role"; "interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role", "pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.", "qualities such as weight, color are not assayed but measured, so they do not fall into this category."; "Analyte role is a role borne by a molecular entity and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role"@en; ; . _:2deed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2deee9 . _:2deee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2deef9 . _:2deef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2def09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "material to be added role"@en; rdfs:subClassOf , _:2def19; "9 March 09 from discussion with PA branch"; "OBI"; "Role Branch"; "drug added to a buffer contained in a tube; substance injected into an animal;"; "material to be added role"; "material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process"@en; ; . _:2def19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2def29 . _:2def29 a owl:Class; owl:intersectionOf _:2def39 . _:2def39 rdf:first ; rdf:rest _:2def59 . _:2def59 rdf:first _:2def49; rdf:rest rdf:nil . _:2def49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "interpreting data"@en; rdfs:subClassOf , _:2def69; "Bjoern Peters"; "Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis."; "PERSON: Bjoern Peters", "PERSON: Jennifer Fostel"; "interpreting data"; "the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions"@en; ; . _:2def69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "planning"@en; rdfs:subClassOf , _:2def79; "7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. "; "Bjoern Peters"; "Bjoern Peters", "PPPB branch"; "planning"; "the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment."; "discuss with OBI whether planning is a planned process, and whether it has a specified output, and whether its output should more generally be a directive information entity (OBI says it has_participant some 'plan specification . . . but it seems liek a specification could only be an output of a planning process, and couldnt a planning process have outputs that are not plan specifications (ie could have output that is an action specification?)."; "a process of creating or modifying a plan."@en; ; . _:2def79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "perturb function"@en; rdfs:subClassOf ; "Bill Bug", "Daniel Schober", "Frank Gibson", "Melanie Courtot"; "A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function."@en; "http://en.wikipedia.org/wiki/Perturbation_biology"@en; "perturb function"@en; ; . a owl:Class; rdfs:label "transfer function"@en; rdfs:subClassOf ; "Bill Bug", "Daniel Schober", "Frank Gibson", "Melanie Courtot"; "A transfer function is a function to displace a material from one location to another."@en; "transfer function"@en; ; . a owl:Class; rdfs:label "solid support function"@en; rdfs:subClassOf ; "Daniel Schober", "Frank Gibson", "Melanie Courtot"; "Taped, glued, pinned, dried or molecularly bonded to a solid support"; "solid support function"; "A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement"@en; ; . a owl:Class; rdfs:label "primer role"@en; rdfs:subClassOf , _:2def89; "(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer"; "a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation."; "primer role"; "a role palyed by oligonucleotides that seed the polymerase-driven replication of a nucleic acid molecule."; ; . _:2def89 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2def99 . _:2def99 a owl:Class; owl:unionOf _:2defa9 . _:2defa9 rdf:first ; rdf:rest _:2defb9 . _:2defb9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "PCR product"@en; rdfs:subClassOf ; "GROUP: OBI BIomaterial Branch"; "GROUP: OBI BIomaterial Branch"; "PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA."; "PCR product"@en; "We are using PCR and not the written out words, as this is the most common used."@en; "is double stranded DNA that is the specified output of a polymerase chain reaction"@en; ; . a owl:Class; rdfs:label "recombinant plasmid"@en; rdfs:subClassOf ; "GROUP: OBI Biomaterial Branch"; "PERSON: Bjoern Peters", "PERSON: Kevin Clancy", "PERSON: Melanie Courtot"; "a plasmid in which extraneous DNA has been inserted."; "obsolete_recombinant plasmid"; "not sure definition aligns with our need. may merge/re-use at some point in future"; "recombinant plasmid"@en; ; . a owl:Class; rdfs:label "cloning insert role"@en; rdfs:subClassOf , _:2defc9; "Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just \"cloning process\"", "Note that we interpret this OBI class to inhere in DNA molecules that are intended to be inserted/cloned into a construct, not in actual parts of constructs that result from the realization of this role. Therefore, this is asserted as a 'material to be added role'."; "GROUP: Role branch"; "OBII and Wikipedia"; "cloning insert role"; "construct insert role"; "cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process."@en; ; . _:2defc9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "extract"@en; rdfs:subClassOf , , _:2defd9; "GROUP: OBI Biomatrial Branch"; "PERSON: Philippe Rocca-Serra"; "Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923"@en; "an extract is a material entity which results from an extraction process"@en; "extract"@en; "extracted material"@en; ; . _:2defd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "averaging objective"@en; rdfs:subClassOf ; "Elisabetta Manduchi", "James Malone"@en; "PERSON: Elisabetta Manduchi"; "A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment."@en; "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation."@en; "averaging objective"@en; ; . a owl:Class; rdfs:label "plasmid"@en; rdfs:subClassOf ; "group:OBI"; "person:Melanie Courtot"; "a double-stranded DNA that is separate from, and can replicate in cells independently of, the chromosomal DNA. They are usually circular, and used to transfer genetic elements between cells. "; "PERSON: Matthew Brush"; "plasmid"@en; ; . a owl:Class; rdfs:label "adding material objective"@en; rdfs:subClassOf , _:2defe9; "BP"; "adding material objective"; "creating a mouse infected with LCM virus"; "material addition to target objective"; "a material combination objective to add new material to some target material, such that this target retains its identity as a specified output that is 'modified' through the material addition process (ie the specified output is shares identity with one of the specified inputs)"; rdfs:comment "The key here is that there is some existing target of material combination that is input into a material combination process. The specified output of this process can be the now larger 'target' material resulting from addition of new material, or it can be the new 'material to be added' that is output in a new context.' The identity of this specified output distinguishes 'physical' from 'contextual' material component combination objectives."; "is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity"@en; ; . _:2defe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2deff9 . _:2deff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "analyte measurement objective"@en; rdfs:subClassOf ; "PERSON: Bjoern Peters"; "PPPB branch"; "The objective to measure the concentration of glucose in a blood sample"; "analyte measurement objective"; "is an assay objective to determine the presence or concentration of an analyte in the evaluant"@en; ; . a owl:Class; rdfs:label "assay objective"@en; rdfs:subClassOf ; "PPPB branch"; "PPPB branch"; "assay objective"; "the objective to determine the weight of a mouse."; "an objective specification to generated data about some evaluant"; "is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role)"@en; ; . a owl:Class; rdfs:label "analyte assay"@en; owl:equivalentClass _:2df009; rdfs:subClassOf , _:2df129; "PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg"; "analyte assay"; "An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant."@en; "Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement."@en; "detection assay"; "example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output"@en; ; . _:2df009 a owl:Class; owl:intersectionOf _:2df019 . _:2df019 rdf:first ; rdf:rest _:2df039 . _:2df039 rdf:first _:2df029; rdf:rest rdf:nil . _:2df029 a owl:Class; owl:intersectionOf _:2df059 . _:2df059 rdf:first _:2df049; rdf:rest _:2df0b9 . _:2df049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df069 . _:2df069 a owl:Class; owl:intersectionOf _:2df079 . _:2df079 rdf:first ; rdf:rest _:2df099 . _:2df099 rdf:first _:2df089; rdf:rest rdf:nil . _:2df089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df0b9 rdf:first _:2df0a9; rdf:rest _:2df119 . _:2df0a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df0c9 . _:2df0c9 a owl:Class; owl:intersectionOf _:2df0d9 . _:2df0d9 rdf:first ; rdf:rest _:2df0f9 . _:2df0f9 rdf:first _:2df0e9; rdf:rest rdf:nil . _:2df0e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df119 rdf:first _:2df109; rdf:rest rdf:nil . _:2df109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "target of material addition role"@en; rdfs:subClassOf , _:2df139; "From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role."; "GROUP: Role Branch"; "OBI"; "peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application."; "target of material addition role"; "target of material addition role is a role realized by an entity into which a material is added in a material addition process"; "a role realized by a planned process in which the bearer is physically modified through the addition of material"; ; . _:2df139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df149 . _:2df149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material transformation objective"@en; rdfs:subClassOf ; "GROUP: OBI PlanAndPlannedProcess Branch"; "PERSON: Bjoern Peters", "PERSON: Frank Gibson", "PERSON: Jennifer Fostel", "PERSON: Melanie Courtot", "PERSON: Philippe Rocca-Serra"; "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS."; "material transformation objective"; """OBI (it is confusing to use the term 'transformation' in this class label, as the description of this class makes it clear that 'transformation' here is not used in the same sense as in the relation of transformation (ie here it is more generally conceived to include any process with material input and material output, whereas the relation of transformation is more strictly defined to refer to a specific kind of processual change to an input material). Suggestion to change label of 'material transformation objective' to 'material processing objective'.) Furthermore, the OBI definition of this class is very general, such that a number of 'objective specification' subclasses that are not subsumed by this class should be (in particular, specimen creation objective) ) Finally, I have re-arranged many of the objective classes I imported form OBI below this calss - should discuss with them If my interpretations and definitions that I apply to these classes are consistent with those in OBI - if not I should not re-use these classes."""; """Material processing is subclassed by applying three axes in the following order: Axis 1 = Process directionality/cardinality/ input-output ration (1->M vs M->1) : This distinction is based on whether input material is meant to be separated or combined. This gives the first level children 'material separation objective' and 'material combination objective'. Axis 2a (for 'material separation objective') = symmetry of the separation: This distinction is based on whether the separation objective specifies an asymmetrical segregation of components of the input target of material separation. If yes, it is a 'material component separation objective'. If not, it is a 'material portioning objective'. Axis 2b (for 'material combination objective'), = presence of a target input entity that is modified and whose identity is preserved: This distinction is based on whether there is a specified target of material combination that serves as input and is modified by the addition of new material (such that its identity is preserved through this modification). If yes, it is a 'material combination with target objective'. If not (ie if no single input is specified as a target that will be output in some modified form), then it is a 'material pooling objective'. Axis 3 (for 'material component separation objective' and 'material combination with target objective') = which output is the specified output, and what type of change has it undergone: This distinction applies to processes that have more than one output. One output represents a 'physically modified' version of some 'target' input material (ie modified through the removal or addition of material). The other represents a 'contextually' modified version of the material that was added or the material that was separated, according to the objective specification (this output undergoes no physical alterations to its self-contained structure or composition, but is merely re-located to some new setting or context). If the specified output to be studied/used by the investigator is of the former type, the objective is subclassed as a 'physical' objective. If the latter, it is subclassed as a 'contextual' objective. -------------------- In addition, 'material manufacturing' and 'material maintenance' objectives represent non-disjoint siblings of the 'material separation' and 'material combination' objectives.""", """As an example of the tricky third axis of classification (physical vs contextual processing objective), consider the following two examples. 1. The objective of 'separating an appendix from an organism': This process specified by this objective has two outputs : the organism now missing its appendix, and the appendix having been removed from the organism. If the 'specified output' (according to the objective specification) is the organism, then we have a 'physical material component separation' - because the specified output organism has been physically altered relative to its state as input material. If the 'specified output' is the appendix, then we have a 'contextual material component separation' - because the appendix itself, as a self-contained unit, has not undergone any internal/inherent physical alterations to its structure or composition. 2. The objective of adding a pathogen to an organism (e.g. by injecting into blood stream): This process has a single output (the organism containing the pathogen), but two possible perspectives regarding what the 'specified output could be. If the 'specified output' is the host organism, then we have a 'physical material combination' - because the organism has been physically altered relative to its state as input material. If the 'specified output' is the pathogen, then we have a 'contextual material combination' - because the pathogen itself, as a self-contained unit, has not undergone any internal/inherent physical alterations to its structure or composition - rather only a change in its context. ReO classifies material component separation and material combination objective classes in such a way as to clearly qualify as a contextual or a physical processing objective. For example, material 'purification', 'extraction', 'collection', and 'selection' objectives are all defined clearly as to indicate a contextual separation objective. Similarly, material 'delivery' is clearly defined to indicate a contextual combination objective. By contrast, material 'removal' and 'addition' are clearly defined to indicate physical a material separation and a physical material combination, respectively. The utility of making these distinctions is that processed materials (particularly specimens) can be classified as being 'experimentally modified' (when they are specified output of some material processing that achieves some physical processing objective), VS unmodified (when they are specified output of some material processing that achieves only contextual processing objectives). This distinction is important for scientists searching for or applying specimens/reagents, and important for interpreting data. The immediate use case motivating this work was to logically represent CL:'experimentally modified cell'."""; "material processing objective"; "an objective specifiction that creates an specific output object from input materials."@en; "artifact creation objective"@en; ; . a owl:Class; rdfs:label "manufacturing objective"@en; rdfs:subClassOf ; "GROUP: OBI PlanAndPlannedProcess Branch"; "PERSON: Bjoern Peters", "PERSON: Frank Gibson", "PERSON: Jennifer Fostel", "PERSON: Melanie Courtot", "PERSON: Philippe Rocca-Serra"; "manufacturing objective"; "obsolete_manufacturing objective"; "is the objective to manufacture a material of a certain function (device)"@en; "seemed to have same definition as device creation objective, and ReO wanted a manufacturing objective class that did not require the specified output to bear some funciton, and covered things like chemical synthesis"; ; . a owl:Class; rdfs:label "study design execution"; owl:equivalentClass _:2df159; rdfs:subClassOf , _:2df1c9, _:2df209, _:2df219; "6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation."; "a planned process that realizes the concretization of a study design"; "branch derived"; "injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design."; "removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired."; "study design execution"; ; . _:2df159 a owl:Class; owl:intersectionOf _:2df169 . _:2df169 rdf:first ; rdf:rest _:2df189 . _:2df189 rdf:first _:2df179; rdf:rest _:2df1b9 . _:2df179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df199 . _:2df199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df1b9 rdf:first _:2df1a9; rdf:rest rdf:nil . _:2df1a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df1c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df1d9 . _:2df1d9 a owl:Class; owl:unionOf _:2df1e9 . _:2df1e9 rdf:first ; rdf:rest _:2df1f9 . _:2df1f9 rdf:first ; rdf:rest rdf:nil . _:2df209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df229 . _:2df229 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "manufacturer role"; rdfs:subClassOf ; "GROUP: Role Branch"; "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process."; "OBI"; "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role."; "manufacturer role"; ; . a owl:Class; rdfs:label "scattered molecular aggregate"@en; rdfs:subClassOf , _:2df239, _:2df249; "scattered molecular aggregate"; "the sodium and chloride ions in a glass of salt water"; "A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates"@en; "Collective"@en; "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349"@en; "PERSON: Alan Ruttenberg"@en; ; . _:2df239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df249 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "material separation objective"; rdfs:subClassOf ; "PPPB branch"; "PPPB branch"; "The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood."; "is an objective to transform a material entity into spatially separated components."; "material separation objective"; "material dissociation objective"; ; . a owl:Class; rdfs:label "fuzzy clustering objective"@en; rdfs:subClassOf ; "PERSON: James Malone", "PERSON: Ryan Brinkman"; "A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori."@en; "James Malone"@en; "fuzzy clustering objective"@en; ; . a owl:Class; rdfs:label "specimen collection"; owl:equivalentClass _:2df259; rdfs:subClassOf , _:2df2c9, _:2df2d9; "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession", "6/9/09: used at workshop"; "Bjoern Peters"; "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.", "Note that, as considered in ReO, specimen creation does not require material processing of the bearer of the specimen role (as opposed to specimen collection) - and thus specimen mcreation is a child of planned process (and not a technique). This is because we believe that 'intent to study as an example of its kind' is what is key for being a specimen - such that the specimen role can be conferred merely by identification of some entity without any material proceessing (e.g., identification of a merekat to be studied in the wild, simply by observation and noting distinguishing characteristics that will allow future recognition and study). Typically, however, specimen creation involves physical processing/collection of a material of interest to be studied or used in an investigation. A specimen collection class was created to cover this most common case, and this 'specimen collection' class is a child of both 'specimen creation' and 'material processing technique -> material component separation technique'."; "a planned process with the objective of obtaining specimen."; "specimen creation"; "Examples of 'collected specimens' include blood collected from an organism, or soil samples collected from some environment. Specimens can also be created without physically collecting them, for example by tagging animals to track them in the wild, or by merely observing the intended specimen and noting distinguishing features that will allow subsequent identification and study. Finally, specimens can also be processed from other specimens, for example the extraction of nuclear material from a cell specimen to generate a nuclear extract specimen."; "a planned process in which some material entity is identified (and typically collected and/or tagged) as an example of its kind for intended study in an investigation."; """OBI - our definition of specimen creation may conflict with OBIs (in the sense that we beleive that identificaiton with intent to study is sufficient to confer a specimen role, wheras OBI is unclear about this). Need to resolve this issue to determine if we can re-use this class from OBI. HOWEVER, it may be the what we call 'specimens that are not collected' OBI would refer to as 'subjects' rather than specimens. In this case, specimens are always collected, and we could rename the specimen creation calss to be 'specimen collection'. This would require that inanimate objects could be subjects."""; ; . _:2df259 a owl:Class; owl:intersectionOf _:2df269 . _:2df269 rdf:first ; rdf:rest _:2df289 . _:2df289 rdf:first _:2df279; rdf:rest rdf:nil . _:2df279 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df299 . _:2df299 a owl:Class; owl:unionOf _:2df2a9 . _:2df2a9 rdf:first ; rdf:rest _:2df2b9 . _:2df2b9 rdf:first ; rdf:rest rdf:nil . _:2df2c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df2d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df2e9 . _:2df2e9 a owl:Class; owl:unionOf _:2df2f9 . _:2df2f9 rdf:first ; rdf:rest _:2df309 . _:2df309 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "statistical hypothesis test objective"@en; rdfs:subClassOf ; "Person:Helen Parkinson", "James Malone"@en; "WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing"; "hypothesis test objective"; "is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation "; "statistical hypothesis test objective"@en; ; . a owl:Class; rdfs:label "portioning objective"; rdfs:subClassOf ; "The objective to obtain multiple aliquots of an enzyme preparation.", "the objective to obtain multiple aliquots of an enzyme preparation, or to obtain multiple sections of a cell or tissue sample"; "is the objective to separate material into multiple portions, each of which contains a similar composition of the input material."; "portioning objective"; "material partitioning objective"; "a material separation objective to separate some input material into multiple portions, where the composition of each portion is not intended to vary in any specified way."; """Note that it is more commonly the case that material separation objectives specify a particullar component of the target of the separation that is to be separated, based on its physical make-up. This, by definition, is not the case for 'material portionings'. Furthermore, the majority of material portionings (e.g. aliquoting, sectioning) are 'complete', in that the target of the portioning is completely portioned and thus ceases to exist. For this reasons, 'material portioning objective' we do not consider the identitiy of and intentions for the possible specified outputs (ie target of material spearation and separated material), such that this class is not subclassed further into contextual vs physical children as is done for 'material component separation objective'. However, subclassing 'material portioning objective' to reflect such a distinction could easily be implemented in a similar way as for 'material component separation objective', to cover cases where indiscriminate parts of an input material are removed but not to completion. In such cases, the target of the separation remains as output, and the separated material or the target of the separation can used in an investigation."""; rdfs:comment """'portioning' here indicates that this is NOT an objective to separate the input asymmetrically into outputs with specified compositional differences (as compared with its parent 'material separation', which more generally refers to any dissociation of some input material into outputs of similar or intentionally different compositions). This ReO definition allows for techniques such as tissue sectioning to have a material protioning objective, as the specification for this process merely aims to partition the tissue, but not to achieve any specified compositional inequality between the sections (of course there will be some compositional differences in the outputs of a sectioning process, but these are not specifically indicated in the objective specification)"""; "material portioning objective"; ; . a owl:Class; rdfs:label "separation into different composition objective"; rdfs:subClassOf , _:2df319; "The objective to obtain cells contained in a sample of blood.", "the objective to separate an appendix from an organism, the objective to separate white blood cells from a blood sample"; "We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives"; "is the objective to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities)"; "separation into different composition objective"; "material component separation objective"; "a material separation objective to process some target material comprised of parts of different types, such that one or more specified parts become discriminately and differentially segregated between the outputs of this separation process. This process is asymmetric in the sense that the outputs exhibit different compositions, according to the objective specification."; rdfs:comment "The reference to 'component' in the label of this class indicates that this is an 'asymmetrical'/'discriminating' material separation into outputs of different composition. This is contrasted with its parent 'material separation objective', which more generally refers to any dissociation of some input material into outputs of similar or intentionally different compositions. This is also contrasted with its sibling 'material portioning objective', which refers to separations without a specific objective to discrimately segregate components of the input material between outputs."; ; . _:2df319 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df329 . _:2df329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df339 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2df349 . _:2df349 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df359 . _:2df359 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "specimen creation objective"; owl:equivalentClass _:2df369; rdfs:subClassOf , _:2df3b9; "A specimen creation objective is to obtain a material entity for potential use as an input during an investigation"; "Bjoern Peters"; "Bjoern Peters"; "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient."; "specimen creation objective"; """Specimen Creation vs Specimen Collection:: As we will model things in ReO, a specimen creation is not a material processing, as specimens can be created purely through observation and planning (for ex, identification of monkeys in a population through observation of distinguishing features) and certainly can be achieved without a collection process (tagging monkeys with a colored dart fired from a dart gun to identify/track the tagged specimen) . Specimen collection in ReO is a type of specimen creation in which the specimen of interest is physically removed from its environment into a lab/in vitro environment for study. The specimen creation objective will thus fall outside the material processing/transformation objective branch, while the specimen collection objective class will reside within this branch (under contextual processing objective > material separation objective> material collection objective). As for the related processes that achieve these objectives, specimen creation will be asserted as a planned process (and inferred to be a technique), and specimen collection asserted as a material processing technique (inferred to be a material collection process)"""; ; . _:2df369 a owl:Class; owl:intersectionOf _:2df379 . _:2df379 rdf:first ; rdf:rest _:2df399 . _:2df399 rdf:first _:2df389; rdf:rest rdf:nil . _:2df389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df3a9 . _:2df3a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df3b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df3c9 . _:2df3c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "creating a mixture of molecules in solution"; rdfs:subClassOf , _:2df3d9, _:2df3e9; "Bjoern Peters"; "PERSON: Helen Parkinson"; "The production of PBS"; "creating a mixture of molecules in solution"; "is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations."; ; . _:2df3d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df3e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material combination objective"; rdfs:subClassOf ; "PPPB branch"; "bp"; "is an objective to obtain an output material that contains several input materials."; "material combination objective"; "a material processing objective to obtain an output material that contains several input materials."; "material association objective"; ; . a owl:Class; rdfs:label "decision tree induction objective"; rdfs:subClassOf ; "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made."; "James Malone"; "decision tree induction objective"; ; . a owl:Class; rdfs:label "recombinant vector"; owl:equivalentClass _:2df3f9, _:2df409; rdfs:subClassOf , , _:2df449, _:2df459, _:2df469; "A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector."; "recombinant vector"; "recombinant construct"; ; ; . _:2df3f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df409 a owl:Class; owl:intersectionOf _:2df419 . _:2df419 rdf:first ; rdf:rest _:2df439 . _:2df439 rdf:first _:2df429; rdf:rest rdf:nil . _:2df429 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df449 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df469 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cloning vector"; owl:equivalentClass _:2df479; rdfs:subClassOf , _:2df4c9; owl:disjointWith ; "A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site."; "cloning vector"; "cloning construct"; "pBluescript"; rdfs:comment "Cloning vectors are used primarily to propagate inserted DNA in some host cell, for the purpose of its maintenance/propagation in some host cell, and for facilitating its transfer to other constructs. It is not used expression of the inserted DNA in some target system."; "cloning vector"; ; ; . _:2df479 a owl:Class; owl:intersectionOf _:2df489 . _:2df489 rdf:first ; rdf:rest _:2df4a9 . _:2df4a9 rdf:first _:2df499; rdf:rest rdf:nil . _:2df499 a owl:Class; owl:complementOf _:2df4b9 . _:2df4b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df4c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material sample role"; rdfs:subClassOf , _:2df4d9, _:2df4e9; "7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off."; "A material sample role is a specimen role borne by a material entity that is the output of a material sampling process."; "a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general."; "material sample role"; "a specimen role inhereing in a material entity collected with the objective of being a representative example of its type for use in an assay."; ; . _:2df4d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df4e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material sampling process"; owl:equivalentClass _:2df4f9; rdfs:subClassOf , , _:2df579, _:2df589, _:2df599; "A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity"; "material sampling process"; "material sample collection"; ; . _:2df4f9 a owl:Class; owl:intersectionOf _:2df509 . _:2df509 rdf:first ; rdf:rest _:2df529 . _:2df529 rdf:first _:2df519; rdf:rest _:2df549 . _:2df519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df549 rdf:first _:2df539; rdf:rest _:2df569 . _:2df539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df569 rdf:first _:2df559; rdf:rest rdf:nil . _:2df559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df599 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material sample"; owl:equivalentClass _:2df5a9 . _:2df5a9 a owl:Class; owl:intersectionOf _:2df5b9 . _:2df5b9 rdf:first ; rdf:rest _:2df5d9 . _:2df5d9 rdf:first _:2df5c9 . _:2df5c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df5d9 rdf:rest rdf:nil . rdfs:subClassOf , , , _:2df5e9, _:2df5f9; "A material entity that has the material sample role"; "OBI: workshop"; "blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general."; "material sample"; "sample population"; "a material entity that is collected with the objective of being a representative example of its type for use in an assay. Unlike a specimen, a sample is necessarily considered as representative of some larger population, portion, or collection."; ; . _:2df5e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df5f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "independent variable specification"@en; rdfs:subClassOf ; "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI."; "PERSON: Alan Ruttenberg", "PERSON: Bjoern Peters", "PERSON: Chris Stoeckert"; "Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables"; "independent variable specification"; "2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled."@en; "a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled"@en; ; . a owl:Class; rdfs:label "dependent variable specification"@en; rdfs:subClassOf ; "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI."; "PERSON: Alan Ruttenberg", "PERSON: Bjoern Peters", "PERSON: Chris Stoeckert"; "WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables"; "dependent variable specification"; "2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled."@en; "dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies."@en; ; . a owl:Class; rdfs:label "controlled variable specification"@en; rdfs:subClassOf ; "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI."; "PERSON: Alan Ruttenberg", "PERSON: Bjoern Peters", "PERSON: Chris Stoeckert"; "WEB: http://en.wikipedia.org/wiki/Control_variable"; "controlled variable specification"; "2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid"@en; "Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent."@en; ; . a owl:Class; rdfs:label "multiple testing correction objective"; rdfs:subClassOf ; "A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously"; "Application of the Bonferroni correction"; "http://en.wikipedia.org/wiki/Multiple_Testing_Correction"; "multiple comparison correction objective"; "multiple testing correction objective"; ; . a owl:Class; rdfs:label "purification objective"; rdfs:subClassOf ; "10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality"; "BP"; "PERSON:Bjoern Peters"; "The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest"; "isolation objective"; "purification objective"; "the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides."; "OBI:purification objective"; rdfs:comment "Note that this differs from an extraction, which attempts to obtain ONLY some specified components of the input material (ie a pure material - however in practice the output extract is rarely pure). Purifications attempt merely to obtain a more pure/concentrated output with respect to some desired components.", "Wikipedia - process of rendering something pure, i.e. clean of foreign elements and/or pollution"; "material purification objective"; "The material component separation objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest"; ; . a owl:Class; rdfs:label "material maintenance objective"; rdfs:subClassOf ; "PERSON: Bjoern Peters"; "is the objective to maintain some or all of the qualities of a material over time."; "material maintenance objective"; ; . a owl:Class; rdfs:label "manufacturer"; owl:equivalentClass _:2df609; rdfs:subClassOf , , _:2df679, _:2df689; "A person or organization that has a manufacturer role"; "manufacturer"; ; . _:2df609 a owl:Class; owl:intersectionOf _:2df629 . _:2df629 rdf:first _:2df619; rdf:rest _:2df669 . _:2df619 a owl:Class; owl:unionOf _:2df639 . _:2df639 rdf:first ; rdf:rest _:2df649 . _:2df649 rdf:first ; rdf:rest rdf:nil . _:2df669 rdf:first _:2df659; rdf:rest rdf:nil . _:2df659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material maintenance"; rdfs:subClassOf ; "a process with that achieves the objective to maintain some or all of the characteristics of an input material over time"; "material maintenance"; ; . a owl:Class; rdfs:label "test substance role"; rdfs:subClassOf ; "A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation"; "Group:OBI"; "Person:Alan Ruttenberg"; "fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally"; "test substance role"; "explanatory variable role", "test substance role", "predictor variable role", "exposure variable role", "input variable role", "controlled variable role", "manipulated variable role"; "independent variable role"; """a role inhering in an object that bears some quality, the controlled variance of which is the subject of an independent variable specification. This role is realized in a study design execution in which some quality of the bearer is varied between experimetnal replicates in order to determine its effect on some measured dependent variable. Axiomatically: 'inheres in' some ('has quality' some ('is subject of' some 'independent variable specification'))"""; """OBI: To relate this role to its bearers, and use it to define classes such as microarrays,may need to wait until OBI determines how to model specified vs measured vs predicted data items in order to more formally/axiomatically model these key relations. Not all independent variables are related to some quality inhering in a mateiral entity - but when they do, this material can be said to bear an independent variable role. We would want to say that an independent variable role inheres in a material entity that bears a quality (is concentration a quality of the scattered molecular aggregate (using towards some solution), or the solution? . . . concentration is often the subject of indep variable specifications, so we should figure this out. . . . may need to be able to say that the bearer of the indep variable role is a part of some larger entity such as a solution in which its concentration is varied) that is described/specified by an independent variable specification."""; ; . a owl:Class; rdfs:label "pattern matching objective"; rdfs:subClassOf ; "A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees."; "Tina Boussard"; "http://en.wikipedia.org/wiki/Pattern_matching"; "pattern matching objective"; ; . a owl:Class; rdfs:label "cell line immortalization"; rdfs:subClassOf , , , , _:2df699, _:2df6e9, _:2df6f9, _:2df709, _:2df719; "Bjoern Peters"; "OBI"; "Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs"; "a technique that confers upon a cell line the ability to divide indefinitely in vitro."; "cell line immortalization"; "is the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro. Has specified output cell line"; rdfs:comment "'cell immortalization' is different from 'cell transformation' in that the former requires only that a cell is able to replicate indefinitely in culture, while the latter further requires that the cell undergoes a set of genetic modifications that confers the properties of cancer - including the ability to grow in the absence of survival factors and the ability to divide without being specifically instructed to do so from outside the cell. In experimental settings, these qualities allow transformed cells to form tumors in animal models, and to escape contact inhibition in culture and thus grow on top of each other."; "cell culture immortalization"; "cell line cell immortalization", "cell culture cell immortalization", "cell line immortalization"; "PERSON: Matthew Brush"; ; . _:2df699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df6a9 . _:2df6a9 a owl:Class; owl:intersectionOf _:2df6b9 . _:2df6b9 rdf:first ; rdf:rest _:2df6d9 . _:2df6d9 rdf:first _:2df6c9; rdf:rest rdf:nil . _:2df6c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df6e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df6f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df709 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "protein extract"; rdfs:subClassOf , _:2df729, _:2df739; "OBI & wikipedia"; "Person: Philippe Rocca-Serra"; "a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,"; "protein extract"; ; . _:2df729 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2df739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Dulbecco's modified Eagle medium"; rdfs:subClassOf ; "A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins."; "D-MEM", "DMEM"; "Dulbecco's modified Eagle medium"; "Logical definition should contain all components listed in textual definition at some point."; "PERSON:Bjoern Peters"; , ; . a owl:Class; rdfs:label "training objective"; rdfs:subClassOf ; "A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package"; "An training objective which is fulfilled by the provision of some training"; "Helen Parkinson"; "OBI"; "training objective"; ; . a owl:Class; rdfs:label "dose specification"; rdfs:subClassOf ; "a directive information entity that describes the dose that will be administered to a target"; "a protocol specifying to administer 1 ml of vaccine to a mouse"; "dose specification"; ; . a owl:Class; rdfs:label "service provision objective"; rdfs:subClassOf ; "A sequencing centre has a service provision objective"; "An objective which is fulfilled by the provision of some service e.g. a training service"; "Helen Parkinson"; "OBI"; "service provision objective"; ; . a owl:Class; rdfs:label "device creation objective"; rdfs:subClassOf ; "OBI"; "PERSON: Helen Parkinson"; "an objective which aims to create a device with a specified function"; "device creation objective"; "instrument creation objective"; ; . a owl:Class; rdfs:label "nucleic acid extract"; rdfs:subClassOf , _:2df749, _:2df759, _:2df769; "An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen."; "PERSON: Jie Zheng"; "UPenn Group"; "nucleic acid extract"; ; . _:2df749 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2df759 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell culture expansion"@en; rdfs:subClassOf , , _:2df779, _:2df7c9; "a technique of culturing cells in vitro that results in an increase in cell numbers."; "MO_758 grow"@en; "PERSON: Chris Stoeckert, Jie Zheng"@en; "PERSON: Matthew Brush"; "a processual entity that results in the increase of cell numbers"@en; "cell culture expansion"@en; "including grow of yeast and bacteria"@en; ; . _:2df779 a owl:Class; owl:intersectionOf _:2df799 . _:2df799 rdf:first _:2df789; rdf:rest _:2df7b9 . _:2df789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df7b9 rdf:first _:2df7a9; rdf:rest rdf:nil . _:2df7a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df7c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetically modified material"@en; owl:equivalentClass _:2df7d9; rdfs:subClassOf , , _:2df889, _:2df8d9; "OBI (discuss possibility of loosening logical definition to allow for genetically modified materials such as in vitro extracts?)"; "a material entity (organism, cell, or cell line) that has been intentionally modified through some genetic modification technique that alters the sequence of its genetic material, or introduces exogenous genetic material that is capable of being stably replicated, and thus heritable by progeny cells or organisms.."; "GROUP: OBI"@en; "stably genetically modified material"; "http://en.wikipedia.org/wiki/Genetic_engineering#Definition"; """The equivalent class axiom defines this class as being any material (organism or cell or cell culture) that is specified output from a stable genetic modification technique, rather than a material that has some nucleic acid as part that bears a sequence alteration. This is because: (1) this class refers to intentionally/experimentally modified materials that gain a sequence alteration as part of some technique, and not naturally occurring material that bear mutations; (2) Not all stable genetic modifications require sequence alterations to existing genetic material - for example, transformation of a bacterial with a plasmid capbable of being replicated and inherited by progeny cells. Finally, it should be noted that we do not consider cases/ouputs of 'unsuccessful' genetic modification techniques wherein the output fails to be modified (because here we define gnetically modified material as being the SPECIFIED output of a genetic modification technique, and the output that is specified is one that is genetically altered. Outputs that are not altered represent outputs but not specified outputs."""; "PERSON: Jie Zheng"@en; "a material entity, organism or cell, that is the output of a genetic transformation process. "@en; "genetically modified material"@en; "term is proposed by BP on Oct 25, 2010 dev call"@en; ; . _:2df7d9 a owl:Class; owl:intersectionOf _:2df7f9 . _:2df7f9 rdf:first _:2df7e9; rdf:rest _:2df849 . _:2df7e9 a owl:Class; owl:unionOf _:2df809 . _:2df809 rdf:first ; rdf:rest _:2df819 . _:2df819 rdf:first ; rdf:rest _:2df829 . _:2df829 rdf:first ; rdf:rest rdf:nil . _:2df849 rdf:first _:2df839; rdf:rest rdf:nil . _:2df839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df859 . _:2df859 a owl:Class; owl:unionOf _:2df869 . _:2df869 rdf:first ; rdf:rest _:2df879 . _:2df879 rdf:first ; rdf:rest rdf:nil . _:2df889 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df899 . _:2df899 a owl:Class; owl:intersectionOf _:2df8a9 . _:2df8a9 rdf:first ; rdf:rest _:2df8c9 . _:2df8c9 rdf:first _:2df8b9; rdf:rest rdf:nil . _:2df8b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df8d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df8e9 . _:2df8e9 a owl:Class; owl:unionOf _:2df8f9 . _:2df8f9 rdf:first ; rdf:rest _:2df909 . _:2df909 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "transfection"@en; rdfs:subClassOf , , _:2df919, _:2df969, _:2df979, _:2df989; "MO_366 transfection"; "transfection"; "Note here that the specified input and output of a transfection is a cell (which may or may not be part of some larger material such as a cell line or orgnaism). This is because the transfection process fundamentally refers the the act of introducing some moelcules into a cell. A transfected cell line or organism is one which has as part trasnfected cells."; """OBI (transfection is asserted as a child of genetic transformation in OBI. But it includes the delivery of non-genetic material such as RNA (e.g. siRNA) to target cells/organisms. OBI should clarify definition of transgenic technique and adjust definition and palcement of transfection accordingly) Also, material other than nucleic acids can be delivered via transfection, including proteins. Note that OBI's genetic transformation (technique) class is defined using the notion of genetic material (the introduction. alteration or integration of genetic material into a cell or organism). But this concept is not defined anywhere, and is ambiguous. Best I can find is in the ExptDesign sandbox version of OBI, where it is defined as \"A nucleic acid macromolecule that is part of an organism and can be replicated within it. In this case, things like siRNA transfections, which would seem to fall under OBI:transfection, would not be considered genetic transformations by OBI's def - yet OBI:transfection is a subclass of OBI:genetic transformation"""; "PERSON: Chris Stoeckert, Jie Zheng"@en; "a technique which relies on the use of physical, electrical, or chemical mechanisms to introduce molecular entities of biological interest into a cell"; "a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell"@en; ; . _:2df919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df929 . _:2df929 a owl:Class; owl:intersectionOf _:2df939 . _:2df939 rdf:first ; rdf:rest _:2df959 . _:2df959 rdf:first _:2df949; rdf:rest rdf:nil . _:2df949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2df989 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2df999 . _:2df999 a owl:Class; owl:intersectionOf _:2df9a9 . _:2df9a9 rdf:first ; rdf:rest _:2df9c9 . _:2df9c9 rdf:first _:2df9b9; rdf:rest rdf:nil . _:2df9b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetic transformation objective"@en; rdfs:subClassOf ; "suggested to be added by BP and AR during Oct 25, 2010 dev call"; "a material transformation objective to generate a genetically modified organism, cell, or cell line that stably carries some altered or novel genetic material capable of being replicated and propagated to progeny."; "Person: Jie Zheng"@en; "Person: Jie Zheng"@en; "a material transformation objective aims to create genetically modified organism or cell"@en; rdfs:comment "genetic modifications can involve the addition or removal of genetic material, or the alteration of specific sites (e.g. point mutations) that doe not invilve material addition or removal."; "genetic modification objective"@en; "genetic transformation objective"@en; "http://en.wikipedia.org/wiki/Genetic_engineering#Definition"; ; . a owl:Class; rdfs:label "assay validation objective"@en; rdfs:subClassOf ; "GROUP: Penn Group"@en; "PERSON: Chris Stoeckert, Jie Zheng"@en; "an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results"@en; "assay validation objective"@en; ; . a owl:Class; rdfs:label "selective organism creation objective"@en; rdfs:subClassOf ; "PERSON: Chris Stoeckert, Jie Zheng"; "an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms."; "selective organism creation objective"@en; ; . a owl:Class; rdfs:label "SNP microarray"@en; rdfs:subClassOf ; "EFO_0002703 SNP array"; "Person: Helen Parkinson"; "a DNA microarray used to detect polymorphisms in DNA samples"; "SNP microarray"@en; ; . a owl:Class; rdfs:label "epigenetic modification identification objective"@en; rdfs:subClassOf ; "A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications."@en; "Chris Stoeckert, Jie Zheng"@en; "Person: Chris Stoeckert"@en; "epigenetic modification identification objective"@en; ; . a owl:Class; rdfs:label "tiling microarray"@en; rdfs:subClassOf ; "EFO_0002704: tiling array"; "Person: Helen Parkinson"; "a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions."; "genome tiling array"; "tiling microarray"@en; ; . a owl:Class; rdfs:label "transcription profiling identification objective"@en; rdfs:subClassOf ; "A molecular feature identification objective that aims to characterize the abundance of transcripts"@en; "Group: Penn Group"@en; "Person: Chris Stoeckert, Jie Zheng"@en; "transcription profiling identification objective"@en; ; . a owl:Class; rdfs:label "protein and DNA interaction identification objective"@en; rdfs:subClassOf ; "A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites."@en; "MO_933 binding_site_identification_design"@en; "Person: Chris Stoeckert, Jie Zheng"@en; "protein and DNA interaction identification objective"@en; ; . a owl:Class; rdfs:label "purification"@en; owl:equivalentClass _:2df9d9; rdfs:subClassOf , ; "A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest"; "MO_406 purify"; "PERSON: Chris Stoeckert, Jie Zheng"; "purification"@en; ; . _:2df9d9 a owl:Class; owl:intersectionOf _:2df9e9 . _:2df9e9 rdf:first ; rdf:rest _:2dfa09 . _:2dfa09 rdf:first _:2df9f9; rdf:rest rdf:nil . _:2df9f9 a owl:Class; owl:intersectionOf _:2dfa29 . _:2dfa29 rdf:first _:2dfa19; rdf:rest _:2dfa49 . _:2dfa19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfa49 rdf:first _:2dfa39; rdf:rest rdf:nil . _:2dfa39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "grant"@en; rdfs:subClassOf ; "A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role."@en; "Group: OBI"@en; "OBI"@en; "grant"@en; ; . a owl:Class; rdfs:label "organism"@en; rdfs:subClassOf , _:2dfa59; "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')"; "GROUP: OBI Biomaterial Branch"; "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en; "CARO 'orgnaism or virus or viroid'?"; "WEB: http://en.wikipedia.org/wiki/Organism"@en; "animal"@en, "fungus"@en, "plant"@en, "virus"@en; "organism"@en; ; . _:2dfa59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfa69 . _:2dfa69 a owl:Class; owl:unionOf _:2dfa79 . _:2dfa79 rdf:first ; rdf:rest _:2dfa89 . _:2dfa89 rdf:first ; rdf:rest rdf:nil . _:2dfa99 a owl:Axiom; "Was originally the axiomn: has_proper_part some 'material genome'. But noted here that we could to be more accurate here and say has_proper_part some (cell or genome), and then to virus had has proper part some genome, and to cellular organism say has proper part some cell (and since cell has proper part some material genome, and has proper part is transitive, then it will be inferred that organisms have proper part some material genome)"; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2dfaa9 . _:2dfaa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfab9 . _:2dfab9 a owl:Class; owl:unionOf _:2dfac9 . _:2dfac9 rdf:first ; rdf:rest _:2dfad9 . _:2dfad9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "phosphate buffered saline solution"@en; rdfs:subClassOf , , _:2dfae9, _:2dfb39, _:2dfb49; "PERSON: Philippe Rocca-Serra", "PERSON: Melanie Courtot"@en, "PERSON: Tina Boussard"@en; "PBS buffer"@en; "PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes."@en; "Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic)."@en; "WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline"@en; "phosphate buffered saline solution"@en; , ; . _:2dfae9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfaf9 . _:2dfaf9 a owl:Class; owl:intersectionOf _:2dfb09 . _:2dfb09 rdf:first ; rdf:rest _:2dfb29 . _:2dfb29 rdf:first _:2dfb19; rdf:rest rdf:nil . _:2dfb19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfb39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfb49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfb59 . _:2dfb59 a owl:Class; owl:intersectionOf _:2dfb69 . _:2dfb69 rdf:first ; rdf:rest _:2dfb89 . _:2dfb89 rdf:first _:2dfb79; rdf:rest rdf:nil . _:2dfb79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfb99 . _:2dfb99 a owl:Class; owl:intersectionOf _:2dfba9 . _:2dfba9 rdf:first ; rdf:rest _:2dfbc9 . _:2dfbc9 rdf:first _:2dfbb9; rdf:rest rdf:nil . _:2dfbb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "specimen"@en; owl:equivalentClass _:2dfbd9; rdfs:subClassOf , _:2dfc19, _:2dfc29; "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen."; "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation."; "PERSON: James Malone", "PERSON: Philippe Rocca-Serra"; rdfs:comment "a 'specimen' is a single example of a class of entities, and unlike a 'sample', is not necessarily considered as representative of some larger population, portion, or collection."; "a material entity that bears a specimen role, gained through a planned process in which it is identified (and typically tagged or collected) as an example of its kind, and realized through its use in an investigation."; "A material entity that has the specimen role."@en; "GROUP: OBI Biomaterial Branch"@en; "specimen"@en; ; . _:2dfbd9 a owl:Class; owl:intersectionOf _:2dfbe9 . _:2dfbe9 rdf:first ; rdf:rest _:2dfc09 . _:2dfc09 rdf:first _:2dfbf9; rdf:rest rdf:nil . _:2dfbf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfc19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfc29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell line cell"@en; rdfs:subClassOf ; "PERSON: Susanna Sansone"; "A material entity that represents generations of a primary culture."@en; "GROUP: OBI Biomaterial Branch"@en; "obsolete_cell line cell"; """Obsoleted becasue of ambiguity of definition of this class : a material entity that represents generations of a primary culture. Not clear if meant to include all cell cultures, only passaged ones, or only immortalized ones. Repalced with ReO class as temporary fix until can sort out cell representation among CL, CLO, OBI, and ReO."""; "PERSON: Matthew Brush"; "A cell culture cell that represents generations of a primary cell culture."; "OBI (class expression in OBI on cell line cell that it is specified output of some establishing cell culture seems inconsistent - given the difference between a cell line and a cell culture)"; "cell line cell"@en; ; . a owl:Class; rdfs:label "cell culture"@en; rdfs:subClassOf , , _:2dfc39, _:2dfc49, _:2dfc59, _:2dfd29, _:2dfd39; "GROUP: OBI Biomaterial Branch"; """Regarding naming conventions, we have attempted to avoid usage of ambiguous/inconsistently applied terms such as 'primary' in crafting preferred labels for our cell culture classes, as such terms have varied meaning in different communities. For example, 'primary' can mean a cell culutre is 'unpassaged' in some circles, and that it is 'mortal' in others. However, we have included these as alternative terms to make them available to different communities wishing to apply them as community-specific labels. For example, 'primary cell culture' is set as an alt term for both 'unpassaged cell culture' and 'mortal cell culture'. Similarly, the term 'line' is subject to varied initerpretation (can refer to a culture that is immortalized, or a culture that has been passaged). Here, we use 'line' only in cases where the culture has been immortalized, and use 'culture' in labels of classes that are not immortal."""; """Classification Axes for the Cell Culture Hierarchy: The cell culture hierarchy is classified first according to origin of the cells in culture (multicellular organism cells vs unicellular organisms), and second (for multicellular organism cultures) based on mortality of the cells comprising the culture (this axis does not apply to unicellular organism cultures). Equivalent Classes: In addition to this primary asserted hierarhcy, several additional equivalent classes can be defined based experimental techniques used in processing/generating a cell culture (e.g. selected cell culture, passaged cell culture, genetically modified cell culutre, etc). Additional dimensions can serve as the basis for equivalent classes such as 'expression cell line', 'disease model cell line', 'adherent cell line'. Several examples are implemented in ReO - primarily under 'immortal cell line' as these represent the cell culture reagents of broadest interest and utility. However these same design patterns could be applied to create simialr defined classes at other levels in the cell culture hierarchy (e.g. cell cultures, unicellular oganism cultures, mortal cell cultures)."""; "OBI (be sure that this class is intended to cover cultures of unicellualr organisms)"; "PERSON: Bjoern Peters"@en; "a cell culture is a material entity consisting of a population of cells that is maintained in vitro"@en; "cell culture"@en; ; ; . _:2dfc39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dfc49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfc59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfc69 . _:2dfc69 a owl:Class; owl:intersectionOf _:2dfc79 . _:2dfc79 rdf:first ; rdf:rest _:2dfc99 . _:2dfc99 rdf:first _:2dfc89; rdf:rest rdf:nil . _:2dfc89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfca9 . _:2dfca9 a owl:Class; owl:intersectionOf _:2dfcb9 . _:2dfcb9 rdf:first ; rdf:rest _:2dfcd9 . _:2dfcd9 rdf:first _:2dfcc9; rdf:rest rdf:nil . _:2dfcc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfce9 . _:2dfce9 a owl:Class; owl:intersectionOf _:2dfcf9 . _:2dfcf9 rdf:first ; rdf:rest _:2dfd19 . _:2dfd19 rdf:first _:2dfd09; rdf:rest rdf:nil . _:2dfd09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfd29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfd39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "primary cell culture"@en; rdfs:subClassOf ; "GROUP: OBI Biomaterial Branch"; "PERSON: Matthew Brush"; "PERSON: Susanna Sansone"; rdfs:comment "Note that the term 'primary' in 'primary cell culture' refers to the fact that the culture has yet to be subcultured/passaged (which makes it a cell line). In contrast, the term 'primary' in 'prmary cell line' indicates that the cell line is not immortal, and will senesce after a limited number of doublings."; "http://www.invitrogen.com/site/us/en/home/References/gibco-cell-culture-basics/introduction-to-cell-culture.html"; "OBI, CLO - clarify definiition of a cell line - does 'line' imply immortalization, or jsut that it has been passaged."; "a cell culture in which the cells are derived from a fresh tissue source and cultured in vitro, but have not undergone their first subculture whereby they are passaged into a new vessel with fresh growth medium to provide room for continued growth. A primary cell culture becomes a cell line upon its first subculture."@en; "a primary cell culture is a cell culture where the cells derive from a fresh tissue source."@en; """obsoleted when implemented new cell culture hierarchy . . . replaced by 'unpassaged mortal cell culture'? or possibly 'mortal cell culture' - depending on intended meaning of this OBI class. log def was = 'cell culture' and (is_specified_output_of exactly 0 'cell subculturing')"""; "primary cell culture"@en; ; . a owl:Class; rdfs:label "synthetic peptide"@en; owl:equivalentClass _:2dfd49; rdfs:subClassOf , , _:2dfd89, _:2dfd99, _:2dfda9; "Bjoern Peters"@en; "IEDB"@en; "synthetic polypeptide"; "Note again here that in ReO the term 'polypeptide' is synonymous with 'peptide' and that these terms do not impose any length/size restrictions/connotations. We will use the term 'oligopeptide' to indicate shorter peptides, and provide a recommended length cutoff for such molecules.", "changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi)."@en; "PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application"@en; "a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment"@en; "synthetic peptide"@en; "the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme"@en; ; ; . _:2dfd49 a owl:Class; owl:intersectionOf _:2dfd59 . _:2dfd59 rdf:first ; rdf:rest _:2dfd79 . _:2dfd79 rdf:first _:2dfd69; rdf:rest rdf:nil . _:2dfd69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfd89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfd99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfda9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "data transformation"@en; owl:equivalentClass _:2dfdb9; rdfs:subClassOf , _:2dfdf9, _:2dfe09, _:2dfe19, _:2dfe29, _:2dfe39; "Philippe Rocca-Serra", "Elisabetta Manduchi"@en, "Helen Parkinson"@en, "James Malone"@en, "Melanie Courtot"@en, "Richard Scheuermann"@en, "Ryan Brinkman"@en, "Tina Hernandez-Boussard"@en; "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value."; "data processing"; " 'data processing' here is distinct from a 'data processing technique'. The former can be perfomed by computational or human agents and described in a plan specification, while the latter is performed by some human agent and described specifically in a protocol."; "A data transformation is a process which produces output data from input data"@en; "Branch editors"@en; "data analysis"@en, "data processing"@en; "data transformation"@en; ; . _:2dfdb9 a owl:Class; owl:intersectionOf _:2dfdc9 . _:2dfdc9 rdf:first ; rdf:rest _:2dfde9 . _:2dfde9 rdf:first _:2dfdd9; rdf:rest rdf:nil . _:2dfdd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfdf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfe09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dfe19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfe29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfe39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "feature extraction objective"@en; rdfs:subClassOf ; "Elisabetta Manduchi", "James Malone"@en; "A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image."@en; "TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction"@en; "feature extraction objective"@en; ; . a owl:Class; rdfs:label "differential expression analysis objective"@en; rdfs:subClassOf ; "A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions."@en; "Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software"@en; "Elisabetta Manduchi"@en; "PERSON: Elisabetta Manduchi"@en; "differential expression analysis objective"@en; ; . a owl:Class; rdfs:label "descriptive statistical calculation objective"@en; rdfs:subClassOf ; "A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability."@en; "Elisabetta Manduchi"@en, "James Malone"@en, "Melanie Courtot"@en, "Monnie McGee"@en; "PERSON: Elisabetta Manduchi"@en, "PERSON: James Malone"@en, "PERSON: Melanie Courtot"@en, "PERSON: Monnie McGee"@en; "descriptive statistical calculation objective"@en; ; . a owl:Class; rdfs:label "sequence analysis objective"@en; rdfs:subClassOf ; "James Malone"; "PERSON: James Malone"; "A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns."@en; "sequence analysis objective"@en; ; . a owl:Class; rdfs:label "survival analysis objective"@en; rdfs:subClassOf ; "A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables"; "Kaplan meier data transformation"; "PERSON: James Malone", "PERSON: Tina Boussard"; "http://en.wikipedia.org/wiki/Survival_analysis"; "survival analysis"; "survival analysis objective"@en; ; . a owl:Class; rdfs:label "inter-rater reliability objective"@en; rdfs:subClassOf ; "Person:Alan Ruttenberg", "Person:Helen Parkinson"; "a data transformation objective of determining the concordance or agreement between human judges."; "http://en.wikipedia.org/wiki/Inter-rater_reliability"; "inter-rater agreement"; "inter-rater reliability objective"; ; . a owl:Class; rdfs:label "data vector reduction objective"@en; rdfs:subClassOf ; "James Malone", "Richard H. Scheuermann"@en; "Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k."@en; "PERSON: Richard H. Scheuermann"@en; "data vector reduction objective"@en; ; . a owl:Class; rdfs:label "data transformation objective"@en; rdfs:subClassOf ; "A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed."@en; "James Malone"@en; "PERSON: James Malone"@en; "data transformation objective"@en; "normalize objective"@en; ; . a owl:Class; rdfs:label "data normalization objective"@en; rdfs:subClassOf ; "Elisabetta Manduchi", "Helen Parkinson", "James Malone"@en; "PERSON: Elisabetta Manduchi", "PERSON: Helen Parkinson", "PERSON: James Malone"@en; "Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as \"quantile normalization\", according to the procedure described e.g. in PMID 12538238."@en; "data normalization objective"@en; ; . a owl:Class; rdfs:label "correction objective"@en; rdfs:subClassOf ; "PERSON: James Malone", "PERSON: Melanie Courtot"; "A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself"@en; "James Malone"@en; "Type I error correction"@en; "correction objective"@en; ; . a owl:Class; rdfs:label "partitioning objective"@en; rdfs:subClassOf ; "Elisabetta Manduchi", "James Malone"@en; "PERSON: Elisabetta Manduchi"; "A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets."@en; "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set."@en; "partitioning objective"@en; ; . a owl:Class; rdfs:label "background correction objective"@en; rdfs:subClassOf ; "Elisabetta Manduchi", "James Malone"@en; "PERSON: Elisabetta Manduchi"; "A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation."@en; "background correction objective"@en; ; . a owl:Class; rdfs:label "curve fitting objective"@en; rdfs:subClassOf ; "Elisabetta Manduchi", "James Malone"@en; "PERSON: Elisabetta Manduchi"; "A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints."@en; "curve fitting objective"@en; ; . a owl:Class; rdfs:label "center calculation objective"@en; rdfs:subClassOf ; "PERSON: James Malone"; "A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set."@en; "A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average."@en; "James Malone"@en; "center calculation objective"@en; ; . a owl:Class; rdfs:label "class discovery objective"@en; rdfs:subClassOf ; "PERSON: Elisabetta Manduchi", "PERSON: James Malone"; "clustering objective", "discriminant analysis objective"@en, "unsupervised classification objective"@en; "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic."@en; "James Malone"@en; "class discovery objective"@en; ; . a owl:Class; rdfs:label "class prediction objective"@en; rdfs:subClassOf ; "PERSON: Elisabetta Manduchi", "PERSON: James Malone"; "classification objective", "supervised classification objective"@en; "James Malone"@en; "class prediction objective"@en; ; . a owl:Class; rdfs:label "spread calculation objective"@en; rdfs:subClassOf ; "Person:Helen Parkinson", "James Malone"@en; "Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean"; "is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set "; "Awaiting English definition from Monnie McGee"@en; "spread calculation objective"@en; ; . a owl:Class; rdfs:label "scaling objective"@en; rdfs:subClassOf ; "Person:Helen Parkinson", "James Malone"@en; "Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13"; "is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum"; "Awaiting English definition from Monnie McGee"@en; "scaling objective"@en; ; . a owl:Class; rdfs:label "error correction objective"@en; rdfs:subClassOf ; "Application of a multiple testing correction method"; "PERSON: James Malone"; "An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself."@en; "James Malone, Helen Parkinson"@en; "error correction objective"@en; ; . a owl:Class; rdfs:label "cross validation objective"@en; rdfs:subClassOf ; "WEB: http://en.wikipedia.org/wiki/Cross_validation"; "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis."@en; "James Malone"@en; "cross validation objective"@en; "rotation estimation objective"@en; ; . a owl:Class; rdfs:label "merging objective"@en; rdfs:subClassOf ; "PERSON: Data Transformation Branch"; "merging objective"; "A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets."@en; "James Malone"@en; "combining objective"@en; "merging of columns from two different data sets"@en; ; . a owl:Class; rdfs:label "correlation study objective"; rdfs:subClassOf ; "A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables."; "PERSON: Tina Boussard"; "correlation study objective"; ; . a owl:Class; rdfs:label "spectrum analysis objective"; rdfs:subClassOf ; "Calculation of characteristic path length in mass spectrometry"; "PERSON: Tina Boussard", "Person:Helen Parkinson"; "is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. "; "spectrum analysis objective"; ; . a owl:Class; rdfs:label "chemical solution"@en; rdfs:subClassOf , _:2dfe49, _:2dfed9; "GROUP: OBI Biomaterial Branch"; "PERSON: Bjoern Peters", "PERSON: Philippe Rocca-Serra"; "solution", "liquid chemical solution"@en; "A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute."@en; rdfs:comment "a chemical solution is a homogeneous mixture composed of only one phase. In such a mixture, a solute is dissolved in another substance, known as a solvent."; "PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution."@en; "chemical solution"@en; ; . _:2dfe49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfe59 . _:2dfe59 a owl:Class; owl:intersectionOf _:2dfe69 . _:2dfe69 rdf:first ; rdf:rest _:2dfe89 . _:2dfe89 rdf:first _:2dfe79; rdf:rest rdf:nil . _:2dfe79 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2dfe99 . _:2dfe99 a owl:Class; owl:intersectionOf _:2dfea9 . _:2dfea9 rdf:first ; rdf:rest _:2dfec9 . _:2dfec9 rdf:first _:2dfeb9; rdf:rest rdf:nil . _:2dfeb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "buffer role"@en; rdfs:subClassOf , _:2dfee9, _:2dfef9; "A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3−) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution"; "OBI"; "Person:Helen Parkinson", "Person:Philippe Rocca-Serra"; "a role which inheres in some molecular entity realized during the process of buffering"; "buffer"; "buffer role"; ; . _:2dfee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dfef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dff09 . _:2dff09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dff19 a owl:Axiom; ""; "axiom exploring the use of the 'exploits' relation"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2dff29 . _:2dff29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "solvent role"@en; rdfs:subClassOf , _:2dff39, _:2dff49; "Philippe Rocca-Serra"; "adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)"; "solvent role"; "OBI (they have axiom that this (and solute role) inhere in a molecular entity . . . but wouldnt it me more accurate to say that it inheres in a chemical entity or pure chemical substance? Because individual molecules cannot act as a solvents, but collections of molecules or a compound can?"; "PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors."@en; "solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation"@en; ; . _:2dff39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2dff49 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "solute role"@en; rdfs:subClassOf , _:2dff59, _:2dff69; "Philippe Rocca-Serra"; "adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)"; "solute role"; "PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure."@en; "solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution"@en; ; . _:2dff59 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2dff69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetically modified organism"@en; owl:equivalentClass _:2dff79; rdfs:subClassOf , , _:2dffe9, _:2e0039; "PERSON: Philippe Rocca-Serra"; "genetically modified organism"; "OBI Biomaterial"@en; rdfs:comment "ReO-preferred definition is intended to be broad enough cover introduction of genetic material that directly encodes gene products expressed in the host organism, as well as genetic material that indirectly controls the expression of some endogenous gene (ie introduction of regulatory elements upstream of some endogenous gene)."; "an organism that is the output of a genetic transformation process"@en; "an organism which has been intentionally modified through some genetic modification technique that alters the sequence of its genetic material, or introduces exogenous genetic material that is capable of being replicated and inherited by offspring cells or organisms."; ; . _:2dff79 a owl:Class; owl:intersectionOf _:2dff89 . _:2dff89 rdf:first ; rdf:rest _:2dffa9 . _:2dffa9 rdf:first _:2dff99; rdf:rest rdf:nil . _:2dff99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dffb9 . _:2dffb9 a owl:Class; owl:unionOf _:2dffc9 . _:2dffc9 rdf:first ; rdf:rest _:2dffd9 . _:2dffd9 rdf:first ; rdf:rest rdf:nil . _:2dffe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2dfff9 . _:2dfff9 a owl:Class; owl:intersectionOf _:2e0009 . _:2e0009 rdf:first ; rdf:rest _:2e0029 . _:2e0029 rdf:first _:2e0019; rdf:rest rdf:nil . _:2e0019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0049 . _:2e0049 a owl:Class; owl:unionOf _:2e0059 . _:2e0059 rdf:first ; rdf:rest _:2e0069 . _:2e0069 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "extraction"@en; rdfs:subClassOf , , _:2e0079; "A material separation in which a desired component of an input material is separated from the remainder"; "Person:Bjoern Peters", "Philippe Rocca-Serra"; "extraction"; "nucleic acid extraction using phenol chloroform"; ; . _:2e0079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "storage"@en; rdfs:subClassOf ; "OBI-Branch"; "Philippe Rocca-Serra"; "storage"; "A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability"@en; "PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10."@en; ; . a owl:Class; rdfs:label "microarray"@en; rdfs:subClassOf , , _:2e0089, _:2e0099, _:2e00a9, _:2e00b9; "An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays."; "PERSON: Chris Stoeckert"; "http://en.wikipedia.org/wiki/Microarray"; "A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position."@en; "microarray probe collection"; "Daniel Schober"@en; "PERSON: Melissa Haendel"; "a material entity that is comprised of a collection of materials arrayed in two dimensions on a solid substrate (typically glass, silicon, plastic, or paraffin), that allows assay of a large number of biological specimens using high-throughput screening methods"; "note that the primary axis for subclassing microarray here is based on the type of entity that is immobilized and that bears the independent variable role. An alternate axis is used to define cellular microarray, which is distinguished based on the identity of the study subject an array is used to investigate (ie a cell) . . . as cellular microarrays can have many types of molecules immobilized on their solid substrate "; rdfs:comment "In ReO we view microarrays as reagents (as opposed to devices as they are viewed in OBI), because the principle components of microarrays are their molecular probes, each of which serves a reagent role in the execution of a microarray experiment. The solid matrix/substrate serves a secondary role to support the organization and presentation of these molecular reagents in the context of an experiment. The ultimate function of the microarray as a whole, then, is realized through the manifold chemical interactions of its molecular probes, which can be conceptually reduced to the realization of reagent roles inhering in these moleuclar entities. Thus, in ReO we consider the microarray as a reagent, rather than a device, as the realization of its function occurs at the molecular level. "; "microarray"@en; ; ; . _:2e0089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e00a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e00b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e00c9 . _:2e00c9 a owl:Class; owl:intersectionOf _:2e00d9 . _:2e00d9 rdf:first ; rdf:rest _:2e00f9 . _:2e00f9 rdf:first _:2e00e9; rdf:rest rdf:nil . _:2e00e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA microarray"@en; rdfs:subClassOf , _:2e0109; "PERSON: Frank Gibson", "PERSON: Daniel Schober"@en; "Web:@2008/03/03"; "A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample."@en; "DNA microarray"@en; "DNA-array"@en, "DNA Chip"@en; "a DNA microarray that is comprised of numerous collections of like DNA oligonucleotides, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed DNA 'probes' are used to determine the identity or quantity of 'target' nucleic acid molecules (or nucleic acid-associated molecules) in some biological specimen of interest, based on quantification of hybridization between specimen nucleic acid targets and immobilized microarray DNA molecules."; "Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). \"Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis\". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115"@en; ; . _:2e0109 a owl:Class; owl:intersectionOf _:2e0119 . _:2e0119 rdf:first ; rdf:rest _:2e0139 . _:2e0139 rdf:first _:2e0129; rdf:rest rdf:nil . _:2e0129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0149 . _:2e0149 a owl:Class; owl:intersectionOf _:2e0159 . _:2e0159 rdf:first ; rdf:rest _:2e0179 . _:2e0179 rdf:first _:2e0169; rdf:rest rdf:nil . _:2e0169 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e0189 . _:2e0189 a owl:Class; owl:intersectionOf _:2e0199 . _:2e0199 rdf:first ; rdf:rest _:2e01b9 . _:2e01b9 rdf:first _:2e01a9; rdf:rest rdf:nil . _:2e01a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "protein microarray"@en; rdfs:subClassOf , _:2e01c9; "PERSON: Daniel Schober"; "protein-binding array"; "a molecular microarray that is comprised of numerous collections of like polypeptides or polypeptide complexes, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed polypeptide 'probes' are used to determine the identity or quantity of some 'target' molecule(s) in a biological specimen of interest, based on quantification of binding between specimen molecular targets and immobilized polypeptide probes. "; "A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions."@en; "Daniel Schober"@en; "The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions."@en; "polypeptide microarray"; "protein microarray"@en; ; . _:2e01c9 a owl:Class; owl:intersectionOf _:2e01d9 . _:2e01d9 rdf:first ; rdf:rest _:2e01f9 . _:2e01f9 rdf:first _:2e01e9; rdf:rest rdf:nil . _:2e01e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0209 . _:2e0209 a owl:Class; owl:intersectionOf _:2e0219 . _:2e0219 rdf:first ; rdf:rest _:2e0239 . _:2e0239 rdf:first _:2e0229; rdf:rest rdf:nil . _:2e0229 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e0249 . _:2e0249 a owl:Class; owl:intersectionOf _:2e0259 . _:2e0259 rdf:first ; rdf:rest _:2e0279 . _:2e0279 rdf:first _:2e0269; rdf:rest rdf:nil . _:2e0269 a owl:Class; owl:intersectionOf _:2e0299 . _:2e0299 rdf:first _:2e0289; rdf:rest _:2e02b9 . _:2e0289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e02b9 rdf:first _:2e02a9; rdf:rest rdf:nil . _:2e02a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "study design"@en; rdfs:subClassOf ; "A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution."; "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available."; "PERSON: Chris Stoeckert"; "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design."@en; "experimental design"@en; "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol."@en; "study design"@en; ; . a owl:Class; rdfs:label "collecting specimen from organism"@en; rdfs:subClassOf , , _:2e02c9, _:2e02d9; "specimen collection from organism"; "IEDB"@en; "PERSON:Bjoern Peters"@en; "a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation"@en; "collecting specimen from organism"@en; "taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient"@en; ; . _:2e02c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e02d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material component separation"@en; owl:equivalentClass _:2e02e9; rdfs:subClassOf , _:2e0329, _:2e0339; "Bjoern Peters"@en; "IEDB"@en; "material component separation technique", "material component separation"@en; "Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification"@en; "a material processing in which components of an input material become segregated in space"@en; ; . _:2e02e9 a owl:Class; owl:intersectionOf _:2e02f9 . _:2e02f9 rdf:first ; rdf:rest _:2e0319 . _:2e0319 rdf:first _:2e0309; rdf:rest rdf:nil . _:2e0309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material portioning"@en; owl:equivalentClass _:2e0349; rdfs:subClassOf ; "OBI branch derived"@en; "PERSON:Bjoern Peters"@en; "a material processing in which the input substance is partitioned into a number of portions that are similar in composition."@en; "aliquoting"@en, "apportioning"@en; "material portioning"@en; "pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock"@en; ; . _:2e0349 a owl:Class; owl:intersectionOf _:2e0359 . _:2e0359 rdf:first ; rdf:rest _:2e0379 . _:2e0379 rdf:first _:2e0369; rdf:rest rdf:nil . _:2e0369 a owl:Class; owl:intersectionOf _:2e0399 . _:2e0399 rdf:first _:2e0389; rdf:rest _:2e03b9 . _:2e0389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e03b9 rdf:first _:2e03a9; rdf:rest rdf:nil . _:2e03a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "cell fixation"@en; rdfs:subClassOf , , _:2e03c9, _:2e03d9; "OBI branch derived"@en; "PERSON:Bjoern Peters"@en; "a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time"@en; "cell fixation"@en; "http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus"@en; "should include capturing what qualities are being preserved"@en; "we could generalize this for other input materials"@en; ; . _:2e03c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e03d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e03e9 . _:2e03e9 a owl:Class; owl:intersectionOf _:2e03f9 . _:2e03f9 rdf:first ; rdf:rest _:2e0419 . _:2e0419 rdf:first _:2e0409; rdf:rest rdf:nil . _:2e0409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "maintaining cell culture"@en; rdfs:subClassOf ; "a material processing technique that is the collection of all techniques directly involved in maintenance of an active cell culture, following its initial establishment."; "Using the CLO cell line maintenance class here (ReO alt term 'cell culture maintenance'), which has same meaning, and same axioms now"; rdfs:comment "Includes processes such as cell culture splitting, cell culture expansion, cell culture feeding. Does not include processes such as establishing cell culture from an anatomical source, or cell culture freezing for long term dormant storage."; "OBI branch derived"@en; "PlanAndPlannedProcess Branch"@en; "When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture"@en; "a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing"@en; "maintaining cell culture"@en; "obsolete_cell culture maintenance"; ; . a owl:Class; rdfs:label "establishing cell culture"@en; rdfs:subClassOf , , , , _:2e0429, _:2e0439, _:2e04c9, _:2e04d9; "Establishing a cell culture could be said to achieve a manufacturing objective, as the cell culture itself is a new entity manufactured from the assembly of input cells. This technique also qualifies as an 'experimental modification' in the sense that the individual cells that are part of this cell culture represent physically modified versions of the input cells (ie that they have been cultured to incorporate nutrients and express surface proteins required for their survival in vitro). This view is taken to support the convention of viewing cultured cells as 'experimentally modified', as established in the Cell Ontology."; "OBI branch derived"@en; "PlanAndPlannedProcess Branch"@en; "establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density."@en; "establishing cell culture"@en; ; . _:2e0429 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0449 . _:2e0449 a owl:Class; owl:intersectionOf _:2e0469 . _:2e0469 rdf:first _:2e0459; rdf:rest _:2e04b9 . _:2e0459 a owl:Class; owl:unionOf _:2e0479 . _:2e0479 rdf:first ; rdf:rest _:2e0499 . _:2e0499 rdf:first _:2e0489; rdf:rest rdf:nil . _:2e0489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e04b9 rdf:first _:2e04a9; rdf:rest rdf:nil . _:2e04a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e04c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e04d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell culture splitting"@en; rdfs:subClassOf , _:2e04e9; "non-selective cell subculturing", "cell culture spllitting"; "cell culture passaging"; "OBI branch derived"@en; "PlanAndPlannedProcess Branch"@en; "The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media."@en; "The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing"@en; "cell culture splitting"@en; ; . _:2e04e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "synthesis"@en; rdfs:subClassOf , , _:2e04f9, _:2e0509, _:2e0519; "synthesis"; "chemical synthesis", "de novo molecular synthesis", "synthesize"@en; "OBI (clarify definition and consider relabeling to indicate this is a molecular/chemical synthesis process)"; "OBI branch derived"@en; "This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription"@en; "PERSON:Kevin Clancy"@en; "a material processing technique whereby a molecular entity is constructed from simpler chemical entities"; "molecular synthesis"; "making cDNA from nucleotides using RNA as a template"@en; "the construction of a biomaterial from simpler biomaterials"@en; ; . _:2e04f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant plasmid cloning"@en; rdfs:subClassOf , _:2e0529; "OBI branch derived"@en; "PERSON:Kevin Clancy"@en; "The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35."@en; "recombinant plasmid cloning"@en; "the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial"@en; ; . _:2e0529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetic transformation"@en; rdfs:subClassOf ; "a technique whereby the sequence of exisitng genetic material of a target cell or organism is altered, or exogneous DNA is introduced into a cell or orgnaism in such a way that it can be stably replicated and thus heritable by progeny."; """1. not clear that my interpretation of this concept is same as in this OBI class, so created own 'genetic modification technique' class and will use this for now. 2. Oddly, when I use the OBI class here it does not infer as a type of experimental modification, but if I duplicate the OBI class and replace all usages of the OBI class with this duplicated class (so essentially this du0plicated class is identical in axioms and usage to the OBI class) - this duplicated class now classifies correctly. Only real difference is in some of the annotation properties ( e.g. all of them live in ReO, and the label of the duplicated class is 'genetic modification technique', as opposed to this being a ReO alternative label for 'genetic transformation' - the original OBI label) All class axioms duplicated on new ReO gneetic modification technique class"""; """OBI (re: clarification of OBI class label 'genetic transformation' . . . note that here we do NOT include cases such as transient transfections where the added genetic material may not be capable of stable replication and propagation to progenitors. While such process allow for expression of exogenous genes in a target cell or organism, there is no stable, heritable changes to what we consider to be the 'genetic material' of the target. This class in OBI (genetic transformation) seems like it may include such cases - if so we should not import here, as meaning is different than what we intend with 'genetic modification technique'. Consider making two classes in ReO: 'genetic modification technique' being more inclusive, and including things like stable transfections (since these are material delivery and thus modifications), and then the subtype 'stable/heritable/integral genetic modification technique' or 'genetic material modification technique' to be equivalent to my current meaning here - where genetic material is truly modified."""; "transient or stable transfection of DNA into a cell or organism. exposure of cells to mutagenizing radiation to introduce random mutations into the genome.", "The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35"@en; "http://en.wikipedia.org/wiki/Genetic_engineering#Definition"; rdfs:comment "Note that here we do NOT include cases such as transient transfections where the added genetic material may not be capable of stable replication and propagation to progenitors. While such process allow for expression of exogenous genes in a target cell or organism, there is no stable, heritable changes to what we consider to be the 'genetic material' of the target."; "MHB:created editor preferred term 'genetic modification technique' in oplace of the OBI label 'genetic transformation' for two reasons: (1) used 'modification' to avoid confusion with 'cell transformation' (a process through which genetic modifications confer properties of cancer upon a cell); (2) appended with 'technique' to clarify that this is a planned process and not a naturally occuring genetic transformation/modification event."; "OBI branch derived"@en; "PERSON:Kevin Clancy"@en; "genetic modification"@en; "genetic transformation"@en; "obsolete_genetic modification technique"@en; "the introduction. alteration or integration of genetic material into a cell or organism"@en; ; . a owl:Class; rdfs:label "DNA transfection"@en; owl:equivalentClass _:2e0539; rdfs:subClassOf , _:2e05b9, _:2e0609, _:2e0659; "DNA transfection"@en; "OBI branch derived"@en; "PERSON:Kevin Clancy"@en; "The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest"@en; "a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell"@en; ; . _:2e0539 a owl:Class; owl:intersectionOf _:2e0549 . _:2e0549 rdf:first ; rdf:rest _:2e0569 . _:2e0569 rdf:first _:2e0559; rdf:rest rdf:nil . _:2e0559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0579 . _:2e0579 a owl:Class; owl:intersectionOf _:2e0589 . _:2e0589 rdf:first ; rdf:rest _:2e05a9 . _:2e05a9 rdf:first _:2e0599; rdf:rest rdf:nil . _:2e0599 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e05b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e05c9 . _:2e05c9 a owl:Class; owl:intersectionOf _:2e05d9 . _:2e05d9 rdf:first ; rdf:rest _:2e05f9 . _:2e05f9 rdf:first _:2e05e9; rdf:rest rdf:nil . _:2e05e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0609 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0619 . _:2e0619 a owl:Class; owl:intersectionOf _:2e0629 . _:2e0629 rdf:first ; rdf:rest _:2e0649 . _:2e0649 rdf:first _:2e0639; rdf:rest rdf:nil . _:2e0639 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant vector cloning"@en; rdfs:subClassOf , , , _:2e0669, _:2e06b9, _:2e06c9, _:2e06d9, _:2e06e9; "molecular cloning"; rdfs:comment "This technique specifically refers to ", "'Empty' DNA constructs (backbones) that carry no 'construct insert' are not considered here to be products of 'recombinant construct cloning', as the term 'cloning' is typically associated with the progagation and characterization of a specific piece of DNA that is inserted into a DNA construct. Insertion of any sequences into the construct for other purposes (e.g. antibiotic resistance, selectble markers, promoters) are considered part of 'DNA construct creation', but not 'recombinant construct cloning'."; """1. Original OBI label was 'recombinant vector cloning'. We created ReO alternative term 'recombinant construct cloning' for display in ReO, for consistency with the REO construct class, and to avoid semantic ambiguity of the term 'vector' in the biomedical domain. 2. Note that we do not consider 'empty' DNA constructs (backbones) that carry no 'construct insert' to be products of 'recombinant construct cloning', as the term 'cloning' is typically associated with the progagation and characterization of a specific piece of DNA that is inserted into a DNA construct. Insertion of any sequences into the construct for other purposes (e.g. antibiotic resistance, selectble markers, promoters) are considered part of 'DNA construct creation', but not 'recombinant construct cloning'."""; "OBI branch derived"@en; "a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material"@en; "pa_branch (Alan, Randi, Kevin, Jay, Bjoern)"@en; "recombinant construct cloning"@en; "recombinant vector cloning"@en; ; . _:2e0669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0679 . _:2e0679 a owl:Class; owl:intersectionOf _:2e0689 . _:2e0689 rdf:first ; rdf:rest _:2e06a9 . _:2e06a9 rdf:first _:2e0699; rdf:rest rdf:nil . _:2e0699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e06b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e06c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e06d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e06e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e06f9 . _:2e06f9 a owl:Class; owl:intersectionOf _:2e0709 . _:2e0709 rdf:first ; rdf:rest _:2e0729 . _:2e0729 rdf:first _:2e0719; rdf:rest rdf:nil . _:2e0719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleic acid extraction"@en; owl:equivalentClass _:2e0739; rdfs:subClassOf , _:2e0779; "OBI branch derived"@en; "Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet."@en; "PlanAndPlannedProcess Branch"@en; "a material separation to recover the nucleic acid fraction of an input material"@en; "nucleic acid extraction"@en; "requested by Helen Parkinson for MO. Could be defined class"@en; ; ; . _:2e0739 a owl:Class; owl:intersectionOf _:2e0749 . _:2e0749 rdf:first ; rdf:rest _:2e0769 . _:2e0769 rdf:first _:2e0759; rdf:rest rdf:nil . _:2e0759 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0779 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transgenic organism"@en; owl:equivalentClass _:2e0789; rdfs:subClassOf , , , _:2e07f9, _:2e0849; "PERSON: Philippe Rocca-Serra", "PERSON: Bjoern Peters"@en; "GROUP:IEDB"@en; "PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application"@en; "a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it"@en; "an organism which has been modified through some transgenic technique to contain exogenous genetic material from a different cell or organism that contibutes to some gene expression process in the organism"; "transgenic organism"@en; ; . _:2e0789 a owl:Class; owl:intersectionOf _:2e0799 . _:2e0799 rdf:first ; rdf:rest _:2e07b9 . _:2e07b9 rdf:first _:2e07a9; rdf:rest rdf:nil . _:2e07a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e07c9 . _:2e07c9 a owl:Class; owl:unionOf _:2e07d9 . _:2e07d9 rdf:first ; rdf:rest _:2e07e9 . _:2e07e9 rdf:first ; rdf:rest rdf:nil . _:2e07f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0809 . _:2e0809 a owl:Class; owl:intersectionOf _:2e0819 . _:2e0819 rdf:first ; rdf:rest _:2e0839 . _:2e0839 rdf:first _:2e0829; rdf:rest rdf:nil . _:2e0829 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0859 . _:2e0859 a owl:Class; owl:unionOf _:2e0869 . _:2e0869 rdf:first ; rdf:rest _:2e0879 . _:2e0879 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "epitope"@en; owl:equivalentClass _:2e0889; rdfs:subClassOf , _:2e08c9, _:2e08d9, _:2e08e9; "epitope"; "antigenic determinant"; "IEDB"@en; "IEDB"@en; "a material entity bearing the epitope role"@en; ; . _:2e0889 a owl:Class; owl:intersectionOf _:2e0899 . _:2e0899 rdf:first ; rdf:rest _:2e08b9 . _:2e08b9 rdf:first _:2e08a9; rdf:rest rdf:nil . _:2e08a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e08c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e08d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e08e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "epitope binding by adaptive immune receptor"@en; rdfs:subClassOf , , _:2e08f9, _:2e0909, _:2e0919, _:2e0929; "epitope binding by adaptive immune receptor"; "IEDB"@en; "IEDB"@en; "OBI : 'significant enough to trigger an immune response' does not necessarily mean an 'adaptive immune response', right? (otherwise this process would apply only for immunogens, and not more generally to any antigen)"; "is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding."@en; ; . _:2e08f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0909 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0929 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "adaptive immune receptor"@en; owl:equivalentClass _:2e0939; rdfs:subClassOf ; "adaptive immune receptor"; "adaptive immune receptor complex"; "GO (this class should eventually come from GO, not OBI)"; "IEDB"@en; "IEDB"@en; "is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes."@en; ; . _:2e0939 a owl:Class; owl:unionOf _:2e0949 . _:2e0949 rdf:first ; rdf:rest _:2e0959 . _:2e0959 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "disposition to be bound by an adaptive immune receptor"@en; rdfs:subClassOf , _:2e0969; "disposition to be bound by an adaptive immune receptor"; "epitope disposition"; "IEDB"@en; "IEDB"@en; "Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor."@en; ; . _:2e0969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "adjuvant role"@en; rdfs:subClassOf , _:2e0979; "adjuvant role"; "adjuvent role"; "Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response."@en; "IEDB"@en; "IEDB"@en; ; . _:2e0979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0989 . _:2e0989 a owl:Class; owl:intersectionOf _:2e0999 . _:2e0999 rdf:first ; rdf:rest _:2e09b9 . _:2e09b9 rdf:first _:2e09a9; rdf:rest rdf:nil . _:2e09a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "immunization"@en; rdfs:subClassOf ; "Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope)."; "immunization"; "IEDB"@en; "IEDB"@en; "The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope."@en; ; . a owl:Class; rdfs:label "pathological bodily process"; rdfs:subClassOf ; "creation date: 2009-06-23T11:54:29Z"; "A bodily process that is clinically abnormal."@en; "Albert Goldfain"; "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf"; . a owl:Class; rdfs:label "disease course"; rdfs:subClassOf ; "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf"; "Albert Goldfain"; "creation date: 2009-06-23T11:55:44Z"; "The totality of all processes through which a given disease instance is realized."@en; . a owl:Class; rdfs:label "pathological formation"; rdfs:subClassOf , , _:2e09c9; "Albert Goldfain"; "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf"; "creation date: 2009-07-13T02:14:59Z"; rdfs:comment "Note that htis class does not classify as a pathological anatomical structure, because such structures are defined in OGMS as being anatomical structures in the FMA sense (ie only cannonical structures)."; "OGMS (is the class restriction placed on this class in ReO in agreement with the intended meaning of this class?)"; "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en; . _:2e09c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "pathological anatomical structure"; owl:equivalentClass _:2e09d9; rdfs:subClassOf , , _:2e0a49; "creation date: 2009-07-13T02:14:05Z"; "OGMS (is class restriction placed on this class in ReO in agreement with the intended meaning of this class? Correct value for the axiom could be 'disease course process' instead of or in addition to 'pathological bodily process'?)"; "Albert Goldfain"; "An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs."@en; "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf"; . _:2e09d9 a owl:Class; owl:intersectionOf _:2e09e9 . _:2e09e9 rdf:first ; rdf:rest _:2e0a09 . _:2e0a09 rdf:first _:2e09f9; rdf:rest rdf:nil . _:2e09f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0a19 . _:2e0a19 a owl:Class; owl:unionOf _:2e0a29 . _:2e0a29 rdf:first ; rdf:rest _:2e0a39 . _:2e0a39 rdf:first ; rdf:rest rdf:nil . _:2e0a49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0a59 . _:2e0a59 a owl:Class; owl:unionOf _:2e0a69 . _:2e0a69 rdf:first ; rdf:rest _:2e0a79 . _:2e0a79 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "portion of pathological body substance"; rdfs:subClassOf , , _:2e0a89; "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf"; "Albert Goldfain"; "creation date: 2009-07-13T02:15:17Z"; "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en; . _:2e0a89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "pathological transformation"; rdfs:subClassOf ; "creation date: 2009-07-13T02:17:07Z"; "Albert Goldfain"; "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf"; "A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure."@en; . a owl:Class; rdfs:label "pathological derivation"; rdfs:subClassOf ; "creation date: 2009-07-13T02:17:24Z"; "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf"; "Albert Goldfain"; "A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier."@en; . a owl:Class; rdfs:label "pathological invasion"; rdfs:subClassOf ; "Albert Goldfain"; "creation date: 2009-07-13T02:17:47Z"; "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf"; "TODO: Define."@en; . a owl:Class; rdfs:label "color"; rdfs:subClassOf ; "A composite chromatic quality composed of hue, saturation and intensity parts."; "colour", "relative color"; , . a owl:Class; rdfs:label "fluorescence"; rdfs:subClassOf ; "A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together."; "PATO (OBIs contention is that fluorescence is a disposition rather than a quality)"; "PATO has this as a quality . . . if we decide this is so, place as child of PATO:luminous flux in the quality branch of ReO"; , . a owl:Class; rdfs:label "biological sex"; rdfs:subClassOf ; "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved."; , . a owl:Class; rdfs:label "morphology"; rdfs:subClassOf ; "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure."; "PERSON: Matthew Brush"; """A physical object quality inhering in the bearer by virtue of the bearer's size or shape or structure. """@en; , . a owl:Class; rdfs:label "size"; rdfs:subClassOf ; "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude."; . a owl:Class; rdfs:label "length"; rdfs:subClassOf ; "A 1-D extent quality which is equal to the distance between two points."; . a owl:Class; rdfs:label "mass"; rdfs:subClassOf ; "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter."; ; , , . a owl:Class; rdfs:label "viability"; rdfs:subClassOf ; "An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population."; , . a owl:Class; rdfs:label "colored"; rdfs:subClassOf ; "A color quality inhering in a bearer by virtue of the bearer's having color."; "need to decide how to treat colored (as a disposition or a quality), since, like fluorescence, the emission of color by an object requires certain conditions to be met (namely, the object must be placed in some amount of light)"; , . a owl:Class; rdfs:label "female"; rdfs:subClassOf ; "A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes."; , . a owl:Class; rdfs:label "male"; rdfs:subClassOf ; "A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes."; , . a owl:Class; rdfs:label "physical quality"; rdfs:subClassOf ; "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities."; "relational physical quality"; "relational physical quality"; . a owl:Class; rdfs:label "physical object quality"; rdfs:subClassOf ; "A quality which inheres in a continuant."; rdfs:comment "Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles."; "monadic quality of a continuant", "multiply inhering quality of a physical entity ", "quality of a continuant", "quality of a single physical entity", "quality of an object", "quality of continuant"; , . a owl:Class; rdfs:label "electromagnetic (EM) radiation quality"; rdfs:subClassOf ; "A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation."; , . a owl:Class; rdfs:label "luminous flux"; rdfs:subClassOf ; "A scalar optical quality which obtains by the magnitude of the light emitted by the bearer."; "debatable here to whether colored is a quality or a disposition, as, similar to fluorescence, the emisison of colored light depends on certain conditions (ie it must be placed in light to emit light of a different wavelength)"; , . a owl:Class; rdfs:label "optical quality"; rdfs:subClassOf ; "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light."; , . a owl:Class; rdfs:label "hermaphrodite"; rdfs:subClassOf ; "A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual."; "intersex"; , . a owl:Class; rdfs:label "cellular quality"; owl:equivalentClass _:2e0a99; rdfs:subClassOf , _:2e0b09; "A monadic quality of continuant that exists at the cellular level of organisation."; "PATO (suggest that PATO consider adopting our modeling for cell qualities and cell morphology. In PATO, cellular quality appears to be disjoint with morphology - but there are cell morphologies captured in PATO under the morphology class. In ReO, we added an equivalent class statement to cellular quality and created a cellular morphology subclass of morphology, so that cellular morphology qualities could be asserted under morphology, and the reasoner would classify them, as inferred children of cellular quality)"; rdfs:comment "cellular qualities inhere in entities at the cellular level of granularity, including cells and cell cultures"; , . _:2e0a99 a owl:Class; owl:intersectionOf _:2e0aa9 . _:2e0aa9 rdf:first ; rdf:rest _:2e0ac9 . _:2e0ac9 rdf:first _:2e0ab9; rdf:rest rdf:nil . _:2e0ab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0ad9 . _:2e0ad9 a owl:Class; owl:unionOf _:2e0ae9 . _:2e0ae9 rdf:first ; rdf:rest _:2e0af9 . _:2e0af9 rdf:first ; rdf:rest rdf:nil . _:2e0b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0b19 . _:2e0b19 a owl:Class; owl:unionOf _:2e0b29 . _:2e0b29 rdf:first ; rdf:rest _:2e0b39 . _:2e0b39 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "adhesivity"; rdfs:subClassOf ; "An emergent molecular quality that arises by virtue of the bearer's disposition to exhibit molecular attraction to another entity in contact."; rdfs:comment "The definition is general enough to cover adhesion arising from different kinds of chemical bonding/forces, although for PATO this term will most commonly used for cellular adhesion. See also GO:0031589 \"cell-substrate adhesion\"."; "adhesiveness"; , . a owl:Class; rdfs:label "cellular adhesivity"; rdfs:subClassOf ; "A cellular quality that exists by virtue of the disposition of the cell to adhere to other cells and molecules, through the emergent action of the molecular parts of the cell surface."; "PATO (this intermediate class seems redundant)"; , . a owl:Class; rdfs:label "solubility"; rdfs:subClassOf ; "A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid."; . a owl:Class; rdfs:label "soluble in"; rdfs:subClassOf ; "A solubility quality inhering in a substance by virtue of the bearer's disposition to dissolve in a liquid."; "soluble"; . a owl:Class; rdfs:label "radiation quality"; rdfs:subClassOf ; "A quality that inheres in an bearer by virtue of how that bearer interacts with radiation."; , . a owl:Class; rdfs:label "activity (of a radionuclide)"; rdfs:subClassOf ; "A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate."; "radioactivity"; , . a owl:Class; rdfs:label "radioactive"; rdfs:subClassOf ; "A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity."; , . a owl:Class; rdfs:label "pseudohermaphrodite"; rdfs:subClassOf ; "A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex."; , . a owl:Class; rdfs:label "male pseudohermaphrodite"; rdfs:subClassOf ; "A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female."; , . a owl:Class; rdfs:label "female pseudohermaphrodite"; rdfs:subClassOf ; "A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male."; , . a owl:Class; rdfs:label "phenotypic sex"; rdfs:subClassOf ; , . a owl:Class; rdfs:label "immortal"; rdfs:subClassOf ; "A quality inhering in a bearer by virtue of the bearer's disposition to being capable of indefinite growth or division."; , . a owl:Class; rdfs:label "organismal quality"; rdfs:subClassOf ; "A quality that inheres in an entire organism or part of an organism."; , . a owl:Class; rdfs:label "molecular quality"; owl:equivalentClass _:2e0b49; rdfs:subClassOf , _:2e0b89; "A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc."; "relational molecular quality"; . _:2e0b49 a owl:Class; owl:intersectionOf _:2e0b59 . _:2e0b59 rdf:first ; rdf:rest _:2e0b79 . _:2e0b79 rdf:first _:2e0b69; rdf:rest rdf:nil . _:2e0b69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0b89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polarity"; rdfs:subClassOf ; "A molecular quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole."; rdfs:comment "Polarity refers to a separation of electric charge leading to a molecule or its chemical groups having an electric dipole or multipole moment. Molecular polarity is dependent on the difference in electronegativity between atoms in a compound and the asymmetry of the compound's structure. Polarity underlies a number of physical properties including surface tension, solubility, and melting- and boiling-points."; . a owl:Class; rdfs:label "polar polarity"; rdfs:subClassOf ; "Polar polarity is a quality that inheres in a molecular entity when the molecular entity is polar, i.e. does possess an electric dipole."; . a owl:Class; rdfs:label "nonpolar polarity"; rdfs:subClassOf ; "A molecular quality which inheres in a molecular entity when the molecular entity does not possess an electrical dipole."; . a owl:Class; rdfs:label "protein"; owl:equivalentClass _:2e0b99; rdfs:subClassOf , _:2e0bd9, _:2e0c19, _:2e0c29; "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA."; rdfs:comment "Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].", "Note that bioengineered proteins produced in cells or extracts via ribosome mediated translation, but as part of some planned process, are included here."; "Note that ChEBI:protein is defined such as to consist minimally of one polypeptide chain synth at the ribosome, such that proteins can consist of more than one polyppetide chain. this is different thatn the PRO:protein class used here, that excludes protein complexes with more than one chain."; "protein polypeptide chain", "protein amino acid chain"; "a polypeptide chain that is synthesized through ribosome-mediated translation"; "ChEBI:protein polypeptide chain (CHEBI_16541)"; "PRO", . _:2e0b99 a owl:Class; owl:intersectionOf _:2e0ba9 . _:2e0ba9 rdf:first ; rdf:rest _:2e0bc9 . _:2e0bc9 rdf:first _:2e0bb9; rdf:rest rdf:nil . _:2e0bb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0bd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0be9 . _:2e0be9 a owl:Class; owl:unionOf _:2e0bf9 . _:2e0bf9 rdf:first ; rdf:rest _:2e0c09 . _:2e0c09 rdf:first ; rdf:rest rdf:nil . _:2e0c19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0c29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "post-translationally modified amino-acid residue"; rdfs:subClassOf ; "A modified amino-acid residue that was modified after its incorporation into an amino acid chain."; rdfs:comment "This includes any residue modification that occurs once translation has begun, and thus includes what are usually considered co-translational modifications."; "post-translationally modified amino acid chain residue"; "obsolete_post-translationally modified amino-acid residue"; . a owl:Class; rdfs:label "pre-translationally modified amino-acid residue"; rdfs:subClassOf ; "A modified amino-acid residue that was modified before its incorporation into an amino acid chain."; rdfs:comment "PRO needs to refer to such residues as distinct from the standard set of amino acids. These are produced exclusively by modification of amino acids acylated to special tRNA before incorporation by ribosomes into proteins. [PSI-MOD]."; "non-standard encoded protein residue", "pre-translationally modified amino acid chain residue"; . a owl:Class; rdfs:label "amino acid chain"; rdfs:subClassOf , , _:2e0c39, _:2e0c49, _:2e0c59, _:2e0c69; "A polymer of amino acids linked by peptide bonds."; "Polypeptides are defined/distinguished from other molecular entities based strictly on structural qualifications, as described in the definition. Subclassing of the polypeptide class is based on how the polypeptide is made, with a first level distinction between 'proteins' generated at the ribosome, and 'synthetic polypeptides' generated by in vitro direct chemical synthesis. Proteins are further subclassed based on mechanism of production into 'bioengineered proteins' that are produced in a host organism that expresses the protein from recombinant DNA , and 'naturally produced proteins' that are generated in the absence of such 'experimental intent'. "; "amino acid chain", "peptide"; "a polymer having monomeric constituents that are amino acids joined via peptide bonds"; "polypeptide"; "ChEBI:peptide (CHEBI_16670)"; "PRO", ; rdfs:comment "polypeptides (aka amino acid chains), as macromolecules, are defined here based on their composition from repating monomeric subunits, and not by some size/molecular weight requirement. Thus, a di-peptide or a 1000 residue protein are both polypeptides." . _:2e0c39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0c49 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e0c59 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e0c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "proteolytic cleavage product"; rdfs:subClassOf ; "An amino acid chain produced as the result of peptide bond cleavage of a longer amino acid chain."; "obsolete_proteolytic cleavage product"; "PRO", ; "not needed for now" . a owl:Class; rdfs:label "modified amino-acid residue"; rdfs:subClassOf ; "An amino-acid residue that is covalently modified by chemical alteration to the side chain or backbone atoms."; "modified amino acid chain residue"; . a owl:Class; rdfs:label "reagent"@en; owl:equivalentClass _:2e0c79; rdfs:subClassOf , _:2e0cb9, _:2e0cc9; """The reagent hierachy contains a core set of reagent classes pulled together from their asserted positions within the material entity hierarchy. The presentation/organization of these classes here is meant for easy and intuitive navigability, and thus presents recognizable classes of reagents as its top level children. As there are also several defined equivalent classes presented in this hierarchy, a given class of reagents may be found in more than one location. For example, a plasmid expressing an siRNA molecule targeted against a cellular gene product will classify as a nucleic acid reagent > DNA construct > siRNA construct, as well as a gene knockdown reagent>RNAi reagent > siRNA reagent (based on the function of the siRNA product of this plasmid)."""; "biomedical research reagent"; rdfs:comment """1. Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily particpate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. 2. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. 3. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique)."""; "a material entity that bears a reagent role, such that it is intended to be applied in a scientific technique to participate in a chemical interaction facilitating the generation of knowledge about some distinct entity, or the generation of some distinct material specified output"; """At the class level, 'reagents' are defined by bearing a 'reagent role'. However, the nebulous/intractable nature of when and how this role is gained for a given instance - in that it relies on knowing which instances are subject to an agents intentional designs - make specifying the extensions of 'reagent' classes a imprecise and impractical pursuit. This is generally true for all 'role-based' classes such as reagents, specimens, study-subjects, etc. For this reason, we were forced to take a more practical (if less ontologically rigorous) approach in modeling ReO, and interpret the bearing of a reagent role loosely to apply to classes whose instances, when processed/prepared in some way, are CONVNETIONALLY are used as reagents. This is relatively straight-forward for materials that exist only as synthetic or manufactured products (ie are not naturally produced) - as all are created de novo according to the intent of some agent. In ReO, classes of synthetic molecules or manufactured materials that are conventionally used as reagents are given a reagent role, even if it may not be the case that every instances will be subject of some agents intent to apply it experimentally as a reagent. Examples include Alexafluors, synthetic oligos, and recombinant plasmids, cell lines, and microarrays. Classes representing materials that are conventionally used as reagents but can occur naturally present a different challenge. Examples include sodium chloride, proteins such as bovine serum albumin (BSA), or antibiotics such as gentimycin. Here, the 'universal' class of all instances of such entities cannot be said to bear a reagent role because not all instances have been processed for human application (e.g. salt in the Great Salt Lake, or BSA in the blood of a grazing cow do not bear reagent roles). In such cases, ReO imports or creates universal classes (e.g. ChEBI:sodium chloride), and subclasses these universals to describe the subset of instances that have been processed so as to be applied as reagents. This subclass is logically defined by bearing a 'reagent role'. For example, ReO:sodium chloride reagent = ChEBI:sodium chloride and has_role some 'reagent role', and the ReO:BSA reagent class bears a 'reagent role' and represents the subset of all BSA that has been processed for potential experimental application. In this way, reagent classes are asserted according to their 'natural type', and a reasoner can create a stand-alone hierarchy of all classes bearing a reagent role under the defined 'reagent' class (= 'material entity' and has_role some 'reagent role')""" . _:2e0c79 a owl:Class; owl:intersectionOf _:2e0c89 . _:2e0c89 rdf:first ; rdf:rest _:2e0ca9 . _:2e0ca9 rdf:first _:2e0c99; rdf:rest rdf:nil . _:2e0c99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0cc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "reagent role"@en; rdfs:subClassOf , _:2e0cd9, _:2e0ce9, _:2e0d39; "OBI (need to have discussions with OBI to clearly define the reagent role, and adopt a common representation in ReO and OBI)"; rdfs:comment "In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique)."; "biomedical research reagent role"; """An Illustrative Example of Experimental Roles ('reagent role', 'evaluant role', 'analyte role', and 'target of material addition role') Realized in a Series of Three Sequential Techniques: 1. A Material Processing Technique to Generatr a Labeled Antibody In a antibody labeling technique, the fluorochrome label plays a 'reagent role' (along with any buffers or enzymes used in the technique), and the antibody plays a 'target of material addition role' (in a material processing technique such as antibody labeling, this role is analogous to the 'evaluant role' in an assay). 2. An Assay to Determine Degree of Labeling In an assay to determine the efficiency of labeling of the antibody, the labeled antibody plays an evaluant role, the fluorochrome plays an analyte role, and any buffers or enzymes used in the assay play reagent roles 3. An Assay to Detect Expression Level and Location of a Protein of Interest In a immunocytochemistry assay applying this validated labeled antibody, the cells play an evaluant role, the endogenous protein of interest plays an analyte role, and the labeled antibody probe plays a reagent role (as do any buffers, fixatives, and detergents, etc use din the assay). This example illustrates how a given material entity (an antibody for example) can bear and realize many different roles (an evaluant role, a reagent role, and a target or material addition role), and how these roles are realized in different processes."""; """At the class level, 'reagents' are defined by bearing a 'reagent role'. However, the nebulous/intractable nature of when and how this role is gained for a given instance - in that it relies on knowing which instances are subject to an agents intentional designs - make specifying the extensions of 'reagent' classes a imprecise and impractical pursuit. This is generally true for all 'role-based' classes such as reagents, specimens, study-subjects, etc. For this reason, we were forced to take a more practical (if less ontologically rigorous) approach in modeling ReO, and interpret the bearing of a reagent role loosely to apply to classes whose instances, when processed/prepared in some way, are CONVNETIONALLY are used as reagents. This is relatively straight-forward for materials that exist only as synthetic or manufactured products (ie are not naturally produced) - as all are created de novo according to the intent of some agent. In ReO, classes of synthetic molecules or manufactured materials that are conventionally used as reagents are given a reagent role, even if it may not be the case that every instances will be subject of some agents intent to apply it experimentally as a reagent. Examples include Alexafluors, synthetic oligos, and recombinant plasmids, cell lines, and microarrays. Classes representing materials that are conventionally used as reagents but can occur naturally present a different challenge. Examples include sodium chloride, proteins such as bovine serum albumin (BSA), or antibiotics such as gentimycin. Here, the 'universal' class of all instances of such entities cannot be said to bear a reagent role because not all instances have been processed for human application (e.g. salt in the Great Salt Lake, or BSA in the blood of a grazing cow do not bear reagent roles). In such cases, ReO imports or creates universal classes (e.g. ChEBI:sodium chloride), and subclasses these universals to describe the subset of instances that have been processed so as to be applied as reagents. This subclass is logically defined by bearing a 'reagent role'. For example, ReO:sodium chloride reagent = ChEBI:sodium chloride and has_role some 'reagent role', and the ReO:BSA reagent class bears a 'reagent role' and represents the subset of all BSA that has been processed for potential experimental application. (NOTE that BSA also bears many other reagent roles - see editor note on this class). In this way, reagent classes are asserted according to their 'natural type', and a reasoner can create a stand-alone hierarchy of all classes bearing a reagent role under the defined 'reagent' class (= 'material entity' and has_role some 'reagent role')""", """Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily particpate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.""", "When we assert that some class of molecules has a more specific reagent role - for example that calcium phosphate has_role some 'transfection reagent role' - we indicate that this class of molecules CONVENTIONALLY is used for the purpose indicated in the role - not that every instance of a calcium phosphate reagent is intended to be used this way (because there are other experimental applications for calcium phosphate as a reagent besides transfections). This understanding may not be ideal/ontologically rigorous - but it is practical for the type of modeling we need to do."; "a role inhering in a material entity intended to be applied in a scientific technique and participate in a chemical interaction that facilitates the generation of knowledge about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer." . _:2e0cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0ce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0cf9 . _:2e0cf9 a owl:Class; owl:intersectionOf _:2e0d09 . _:2e0d09 rdf:first ; rdf:rest _:2e0d29 . _:2e0d29 rdf:first _:2e0d19; rdf:rest rdf:nil . _:2e0d19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0d39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0d49 . _:2e0d49 a owl:Class; owl:intersectionOf _:2e0d59 . _:2e0d59 rdf:first ; rdf:rest _:2e0d79 . _:2e0d79 rdf:first _:2e0d69; rdf:rest rdf:nil . _:2e0d69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0d89 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e0d99 . _:2e0d99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0da9 . _:2e0da9 a owl:Class; owl:intersectionOf _:2e0db9 . _:2e0db9 rdf:first ; rdf:rest _:2e0dd9 . _:2e0dd9 rdf:first _:2e0dc9; rdf:rest rdf:nil . _:2e0dc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "antibody reagent"; owl:equivalentClass _:2e0de9; rdfs:subClassOf , , , _:2e0e29, _:2e0e39, _:2e0ec9; "A reagent that is comprised of immunoglobulins produced by B cells in response to an immunogen. Antibody reagents are typically bioengineered to be applied in some experimental technique to recognize and probe a specific molecular antigen, or larger material antibody target containing such an antigen. This recognition can be exploited to detect or isolate some target, or to modulate the activity of some target molecule. "; "Consult the Antibody Ontology group (http://neurocommons.org/page/Semantic_resources_project/Antibodies) to coordinate development and implementation of this model in ReO and OBI."; "nearly all antibody reagents are 'bioengineered' through some 'antibody production' process (ie manufactured using an organism experimentally immunized to produce an antibody of interest). A rare exception are those that are collected from some organism that was not subject to some controlled immunization technique, but rather naturally exposed to some immunogen that resulted in production of an antibody that has experimental value as a reagent. To account for these outliers, 'antibody reagent' is not placed below 'bioengineered protein reagent', and antibodies are modeled as being the specified output of some 'antibody production' or 'specimen collection from organism'." . _:2e0de9 a owl:Class; owl:intersectionOf _:2e0df9 . _:2e0df9 rdf:first ; rdf:rest _:2e0e19 . _:2e0e19 rdf:first _:2e0e09; rdf:rest rdf:nil . _:2e0e09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0e39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0e49 . _:2e0e49 a owl:Class; owl:intersectionOf _:2e0e59 . _:2e0e59 rdf:first ; rdf:rest _:2e0e79 . _:2e0e79 rdf:first _:2e0e69; rdf:rest rdf:nil . _:2e0e69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0e89 . _:2e0e89 a owl:Class; owl:intersectionOf _:2e0e99 . _:2e0e99 rdf:first ; rdf:rest _:2e0eb9 . _:2e0eb9 rdf:first _:2e0ea9; rdf:rest rdf:nil . _:2e0ea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e0ec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0ed9 . _:2e0ed9 a owl:Class; owl:unionOf _:2e0ee9 . _:2e0ee9 rdf:first ; rdf:rest _:2e0ef9 . _:2e0ef9 rdf:first ; rdf:rest rdf:nil . _:2e0f09 a owl:Axiom; "note here that we include in the axiom the part about being output from an antibody production technique or an antibody colleciton technique because we need to account for antibodies that are collected from some natural source with the intention of using then as a reagent."; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e0f19 . _:2e0f19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e0f29 . _:2e0f29 a owl:Class; owl:unionOf _:2e0f39 . _:2e0f39 rdf:first ; rdf:rest _:2e0f49 . _:2e0f49 rdf:first ; rdf:rest rdf:nil . _:2e0f59 a owl:Axiom; "Note here that we apply the more specific reagent role: 'molecular probe role'. This is becasue all antibody reagents are considered molecular probes, as their applications include serving as labels/trackers, molecular 'captors', or molecular effectors that activate or inhibit/block some molecular target."; owl:annotatedSource ; owl:annotatedProperty owl:equivalentClass; owl:annotatedTarget _:2e0f69 . _:2e0f69 a owl:Class; owl:intersectionOf _:2e0f79 . _:2e0f79 rdf:first ; rdf:rest _:2e0f99 . _:2e0f99 rdf:first _:2e0f89; rdf:rest rdf:nil . _:2e0f89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleic acid reagent"; owl:equivalentClass _:2e0fa9; rdfs:subClassOf , , _:2e1019; owl:disjointWith ; "PERSON: Melissa Haendel"; "a nucleic acid or nucleic acid analog that bears a reagent role, in virtue of its being intended for application in a scientific technique to participate in a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material output."; "http://en.wikipedia.org/wiki/Nucleic_acid"; "ERO (if they import this class, need to agree that things like nucleic acid analogs are included. Likely OK as ERO has morpholino as a nucleic acid reagent. . . also consider possibility of including things like nucleotides, if this will be intuitive/useful for users???)"; rdfs:comment "nucleic acid reagents are nucleic acids or nucleic acid analogs that are applied experimentally as reagents in an assay or technique, and include things like primers, oligonucleotides, siRNAs, and recombinant plasmids and other DNA constructs."; . _:2e0fa9 a owl:Class; owl:intersectionOf _:2e0fc9 . _:2e0fc9 rdf:first _:2e0fb9; rdf:rest _:2e1009 . _:2e0fb9 a owl:Class; owl:unionOf _:2e0fd9 . _:2e0fd9 rdf:first ; rdf:rest _:2e0fe9 . _:2e0fe9 rdf:first ; rdf:rest rdf:nil . _:2e1009 rdf:first _:2e0ff9; rdf:rest rdf:nil . _:2e0ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "chemical reagent"; owl:equivalentClass _:2e1029; rdfs:subClassOf , _:2e10b9, _:2e10c9; "a molecular entity that is not an information macromolecule (ie not a nucleic acid, polypeptide, or analogs of these macromolecules), and which bears a reagent role in virtue of its being intended for application in a scientific technique to participate in a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material output."; "Chemical reagents by definition do not carry genetic sequence information, and can include 'small molecules', salts, ions, and atomic entities, as well as carbohydrate and lipid molecules."; """A chemical reagent is a molecular reagent that is not an information macromolecule (ie is not composed of repeating residues or amino acid or nucleotide or their analogs, and thus excludes protein reagents and nucleic acid reagents). This distinction is made as such a high level to reflect the special status that nucleic acid and proteins hold in biomedical research - and the special attributes andd applications they have - owing in part to their genetic biological origin and bearing of genetic sequence information. Accordingly, these classes afforded their own high level category in the ReO reagent hierarchy. Chemical reagents are primarily bioactive organic small molecules, but also include things like lipids and carbohydrates and inorganic salts and atomic/elemental entities."""; """ERO - this class should replace the ERO chemical reagent class, however, the subclasses in ERO are defined as 'compounds'. Problems with this include (1) the notion of a compound has is not modeled in ChEBI or other OBO Foundry ontologies (or is it . . . i think ChEBI classes are constured to represent compunds), and this its use here hinders interoperability; (2) restricting chemical reagents to compounds means that things like molecular oxygen or P32 cannot be included - as these are not truly compounds (ie they are not composed of more than one kind of atom/element) (but at least in the case of P32 as a reagent - this never come as free-standing atoms - but rather as part of some larger molecule). Seems like ERO should adopt the use of ChEBI:'molecular entity' here, as this class considers atoms, elements, molecules comprised of only one type of atom, ionic compounds and salts, and molecular complexes - which should cover all ERO's use cases. ERO could then use a ERO-specific label to present these classes as deisred to users (if they want to continue to call these compounds)"""; . _:2e1029 a owl:Class; owl:intersectionOf _:2e1039 . _:2e1039 rdf:first ; rdf:rest _:2e1059 . _:2e1059 rdf:first _:2e1049; rdf:rest _:2e10a9 . _:2e1049 a owl:Class; owl:complementOf _:2e1069 . _:2e1069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1079 . _:2e1079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1089 . _:2e1089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e10a9 rdf:first _:2e1099; rdf:rest rdf:nil . _:2e1099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e10b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e10c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polypeptide reagent"; owl:equivalentClass _:2e10d9; rdfs:subClassOf , , _:2e1149; "a polypeptide or polypeptide complex that bears a reagent role, in virtue of its being intended for application in a scientific technique to participate in a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material output."; "peptide reagent", "amino acid chain reagent"; "Note here that the term 'polypeptide' is synonymous in ReO with 'peptide' and that these terms do not formally impose any length/size restrictions/connotations. We will use the term 'oligopeptide' to indicate shorter peptides, and provide a recommended length cutoff for such molecules."; . _:2e10d9 a owl:Class; owl:intersectionOf _:2e10f9 . _:2e10f9 rdf:first _:2e10e9; rdf:rest _:2e1139 . _:2e10e9 a owl:Class; owl:unionOf _:2e1109 . _:2e1109 rdf:first ; rdf:rest _:2e1119 . _:2e1119 rdf:first ; rdf:rest rdf:nil . _:2e1139 rdf:first _:2e1129; rdf:rest rdf:nil . _:2e1129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "reagent library"; owl:equivalentClass _:2e1159; rdfs:subClassOf , , _:2e1299, _:2e1319, _:2e1399; "a reagent that is a collection of reagents of the same type. Each member of this collection is either a single reagent (e.g. an organism or cell line), or, more typically, each member of the collection is itself a collection of a single type of molecule (e.g. a collection of identical molecules, or genetically identical bacteria)."; . _:2e1159 a owl:Class; owl:intersectionOf _:2e1169 . _:2e1169 rdf:first ; rdf:rest _:2e1189 . _:2e1189 rdf:first _:2e1179; rdf:rest _:2e1219 . _:2e1179 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e1199 . _:2e1199 a owl:Class; owl:intersectionOf _:2e11a9 . _:2e11a9 rdf:first ; rdf:rest _:2e11c9 . _:2e11c9 rdf:first _:2e11b9; rdf:rest rdf:nil . _:2e11b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e11d9 . _:2e11d9 a owl:Class; owl:unionOf _:2e11e9 . _:2e11e9 rdf:first ; rdf:rest _:2e11f9 . _:2e11f9 rdf:first ; rdf:rest rdf:nil . _:2e1219 rdf:first _:2e1209; rdf:rest rdf:nil . _:2e1209 a owl:Restriction; owl:onProperty ; owl:onClass _:2e1229; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e1229 a owl:Class; owl:intersectionOf _:2e1239 . _:2e1239 rdf:first ; rdf:rest _:2e1259 . _:2e1259 rdf:first _:2e1249; rdf:rest rdf:nil . _:2e1249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1269 . _:2e1269 a owl:Class; owl:unionOf _:2e1279 . _:2e1279 rdf:first ; rdf:rest _:2e1289 . _:2e1289 rdf:first ; rdf:rest rdf:nil . _:2e1299 a owl:Restriction; owl:onProperty ; owl:onClass _:2e12a9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e12a9 a owl:Class; owl:intersectionOf _:2e12b9 . _:2e12b9 rdf:first ; rdf:rest _:2e12d9 . _:2e12d9 rdf:first _:2e12c9; rdf:rest rdf:nil . _:2e12c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e12e9 . _:2e12e9 a owl:Class; owl:unionOf _:2e12f9 . _:2e12f9 rdf:first ; rdf:rest _:2e1309 . _:2e1309 rdf:first ; rdf:rest rdf:nil . _:2e1319 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e1329 . _:2e1329 a owl:Class; owl:intersectionOf _:2e1339 . _:2e1339 rdf:first ; rdf:rest _:2e1359 . _:2e1359 rdf:first _:2e1349; rdf:rest rdf:nil . _:2e1349 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1369 . _:2e1369 a owl:Class; owl:unionOf _:2e1379 . _:2e1379 rdf:first ; rdf:rest _:2e1389 . _:2e1389 rdf:first ; rdf:rest rdf:nil . _:2e1399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA construct"; owl:equivalentClass _:2e13a9; rdfs:subClassOf , , _:2e1409, _:2e1419, _:2e1429; "A double-stranded DNA molecule capable of autonomous replication, used as a vehicle to transfer foreign genetic material into a host cell. Constructs can be engineered to carry inserts of DNA from external sources, for purposes of cloning and propagation or gene expression in host cells."; "DNA vector", "vector replicon", "recombinant DNA construct", "recombinant construct", "recombinant DNA vector", "engineered DNA vector", "construct", " engineered DNA construct"; "OBI_0000731 recombinant vector"; "OBI (consider aligning/merging/importing OBI 'recombinant vector' class)"; """1. Note that 'DNA construct' in ReO includes both empty/backbone vectors as well as 'recombinant constructs' into which some sequences of interest have been cloned. Its primary children include 'artificial chromosome' and 'plasmid construct', which likewise account for both empty and recombinant versions. 2. We have created a defined 'recombinant construct' class to illustrate modeling of constructs that contain a cloned insert. Note that these constructs are outputs not merely of a 'DNA construct engineering' technique, but of a 'recombinant construct cloning' technique. For example, 'genomic DNA construct', and the various recombiant plasmid classes, are asserted to contain such a cloned insert, and are specified as outputs of some' recombiannt construct cloning' technique. 3. We have also created the disjoint defined classes 'cloning construct' and 'expression constirct' to illustrate modeling of these key types of constructs distinguished by their capacity to express the cloned insert in some biological system. 4. Several additional defined classes of constructs (mainly plasmids) have been implemented to illustrate the types of modeling that can be done with ReO.""" . _:2e13a9 a owl:Class; owl:intersectionOf _:2e13b9 . _:2e13b9 rdf:first ; rdf:rest _:2e13d9 . _:2e13d9 rdf:first _:2e13c9; rdf:rest _:2e13f9 . _:2e13c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e13f9 rdf:first _:2e13e9; rdf:rest rdf:nil . _:2e13e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1429 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "BAC"; rdfs:subClassOf ; "An artificial chromosome vector that contains portions of the bacterial fertility plasmid (F-plasmid). Used for transforming and cloning in bacteria, usually E. coli."; "bacterial artificial chromosome"; "http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome" . a owl:Class; rdfs:label "HAC"; rdfs:subClassOf ; "An artificial chromosome containing chromosomal features needed for replication and preservation in human cells, and used to propagate large sequences of DNA."; "Human artificial chromosome" . a owl:Class; rdfs:label "PAC"; rdfs:subClassOf ; "An artificial chromosome derived from the genome of the P1 bacteriophage. Used for transforming and cloning in bacteria, usually E. coli."; "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome" . a owl:Class; rdfs:label "YAC"; rdfs:subClassOf ; "An artificial chromosome containing chromosomal features needed for replication and preservation in yeast cells (origin, telomere, and centromere). A YAC is built using an initial circular plasmid, which is typically broken into two linear molecules using restriction enzymes to allow ligation of a sequence or gene of interest and form a single large linear piece of DNA. YACs are useful for the physical mapping of complex genomes and for the cloning of large genes. "; "http://en.wikipedia.org/wiki/Yeast_artificial_chromosome"; "yeast artificial chromosome" . a owl:Class; rdfs:label "recombinant plasmid"; owl:equivalentClass _:2e1439; rdfs:subClassOf , , _:2e1479, _:2e1489, _:2e1499, _:2e14a9; "A plasmid construct engineered in vitro to contain exogenous DNA sequences called 'construct inserts' or 'cloned inserts'. These cloned regions of DNA are maintained in some host cell through the action of various functional elements in the construct that facilitate plasmid amplification, selection, and antibiotic resistance."; "PERSON: Matthew Brush"; "engineered plasmid", "plasmid construct"; "OBI (merge with OBI_0000410:recombinant plasmid . . . but they define recombinant plasmid as expression plasmid - which is not our intent here . . note recomb plasmid OBI class is already in Obsolete classes above)"; rdfs:comment "recombinant plasmids include those intended to amplify DNA in host cell for the purpose of maintenance and cloning into other constructs (cloning plasmids), and those intended to express DNA in some target system (expression constructs)" . _:2e1439 a owl:Class; owl:intersectionOf _:2e1449 . _:2e1449 rdf:first ; rdf:rest _:2e1469 . _:2e1469 rdf:first _:2e1459; rdf:rest rdf:nil . _:2e1459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e14a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA interference plasmid"; owl:equivalentClass _:2e14b9; rdfs:subClassOf , , , _:2e1549, _:2e1559, _:2e15f9 . _:2e14b9 a owl:Class; owl:intersectionOf _:2e14c9 . _:2e14c9 rdf:first ; rdf:rest _:2e14e9 . _:2e14e9 rdf:first _:2e14d9; rdf:rest rdf:nil . _:2e14d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e14f9 . _:2e14f9 a owl:Class; owl:intersectionOf _:2e1509 . _:2e1509 rdf:first ; rdf:rest _:2e1529 . _:2e1529 rdf:first _:2e1519; rdf:rest rdf:nil . _:2e1519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1539 . _:2e1539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1549 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1569 . _:2e1569 a owl:Class; owl:intersectionOf _:2e1579 . _:2e1579 rdf:first ; rdf:rest _:2e1599 . _:2e1599 rdf:first _:2e1589; rdf:rest rdf:nil . _:2e1589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e15a9 . _:2e15a9 a owl:Class; owl:intersectionOf _:2e15b9 . _:2e15b9 rdf:first ; rdf:rest _:2e15d9 . _:2e15d9 rdf:first _:2e15c9; rdf:rest rdf:nil . _:2e15c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e15e9 . _:2e15e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e15f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1609 . _:2e1609 a owl:Class; owl:intersectionOf _:2e1619 . _:2e1619 rdf:first ; rdf:rest _:2e1639 . _:2e1639 rdf:first _:2e1629; rdf:rest rdf:nil . _:2e1629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1649 . _:2e1649 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf _:2e1659; "A recombinant plasmid expressing transcripts that are processed into small RNA molecules which target genes for post-transcriptional silencing through the RNAi pathway."; "RNAi plasmid"; . _:2e1659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1669 . _:2e1669 a owl:Class; owl:intersectionOf _:2e1679 . _:2e1679 rdf:first ; rdf:rest _:2e1699 . _:2e1699 rdf:first _:2e1689; rdf:rest rdf:nil . _:2e1689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e16a9 . _:2e16a9 a owl:Class; owl:intersectionOf _:2e16b9 . _:2e16b9 rdf:first ; rdf:rest _:2e16d9 . _:2e16d9 rdf:first _:2e16c9; rdf:rest rdf:nil . _:2e16c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e16e9 a owl:Axiom; """should the axiom say gene expression and (has_specified_output some (capable_of . . . ? . . . core question here is can a biological process have a specified output if it occurs as a specified part of a technique? """; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e16f9 . _:2e16f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1709 . _:2e1709 a owl:Class; owl:intersectionOf _:2e1719 . _:2e1719 rdf:first ; rdf:rest _:2e1739 . _:2e1739 rdf:first _:2e1729; rdf:rest rdf:nil . _:2e1729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1749 . _:2e1749 a owl:Class; owl:intersectionOf _:2e1759 . _:2e1759 rdf:first ; rdf:rest _:2e1779 . _:2e1779 rdf:first _:2e1769; rdf:rest rdf:nil . _:2e1769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1789 . _:2e1789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1799 a owl:Axiom; ""; "exploratory axiom - not sure if use of participates_in is accurate here"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e17a9 . _:2e17a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e17b9 . _:2e17b9 a owl:Class; owl:intersectionOf _:2e17c9 . _:2e17c9 rdf:first ; rdf:rest _:2e17e9 . _:2e17e9 rdf:first _:2e17d9; rdf:rest rdf:nil . _:2e17d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e17f9 . _:2e17f9 a owl:Class; owl:intersectionOf _:2e1809 . _:2e1809 rdf:first ; rdf:rest _:2e1829 . _:2e1829 rdf:first _:2e1819; rdf:rest rdf:nil . _:2e1819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dsRNA plasmid"; rdfs:subClassOf , _:2e1839; "An RNA interference plasmid engineered to express complementary strands of RNA that form double-stranded duplexes, which are processed through the RNAi pathway into short interfering RNA (siRNA) molecules used to silence target gene expression."; "double-stranded RNA plasmid" . _:2e1839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1849 . _:2e1849 a owl:Class; owl:intersectionOf _:2e1859 . _:2e1859 rdf:first ; rdf:rest _:2e1879 . _:2e1879 rdf:first _:2e1869; rdf:rest rdf:nil . _:2e1869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1889 . _:2e1889 a owl:Class; owl:intersectionOf _:2e1899 . _:2e1899 rdf:first ; rdf:rest _:2e18b9 . _:2e18b9 rdf:first _:2e18a9; rdf:rest rdf:nil . _:2e18a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e18c9 . _:2e18c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e18d9 . _:2e18d9 a owl:Class; owl:intersectionOf _:2e18e9 . _:2e18e9 rdf:first ; rdf:rest _:2e1909 . _:2e1909 rdf:first _:2e18f9; rdf:rest rdf:nil . _:2e18f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA plasmid"; rdfs:subClassOf , _:2e1919; "An RNA interference plasmid that expresses a short sequence of RNA that includes elements required for processing by endogenous microRNA processing machinery into active microRNA molecules. "; rdfs:comment "The gene specific targeting sequences in these small RNAs may or may not represent a naturally occurring miRNA, but they will contain flanking RNA regions that allow processing by endogenous miRNA pathway."; "microRNA plasmid" . _:2e1919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1929 . _:2e1929 a owl:Class; owl:intersectionOf _:2e1939 . _:2e1939 rdf:first ; rdf:rest _:2e1959 . _:2e1959 rdf:first _:2e1949; rdf:rest rdf:nil . _:2e1949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1969 . _:2e1969 a owl:Class; owl:intersectionOf _:2e1979 . _:2e1979 rdf:first ; rdf:rest _:2e1999 . _:2e1999 rdf:first _:2e1989; rdf:rest rdf:nil . _:2e1989 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e19a9 . _:2e19a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "shRNA plasmid"; rdfs:subClassOf , _:2e19b9; "An RNA interference plasmid that expresses a short sequence of RNA that forms a short hairpin duplex. This gene product is processed by endogenous RNAi pathway machinery into a small interfering RNA (siRNA) molecule used to silence target gene expression."; "http://www.medterms.com/script/main/art.asp?articlekey=25734"; "short hairpin RNA plasmid", "small hairpin RNA plasmid" . _:2e19b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e19c9 . _:2e19c9 a owl:Class; owl:intersectionOf _:2e19d9 . _:2e19d9 rdf:first ; rdf:rest _:2e19f9 . _:2e19f9 rdf:first _:2e19e9; rdf:rest rdf:nil . _:2e19e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1a09 . _:2e1a09 a owl:Class; owl:intersectionOf _:2e1a19 . _:2e1a19 rdf:first ; rdf:rest _:2e1a39 . _:2e1a39 rdf:first _:2e1a29; rdf:rest rdf:nil . _:2e1a29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1a49 . _:2e1a49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cDNA plasmid"; owl:equivalentClass _:2e1a59; rdfs:subClassOf , _:2e1ad9, _:2e1b29; "A plasmid with an insert derived from a cDNA molecule."; "PERSON: Nicole Vasilevsky"; . _:2e1a59 a owl:Class; owl:intersectionOf _:2e1a69 . _:2e1a69 rdf:first ; rdf:rest _:2e1a89 . _:2e1a89 rdf:first _:2e1a79; rdf:rest rdf:nil . _:2e1a79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1a99 . _:2e1a99 a owl:Class; owl:intersectionOf _:2e1aa9 . _:2e1aa9 rdf:first ; rdf:rest _:2e1ac9 . _:2e1ac9 rdf:first _:2e1ab9; rdf:rest rdf:nil . _:2e1ab9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e1ad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1ae9 . _:2e1ae9 a owl:Class; owl:intersectionOf _:2e1af9 . _:2e1af9 rdf:first ; rdf:rest _:2e1b19 . _:2e1b19 rdf:first _:2e1b09; rdf:rest rdf:nil . _:2e1b09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e1b29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1b39 . _:2e1b39 a owl:Class; owl:intersectionOf _:2e1b49 . _:2e1b49 rdf:first ; rdf:rest _:2e1b69 . _:2e1b69 rdf:first _:2e1b59; rdf:rest rdf:nil . _:2e1b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1b79 . _:2e1b79 a owl:Class; owl:intersectionOf _:2e1b89 . _:2e1b89 rdf:first ; rdf:rest _:2e1ba9 . _:2e1ba9 rdf:first _:2e1b99; rdf:rest rdf:nil . _:2e1b99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA cDNA plasmid"; rdfs:subClassOf ; "A cDNA plasmid that carries a small cDNA insert from a pool of size-selected cDNAs, representing putative endogenous miRNAs."; "PERSON: Matthew Brush"; "micro RNA cDNA plasmid" . a owl:Class; rdfs:label "cosmid"; rdfs:subClassOf ; "A recombinant plasmid that contains cos DNA sequences derived from the Lambda bacteriophage, which allow for DNA packaging in phage capsids for delivery by viral transduction."; "PERSON: Nicole Vasilevsky"; "cosmid"; "http://en.wikipedia.org/wiki/Cosmid" . a owl:Class; rdfs:label "fosmid"; rdfs:subClassOf ; "A recombinant plasmid that contains sequences from the bacterial F-plasmid to enable packaging in lambda phage for delivery by viral transduction."; "PERSON: Nicole Vasilevsky"; "fosmid"; "http://en.wikipedia.org/wiki/Fosmid" . a owl:Class; rdfs:label "gene trap plasmid"; rdfs:subClassOf ; "A recombinant plasmid containing a reporter gene that is only expressed upon integration in a functional gene."; "http://www.nature.com/nbt/journal/v19/n6/full/nbt0601_579.html"; . a owl:Class; rdfs:label "phagemid"; rdfs:subClassOf ; "A hybrid plasmid that carries elements from the filamentous bacteriophage M13, including the M13 origin. A phagemid can be replicated form its plasmid origin as a circular double-stranded plasmid, or replicated from its M13 origin and packaged as single stranded DNA in viral particles in the presence of a helper phage."; "http://en.wikipedia.org/wiki/Phagemid" . a owl:Class; rdfs:label "viral shuttle plasmid"; rdfs:subClassOf , _:2e1bb9; "A recombinant plasmid into which a gene of interest can be inserted, and which contains flanking sequence elements that allow for packaging of this genetic cargo into viral capsids. Viral shuttle plasmids may contain additional genes required for capsid protein production and assembly, or may require helper plasmids which produce these proteins. Cloning the gene of interest into a shuttle vector allows transferring the gene into the viral genome by means of homologous recombination in an viral packaging cell line."; "Viral shuttle plasmids are typically cloning plasmids, but some contain promoter elements that allow for direct transient expression in target cell lines (thus, they do not classify here as a type of cloning construct)"; rdfs:comment "Here we consider 'shuttle vectors/plasmids' to be those into which a gene of interest is cloned, and from which it is packaged into the viral genome/capsid for replication and expression. Notably, there are many different commercialized systems for insertion of a gene of interest into a recombiannt virus, and the 'shuttle' vectors in these systems may go by different names (e.g. 'destinationvectors/plasmids' (DEST) in Invitrogen systems that use the Gateway cloning system)."; "viral plasmid", "viral shuttle vector", "viral destination vector", "viral destination plasmid"; "http://en.wikipedia.org/wiki/Viral_vector"; . _:2e1bb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1bc9 . _:2e1bc9 a owl:Class; owl:intersectionOf _:2e1bd9 . _:2e1bd9 rdf:first ; rdf:rest _:2e1bf9 . _:2e1bf9 rdf:first _:2e1be9; rdf:rest rdf:nil . _:2e1be9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "adeno-associated virus shuttle plasmid"; rdfs:subClassOf ; "A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into baculoviral capsids for expression in target cells. Adeno-associated viral expression systems can be used with non-dividing cells, and cargo DNA has the ability to stably integrate into the host cell genome at a specific site (designated AAVS1) in the human chromosome 19."; "AAV plasmid", "adeno-associated viral plasmid"; "" . a owl:Class; rdfs:label "adenoviral shuttle plasmid"; rdfs:subClassOf ; "A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into adenoviral capsids for expression in target cells. DNA delivered by andenoviral systems does not integrate into the genome and is not replicated during cell division. The adenovirus is able to infect post-mitotic cells, making them especially useful for gene transfer into neuronal cells. "; "adenoviral plasmid" . a owl:Class; rdfs:label "baculoviral shuttle plasmid"; rdfs:subClassOf ; "A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into baculoviral capsids for expression in target cells. Baculoviral expression systems are used for transient and stable protein expression in insect cells (and related invertebrates such as arachnids and crustaceans). "; "http://cshprotocols.cshlp.org/cgi/content/extract/2006/3/pdb.prot4512"; "baculoviral plasmid" . a owl:Class; rdfs:label "lentiviral shuttle plasmid"; rdfs:subClassOf ; "A viral plasmid that is used to introduce genes into cells, which has the ability to integrate into the genome of non-dividing cells."; "http://en.wikipedia.org/wiki/Viral_vector"; "lentiviral plasmid" . a owl:Class; rdfs:label "retroviral shuttle plasmid"; rdfs:subClassOf ; "A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into retroviral capsids for expression in target cells. DNA delivered by retroviral systems can be integrated into the host genome in a stable fashion in dividing cells. "; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Viral_vector"; "retroviral plasmid" . a owl:Class; rdfs:label "yeast two-hybrid construct"; rdfs:subClassOf , _:2e1c09, _:2e1c59; "A construct used for yeast two hybrid screening assays, which is engineered to express a protein of interest fused to either the DNA-binding domain (BD) fragment or activation domain (AD) of a transcription factor. Yeast two hybrid constructs are typically plasmids or phagemids."; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Two-hybrid_screening"; . _:2e1c09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1c19 . _:2e1c19 a owl:Class; owl:intersectionOf _:2e1c29 . _:2e1c29 rdf:first ; rdf:rest _:2e1c49 . _:2e1c49 rdf:first _:2e1c39; rdf:rest rdf:nil . _:2e1c39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1c59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA reagent"; owl:equivalentClass _:2e1c69; rdfs:subClassOf , , _:2e1ca9; "deoxyribonucleic acid reagent"; "DNA oligos, DNA constructs"; "a deoxyribonucleic acid or a deoxyribonucleic acid analog that bears a reagent role"; . _:2e1c69 a owl:Class; owl:intersectionOf _:2e1c79 . _:2e1c79 rdf:first ; rdf:rest _:2e1c99 . _:2e1c99 rdf:first _:2e1c89; rdf:rest rdf:nil . _:2e1c89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1ca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA oligonucleotide"; rdfs:subClassOf , , _:2e1cb9; "DNA oligo"; "ChEBI? SOM? . . . seems like this class should exist somewhere"; "a deoxyribonucleic acid moelcule consisting of a short, linear single strand of typically 100 or fewer nucleotides" . _:2e1cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA probe"; owl:equivalentClass _:2e1cc9; rdfs:subClassOf , , _:2e1d09; "DNA-based molecular labels and microarray probes, as well as DNAs used to activate or repress the activity of some target, are all considered probes."; rdfs:comment "Note here that the term 'probe' here is interpreted generally to cover targeted molecular effectors. Application in a technique serves to target some molecular entity for a range of purposes, including detection of some target (e.g. molecular labels as probes), isolation of some target (e.g. microarray probes), or altering some biochemical property of some target (e.g. probes used for activation or inhibition of some activity, blocking progress of a polymerase, etc)."; "a DNA oligonucleotide reagent that is a single-stranded DNA molecule applied experimentally to probe the biomolecular environment of some specimen. Typically used to detect, isolate, or affect the activity of nucleic acid molecules bearing complementary sequence among a mixture of other nucleic acid molecules"; "DNA oligonucleotide label" . _:2e1cc9 a owl:Class; owl:intersectionOf _:2e1cd9 . _:2e1cd9 rdf:first ; rdf:rest _:2e1cf9 . _:2e1cf9 rdf:first _:2e1ce9; rdf:rest rdf:nil . _:2e1ce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1d09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA primer"; owl:equivalentClass _:2e1d19; rdfs:subClassOf , , _:2e1d59; "PERSON: Melissa Haendel"; "an DNA oligonucleotide that binds to some complementary nucleic acid template to serve as a starting for nucleic acid synthesis."; "http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29" . _:2e1d19 a owl:Class; owl:intersectionOf _:2e1d29 . _:2e1d29 rdf:first ; rdf:rest _:2e1d49 . _:2e1d49 rdf:first _:2e1d39; rdf:rest rdf:nil . _:2e1d39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1d59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA reagent"; owl:equivalentClass _:2e1d69; rdfs:subClassOf , , _:2e1da9; "ribonucleic acid reagent"; "an siRNa oligo, an RNA primer, a ribozyme"; "a ribonucleic acid or a ribonucleic acid analog that bears a reagent role"; . _:2e1d69 a owl:Class; owl:intersectionOf _:2e1d79 . _:2e1d79 rdf:first ; rdf:rest _:2e1d99 . _:2e1d99 rdf:first _:2e1d89; rdf:rest rdf:nil . _:2e1d89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1da9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA oligonucleotide"; rdfs:subClassOf , , _:2e1db9; "RNA oligo"; "ChEBI? SOM? . . . seems like this class should exist somewhere"; "a ribonucleic acid molecule consisting of a short, linear single strand of typically 100 or fewer nucleotides" . _:2e1db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA interference oligonucleotide reagent"; owl:equivalentClass _:2e1dc9; rdfs:subClassOf , , , _:2e1e09; "RNAi oligonucleotide", "RNAi oligo"; "an RNA oligonucleotide that can be applied experimentally to silence expression of a target gene through the RNAi pathway." . _:2e1dc9 a owl:Class; owl:intersectionOf _:2e1dd9 . _:2e1dd9 rdf:first ; rdf:rest _:2e1df9 . _:2e1df9 rdf:first _:2e1de9; rdf:rest rdf:nil . _:2e1de9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1e09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dsRNA oligonucleotide reagent"; rdfs:subClassOf , , _:2e1e19; "dsRNA oligo", "dsRNA oligonucleotide"; "an RNA interference oligonucleotide reagent comprised of complementary strands of RNA that form double-stranded duplexes, and can be processed through the RNAi pathway into short interfering RNA (siRNA) molecules used to silence target gene expression." . _:2e1e19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA oligonucleotide reagent"; rdfs:subClassOf , , _:2e1e29; "miRNA oligo", "miRNA oligonucleotide"; rdfs:comment "The gene specific targeting sequences in these RNA oligonucleotides may or may not represent a naturally occurring miRNA, but they will contain flanking RNA regions that allow processing by endogenous miRNA pathway."; "An RNA interference oligonucleotide reagent that includes gene-specific targeting sequences intended to silence expression of a target gene through the RNAi pathway, and also contains flanking miRNA sequence elements that allow for processing by cellular microRNA processing machinery into active miRNA molecules. " . _:2e1e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "siRNA oligonucleotide reagent"; rdfs:subClassOf , , _:2e1e39; "siRNA oligo", "siRNA oligonucleotide"; "an RNA interference oligonucleotide reagent capable of silencing expression of a target gene through the RNAi pathway. siRNAs are synthesized as single-stranded molecules, typically 19-25 nucleotides in length, and paired with complementary sequences to form duplexes that serve as substrates for cellular RNAi processing machinery." . _:2e1e39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA inhibitor siRNA oligonucleotide reagent"; rdfs:subClassOf ; "miRNA inhibitor siRNA oligo"; "an siRNA oligonucleotide that is used to specifically inhibit endogenous miRNA function in cells." . a owl:Class; rdfs:label "RNA probe"; owl:equivalentClass _:2e1e49; rdfs:subClassOf , , _:2e1e89; "an RNA oligonucleotide reagent that is a single-stranded RNA molecule applied experimentally to probe the biomolecular environment of some specimen. Typically used to detect, isolate, or affect the activity of nucleic acid molecules bearing complementary sequence among a mixture of other nucleic acid molecules"; "riboprobe"; "RNA-based molecular labels and microarray probes, as well as RNAs used to activate or repress the activity of some target, are all considered probes."; rdfs:comment "Note here that the term 'probe' here is interpreted generally to cover targeted molecular effectors. Application in a technique serves to target some molecular entity for a range of purposes, including detection of some target (e.g. molecular labels as probes), isolation of some target (e.g. microarray probes), or altering some biochemical property of some target (e.g. probes used for activation or inhibition of some activity, blocking progress of a polymerase, etc)." . _:2e1e49 a owl:Class; owl:intersectionOf _:2e1e59 . _:2e1e59 rdf:first ; rdf:rest _:2e1e79 . _:2e1e79 rdf:first _:2e1e69; rdf:rest rdf:nil . _:2e1e69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1e89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "morpholino"; rdfs:subClassOf , , _:2e1e99, _:2e1ea9; "Nucleic acid reagent that is a short strand of nucleic acid where the bases are bound to morpholine rings instead of deoxyribose rings and linked through phosphorodiamidate groups instead of phosphates. Morpholinos are used to knockdown gene expression via antisense binding."; "PERSON:Melissa Haendel"; "http://en.wikipedia.org/wiki/Morpholino"; "morpholino oligonucleotide", "morpholino oligo" . _:2e1e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1ea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "artificial chromosome"; rdfs:subClassOf , _:2e1eb9, _:2e1ec9, _:2e1ed9; owl:disjointWith ; "PERSON: Matthew Brush"; "a DNA construct that is generated by inserting exogenous DNA into a plasmid containing features of a eukaryotic chromosome or prokaryotic episome that support replication and preservation in a host cell. Artificial chromosomes are used to clone large DNA fragments between 100,000 bases and 3,000,000 bases in size. "; . _:2e1eb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1ec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA primer"@en; owl:equivalentClass _:2e1ee9; rdfs:subClassOf , , _:2e1f29; "a RNA oligonucleotide that binds to some complementary nucleic acid template to serve as a starting point for nucleic acid synthesis" . _:2e1ee9 a owl:Class; owl:intersectionOf _:2e1ef9 . _:2e1ef9 rdf:first ; rdf:rest _:2e1f19 . _:2e1f19 rdf:first _:2e1f09; rdf:rest rdf:nil . _:2e1f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1f29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "complementary DNA"@en; rdfs:subClassOf , _:2e1f39, _:2e1f49; "http://en.wikipedia.org/wiki/Complementary_DNA"; "cDNA"; "a DNA moelcule representing sequence reverse transcribed from a messenger RNA template, in a reaction catalyzed by the enzyme reverse transcriptase and the enzyme DNA polymerase." . _:2e1f39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e1f49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA primer pair"@en; rdfs:subClassOf , _:2e1f59; "a primer pair comprised of two DNA primers that are complementary to a specified stretch of nucleic acid sequence, and used in a polymerase chain reaction to amplify this segment of DNA" . _:2e1f59 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "construct insert"@en; rdfs:subClassOf , _:2e1f69, _:2e1fc9; "cloned insert"; """1. Note that this class refers to actual parts of constructs, not DNA molecules that are intended to be inserted into a construct. The latter are bearers of a construct insert role, the former are the result of the realization of this role. 2. Note that as physical part of a DNA construct, the boundaries of the insert is determined by the specification of some agent, and includes the region of interest in an experimental context (ie restriction fragments and leader sequences included to get the insert into the construct that are of no subsequent experimental interest may not be included). This distinction allows us to say, for example, that a 'genomimc DNA construct' has_proper_part some ('construct insert' and (bears_concretization_of ONLY 'natural genomic sequence region')."""; "a material DNA span that is part of a DNA construct, inserted into its cloning site to allow for its replication, and often expression of genes carried in the inserted sequence." . _:2e1f69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1f79 . _:2e1f79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e1f89 . _:2e1f89 a owl:Class; owl:intersectionOf _:2e1f99 . _:2e1f99 rdf:first ; rdf:rest _:2e1fb9 . _:2e1fb9 rdf:first _:2e1fa9; rdf:rest rdf:nil . _:2e1fa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e1fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "pathological cell"@en; owl:equivalentClass _:2e1fd9; rdfs:subClassOf , , _:2e2019, _:2e2029; "a cell in vivo that has undergone a pathological transformation that contributes to or results from the disease course processes of some disease"; "PERSON: Matthew Brush"; . _:2e1fd9 a owl:Class; owl:intersectionOf _:2e1fe9 . _:2e1fe9 rdf:first ; rdf:rest _:2e2009 . _:2e2009 rdf:first _:2e1ff9; rdf:rest rdf:nil . _:2e1ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2029 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "pathological anatomical entity"@en; owl:equivalentClass _:2e2039; rdfs:subClassOf , _:2e2079; rdfs:comment "an equivalent class to subsume all classes that are outputs of some pathological process (pathological formation, pathological anatomical structure, portion of pathological body substance, and pathological cell)"; "PERSON: Matthew Brush"; "a material anatomical entity that is transformed or derived through some pathological bodily process (e.g. a tumor, a portion of infected blood, an dulcer), or bears parts what have been derived or transformed in such a manner (e.g. a carcinomatous colon, a blistered toe, or ulcerated stomach)" . _:2e2039 a owl:Class; owl:intersectionOf _:2e2049 . _:2e2049 rdf:first ; rdf:rest _:2e2069 . _:2e2069 rdf:first _:2e2059; rdf:rest rdf:nil . _:2e2059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organic macromolecule chemical reagent"; owl:equivalentClass _:2e2089; rdfs:subClassOf , , _:2e2119; "An organic chemical reagent whose structure essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass (ie polymerization). As a result, such macromolecules typically display a high molecular mass (relative to small molecules)."; rdfs:comment "Note that key to the definition here is (1) being comprised or repetition of some monomeric building block, and not any specific size constraint. As a result, ReO would consider even a disaccharide or trisaccharide to be a macromolecule chemical reagent, and (2) the fact that nucleic acid and polypeptide macromolecules are not considered here to be 'chemical reagents', for reasons specified in the annotations on this class." . _:2e2089 a owl:Class; owl:intersectionOf _:2e2099 . _:2e2099 rdf:first ; rdf:rest _:2e20b9 . _:2e20b9 rdf:first _:2e20a9; rdf:rest _:2e2109 . _:2e20a9 a owl:Class; owl:complementOf _:2e20c9 . _:2e20c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e20d9 . _:2e20d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e20e9 . _:2e20e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2109 rdf:first _:2e20f9; rdf:rest rdf:nil . _:2e20f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "mortal"@en; rdfs:subClassOf ; "PATO (placeholder for PATO term?)" . a owl:Class; rdfs:label "obsolete_morphology"@en; rdfs:subClassOf ; "a physical object qualilty inhering in its bearer by virtue of the bearer's size or shape or structure."; rdfs:comment "replace with PATO:morphology"; "replaced with PATO:morphology" . a owl:Class; rdfs:label "fibroblastic morphology"@en; rdfs:subClassOf ; "http://www.invitrogen.com/site/us/en/home/References/gibco-cell-culture-basics/cell-morphology.html"; "Fibroblastic cells are bipolar or multipolar, have elongated shapes, and grow attached to a substrate."; "fibroblast-like morphology", "fibroblastoid morphology"; "PERSON:Matthew Brush" . a owl:Class; rdfs:label "epithelial morphology"@en; rdfs:subClassOf ; "epithelial-like morphology", "epithelioid morphology"; "Cells with epithelial morphology are polygonal in shape with more regular dimensions, and grow attached to a substrate in discrete patches."; "PERSON: Matthew Brush"; "http://www.invitrogen.com/site/us/en/home/References/gibco-cell-culture-basics/cell-morphology.html" . a owl:Class; rdfs:label "endothelial morphology"@en; rdfs:subClassOf ; "endothelioid morphology" . a owl:Class; rdfs:label "lymphoblastic morphology"@en; rdfs:subClassOf ; "PERSON:Matthew Brush"; "Lymphoblastic cells are spherical in shape and usually grown in suspension without attaching to a surface."; "lymphoblast-like morphology", "lymphoblastoid morphology"; "http://www.invitrogen.com/site/us/en/home/References/gibco-cell-culture-basics/cell-morphology.html" . a owl:Class; rdfs:label "myeloblast-like morphology"@en; rdfs:subClassOf ; "myeloblastoid morphology" . a owl:Class; rdfs:label "myoblast-like morphology"@en; rdfs:subClassOf ; "myoblastoid morphology" . a owl:Class; rdfs:label "myofibroblast-like morphology"@en; rdfs:subClassOf ; "myofibroblastoid morphology" . a owl:Class; rdfs:label "stem cell-like morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "neuroepithelial morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "monocyte-like morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "macrophage-like morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "polygonal morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "large multinucleate morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "Schwann cell-like morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "stellar morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "refractile morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "dendritic morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "amoeboid morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "spindle-like morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "bipolar morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "multipolar morphology"@en; rdfs:subClassOf . a owl:Class; rdfs:label "technique"@en; rdfs:subClassOf , _:2e2129, _:2e2169, _:2e21a9, _:2e21b9; "A (scientific) technique is a planned process with precise and focused objectives that are scientific in nature (ie they produce scientific data or research materials to be used in a scientific investigation, according to a plan specification outlined in a protocol). "; "http://en.wikipedia.org/wiki/Scientific_technique"; """In naming of technique classes, labels are appended with 'technique' in cases where it is required to distinguish the class from other (non-technique) processes that could be described with a similar name. For example the technique of genetic modicication is labeled as 'genetic modification technique', because the more general process of 'genetic modification' can occur naturally through biological or pathological processes, or intentionally throguh a planned experimental technique. Similarly, the technique of cell line immortalization is labeled as 'cell line immortalization technique', because the more general process of 'cell line immortalization' can occur naturally/spontaneously or intentionally through a planned technique. Note also that any material that you indicate to be output from a material processing technique will be inferred to be a research material.""", """Convention for creating technique classes should be to record (1) objectives where applicable, (2) the specified inputs and outputs, and (3) and the specific roles the inputs bear and/or are realized in a technique. For example, 'recombinant construct cloning' has the following axioms: - has_specified_input some ('nucleic acid' and ('has role' some 'construct insert role')) - has_specified_input some ('DNA construct' and ('has role' some 'target of material addition role')) - has_specified_ouptut some 'DNA construct' And 'moelcular label detection assay' is described as: - realizes some ('evaluant role' and ('inheres in' some 'labeled material')) - has_specified_input some ('labeled material' and ('has role' some 'evaluant role') - has_specified_output some ('measurement datum' and ('is about' some 'labeled material')) This allows for inferred classification of techniques under multiple parents."""; "scientific technique"; """OBI: 1. Note that OBI prefers to use the realizes relation to link processes to plan specifications they achieve (realizes some (concretizes some protocol)). I dont agree here, and created the 'achieves_plan_specification' property for this need. 2. Would like their opinion on this class, and the value of organizing protocol-driven techniques under planned process. Esp in reagrd to the now obsolete OBI class 'protocol application', which sounds like it may have been intended to represent what ReO here calls techniques. (OBI:0000069 'protocol application' = a process carried out to bring about the objective defined in the protocol applied. Every protocol_application has one or more inputs and outputs definition_source: OBI. a protocol_application is a planned process realizes a process in which the objective of the protocol is achieved. The manipulation of materials and information on materials as part of an investigation) 3. Also look at the former OBI:0000011 class 'objective-driven process' = a process which is initiataed by one or more human participants with an overall objective they wish to achieve. The participantes do not necessarily have to have a plan how to achieve it. - this is wehre things like assay were once colleced, and it was a sibling of planned process . . . I (BP) felt the need for this upper class, as processes like planning or interpreting data clearly have an objective but do not have a plan. This distinction may get tricky."""; """ 'Technique' is not implemented as a defined class, given the subtle and subjective nature of its defining distinctions (however, we could define it as 'a planned process that realizes / achieves_plan_specification some protocol'). For now, any planned processes qualifying as scientific techniques will be asserted here as either assays or material porcessing techniques or data processing techniques. Techniques in scope here should be those related to reagents (ie material processing techniques used to generate a reagent or techniques/assays in which reagents are used). These classes are referenced as such in logical definitions of reagent classes."""; rdfs:comment """Scientific techniques are distinguished from planned processes in that: (1) they have objectives that are 'scientific' in nature (admittedly a rather vague requirement) (2) they are focused/limited in scope, such that they are amenable to capturing in a 'protocol' plan specification (as opposed to a broader 'plan specifications' such as a 'grant' or 'study design', which may incorporate many techniques). (3) they are performed by some human agent (as opposed to a computer or software agent), such that computational data transformations and statistical analyses do not qualify as techniques (these planned processes would be described by 'plan specifications' such as an 'algorithm' or 'software', not a 'protocol').""" . _:2e2129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2139 . _:2e2139 a owl:Class; owl:unionOf _:2e2149 . _:2e2149 rdf:first ; rdf:rest _:2e2159 . _:2e2159 rdf:first ; rdf:rest rdf:nil . _:2e2169 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2179 . _:2e2179 a owl:Class; owl:unionOf _:2e2189 . _:2e2189 rdf:first ; rdf:rest _:2e2199 . _:2e2199 rdf:first ; rdf:rest rdf:nil . _:2e21a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e21b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e21c9 a owl:Axiom; "Note that OBI prefers to use the realizes relation to link processes to plan specifications they achieve (realizes some (concretizes some protocol)). I dont agree here, and created the 'achieves_plan_specification' property for this need. "; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e21d9 . _:2e21d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_construct reagent role"@en; rdfs:subClassOf ; "OBI (consider aligning and merging with OBI_0000411 cloning vector role)"; "need to ask/be sure that all roles we implement as children of reagent role are indeed reagent roles . . . construct reagent role was deemed that this is not. rather, it can be replaced by a function (genetic material vector function)"; "adapted from OBI_0000411 'cloning vector role'"; "a reagent role inhering in a DNA construct, and realized in a process whereby foreign DNA is inserted into the construct during the process of cloning."; "PERSON: Matthew Brush" . a owl:Class; rdfs:label "gene knockdown function"@en; rdfs:subClassOf ; "gene repression function", "gene silencing function"; "a perturb function that inheres in molecular entities that are directly capable of reducing expression levels of some target gene in eukaryotic cells, or in plasmids created to produce such molecules" . a owl:Class; rdfs:label "RNA interference function"@en; rdfs:subClassOf , _:2e21e9; "GO (currently no RNAi or miRNA function in GO)"; "RNAi function"; "a gene knockdown function that inheres in small RNA molecules that are capable of RNA-mediated gene silencing in eukaryotic cells, or plasmids created to produce such small RNA molecules" . _:2e21e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetic locus"@en; rdfs:subClassOf , _:2e21f9, _:2e2209; "SO? (Placeholder until SO implements a suitable class. Submit to SO term tracker)"; "a nucleic acid sequence region that is part of a genome and represents a specified location on a chromosome. " . _:2e21f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2209 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e2219 . _:2e2219 a owl:Class; owl:unionOf _:2e2229 . _:2e2229 rdf:first ; rdf:rest _:2e2239 . _:2e2239 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "obsolete_cellular adhesivity"@en; rdfs:subClassOf ; "replaced with PATO:cellular adhesivity"; rdfs:comment "Placeholder - replace with PATO:cellular adhesivity" . a owl:Class; rdfs:label "site-directed mutagenesis"; rdfs:subClassOf , , _:2e2249, _:2e2259, _:2e22a9; "A technique in which a mutation is created at a defined site in a DNA molecule for research purposes."; "Oligonucleotide directed mutagenesis", "Oligonucleotide-directed mutagenesis", "Site specific mutagenesis", "Site-specific mutagenesis"; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Site-directed_mutagenesis"; "not an experimental modification because the output is not derived from the input DNA template . . . so the specified output REPRESENTS a modified version of the input, but physically it is not one." . _:2e2249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2269 . _:2e2269 a owl:Class; owl:intersectionOf _:2e2279 . _:2e2279 rdf:first ; rdf:rest _:2e2299 . _:2e2299 rdf:first _:2e2289; rdf:rest rdf:nil . _:2e2289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e22a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e22b9 . _:2e22b9 a owl:Class; owl:intersectionOf _:2e22c9 . _:2e22c9 rdf:first ; rdf:rest _:2e22e9 . _:2e22e9 rdf:first _:2e22d9; rdf:rest rdf:nil . _:2e22d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "yeast two hybrid screening"; rdfs:subClassOf , , _:2e22f9, _:2e2349; "A technique used to discover protein-protein interactions and protein-DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively."; "PERSON: Nicole Vasilevsky"; "Yeast two hybrid interaction screening"; "http://en.wikipedia.org/wiki/Two-hybrid_screening"; "may want to change logical def to has_specified_output ONLY 'data item'?"; . _:2e22f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2309 . _:2e2309 a owl:Class; owl:intersectionOf _:2e2319 . _:2e2319 rdf:first ; rdf:rest _:2e2339 . _:2e2339 rdf:first _:2e2329; rdf:rest rdf:nil . _:2e2329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2349 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_gene trapping "; rdfs:subClassOf ; "A technique that is used to introduce insertional mutations across the mammalian genome using a gene trap vector. "; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Gene_trapping"; "may be reimplemented later, but not needed yet" . a owl:Class; rdfs:label "adherent"@en; rdfs:subClassOf ; "a cellular adhesivity quality characterized by firm attachment and flattening/spreading of cells to the surface of a growth substrate in vitro."; "PERSON: Matthew Brush"; "CLO (inquire as to thinking behind their 'adherent growth mode' property, and possibility for merging/adopting a more PATO-oriented approach)"; "CLO_0000028 adherent cell culture growth mode" . a owl:Class; rdfs:label "suspension"@en; rdfs:subClassOf ; "CLO (inquire as to thinking behind their 'suspension growth mode' property, and possibility for merging/adopting a more PATO-oriented approach)"; "PERSON: Matthew Brush"; "CLO_0000029 suspension cell culture growth mode"; "a cellular adhesivity quality characterized by cellular growth free-floating in culture media. " . a owl:Class; rdfs:label "RNA primer pair"@en; rdfs:subClassOf , _:2e2359; "a primer pair comprised of two RNA primers that are complementary to a specified stretch of nucleic acid sequence, and used in a polymerase chain reaction to amplify this segment of nucleic acid" . _:2e2359 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "obsolete_primer reagent role"@en; rdfs:subClassOf ; "not needed"; "a reagent role inhering in a DNA or RNA primer intended to be used in a technique to seed the polymerase-driven synthesis of a double stranded nucleic acid molecule." . a owl:Class; rdfs:label "targeted tracker role"@en; rdfs:subClassOf , , _:2e2369; rdfs:comment "A molecular tracker typically acts as an intermediary between an analyte (or label associated with an analyte) and a reporter, by either (1) having as part some reporter that was covalently attached prior to applicaiton of the label, or (2) having as part some moiety that specifically interacts with a reporter. Examples of (1) include probe-reporter conjugates such as a P33 labeled oligonucleotide probe, or a fluorochrome-conjugated antibody. Examples of (2) include biotin incorporated into a oligonucleotide probe that recruits a fluorochrome-conjugated streptavidin molecule, or a primary antibody that recruits a labeled secondary antibody in a western blot."; """Case 1: Nucleotides synthesized with the incorporation of biotin were used to synthesize a cDNA probe, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. Here, biotin bears a tracker role, the fluorochrome bears a reporter role, and the antibody bears a probe role. Case 2 : An oligonucleotide synthesized with radioactive P33 and used to detect the presence of complementary sequence on a southern blot. Here, P33 bears a reporter role, and the oligo bears a probe role. Case 3: a protein labeling assay involving the detection of S35-labeled methionine incorporated into newly synthesized proteins in a cell culture cells. Here, S35 bears a reporter role, and there is no probe role realized. Case 4: Covalent attachment of an fluorochrome into a primary antibody to detect a specific cellular protein in an immunocytochemistry assay. Here, the fluorochrome bears a reporter role, and the antibody bears the probe role. Case 5: Immunosytochemical detection of a FLAG epitope tag in an overexpressed protein in cell culture cells, using a fluorochrome conjugated anti-FLAG antibody. Here, as in Case 4, the fluorochrome bears a reporter role and the antibody bears the probe role. In addition, the FLAG tag also bears a tracker role. Case 6: Phalloidin molecules (a fungal toxin that binds F-actin) are conjugated to rhodamine fluorochrome and applied to a slide of fixed cells to detect actin fibers by fluorescent microscopy. Here, phalloidin bears a probe role (it binds non-covalently to actin), and rhodamine bears a reporter role."""; "a molecular tracker role inhering in a molecular entity that is not capable of producing a detectable signal, but is capable of autonomous non-covalent association with a molecular target." . _:2e2369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2379 . _:2e2379 a owl:Class; owl:intersectionOf _:2e2389 . _:2e2389 rdf:first ; rdf:rest _:2e23a9 . _:2e23a9 rdf:first _:2e2399; rdf:rest rdf:nil . _:2e2399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e23b9 . _:2e23b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "primer"@en; owl:equivalentClass _:2e23c9; rdfs:subClassOf , _:2e2409; "http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29"; "oligonucleotide that binds to some complementary nucleic acid template to serve as a starting for nucleic acid synthesis." . _:2e23c9 a owl:Class; owl:intersectionOf _:2e23d9 . _:2e23d9 rdf:first ; rdf:rest _:2e23f9 . _:2e23f9 rdf:first _:2e23e9; rdf:rest rdf:nil . _:2e23e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "gene knockdown reagent"@en; owl:equivalentClass _:2e2419; rdfs:subClassOf , _:2e2479, _:2e2489; "a molecular reagent that is capable of reducing the expression of a target gene in a biological system"; rdfs:comment "These are primarily RNAi reagents/siRNA and related reagents, including oligos that directly downregulate some target, or plasmids that generate RNA molecues that are processed into such oligos. In addition to these RNAi reagents, chemical or biological agents that target specific genes/promoters, or that target specific proteins for degradataion can also qualify as gene knockdown reagents."; "genetic knockdown reagent"; . _:2e2419 a owl:Class; owl:intersectionOf _:2e2429 . _:2e2429 rdf:first ; rdf:rest _:2e2449 . _:2e2449 rdf:first _:2e2439; rdf:rest _:2e2469 . _:2e2439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2469 rdf:first _:2e2459; rdf:rest rdf:nil . _:2e2459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "expression construct"@en; owl:equivalentClass _:2e2499; rdfs:subClassOf , _:2e24d9, _:2e24e9, _:2e2509; "expression vector"; "a DNA construct that is engineered to express some gene product (RNA or protein) encoded in its insert. Expression constructs contain one or more genetic sequences to be transcribed, as driven by the necessary promoter and regulatory elements."; rdfs:comment "Expression constructs typically contain regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. "; . _:2e2499 a owl:Class; owl:intersectionOf _:2e24a9 . _:2e24a9 rdf:first ; rdf:rest _:2e24c9 . _:2e24c9 rdf:first _:2e24b9; rdf:rest rdf:nil . _:2e24b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e24d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e24e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e24f9 . _:2e24f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2519 . _:2e2519 a owl:Class; owl:intersectionOf _:2e2529 . _:2e2529 rdf:first ; rdf:rest _:2e2549 . _:2e2549 rdf:first _:2e2539; rdf:rest rdf:nil . _:2e2539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2559 . _:2e2559 a owl:Class; owl:intersectionOf _:2e2569 . _:2e2569 rdf:first ; rdf:rest _:2e2589 . _:2e2589 rdf:first _:2e2579; rdf:rest rdf:nil . _:2e2579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2599 a owl:Axiom; "consider the axiom on OBI recombinant plasmid : has_function some (is realized by some (gene expression)) . . . is it ok to say both the reagent role and some function are both realized by gene expression as part of some technique?"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e25a9 . _:2e25a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e25b9 . _:2e25b9 a owl:Class; owl:intersectionOf _:2e25c9 . _:2e25c9 rdf:first ; rdf:rest _:2e25e9 . _:2e25e9 rdf:first _:2e25d9; rdf:rest rdf:nil . _:2e25d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e25f9 . _:2e25f9 a owl:Class; owl:intersectionOf _:2e2609 . _:2e2609 rdf:first ; rdf:rest _:2e2629 . _:2e2629 rdf:first _:2e2619; rdf:rest rdf:nil . _:2e2619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA interference reagent"@en; owl:equivalentClass _:2e2639; rdfs:subClassOf , , , _:2e2699, _:2e26a9; "Given the importance of RNA interference technology in biomedical research, we have included this defined class, based on bearing a function to knockdown gene expression through the RNAi pathway, as a secondary axis of classification (as it includes children of two classes distinguished along our primary axis - DNA reagent vs RNA reagent)"; "a nucleic acid reagent that is capable of reducing the expression of a target gene in a biological system through the RNA interference pathway"; "examples include siRNAi, dsRNA, or miRNA oligos, or plasmids engineered to produce such reagents in cells"; "RNAi reagent"; . _:2e2639 a owl:Class; owl:intersectionOf _:2e2649 . _:2e2649 rdf:first ; rdf:rest _:2e2669 . _:2e2669 rdf:first _:2e2659; rdf:rest _:2e2689 . _:2e2659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2689 rdf:first _:2e2679; rdf:rest rdf:nil . _:2e2679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e26a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant artificial chromosome cloning"@en; rdfs:subClassOf . a owl:Class; rdfs:label "primer pair"@en; rdfs:subClassOf , , _:2e26b9, _:2e26c9, _:2e26d9, _:2e26e9; "a reagent comprised of two primers that are complementary to a specified stretch of nucleic acid sequence, and used in a polymerase chain reaction to amplify this segment of nucleic acid"; "Note that primer pair is considered here at a MOLECULAR level, ie. as the aggregate pair of two molecules. By contrast, 'reagent libraries' are considered at a MACROSCOPIC level, ie. as aggregates of collections of individual molecules or organisms. This is reflected in the logical descriptions of each." . _:2e26b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e26c9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e26d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e26e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e26f9 . _:2e26f9 a owl:Class; owl:intersectionOf _:2e2709 . _:2e2709 rdf:first ; rdf:rest _:2e2729 . _:2e2729 rdf:first _:2e2719; rdf:rest rdf:nil . _:2e2719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_cell"@en; rdfs:subClassOf ; "a material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane."; "adapted from CARO"; "PERSON: Matthew Brush"; "replaced by CL cell" . a owl:Class; rdfs:label "obsolete_cell specimen"@en; rdfs:subClassOf ; "a cell that is intended to be used in some technique or investigation as an example of its type"; "OBI (clarify that they intend their cell specimen class to refer to a collection of cells, and only multicellular orgnism cells)"; "out fo scope for ReO, and no want to deal with conflicting defs vs OBI:cell specimen"; . a owl:Class; rdfs:label "molecular binding disposition"@en; rdfs:subClassOf , _:2e2739; "a disposition inhering in a molecular entity to form selective, non-covalent, often stoichiometric, interactions with one or more specific sites on another molecule."; "selective binding disposition", "non-covalent binding disposition"; "adapted from GO:binding (MF)" . _:2e2739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "hybridizing disposition"@en; rdfs:subClassOf , _:2e2749; "http://en.wikipedia.org/wiki/Nucleic_acid_hybridisation#Hybridization"; "a disposition, inhering in a single-stranded nucleic acid or nucleic acid analog, to form a non-covalent, sequence-specific interaction with other single-stranded nucleic acids or analogs exhibitiing a complementary sequence " . _:2e2749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2759 . _:2e2759 a owl:Class; owl:unionOf _:2e2769 . _:2e2769 rdf:first ; rdf:rest _:2e2779 . _:2e2779 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "expression cell line"@en; owl:equivalentClass _:2e2789; rdfs:subClassOf , _:2e2809, _:2e2899; "a cell line that exhibits stable expression of an exogenous gene introduced in some DNA construct via some genetic transformation technique "; "example equivalent class illustrating design pattern for defining cell lines that express some exogenous gene"; rdfs:comment "In most cases this will also be a transgenic cell line, but in cases wehre the expressed gene represents seqeunce found in the host cells own genome, as is done in some over-expression studies, this is not considered transgenic."; . _:2e2789 a owl:Class; owl:intersectionOf _:2e2799 . _:2e2799 rdf:first ; rdf:rest _:2e27b9 . _:2e27b9 rdf:first _:2e27a9; rdf:rest rdf:nil . _:2e27a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e27c9 . _:2e27c9 a owl:Class; owl:intersectionOf _:2e27d9 . _:2e27d9 rdf:first ; rdf:rest _:2e27f9 . _:2e27f9 rdf:first _:2e27e9; rdf:rest rdf:nil . _:2e27e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2809 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2819 . _:2e2819 a owl:Class; owl:intersectionOf _:2e2829 . _:2e2829 rdf:first ; rdf:rest _:2e2849 . _:2e2849 rdf:first _:2e2839; rdf:rest rdf:nil . _:2e2839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2859 . _:2e2859 a owl:Class; owl:intersectionOf _:2e2869 . _:2e2869 rdf:first ; rdf:rest _:2e2889 . _:2e2889 rdf:first _:2e2879; rdf:rest rdf:nil . _:2e2879 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e28a9 . _:2e28a9 a owl:Class; owl:intersectionOf _:2e28b9 . _:2e28b9 rdf:first ; rdf:rest _:2e28d9 . _:2e28d9 rdf:first _:2e28c9; rdf:rest rdf:nil . _:2e28c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "mutant cell line"@en; owl:equivalentClass _:2e28e9; rdfs:subClassOf , _:2e2939; "example equivalent class illustrating design pattern for defining cell lines comprised of cells that carry a characterized genetic mutation in a targeted endogenous gene. ", "Modeling here may not yet be correct or complete yet, as this equivalent class is intended to describe cell lines displaying characterized/directed mutations in a specific endogenous gene, tyically that give rise to some known mutant gene product whose function will be studied. We intend for this to excludes tumor-derived cell lines such as HeLa cells, which contain a host of uncharacterized genomic mutations that resulted in transformation to a cancer phenotype. However, we are not sure yet how to formally model this requirement that 'mutant cell lines' are only those that carry specific, characterized mutations - and thus rely on an objective created to define this class."; "a multicellular organism cell culture with an established genetic alteration in a specific gene of interest. This mutation is typiclly made to alter the activity of this target gene in order to study its function."; ; . _:2e28e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e28f9 . _:2e28f9 a owl:Class; owl:intersectionOf _:2e2909 . _:2e2909 rdf:first ; rdf:rest _:2e2929 . _:2e2929 rdf:first _:2e2919; rdf:rest rdf:nil . _:2e2919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2939 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e2949 . _:2e2949 a owl:Class; owl:intersectionOf _:2e2959 . _:2e2959 rdf:first ; rdf:rest _:2e2979 . _:2e2979 rdf:first _:2e2969; rdf:rest rdf:nil . _:2e2969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2989 . _:2e2989 a owl:Class; owl:intersectionOf _:2e2999 . _:2e2999 rdf:first ; rdf:rest _:2e29b9 . _:2e29b9 rdf:first _:2e29a9; rdf:rest rdf:nil . _:2e29a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "adherent cell line"@en; owl:equivalentClass _:2e29c9; rdfs:subClassOf , _:2e2a09; "example equivalent class illustrating design pattern for describing adherence growth mode charateristics of a cell line"; "an immortal cell line whose cells proliferate while attached to some substratum in a cell culture container (petri dish, flask)"; . _:2e29c9 a owl:Class; owl:intersectionOf _:2e29d9 . _:2e29d9 rdf:first ; rdf:rest _:2e29f9 . _:2e29f9 rdf:first _:2e29e9; rdf:rest rdf:nil . _:2e29e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2a09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "myeloma"@en; rdfs:subClassOf ; "PERSON: Matthew Brush"; "a neoplasm resulting from the uncontrolled proliferation of plasma cells, a type of white blood cell normally responsible for the production of antibodies."; "http://en.wikipedia.org/wiki/Myeloma"; . a owl:Class; rdfs:label "fibroblastic cell line"@en; owl:equivalentClass _:2e2a19; rdfs:subClassOf , _:2e2a99; """example equivalent class illustrating design pattern for describing cell line cell morphology. note that these cell lines need not be derived from a fibroblast, but rather have cells with a morphology that is considered 'fibroblast-like'"""; "an immortal cell line whose cells exhibit a fibroblast-like morphology when grown in culture"; . _:2e2a19 a owl:Class; owl:intersectionOf _:2e2a29 . _:2e2a29 rdf:first ; rdf:rest _:2e2a49 . _:2e2a49 rdf:first _:2e2a39; rdf:rest rdf:nil . _:2e2a39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e2a59 . _:2e2a59 a owl:Class; owl:intersectionOf _:2e2a69 . _:2e2a69 rdf:first ; rdf:rest _:2e2a89 . _:2e2a89 rdf:first _:2e2a79; rdf:rest rdf:nil . _:2e2a79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2a99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e2aa9 . _:2e2aa9 a owl:Class; owl:intersectionOf _:2e2ab9 . _:2e2ab9 rdf:first ; rdf:rest _:2e2ad9 . _:2e2ad9 rdf:first _:2e2ac9; rdf:rest rdf:nil . _:2e2ac9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "hybridoma cell line"@en; owl:equivalentClass _:2e2ae9; rdfs:subClassOf , _:2e2b39, _:2e2b49, _:2e2b59; "http://medical-dictionary.thefreedictionary.com/hybridoma"; "A cell line consisting of cells produced in vitro by the fusion of a lymphocyte B-cell that produces antibodies and a myeloma tumor cell. It proliferates into clones that produce a continuous supply of a specific antibody reagent." . _:2e2ae9 a owl:Class; owl:intersectionOf _:2e2b09 . _:2e2b09 rdf:first _:2e2af9; rdf:rest _:2e2b29 . _:2e2af9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2b29 rdf:first _:2e2b19; rdf:rest rdf:nil . _:2e2b19 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e2b39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2b49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2b59 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "mammalian expression construct"@en; owl:equivalentClass _:2e2b69; rdfs:subClassOf , _:2e2c29, _:2e2cb9; "An expression construct that contains promoter elements to drive expression of downstream genes in mammalian cells or mammal-derived in vitro expression systems."; . _:2e2b69 a owl:Class; owl:intersectionOf _:2e2b79 . _:2e2b79 rdf:first ; rdf:rest _:2e2b99 . _:2e2b99 rdf:first _:2e2b89; rdf:rest rdf:nil . _:2e2b89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2ba9 . _:2e2ba9 a owl:Class; owl:intersectionOf _:2e2bb9 . _:2e2bb9 rdf:first ; rdf:rest _:2e2bd9 . _:2e2bd9 rdf:first _:2e2bc9; rdf:rest rdf:nil . _:2e2bc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2be9 . _:2e2be9 a owl:Class; owl:unionOf _:2e2bf9 . _:2e2bf9 rdf:first ; rdf:rest _:2e2c19 . _:2e2c19 rdf:first _:2e2c09; rdf:rest rdf:nil . _:2e2c09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2c29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2c39 . _:2e2c39 a owl:Class; owl:intersectionOf _:2e2c49 . _:2e2c49 rdf:first ; rdf:rest _:2e2c69 . _:2e2c69 rdf:first _:2e2c59; rdf:rest rdf:nil . _:2e2c59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2c79 . _:2e2c79 a owl:Class; owl:unionOf _:2e2c89 . _:2e2c89 rdf:first ; rdf:rest _:2e2ca9 . _:2e2ca9 rdf:first _:2e2c99; rdf:rest rdf:nil . _:2e2c99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2cc9 . _:2e2cc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2cd9 . _:2e2cd9 a owl:Class; owl:intersectionOf _:2e2ce9 . _:2e2ce9 rdf:first ; rdf:rest _:2e2d09 . _:2e2d09 rdf:first _:2e2cf9; rdf:rest rdf:nil . _:2e2cf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2d19 . _:2e2d19 a owl:Class; owl:intersectionOf _:2e2d29 . _:2e2d29 rdf:first ; rdf:rest _:2e2d49 . _:2e2d49 rdf:first _:2e2d39; rdf:rest rdf:nil . _:2e2d39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2d59 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e2d69 . _:2e2d69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2d79 . _:2e2d79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2d89 . _:2e2d89 a owl:Class; owl:intersectionOf _:2e2d99 . _:2e2d99 rdf:first ; rdf:rest _:2e2db9 . _:2e2db9 rdf:first _:2e2da9; rdf:rest rdf:nil . _:2e2da9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2dc9 . _:2e2dc9 a owl:Class; owl:intersectionOf _:2e2dd9 . _:2e2dd9 rdf:first ; rdf:rest _:2e2df9 . _:2e2df9 rdf:first _:2e2de9; rdf:rest rdf:nil . _:2e2de9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "PC12 HD-Q74"@en; rdfs:subClassOf , , , _:2e2e09, _:2e2e19, _:2e2e29, _:2e2f39, _:2e2fc9, _:2e30e9; rdfs:comment "example particular cell line, axiomatized such that it will be subsumed by several defined cell line classes to illustrate reasoning/inferfence that can be done within the cell culture hierarchy"; "http://www.enterprise.cam.ac.uk/uploads/File/Licensing_Opps/Life/Cell%20Culture%20Model%20for%20Huntingdon%27s%20Disease%20-%20Rub-1856-07.pdf"; "a stable inducible rat phaeochromocytoma (PC12) cell line expressing GFP-tagged exon 1 of the huntingtin gene with 74 glutamine repeats, driven by a doxycycline-dependent Tet-On promoter. This cell line can be used for in vitro studies to evaluate compounds to treat Huntington’s disease."; . _:2e2e09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2e19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2e39 . _:2e2e39 a owl:Class; owl:intersectionOf _:2e2e49 . _:2e2e49 rdf:first ; rdf:rest _:2e2e69 . _:2e2e69 rdf:first _:2e2e59; rdf:rest rdf:nil . _:2e2e59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2e79 . _:2e2e79 a owl:Class; owl:intersectionOf _:2e2e89 . _:2e2e89 rdf:first ; rdf:rest _:2e2ea9 . _:2e2ea9 rdf:first _:2e2e99; rdf:rest rdf:nil . _:2e2e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2eb9 . _:2e2eb9 a owl:Class; owl:intersectionOf _:2e2ec9 . _:2e2ec9 rdf:first ; rdf:rest _:2e2ee9 . _:2e2ee9 rdf:first _:2e2ed9; rdf:rest rdf:nil . _:2e2ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2ef9 . _:2e2ef9 a owl:Class; owl:intersectionOf _:2e2f09 . _:2e2f09 rdf:first ; rdf:rest _:2e2f29 . _:2e2f29 rdf:first _:2e2f19; rdf:rest rdf:nil . _:2e2f19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2f39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2f49 . _:2e2f49 a owl:Class; owl:intersectionOf _:2e2f59 . _:2e2f59 rdf:first ; rdf:rest _:2e2f79 . _:2e2f79 rdf:first _:2e2f69; rdf:rest rdf:nil . _:2e2f69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2f89 . _:2e2f89 a owl:Class; owl:intersectionOf _:2e2f99 . _:2e2f99 rdf:first ; rdf:rest _:2e2fb9 . _:2e2fb9 rdf:first _:2e2fa9; rdf:rest rdf:nil . _:2e2fa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e2fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e2fd9 . _:2e2fd9 a owl:Class; owl:intersectionOf _:2e2fe9 . _:2e2fe9 rdf:first ; rdf:rest _:2e3009 . _:2e3009 rdf:first _:2e2ff9; rdf:rest rdf:nil . _:2e2ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3019 . _:2e3019 a owl:Class; owl:intersectionOf _:2e3029 . _:2e3029 rdf:first ; rdf:rest _:2e3049 . _:2e3049 rdf:first _:2e3039; rdf:rest rdf:nil . _:2e3039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3059 . _:2e3059 a owl:Class; owl:intersectionOf _:2e3069 . _:2e3069 rdf:first ; rdf:rest _:2e3089 . _:2e3089 rdf:first _:2e3079; rdf:rest rdf:nil . _:2e3079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3099 . _:2e3099 a owl:Class; owl:intersectionOf _:2e30a9 . _:2e30a9 rdf:first ; rdf:rest _:2e30c9 . _:2e30c9 rdf:first _:2e30b9; rdf:rest rdf:nil . _:2e30b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e30d9 . _:2e30d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e30e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e30f9 . _:2e30f9 a owl:Class; owl:intersectionOf _:2e3109 . _:2e3109 rdf:first ; rdf:rest _:2e3129 . _:2e3129 rdf:first _:2e3119; rdf:rest rdf:nil . _:2e3119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3139 . _:2e3139 a owl:Class; owl:intersectionOf _:2e3149 . _:2e3149 rdf:first ; rdf:rest _:2e3169 . _:2e3169 rdf:first _:2e3159; rdf:rest rdf:nil . _:2e3159 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_in vitro cell morphology"@en; rdfs:subClassOf ; "decided that cell line cell morpholgies fall under PATO morphology" . a owl:Class; rdfs:label "GFP expression plasmid"@en; owl:equivalentClass _:2e3179; rdfs:subClassOf , , _:2e3239, _:2e32c9; "an expression construct that is engineered to express the GFP protein or any protein with a GFP tag"; . _:2e3179 a owl:Class; owl:intersectionOf _:2e3189 . _:2e3189 rdf:first ; rdf:rest _:2e31a9 . _:2e31a9 rdf:first _:2e3199; rdf:rest rdf:nil . _:2e3199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e31b9 . _:2e31b9 a owl:Class; owl:intersectionOf _:2e31c9 . _:2e31c9 rdf:first ; rdf:rest _:2e31e9 . _:2e31e9 rdf:first _:2e31d9; rdf:rest rdf:nil . _:2e31d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e31f9 . _:2e31f9 a owl:Class; owl:intersectionOf _:2e3209 . _:2e3209 rdf:first ; rdf:rest _:2e3229 . _:2e3229 rdf:first _:2e3219; rdf:rest rdf:nil . _:2e3219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3249 . _:2e3249 a owl:Class; owl:intersectionOf _:2e3259 . _:2e3259 rdf:first ; rdf:rest _:2e3279 . _:2e3279 rdf:first _:2e3269; rdf:rest rdf:nil . _:2e3269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3289 . _:2e3289 a owl:Class; owl:intersectionOf _:2e3299 . _:2e3299 rdf:first ; rdf:rest _:2e32b9 . _:2e32b9 rdf:first _:2e32a9; rdf:rest rdf:nil . _:2e32a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e32c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e32d9 . _:2e32d9 a owl:Class; owl:intersectionOf _:2e32e9 . _:2e32e9 rdf:first ; rdf:rest _:2e3309 . _:2e3309 rdf:first _:2e32f9; rdf:rest rdf:nil . _:2e32f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3319 a owl:Axiom; ""; "testing use of 'genetically derives into' property"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e3329 . _:2e3329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3339 . _:2e3339 a owl:Class; owl:intersectionOf _:2e3349 . _:2e3349 rdf:first ; rdf:rest _:2e3369 . _:2e3369 rdf:first _:2e3359; rdf:rest rdf:nil . _:2e3359 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "GFP expression cell line"@en; owl:equivalentClass _:2e3379; rdfs:subClassOf , , _:2e34b9; "Class definition implements a proposed design pattern for linking expression cell lines with the genes/proteins they are engineered to express."; "an expression cell line that expresses GFP protein or any protein with a GFP tag"; . _:2e3379 a owl:Class; owl:intersectionOf _:2e3389 . _:2e3389 rdf:first ; rdf:rest _:2e33a9 . _:2e33a9 rdf:first _:2e3399; rdf:rest rdf:nil . _:2e3399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e33b9 . _:2e33b9 a owl:Class; owl:intersectionOf _:2e33c9 . _:2e33c9 rdf:first ; rdf:rest _:2e33e9 . _:2e33e9 rdf:first _:2e33d9; rdf:rest rdf:nil . _:2e33d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e33f9 . _:2e33f9 a owl:Class; owl:intersectionOf _:2e3409 . _:2e3409 rdf:first ; rdf:rest _:2e3429 . _:2e3429 rdf:first _:2e3419; rdf:rest rdf:nil . _:2e3419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3439 . _:2e3439 a owl:Class; owl:intersectionOf _:2e3449 . _:2e3449 rdf:first ; rdf:rest _:2e3469 . _:2e3469 rdf:first _:2e3459; rdf:rest rdf:nil . _:2e3459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3479 . _:2e3479 a owl:Class; owl:intersectionOf _:2e3489 . _:2e3489 rdf:first ; rdf:rest _:2e34a9 . _:2e34a9 rdf:first _:2e3499; rdf:rest rdf:nil . _:2e3499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e34b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e34c9 . _:2e34c9 a owl:Class; owl:intersectionOf _:2e34d9 . _:2e34d9 rdf:first ; rdf:rest _:2e34f9 . _:2e34f9 rdf:first _:2e34e9; rdf:rest rdf:nil . _:2e34e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3509 . _:2e3509 a owl:Class; owl:intersectionOf _:2e3519 . _:2e3519 rdf:first ; rdf:rest _:2e3539 . _:2e3539 rdf:first _:2e3529; rdf:rest rdf:nil . _:2e3529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3549 . _:2e3549 a owl:Class; owl:intersectionOf _:2e3559 . _:2e3559 rdf:first ; rdf:rest _:2e3579 . _:2e3579 rdf:first _:2e3569; rdf:rest rdf:nil . _:2e3569 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3589 . _:2e3589 a owl:Class; owl:intersectionOf _:2e3599 . _:2e3599 rdf:first ; rdf:rest _:2e35b9 . _:2e35b9 rdf:first _:2e35a9; rdf:rest rdf:nil . _:2e35a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Huntington gene"@en; rdfs:subClassOf , _:2e35c9, _:2e35e9, _:2e35f9; "OBO Foundry (need to establish a design approach for representing genes, either as GDCs or material entities. At present there is no ontological representation of individual genes (as there is for proteins in PRO). As the Entrez Gene database represents the most complete and rigorous and widely used database of genes, one temporary approach would be to map ad hoc gene classes to their entrez gene equivalents using data properties such as has_entrez_gene_id and/or has_entrez_gene_symbol.)"; "a gene that includes all of the sequence elements in a geneome necessary to encode a functional transcript that can be translated into a Huntingtin protein by de novo ribosome-mediated translation."; rdfs:comment "MHB: this is a test class, for demonstrating one proposed design pattern for modeling a specific gene class by linking it to its entrez gene record."; . _:2e35c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e35d9 . _:2e35d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e35e9 a owl:Restriction; owl:onProperty ; owl:hasValue "3064" . _:2e35f9 a owl:Restriction; owl:onProperty ; owl:hasValue "HTT" . _:2e3609 a owl:Axiom; "exploratory axiom to test design pattern linking a gene to its expressed physical products"; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e3619 . _:2e3619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3629 . _:2e3629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "mammalian cell line"@en; owl:equivalentClass _:2e3639; rdfs:subClassOf , _:2e36f9 . _:2e3639 a owl:Class; owl:intersectionOf _:2e3649 . _:2e3649 rdf:first ; rdf:rest _:2e3669 . _:2e3669 rdf:first _:2e3659; rdf:rest rdf:nil . _:2e3659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3679 . _:2e3679 a owl:Class; owl:intersectionOf _:2e3689 . _:2e3689 rdf:first ; rdf:rest _:2e36a9 . _:2e36a9 rdf:first _:2e3699; rdf:rest rdf:nil . _:2e3699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e36b9 . _:2e36b9 a owl:Class; owl:intersectionOf _:2e36c9 . _:2e36c9 rdf:first ; rdf:rest _:2e36e9 . _:2e36e9 rdf:first _:2e36d9; rdf:rest rdf:nil . _:2e36d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e36f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3709 . _:2e3709 a owl:Class; owl:intersectionOf _:2e3719 . _:2e3719 rdf:first ; rdf:rest _:2e3739 . _:2e3739 rdf:first _:2e3729 . _:2e3729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3749 . _:2e3749 a owl:Class; owl:intersectionOf _:2e3759 . _:2e3759 rdf:first ; rdf:rest _:2e3779 . _:2e3779 rdf:first _:2e3769; rdf:rest rdf:nil . _:2e3769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3739 rdf:rest rdf:nil . "For now we will make taxonomic lineage the basis for the primary axis of classification for cell lines, and assert any particular cell line classes here. Here we show the design pattern for cell lines derived from cells of mammalian origin"; "a cell line deriving from a cell or cells of some mammal"; . a owl:Class; rdfs:label "disease model cell line"@en; owl:equivalentClass _:2e3789; rdfs:subClassOf , _:2e37c9; "example equivalent class illustrating design pattern for defining cell lines that are models for disease"; "an immortal cell line that is used in scientific experiments as a model for disease"; . _:2e3789 a owl:Class; owl:intersectionOf _:2e3799 . _:2e3799 rdf:first ; rdf:rest _:2e37b9 . _:2e37b9 rdf:first _:2e37a9; rdf:rest rdf:nil . _:2e37a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e37c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "hybridoma cell"@en; owl:equivalentClass _:2e37d9; rdfs:subClassOf , _:2e3859; "CLO (align/merge with CLO:0036932 Hybridoma. Note that this class is also represented in BRENDA, as is hybridoma cel lline) " . _:2e37d9 a owl:Class; owl:intersectionOf _:2e37e9 . _:2e37e9 rdf:first ; rdf:rest _:2e3809 . _:2e3809 rdf:first _:2e37f9; rdf:rest rdf:nil . _:2e37f9 a owl:Class; owl:intersectionOf _:2e3829 . _:2e3829 rdf:first _:2e3819; rdf:rest _:2e3849 . _:2e3819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3849 rdf:first _:2e3839; rdf:rest rdf:nil . _:2e3839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3859 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3869 . _:2e3869 a owl:Class; owl:intersectionOf _:2e3879 . _:2e3879 rdf:first ; rdf:rest _:2e3899 . _:2e3899 rdf:first _:2e3889; rdf:rest rdf:nil . _:2e3889 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "myeloma cell"@en; rdfs:subClassOf , _:2e38a9, _:2e38b9; rdfs:comment "example pathological cell class, used in definition of hybridoma cell" . _:2e38a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e38b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e38c9 . _:2e38c9 a owl:Class; owl:intersectionOf _:2e38d9 . _:2e38d9 rdf:first ; rdf:rest _:2e38f9 . _:2e38f9 rdf:first _:2e38e9; rdf:rest rdf:nil . _:2e38e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleic acid library"@en; owl:equivalentClass _:2e3909; rdfs:subClassOf , _:2e39e9, _:2e3a39, _:2e3a49; "a reagent library comprised of a pools of different nucleic acid molecules, each pool being a uniform collection of one type of molecule. The individual nucleic acid members of such libraries are often stored as cloned in DNA constructs that are propagated in host micro-organisms such as bacteria, yeast, or virus." . _:2e3909 a owl:Class; owl:intersectionOf _:2e3919 . _:2e3919 rdf:first ; rdf:rest _:2e3939 . _:2e3939 rdf:first _:2e3929; rdf:rest _:2e3999 . _:2e3929 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e3949 . _:2e3949 a owl:Class; owl:intersectionOf _:2e3959 . _:2e3959 rdf:first ; rdf:rest _:2e3979 . _:2e3979 rdf:first _:2e3969; rdf:rest rdf:nil . _:2e3969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3999 rdf:first _:2e3989; rdf:rest rdf:nil . _:2e3989 a owl:Restriction; owl:onProperty ; owl:onClass _:2e39a9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e39a9 a owl:Class; owl:intersectionOf _:2e39b9 . _:2e39b9 rdf:first ; rdf:rest _:2e39d9 . _:2e39d9 rdf:first _:2e39c9; rdf:rest rdf:nil . _:2e39c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e39e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e39f9 . _:2e39f9 a owl:Class; owl:intersectionOf _:2e3a09 . _:2e3a09 rdf:first ; rdf:rest _:2e3a29 . _:2e3a29 rdf:first _:2e3a19; rdf:rest rdf:nil . _:2e3a19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3a39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3a49 a owl:Restriction; owl:onProperty ; owl:onClass _:2e3a59; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e3a59 a owl:Class; owl:intersectionOf _:2e3a69 . _:2e3a69 rdf:first ; rdf:rest _:2e3a89 . _:2e3a89 rdf:first _:2e3a79; rdf:rest rdf:nil . _:2e3a79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "primer library"@en; owl:equivalentClass _:2e3a99; rdfs:subClassOf , _:2e3b79, _:2e3bc9, _:2e3c19; "http://www.realtimeprimers.com/hustceprli.html"; "a nucleic acid library consisting of a collection of primers, stored as uniform aliquots of primers of a given sequence used for amplification of target nucleic acid sequences." . _:2e3a99 a owl:Class; owl:intersectionOf _:2e3aa9 . _:2e3aa9 rdf:first ; rdf:rest _:2e3ac9 . _:2e3ac9 rdf:first _:2e3ab9; rdf:rest _:2e3b29 . _:2e3ab9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e3ad9 . _:2e3ad9 a owl:Class; owl:intersectionOf _:2e3ae9 . _:2e3ae9 rdf:first ; rdf:rest _:2e3b09 . _:2e3b09 rdf:first _:2e3af9; rdf:rest rdf:nil . _:2e3af9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3b29 rdf:first _:2e3b19; rdf:rest rdf:nil . _:2e3b19 a owl:Restriction; owl:onProperty ; owl:onClass _:2e3b39; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e3b39 a owl:Class; owl:intersectionOf _:2e3b49 . _:2e3b49 rdf:first ; rdf:rest _:2e3b69 . _:2e3b69 rdf:first _:2e3b59; rdf:rest rdf:nil . _:2e3b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3b79 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e3b89 . _:2e3b89 a owl:Class; owl:intersectionOf _:2e3b99 . _:2e3b99 rdf:first ; rdf:rest _:2e3bb9 . _:2e3bb9 rdf:first _:2e3ba9; rdf:rest rdf:nil . _:2e3ba9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3bc9 a owl:Restriction; owl:onProperty ; owl:onClass _:2e3bd9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e3bd9 a owl:Class; owl:intersectionOf _:2e3be9 . _:2e3be9 rdf:first ; rdf:rest _:2e3c09 . _:2e3c09 rdf:first _:2e3bf9; rdf:rest rdf:nil . _:2e3bf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3c19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unicellular organism culture"@en; owl:equivalentClass _:2e3c29; rdfs:subClassOf , _:2e3c69, _:2e3c79; owl:disjointWith ; "a cell culture consisting of unicellular organisms (e.g. bacteria, yeast, protists) maintained in vitro"; . _:2e3c29 a owl:Class; owl:intersectionOf _:2e3c39 . _:2e3c39 rdf:first ; rdf:rest _:2e3c59 . _:2e3c59 rdf:first _:2e3c49; rdf:rest rdf:nil . _:2e3c49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3c69 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e3c79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_cell strain"@en; rdfs:subClassOf ; """A cell line resulting from the positive selection of a subpopulation of cells from a cell line, by cloning or some other method (physical cell separation, drug selection, environmental selection, etc.) A cell strain often acquires additional genetic changes subsequent to the initiation of the parent line."""; "selected cell line"; "PERSON: Matthew Brush"; "obsoleted after OBI fall '11 workshop when we decided to pursue a cell culture classification approach where classes will be named according to techniques used in generating them"; "http://www.invitrogen.com/site/us/en/home/References/gibco-cell-culture-basics/introduction-to-cell-culture.html, and http://histologia.ugr.es/pdf/cac013.pdf" . a owl:Class; rdfs:label "obsolete_clonal cell line"@en; rdfs:subClassOf ; "obsoleted when implemented new cell culture hierarchy . . ."; "clonal cell strain"; """Are most established heterologous cell lines (e.g.3T3, HeLa, 293 cells) clonal in the sense that they originate from a single cell? . . . if so, we may want to distinguish between 'clonality' in the sense of establishing the original cell line from a single cell from some anatomical structure (ie derives/originates_from exactly 1 (cell and (part_ofsome anatomical structure)) ), versus clonality in the sense of establishing a cell line from a single cell of an existing cell line (ie derives/originates_from exactly 1 (cell and (grain_of some cell line)) ). Depending on the outcome of this decision, it may be neccessary to remove or modify the axiom 'is_specified_output of some 'cell culture cloning' (since this implies it derives from another cell line, given the definition of cell culture cloning, and ignores derivation from a single cell from some anatomical structure . . . may need to create a technique for establishing a clonal cell line from a cell in vivo, to include with the technique of establishing a clonal cell line from a cell line cell)"""; "A cell line that is descended from a single ancestor cell. Clonal cell lines are the result of a cell selection process that yeilds a single cell which is expanded into a new cell line."; "PERSON: Matthew Brush" . a owl:Class; rdfs:label "selective cell subculturing"@en; rdfs:subClassOf , _:2e3c89, _:2e3c99; "PERSON: Matthew Brush"; "A material processing technique whereby a specified subset of cells from an input cell culture is selected based on their exhibiting some desired feature, and propagated into a new cell culture. Selection can be based on physical cell separation, drug selection, environmental selection, or other approaches." . _:2e3c89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3c99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell culture transformation"@en; rdfs:subClassOf , , , _:2e3ca9, _:2e3cb9, _:2e3d09, _:2e3d19; "cell line immortalization", "in vitro cell transformation", "cell line cell transformation", "cell culture cell transformation"; rdfs:comment "'cell immortalization' is different from 'cell transformation' in that the former requires only that a cell is able to replicate indefinitely in culture, while the latter further requires that the cell undergoes a set of genetic modifications that confers the properties of cancer - including the ability to grow in the absence of survival factors and the ability to divide without being specifically instructed to do so from outside the cell. In experimental settings, these qualities allow transformed cells to form tumors in animal models, and to escape contact inhibition in culture and thus grow on top of each other."; "PERSON: Matthew Brush"; "a process by which cultured cells are manipulated to undergo genetic modifications, such that they display properties of cancer, including the ability to grow in the absence of survival factors and the ability to divide without being specifically instructed to do so from outside the cell." . _:2e3ca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3cc9 . _:2e3cc9 a owl:Class; owl:intersectionOf _:2e3cd9 . _:2e3cd9 rdf:first ; rdf:rest _:2e3cf9 . _:2e3cf9 rdf:first _:2e3ce9; rdf:rest rdf:nil . _:2e3ce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3d09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3d19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell culture cell"@en; owl:equivalentClass _:2e3d29; rdfs:subClassOf , _:2e3d69, _:2e3db9, _:2e3dc9, _:2e3dd9; "PERSON: Matthew Brush"; "a cell in vitro that is propagated in vitro as part of a cell culture"; """here we have modeled all cell culture cells such that they are NOT considered 'cells ex vivo', as we consider 'ex vivo' to mean that a cell (or other anatomical entity) was once a part of an organism (as opposed to the looser requirement that it is not currently part of an organism). Cell culture cells are derived from cells in vivo, but themselves, in most cases, were never actually a part of an organism (a notable exception would be in a primary cell culture immediately after its creation, before cells have doubled and derived into new cells, or a culture of cells that never divide but are maintained in culture for a period of time before they scenesce) esp strange is that if I assert this as a type of cell, it infers as a type of cell in vitro and as a type of experimetnally modified cell, but not as a type of experimentally modified cell in vitro!!"""; "12-12-11 CL: we believe that the CL class 'cell line cell' is meant to cover all cultured cells (and not only those derived from multicellular organisms). If true, they will rename this class 'cell culture cell', and ReO will import it here." . _:2e3d29 a owl:Class; owl:intersectionOf _:2e3d39 . _:2e3d39 rdf:first ; rdf:rest _:2e3d59 . _:2e3d59 rdf:first _:2e3d49; rdf:rest rdf:nil . _:2e3d49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3d69 a owl:Class; owl:complementOf _:2e3d79 . _:2e3d79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3d89 . _:2e3d89 a owl:Class; owl:unionOf _:2e3d99 . _:2e3d99 rdf:first ; rdf:rest _:2e3da9 . _:2e3da9 rdf:first ; rdf:rest rdf:nil . _:2e3db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3dc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3dd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3de9 . _:2e3de9 a owl:Class; owl:intersectionOf _:2e3df9 . _:2e3df9 rdf:first ; rdf:rest _:2e3e19 . _:2e3e19 rdf:first _:2e3e09; rdf:rest rdf:nil . _:2e3e09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3e29 . _:2e3e29 a owl:Class; owl:unionOf _:2e3e39 . _:2e3e39 rdf:first ; rdf:rest _:2e3e49 . _:2e3e49 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "benign neoplasm"@en; rdfs:subClassOf ; "benign tumor"; . a owl:Class; rdfs:label "malignant neoplasm"@en; rdfs:subClassOf ; "cancer", "malignant tumor"; . a owl:Class; rdfs:label "cell culture technique"@en; owl:equivalentClass _:2e3e59; rdfs:subClassOf , _:2e3ec9, _:2e3ed9; "a technique in which cells are maintained or manipulated in an artificial environment" . _:2e3e59 a owl:Class; owl:intersectionOf _:2e3e69 . _:2e3e69 rdf:first ; rdf:rest _:2e3e89 . _:2e3e89 rdf:first _:2e3e79; rdf:rest rdf:nil . _:2e3e79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3e99 . _:2e3e99 a owl:Class; owl:unionOf _:2e3ea9 . _:2e3ea9 rdf:first ; rdf:rest _:2e3eb9 . _:2e3eb9 rdf:first ; rdf:rest rdf:nil . _:2e3ec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3ee9 . _:2e3ee9 a owl:Class; owl:unionOf _:2e3ef9 . _:2e3ef9 rdf:first ; rdf:rest _:2e3f09 . _:2e3f09 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "obsolete_phosphorus atom"; rdfs:subClassOf ; "CHEBI_28659 phosphorus atom" . a owl:Class; rdfs:label "cellular morphology"@en; rdfs:subClassOf , , _:2e3f19; rdfs:comment "MHB: subclasses based on 'morphology' fields of cell line catalogs and databases including ATCC, CLBD, CABRI. This attribute captures appearance of cells growing in culture, based on shape (polygonal, spindle-like), symmetry (bipolar, multipolar), physical characteristics (refractile), or similarity to appearance of in vivo cell types such as fibroblasts or epithelial cells."; "a morphology quality that describes the appearance of a cell" . _:2e3f19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "clonal cell subculturing"@en; rdfs:subClassOf , _:2e3f29, _:2e3f39; "Clarification: cell culture cell cloning is not a type of cell culture cell selection because cloning does not require active selection of a cell exhibiting for some desired attribute in cells to start a new culture. This active selection based on cell attribute(s) is a key aspect of selection."; "A cell culture selection process whereby a single cell is isolated from a cell culture, and propagated into a new cell culture." . _:2e3f29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3f39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell subculturing"@en; rdfs:subClassOf , _:2e3f49, _:2e3fa9, _:2e3fb9; "Class restrictions here need work. I don't think OWL is expressive enough to assert that the output cell culture container from this process contains a proper_part_of the cell culture that was input to the process."; "a technique that takes a cell culture as input and removes some subset of cell culture cells (either through some non-selective splitting, or some cell selection process), and outputs one or more cell culture containers containing this subset of input cell culture cells."; """Here, we define subculturing as any technique that results in the growth of a proper subset of cells from some input cell culture container (dish/flask) in an output cell culture container. Most often, subculturing involves cell culture splitting, whereby a non-slective process separates out some subset of cells into a new cell culture container. However, subculturing can also be achieved through a selection process, where a specified subset of cells from the input culture are killed or removed, leaving some desired subset for continued culturing. Note that the definition intentionally references the container in which passaged cells are grown, stating that subculturing results in a proper subset of the input cells is contained in an output cell culture container. This is because cell culture splitting can involve re-culturing of ALL input cells, split between several new containers. For example, a 1:5 spllit of an input container of cells into 5 new dishes. Here, at the level of the cells, the output is NOT a proper subset of the input (becasue all input cells remain in the output culture). Rather, at the level of an cell culture container, there is some container that contains a proper subset of the input cells.""" . _:2e3f49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3f59 . _:2e3f59 a owl:Class; owl:intersectionOf _:2e3f69 . _:2e3f69 rdf:first ; rdf:rest _:2e3f89 . _:2e3f89 rdf:first _:2e3f79; rdf:rest rdf:nil . _:2e3f79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e3f99 . _:2e3f99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3fa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3fb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell culture container"@en; rdfs:subClassOf , _:2e3fc9; "PERSON: Matthew Brush"; "cell culture receptacle"; "a processed material (usually a plastic petri dish or flask) used to hold cells when they are actively cultured in vitro." . _:2e3fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "in vivo cell transformation"; rdfs:subClassOf , , _:2e3fd9, _:2e3fe9; "a pathological transformation by which cells in vivo undergo genetic modifications that confer upon them properties of cancer. "; rdfs:comment "a pathological cell transformation is a 'biological process' in that it has input some in vivo cell and does not realize the objective of a planned or experimental process."; "PERSON: Matthew Brush" . _:2e3fd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e3fe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transformed cell"@en; owl:equivalentClass _:2e3ff9, _:2e4009; rdfs:subClassOf , _:2e4049; "a cell that has undergone genetic modifications that confer upon it properties of cancer, including the capacity for uncontrolled growth, invasion into adjacent tissues, and metastasis to distant sites in the body. When cultured in vitro, transformed cells have the ability to replicate indefinitely."; "http://en.wikipedia.org/wiki/Cancer"; rdfs:comment "transformed cells can arise from natural or experimental processes, and can exist in vivo or in vitro." . _:2e3ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4009 a owl:Class; owl:intersectionOf _:2e4019 . _:2e4019 rdf:first ; rdf:rest _:2e4039 . _:2e4039 rdf:first _:2e4029; rdf:rest rdf:nil . _:2e4029 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell transformation"@en; owl:equivalentClass _:2e4059; rdfs:subClassOf , _:2e4099; "a process by which cells undergo genetic modifications that confer upon them properties of cancer, including the ability to replicate indefinitely if cultured in vitro. Transformation refers to the conversion of a cell from a normal phenotype, which undergoes a limited number of mitotic divisions, into an aberrant phenotype that is immortal and divides indefinitely. Transformed cells no longer retain cell-cycle checkpoints and may ultimately become malignant cancer cells via additional genetic mutations, or damaging environmental events."; "PERSON: Matthew Brush"; "NCI Thesaurus and http://en.wikipedia.org/wiki/Malignant_transformation" . _:2e4059 a owl:Class; owl:intersectionOf _:2e4069 . _:2e4069 rdf:first ; rdf:rest _:2e4089 . _:2e4089 rdf:first _:2e4079; rdf:rest rdf:nil . _:2e4079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transgenic cell line"@en; owl:equivalentClass _:2e40a9; rdfs:subClassOf , , _:2e40e9, _:2e4179; "example equivalent class illustrating design pattern for defining cell lines that carry a transgene"; "a cell line which or derives from some transgenic organism or has itself been modified through some transgenic technique, such that it contains exogenous genetic material from a different cell or organism than that from which it was derived. This exogenous genetic material is capable of being stably replicated and inherited through subsequent generations of the transgenic cell line."; . _:2e40a9 a owl:Class; owl:intersectionOf _:2e40b9 . _:2e40b9 rdf:first ; rdf:rest _:2e40d9 . _:2e40d9 rdf:first _:2e40c9; rdf:rest rdf:nil . _:2e40c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e40e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e40f9 . _:2e40f9 a owl:Class; owl:intersectionOf _:2e4109 . _:2e4109 rdf:first ; rdf:rest _:2e4129 . _:2e4129 rdf:first _:2e4119; rdf:rest rdf:nil . _:2e4119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4139 . _:2e4139 a owl:Class; owl:intersectionOf _:2e4149 . _:2e4149 rdf:first ; rdf:rest _:2e4169 . _:2e4169 rdf:first _:2e4159; rdf:rest rdf:nil . _:2e4159 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "targeting construct"@en; owl:equivalentClass _:2e4189; rdfs:subClassOf , _:2e4249; "SO:0001644 'targeting_vector'"; "a DNA construct that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications."; . _:2e4189 a owl:Class; owl:intersectionOf _:2e4199 . _:2e4199 rdf:first ; rdf:rest _:2e41b9 . _:2e41b9 rdf:first _:2e41a9; rdf:rest rdf:nil . _:2e41a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e41c9 . _:2e41c9 a owl:Class; owl:intersectionOf _:2e41d9 . _:2e41d9 rdf:first ; rdf:rest _:2e41f9 . _:2e41f9 rdf:first _:2e41e9; rdf:rest rdf:nil . _:2e41e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4209 . _:2e4209 a owl:Class; owl:intersectionOf _:2e4219 . _:2e4219 rdf:first ; rdf:rest _:2e4239 . _:2e4239 rdf:first _:2e4229; rdf:rest rdf:nil . _:2e4229 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4259 . _:2e4259 a owl:Class; owl:intersectionOf _:2e4269 . _:2e4269 rdf:first ; rdf:rest _:2e4289 . _:2e4289 rdf:first _:2e4279; rdf:rest rdf:nil . _:2e4279 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4299 . _:2e4299 a owl:Class; owl:intersectionOf _:2e42a9 . _:2e42a9 rdf:first ; rdf:rest _:2e42c9 . _:2e42c9 rdf:first _:2e42b9; rdf:rest rdf:nil . _:2e42b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "homologous recombination"@en; rdfs:subClassOf ; "a biological process that is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA."; "placeholder for appropriate term from a reference ontology such as GO"; "PERSON: Matthew Brush"; "http://en.wikipedia.org/wiki/Homologous_recombination" . a owl:Class; rdfs:label "obsolete_chromosome"@en; rdfs:subClassOf ; "replaced by GO:chromosome"; "GO"; "a cell component composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. " . a owl:Class; rdfs:label "transgenic modification technique"@en; rdfs:subClassOf , _:2e42d9, _:2e4369, _:2e4439; "a genetic modification technique whereby a cell or organism is engineered to stably carry exogenous genetic material from some other cell or organism (ie a gene or nucleic acid sequence that is not normally a part of it)"; "PERSON: Matthew Brush"; rdfs:comment """is a narrower kind of genetic modification technique, in that it covers only stable addition of exogenous genetic material, and not any mutation or deletion of existing genetic material. Genetic material here is considered to be any nucleic acid that is capable of being replicated and inherited by offspring cells or viorions. Thus, things like transient DNA transfections where no stable change is made to the heritable gentic content of the target cell, or morpholino or siRNA transfections that impact post-transcriptional gene expression, do not qualify.""" . _:2e42d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e42e9 . _:2e42e9 a owl:Class; owl:intersectionOf _:2e4309 . _:2e4309 rdf:first _:2e42f9; rdf:rest _:2e4359 . _:2e42f9 a owl:Class; owl:unionOf _:2e4319 . _:2e4319 rdf:first ; rdf:rest _:2e4329 . _:2e4329 rdf:first ; rdf:rest _:2e4339 . _:2e4339 rdf:first ; rdf:rest rdf:nil . _:2e4359 rdf:first _:2e4349; rdf:rest rdf:nil . _:2e4349 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4379 . _:2e4379 a owl:Class; owl:intersectionOf _:2e4399 . _:2e4399 rdf:first _:2e4389; rdf:rest _:2e43e9 . _:2e4389 a owl:Class; owl:unionOf _:2e43a9 . _:2e43a9 rdf:first ; rdf:rest _:2e43b9 . _:2e43b9 rdf:first ; rdf:rest _:2e43c9 . _:2e43c9 rdf:first ; rdf:rest rdf:nil . _:2e43e9 rdf:first _:2e43d9; rdf:rest rdf:nil . _:2e43d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e43f9 . _:2e43f9 a owl:Class; owl:intersectionOf _:2e4409 . _:2e4409 rdf:first ; rdf:rest _:2e4429 . _:2e4429 rdf:first _:2e4419; rdf:rest rdf:nil . _:2e4419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetically modified cell line"@en; owl:equivalentClass _:2e4449; rdfs:subClassOf , , _:2e4489, _:2e4499, _:2e44a9; "an immortal cell line which has been intentionally modified through some genetic modification technique intended to alter the sequence of its genetic material, or introduce exogenous genetic material that is capable of being stably replicated and inherited through subsequent generations of cells."; "example equivalent class illustrating design pattern for describing cell line resulting from some modification technique. This could be a cell line subjected to a mutagen to induce mutations in endogenous genetic material, or a cell line into which exogenous DNA has been introduced in such a way that it is stably replicated."; . _:2e4449 a owl:Class; owl:intersectionOf _:2e4459 . _:2e4459 rdf:first ; rdf:rest _:2e4479 . _:2e4479 rdf:first _:2e4469; rdf:rest rdf:nil . _:2e4469 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e44a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "transgenic material"@en; owl:equivalentClass _:2e44b9; rdfs:subClassOf , _:2e4569, _:2e45b9; "a material entity, arising from an organism, cell, or cell line, which has been modified through some transgenic technique to contain exogenous genetic material from a different cell or organism (i.e. genetic material that is not normally part of the target material)"; rdfs:comment "is a narrower than genetically modified material, in that it covers only materials that stably carry exogenous genetic material that is not normally a part of the target material. The notion of 'stably' means that things like transiently transfected cells or organisms are not included here. The notion of 'exogenous' means that or materials that are subject to alteration/mutation/deletion of existing genetic material are not included. Genetic material here is considered to be any nucleic acid that is capable of being replicated and inherited by offspring cells or organisms." . _:2e44b9 a owl:Class; owl:intersectionOf _:2e44d9 . _:2e44d9 rdf:first _:2e44c9; rdf:rest _:2e4529 . _:2e44c9 a owl:Class; owl:unionOf _:2e44e9 . _:2e44e9 rdf:first ; rdf:rest _:2e44f9 . _:2e44f9 rdf:first ; rdf:rest _:2e4509 . _:2e4509 rdf:first ; rdf:rest rdf:nil . _:2e4529 rdf:first _:2e4519; rdf:rest rdf:nil . _:2e4519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4539 . _:2e4539 a owl:Class; owl:unionOf _:2e4549 . _:2e4549 rdf:first ; rdf:rest _:2e4559 . _:2e4559 rdf:first ; rdf:rest rdf:nil . _:2e4569 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4579 . _:2e4579 a owl:Class; owl:intersectionOf _:2e4589 . _:2e4589 rdf:first ; rdf:rest _:2e45a9 . _:2e45a9 rdf:first _:2e4599; rdf:rest rdf:nil . _:2e4599 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e45b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e45c9 . _:2e45c9 a owl:Class; owl:unionOf _:2e45d9 . _:2e45d9 rdf:first ; rdf:rest _:2e45e9 . _:2e45e9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "genetically modified cell"@en; owl:equivalentClass _:2e45f9; rdfs:subClassOf , , _:2e4639, _:2e4689; "a cell which has been intentionally modified through some genetic modification technique that alters the sequence of its genetic material, or introduces exogenous genetic material that is capable of being stably replicated and thus be heritable by the cell's progeny."; . _:2e45f9 a owl:Class; owl:intersectionOf _:2e4609 . _:2e4609 rdf:first ; rdf:rest _:2e4629 . _:2e4629 rdf:first _:2e4619; rdf:rest rdf:nil . _:2e4619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4639 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4649 . _:2e4649 a owl:Class; owl:intersectionOf _:2e4659 . _:2e4659 rdf:first ; rdf:rest _:2e4679 . _:2e4679 rdf:first _:2e4669; rdf:rest rdf:nil . _:2e4669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material processing technique"@en; owl:equivalentClass _:2e4699; rdfs:subClassOf , , _:2e46d9, _:2e46e9, _:2e46f9, _:2e4709, _:2e4719; """Convention for creating 'material processing technique' classes should be to record objectives, and the specified inputs and outputs and the specific roles they realize in such techniques. For example, 'recombinant construct cloning' is described as: has_specified_input some ('nucleic acid' and ('has role' some 'construct insert role')) has_specified_input some ('DNA construct' and ('has role' some 'target of material addition role')) has_specified_ouptut some 'DNA construct' This allows for inferred classification of techniques under multiple parents.""", """(Ultimately, clean this annotation up and split into ReO modeling approach and ReO development convention annotations and ReO developer note) Modeling Approach: THE ALTERNATE APPROACH I WILL TRY HERE is to assert material processing techniques under material processing technique, and say that a material processing technique has output only some research material. Then I could say that a research material is anything that has a research material role or is output of a material processing technique (actually, dont even need to put this last part in the log def of research material becaseu of the fact that mat proc techniques have output ONLY research material). Development convention: As a result, i would not have to worry about developers having to indicate axiomatically that material processings with an output that is a research material 'has_specified_output some (has_role some 'research material role'))' (and I could remove all such existing axioms) . . . which seems more convenient. The burden then is on developers to be sure to assert material processings that have research material outputs as material processing techniques (which should be easy, as nearly all material processings in OBi and ReO are techniques. Modeling Approach: With this new approach, things will be inferred to be a research material based on their being output from a material processing technique, instead of the reverse (things being inferred to be techniques based on their having a outputs that have a research material role). I think this is more useful and intuitive to expect developers to model and users to understand. Development Convention: So be sure that all outputs of processes asserted to be 'materail processing techniques' are indeed 'research materials' . . . and no need to have axiom saying that output has a research amterial role, because this will be inferred from fact that material processing techniques have ouput only research material. Developer Note: What implicaitons would this new approach have if I decide to elim the material processing technique class and just use OBI material processing . . . then I would have a situation where a research material is defined as being output of a material processing - which is not correct. So be aware of the issues this could cause. ALSO, DO I NEED TO SAY HAS OUTPUT SOME RESEARCH MATERIAL AND ONLY RESEARCH MATERIAL - OR IS THE AXIOM WITH 'ONLY' SUFFICEINT?""", "Developers should ASSERT all material processings that have as specified output only some research material to be materail processing techniques. Also note that any material indicated to be output from a material processing technique will be inferred to be a research material"; "This class is used to subsume all techniques that generate or prepare materials for potential use in an investigation (ie via synthesis, collection, purification, etc). Investigations here are considered broadly to include any planned processes aimed at producing information of a scientific nature, including activities as simple as collecting and storing a specimen for visual observation, where the visual observation is a type of scientific analysis where data about the physical properties of the specimen are gathered and analyzed."; "PERSON: Matthew Brush"; "material preparation technique"; "a material processing in which specified physical changes are made to some material input to generate a material output that has a research material role. "; rdfs:comment "In this definition, 'physical change' is considered broadly as any re-arrangement of matter in the input material, such that techniques resulting in material separation, material collection, and material combination are considered material processing. ", "MHB: in logically defining material processing technique, a requirement for having specified input some material entity was omitted, because this should be true of any process that has_specified_output some material entity (matter cannot be created from nothing)"; """Convention for creating 'material processing technique' classes should be to record objectives, and the specified inputs and outputs and the specific roles they realize in such techniques. For example, 'recombinant construct cloning' is described as: has_specified_input some ('nucleic acid' and ('has role' some 'construct insert role')) has_specified_input some ('DNA construct' and ('has role' some 'target of material addition role')) has_specified_ouptut some 'DNA construct' This allows for inferred classification of techniques under multiple parents."""; . _:2e4699 a owl:Class; owl:intersectionOf _:2e46a9 . _:2e46a9 rdf:first ; rdf:rest _:2e46c9 . _:2e46c9 rdf:first _:2e46b9; rdf:rest rdf:nil . _:2e46b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e46d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e46e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e46f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4709 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e4719 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "obsolete_assay"@en; rdfs:subClassOf ; "material analysis technique"; "replaced with OBI:assay" . a owl:Class; rdfs:label "molecular biology technique"@en; owl:equivalentClass _:2e4729; rdfs:subClassOf ; rdfs:comment "example equivalent class, based on nature of input and output of a technique. Obviously out of scope for a reagetn ontology but could be used in eagle-i or OBI."; . _:2e4729 a owl:Class; owl:intersectionOf _:2e4739 . _:2e4739 rdf:first ; rdf:rest _:2e4759 . _:2e4759 rdf:first _:2e4749; rdf:rest rdf:nil . _:2e4749 a owl:Class; owl:intersectionOf _:2e4779 . _:2e4779 rdf:first _:2e4769; rdf:rest _:2e4799 . _:2e4769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4799 rdf:first _:2e4789; rdf:rest rdf:nil . _:2e4789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e47a9 . _:2e47a9 a owl:Class; owl:unionOf _:2e47b9 . _:2e47b9 rdf:first ; rdf:rest _:2e47d9 . _:2e47d9 rdf:first _:2e47c9; rdf:rest rdf:nil . _:2e47c9 a owl:Class; owl:intersectionOf _:2e47e9 . _:2e47e9 rdf:first ; rdf:rest _:2e4809 . _:2e4809 rdf:first _:2e47f9; rdf:rest rdf:nil . _:2e47f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "fibroblast-derived cell line"@en; owl:equivalentClass _:2e4819; rdfs:subClassOf , _:2e4859, _:2e4869; "example equivalent class illustrating design pattern for describing cell line cell deriving from a particular cell type"; "an immortal cell line that is derived from a fibroblast cell type"; . _:2e4819 a owl:Class; owl:intersectionOf _:2e4829 . _:2e4829 rdf:first ; rdf:rest _:2e4849 . _:2e4849 rdf:first _:2e4839; rdf:rest rdf:nil . _:2e4839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4859 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4879 . _:2e4879 a owl:Class; owl:intersectionOf _:2e4889 . _:2e4889 rdf:first ; rdf:rest _:2e48a9 . _:2e48a9 rdf:first _:2e4899; rdf:rest rdf:nil . _:2e4899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "embryonic cell line"@en; owl:equivalentClass _:2e48b9; rdfs:subClassOf , _:2e49b9 . _:2e48b9 a owl:Class; owl:intersectionOf _:2e48c9 . _:2e48c9 rdf:first ; rdf:rest _:2e48e9 . _:2e48e9 rdf:first _:2e48d9; rdf:rest rdf:nil . _:2e48d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e48f9 . _:2e48f9 a owl:Class; owl:intersectionOf _:2e4909 . _:2e4909 rdf:first ; rdf:rest _:2e4929 . _:2e4929 rdf:first _:2e4919; rdf:rest rdf:nil . _:2e4919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4939 . _:2e4939 a owl:Class; owl:intersectionOf _:2e4949 . _:2e4949 rdf:first ; rdf:rest _:2e4969 . _:2e4969 rdf:first _:2e4959; rdf:rest rdf:nil . _:2e4959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4979 . _:2e4979 a owl:Class; owl:intersectionOf _:2e4989 . _:2e4989 rdf:first ; rdf:rest _:2e49a9 . _:2e49a9 rdf:first _:2e4999; rdf:rest rdf:nil . _:2e4999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e49b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e49c9 . _:2e49c9 a owl:Class; owl:intersectionOf _:2e49d9 . _:2e49d9 rdf:first ; rdf:rest _:2e49f9 . _:2e49f9 rdf:first _:2e49e9; rdf:rest rdf:nil . _:2e49e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4a09 . _:2e4a09 a owl:Class; owl:intersectionOf _:2e4a19 . _:2e4a19 rdf:first ; rdf:rest _:2e4a39 . _:2e4a39 rdf:first _:2e4a29; rdf:rest rdf:nil . _:2e4a29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4a49 . _:2e4a49 a owl:Class; owl:intersectionOf _:2e4a59 . _:2e4a59 rdf:first ; rdf:rest _:2e4a79 . _:2e4a79 rdf:first _:2e4a69; rdf:rest rdf:nil . _:2e4a69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . "an example equivalent class illustrating design pattern for defining cell lines that are derived from an organism in a particualr life cycle stage."; "an immortal cell line that derives from cells isolated from an organism during its embryonic life cycle stage"; . a owl:Class; rdfs:label "semi-adherent"@en; rdfs:subClassOf ; "a cellular adhesivity quality characterized by loose attachment and little to no spreading or flattening of cells on an in vitro growth substrate. Such cells often exhibit a tendency to cluster, and are often found floating in suspension in cell culture media."; "PERSON: Matthew Brush" . a owl:Class; rdfs:label "genomic sequence alteration"@en; owl:equivalentClass _:2e4a89; rdfs:subClassOf , , _:2e4b09, _:2e4b59; "a sequence alteration that is part of a genome that is encoded in the material genome of some cell or virion"; """1. Note here that, unlike for 'genome' and 'genomic sequence feature', here it is necessary for a genomic sequence alteration to be encoded in some 'genetic material' that is part of some 'material genome' and physcally part of some cell or virion (as we consdier this context to be important). As a result, an alteration in the insert of some genomic DNA construct would qualify as a sequence alteration but not a genomic sequence alteration (it makes no ssnese here to consider such an insert to be 'transgenic', for example, without any organism context). We will, however, continue to evaluate use cases as they emerge in regard to this decision. 2. Note that in ReO we consider epi-chromosomal genomic sequence to represent a type of genomic sequence alteration, in the sense that it alters the total sequence content of a genome. Epi-chromosomal genomic sequence is nucleic acid sequence that is encoded by some epi-chromosomal element such as a replicative plasmid or transposon, that becomes part of the genome of some cell. 3. Note that this does not classify as a type of 'genomic sequence region' because deletions are a type of sequene alteration and they have an extent of zero, and thus do not qualify as regions""" . _:2e4a89 a owl:Class; owl:intersectionOf _:2e4a99 . _:2e4a99 rdf:first ; rdf:rest _:2e4ab9 . _:2e4ab9 rdf:first _:2e4aa9; rdf:rest rdf:nil . _:2e4aa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4ac9 . _:2e4ac9 a owl:Class; owl:intersectionOf _:2e4ad9 . _:2e4ad9 rdf:first ; rdf:rest _:2e4af9 . _:2e4af9 rdf:first _:2e4ae9; rdf:rest rdf:nil . _:2e4ae9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4b19 . _:2e4b19 a owl:Class; owl:intersectionOf _:2e4b29 . _:2e4b29 rdf:first ; rdf:rest _:2e4b49 . _:2e4b49 rdf:first _:2e4b39; rdf:rest rdf:nil . _:2e4b39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_research material role"@en; rdfs:subClassOf ; "Note that all subclasses of this role describe more specific uses for bearers in a technique or investigation, but that each of these intended uses is necessarily preceded by the intent to use in a technique or an investigation in the first place)"; """decided to elim research material and research material role - was not necessary - esp after not needing it ti define technique becasue decided this would not be a defined class, and all techniques would be asserted as such previous superclass axioms: 1. 'inheres in' some material_entity 2. 'is realized by' some (technique or (has_part some technique) or (part_of some technique)) (questionable axiom - how better specify this? note that we specify that it can be realized by part_of a technique for cases where the role is realized in a biological process that occurs as part_of a technique note that if we leave has_part and part_of as reflexive, done need to say that this is realized in a technique - as this is implied by (both of) the above) 3. gained_through some (planning and (has_specified_output some 'research material specification'))"""; """Optional usage convention: - This role (or any of its subroles) can be applied in axioms describing input to techniques, to indicate that these inputs bear a 'research material role' (since by definition any material specified as input into a technique is a research material). For ex, 'site-directed mutagenesis' has_specified_input some ('nucleic acid' and (has_role some 'research material role'))"""; "a role inhering in a processed material that is gained through a planning process which specifies an agent's intent for its use in a scientific technique or investigation, and realized through the bearer's participation in the intended process, as input into either an assay or some material processing technique that generates other research materials." . a owl:Class; rdfs:label "inducible promoter sequence region"@en; rdfs:subClassOf ; "inducible promoter", "experimentally inducible promoter sequence region"; "a promoter containing sequence elements that allow for controlled regulation of downstream transcriptional activity by the experimental use of some biotic or abiotic factor"; "PERSON: Matthew Brush"; "http://www.patentlens.net/daisy/promoters/271.html" . a owl:Class; rdfs:label "inducible-expression cell line"@en; owl:equivalentClass _:2e4b69; rdfs:subClassOf , _:2e4c39; "In most cases this will also be a transgenic cell line, but in cases wehre the inducibly expressed gene represents seqeunce found in the host cells own genome, as is done in some over-expression studies, this is not considered transgenic."; "an immortal cell line that is capable of varied levels of expression of some exogenous genetic material in response to some environmetnal condition or chemical agent."; . _:2e4b69 a owl:Class; owl:intersectionOf _:2e4b79 . _:2e4b79 rdf:first ; rdf:rest _:2e4b99 . _:2e4b99 rdf:first _:2e4b89; rdf:rest rdf:nil . _:2e4b89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4ba9 . _:2e4ba9 a owl:Class; owl:intersectionOf _:2e4bb9 . _:2e4bb9 rdf:first ; rdf:rest _:2e4bd9 . _:2e4bd9 rdf:first _:2e4bc9; rdf:rest rdf:nil . _:2e4bc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4be9 . _:2e4be9 a owl:Class; owl:intersectionOf _:2e4bf9 . _:2e4bf9 rdf:first ; rdf:rest _:2e4c19 . _:2e4c19 rdf:first _:2e4c09; rdf:rest rdf:nil . _:2e4c09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4c29 . _:2e4c29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4c39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4c49 . _:2e4c49 a owl:Class; owl:intersectionOf _:2e4c59 . _:2e4c59 rdf:first ; rdf:rest _:2e4c79 . _:2e4c79 rdf:first _:2e4c69; rdf:rest rdf:nil . _:2e4c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4c89 . _:2e4c89 a owl:Class; owl:intersectionOf _:2e4c99 . _:2e4c99 rdf:first ; rdf:rest _:2e4cb9 . _:2e4cb9 rdf:first _:2e4ca9; rdf:rest rdf:nil . _:2e4ca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4cc9 . _:2e4cc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_genetically modified DNA"@en; rdfs:subClassOf ; """decided was not a valid/useful class. former eq calss axiom : 'deoxyribonucleic acid' and (is_specified_output_of some 'genetic modification technique') former superclass axiom: 'is bearer of' some (concretizes some sequence_alteration)""" . a owl:Class; rdfs:label "obsolete_detector reagent role"@en; rdfs:subClassOf ; "a reagent role that inheres in a molecular entity and is realized in an analyte assay that measures the presence, location, or abundance of some analyte of interest."; "had grouped probe role and reporter role, but not label role. may end up grouping lable role if we decide the label role is realized during an analyte assay rather than a material labeling technique." . a owl:Class; rdfs:label "molecular label role"@en; rdfs:subClassOf , _:2e4cd9, _:2e4ce9; """OBI: (1) OBI currently does not implement anything but thelabel role (and detector but this is clearly borkena nd not being used) - but their notes indicate how they might implement related roles such as detector and reporter: 'Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion'. ReO uses different terms for these concepts (would say that the the fluorochrome bears a covalent reporter role, the antibody a targeted reporter role, and the biotin a covalent tracker role)- need to clarify and rectify with OBI. (2) OBI wants to use 'molecular tracer role' instead of 'molecular label role' - but ReO no approve because 'tracer' does not suggest a molecular bond is formed that associates a label with an analyte, which is at the heart of the labeling process. 'tracer;' merely implies that the bearer is physically co-located with an analyte or evaluant (ie a barium tracer in stool, or dye tracer in the blood))"""; rdfs:comment "Note that in some cases the molecular target of the label is the analyte itself (e.g. a radiolabeld oligo probe that binds a target gene in a FISH assay), but in other cases (e.g. secondary antibodies in a ICC assay), the molecular target is another label)"; """Molecular label role has four asserted subclass leaf nodes, distinguished along two axes. The first here is their ability to emit or produce some detectable signal - 'reporter' if capable, 'tracker' if not. The second is the nature of their association with a molecular target - 'covalent' vs. 'targeted' (non-covalent). 1. 'covalent reporter role', inhereing in a 'covalent reporter' that emits some detectable signal and is incorporated covalently into an analyte of interest or some other label that can target such an analyte. Examples include a radioactive dATP[P33] (that can be incorporated into an oligonucleotide probe), or a Cy5 fluorochrome (that can be covalently linked to an antibody probe), or a GFP tag (that must be covalently linked to a recombinant protein of interest), or radioactive methionine[S35] (that can be covalently incorporated into proteins of interest) 2. a 'covalent tracker role', inhereing in a 'covalent tracker' that must be covalently bound or incorporated into analyte or probe, and does not emit a detectable signal. Examples include biotin incorporated into a oligonucleotide probe, or a FLAG epitope tag incorporated into a recombinant protein. 3. a 'targeted reporter role', inhereing in a 'targeted reporter' that non-covalently binds to an analyte and emits a detectable signal. Examples include toluidine blue (a blue stain that that targets heparin to detect mast cells in histochemistry), DAPI stain (binds to DNA and fluoresces under UV light), and Ponceau S stain (a red stain which binds generally to protein). Examples also include oligonucleotides or antibodies that have been conjugated with some detectable label (e.g. [P33]-labeled oligos, cy5-conjugated antibodies) 4. a 'targeted tracker role', inhereing in a 'targeted tracker' that non-covalently binds a molecular target but itself does not produce a detectable signal. Examples include a biotin-labeled oligonucleotide probe used to associate with chromosomes in a FISH assay, an antibody used to target a specific protein in a immunhohistochemical assay."""; """Case 1: Nucleotides synthesized to contain a biotin moiety were used to synthesize a cDNA probe, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. Here, biotin bears a covalent tracker role, the biotin-conjugated probe bears a targeted tracker role, and the fluorochrome-conjugated antibody bears a targeted reporter role. Case 2 : An oligonucleotide synthesized with radioactive P33 and used to detect the presence of complementary sequence on a southern blot. Here, P33 bears a covalent reporter role, and the P33-containing oligo bears a targeted reporter role. Case 3: a protein labeling assay involving the detection of S35-labeled methionine incorporated into newly synthesized proteins in a cell culture cells. Here, S35 bears a covalent reporter role (the label is incorporated directly into the analyte in this example, so no additional label is needed) Case 4: An immunocytochemistry assay where a fluorochrome-labeled primary antibody is used to detect a specific cellular protein on a fixed slide. Here, the fluorochrome alone bears a covalent reporter role, the antibody alone bears a targeted tracker role, and the fluorochrome-antibody conjugate bears a targeted reporter role. Case 5: Immunocytochemical detection of a FLAG epitope tag in an overexpressed protein in cell culture cells, using a fluorochrome conjugated anti-FLAG antibody. Here, as in Case 4, the fluorochrome alone bears a covalent reporter role, the antibody alone bears a targeted tracker role, and the fluorochrome-antibody conjugate bears a targeted reporter role. In addition, the FLAG tag also bears a covalent tracker role. Case 6: Phalloidin molecules (a fungal toxin that binds F-actin) are conjugated to rhodamine fluorochrome and applied to a slide of fixed cells to detect actin fibers by fluorescent microscopy. Here, phalloidin bears a targeted tracker role, the rhodamine bears a covalent reporter role, and the rhodamine-phalloidin conjugate bears a targeted reporter role."""; "a reagent role inhering in a molecular entity intended to associate with some molecular target to allow its detection in a molecular label detection technique, wherein the bearer serves as a proxy for the presence, abundance, or location of this molecular target."; "molecular tracer role" . _:2e4cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4ce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_analyte label role"@en; rdfs:subClassOf ; "a detector role that inheres in a molecular entity, and is realized in a material labeling technique in which it binds or is incorporated into an analyte of interest in some specimen that will serve as the evaluant in an anaytel assay"; "tracer"; "decided this was an unneccessary class"; "an analyte label role is realized in the following processes: Incorportion of methionine containing radioactive S35 into newly synthesized proteins in a cell, engineering a protein produced by an expression construct to carry an epitope tag." . a owl:Class; rdfs:label "obsolete_probe label role"@en; rdfs:subClassOf ; "a probe label role is realized in the following processes: incorportion of biotin or P33 into an oligonucleotide probe, covalent attachment of an Alexafluor molecule onto a primary antibody used for immunocytochemistry, covalent attachment of horseradish peroxidase (HRP) to a secondary IgG used in western blotting."; "a label role that inheres in a molecular entity, and is realized in a probe labeling technique in which it binds or is incorporated into a probe that will be used to detect an analyte in an analyte assay. "; "decided this was an unneccessary class" . a owl:Class; rdfs:label "targeted reporter role"@en; rdfs:subClassOf , , _:2e4cf9; "molecular stain role", "molecular dye role"; "Examples include toluidine blue (a blue stain that that targets heparin to detect mast cells in histochemical studies), DAPI stain (binds to DNA and fluoresces under UV light), and probe-reporter conjugates such as antibodies linked to fluorophores, or oligo probes with incorporated P33."; "a molecular reporter role inhering in a molecular entity that is capable of producing a detectable signal, and capable of autonomous, non-covalent association with a molecular target"; "http://stainsfile.info/StainsFile/theory/bonds.htm" . _:2e4cf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4d09 . _:2e4d09 a owl:Class; owl:intersectionOf _:2e4d19 . _:2e4d19 rdf:first ; rdf:rest _:2e4d39 . _:2e4d39 rdf:first _:2e4d29; rdf:rest rdf:nil . _:2e4d29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4d49 . _:2e4d49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular label target role"; rdfs:subClassOf , _:2e4d59, _:2e4d69; rdfs:comment "This association of a molecule with its target is typically through a non-covalent targeted binding. However in some cases such as that of a covalent molecular label, the association is mediated through creation of a direct covalent bond (e.g. incorporation of P33 into an oligonucleotide probe, or conjugation of Cy3 to a secondary antibody)"; "the bearer will not always directly be an analyte (e.g. in the case where a molecular label targets some other molecular label - such as a secondary antibody binding a primary antibody in a immunocytochemistry assay). But the ultumate target is always some analyte."; "a molecular target role inhering in a molecular entity that is is the intended target for association with a molecular label during some molecular labeling technique" . _:2e4d59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4d69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "labeled material"@en; owl:equivalentClass _:2e4d79; rdfs:subClassOf , _:2e4dd9, _:2e4de9; rdfs:comment "A labeled material can be a molecular entity (in which case it would serve as an analyte in a detction of label assay), or a larger grained material entity (in which case it would serve as an evaluant in a detection of label assay and the molecular entity targeted by the label would serves as an analyte)."; "A material entity created through a molecular labeling technique that contains a molecular label to allow its analysis in a detection of label assay. "; "a material entity created through a molecular labeling technique that contains a molecular label to allow for the detection of the molecular target of this label in a molecular label detection assay"; "an OBI:labeled material class, once created. Proposed definition in OBI: a processed material entity created in a material labeling process that contains a material label to allow its detection in an assay." . _:2e4d79 a owl:Class; owl:intersectionOf _:2e4d89 . _:2e4d89 rdf:first ; rdf:rest _:2e4da9 . _:2e4da9 rdf:first _:2e4d99; rdf:rest _:2e4dc9 . _:2e4d99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4dc9 rdf:first _:2e4db9; rdf:rest rdf:nil . _:2e4db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4dd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4de9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular labeling technique"@en; rdfs:subClassOf , _:2e4df9, _:2e4e49, _:2e4e99, _:2e4ee9, _:2e4ef9, _:2e4f09; "molecular labeling technique"; "OBI:material labeling process, to be implemented soon"; "a material processing technique that adds a molecular label to some input material entity, in order to allow detection of the molecular target of this label through some molecular label detection assay."; rdfs:comment "A labeled material can be a molecular entity or a larger material entity. If the labeled material itself is a molecular entity, it serves as an analyte in this assay. If the labeled material is a larger material entity, it serves as an evaluant in the assay and the molecular entity targeted by the label serves as an analyte."; . _:2e4df9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4e09 . _:2e4e09 a owl:Class; owl:intersectionOf _:2e4e19 . _:2e4e19 rdf:first ; rdf:rest _:2e4e39 . _:2e4e39 rdf:first _:2e4e29; rdf:rest rdf:nil . _:2e4e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4e49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4e59 . _:2e4e59 a owl:Class; owl:intersectionOf _:2e4e69 . _:2e4e69 rdf:first ; rdf:rest _:2e4e89 . _:2e4e89 rdf:first _:2e4e79; rdf:rest rdf:nil . _:2e4e79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4ea9 . _:2e4ea9 a owl:Class; owl:intersectionOf _:2e4eb9 . _:2e4eb9 rdf:first ; rdf:rest _:2e4ed9 . _:2e4ed9 rdf:first _:2e4ec9; rdf:rest rdf:nil . _:2e4ec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4ee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4ef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4f19 . _:2e4f19 a owl:Class; owl:intersectionOf _:2e4f29 . _:2e4f29 rdf:first ; rdf:rest _:2e4f49 . _:2e4f49 rdf:first _:2e4f39; rdf:rest rdf:nil . _:2e4f39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e4f59 a owl:Axiom; "this is an alternate way to link the technique to the melcular label and its 'material to be added role'. Shoudl I use this, or the 'has_specified_input some moelcular label and has role some mateiral to be added role' approach? Or both?"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e4f69 . _:2e4f69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e4f79 . _:2e4f79 a owl:Class; owl:intersectionOf _:2e4f89 . _:2e4f89 rdf:first ; rdf:rest _:2e4fa9 . _:2e4fa9 rdf:first _:2e4f99; rdf:rest rdf:nil . _:2e4f99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "covalent reporter role"@en; rdfs:subClassOf ; "a molecular reporter role inhering in a molecular entity that is capable of producing a detectable signal, but not capable of autonomous non-covalent association with a molecular target (such that it must be covalenly attached to an analyte of interest, or to a targeted molecular label that can direct it to an analyte)."; rdfs:comment "Reporters must be covalently attached to their target (analyte or probe), as they contain no inherent structural element that specifically binds a target. The molecular reporter role inheres only in the part of a molecule that emits a detectable signal (ie the fluorochrome on part of a conjugated antibody, or the radioactive atoms of a labeled oligonucleotide probe, or the GFP moiety in a GFP-fusion protein)."; """Case 1: Nucleotides synthesized with the incorporation of biotin were used to synthesize a cDNA probe, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. Here, biotin bears a tracker role, the fluorochrome bears a reporter role, and the antibody bears a probe role. Case 2 : An oligonucleotide synthesized with radioactive P33 and used to detect the presence of complementary sequence on a southern blot. Here, P33 bears a reporter role, and the oligo bears a probe role. Case 3: a protein labeling assay involving the detection of S35-labeled methionine incorporated into newly synthesized proteins in a cell culture cells. Here, S35 bears a reporter role, and there is no probe role realized. Case 4: Covalent attachment of an fluorochrome into a primary antibody to detect a specific cellular protein in an immunocytochemistry assay. Here, the fluorochrome bears a reporter role, and the antibody bears the probe role. Case 5: Immunosytochemical detection of a FLAG epitope tag in an overexpressed protein in cell culture cells, using a fluorochrome conjugated anti-FLAG antibody. Here, as in Case 4, the fluorochrome bears a reporter role and the antibody bears the probe role. In addition, the FLAG tag also bears a tracker role. Case 6: Phalloidin molecules (a fungal toxin that binds F-actin) are conjugated to rhodamine fluorochrome and applied to a slide of fixed cells to detect actin fibers by fluorescent microscopy. Here, phalloidin bears a probe role (it binds non-covalently to actin), and rhodamine bears a reporter role.""" . a owl:Class; rdfs:label "obsolete_analyte labeling technique"@en; rdfs:subClassOf ; "a technique that attaches or incorporates some molecular label into a molecular entity intended to serve as an analyte in some assay" . a owl:Class; rdfs:label "obsolete_tracker labeling technique"@en; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_chemical reagent role"@en; rdfs:subClassOf ; "obsoleted when implemented the info vs non-info molecular entity divied to classify chemical reagents"; "a reagent role played by a non-protein or nucleic acid molecular entity, and realized during an investigation through its participation in a chemical reaction that detects, measures, modifies, or produces other molecular entities." . a owl:Class; rdfs:label "environment"; rdfs:subClassOf ; "term from environment ontology?"; "organism environment"; "The external elements and conditions which surround, influence, and affect the life and development of an organism or population."; rdfs:comment "Note that environment as used here applies specifically to organisms and populations of organisms, and not to inanimate objects"; "PERSON: Matthew Brush"; "MeSH: environment" . a owl:Class; rdfs:label "organic chemical reagent"@en; owl:equivalentClass _:2e4fb9; rdfs:subClassOf , , _:2e5049; owl:disjointWith ; "an chemical reagent that is an organic molecule (contains some carbon atom), and that is not an information macromolecule (nucleic acid, polypeptide, or analogs of these macromolecules). Organic chemical reagents can include organic small molecules, as well as larger carbohydrates and lipids molecules." . _:2e4fb9 a owl:Class; owl:intersectionOf _:2e4fc9 . _:2e4fc9 rdf:first ; rdf:rest _:2e4fe9 . _:2e4fe9 rdf:first _:2e4fd9; rdf:rest _:2e5039 . _:2e4fd9 a owl:Class; owl:complementOf _:2e4ff9 . _:2e4ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5009 . _:2e5009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5019 . _:2e5019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5039 rdf:first _:2e5029; rdf:rest rdf:nil . _:2e5029 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "inorganic chemical reagent"@en; owl:equivalentClass _:2e5059; rdfs:subClassOf , , _:2e5099; rdfs:comment "Inorganic compounds do not contain chemical moieties consisting of carbon and hydrogen bonded together. Here, we include atomic and elemental reagents such as phosphorus or iodine as inorganic reagents, as they contain no carbon-hydrogen bonds"; "a chemical reagent that is an inorganic molecular entity (ie lacks carbon atoms)"; "sodium chloride salt, phosphorus-32 atoms, iodine, hydrogen chloride acid, sodium hydroxide base" . _:2e5059 a owl:Class; owl:intersectionOf _:2e5069 . _:2e5069 rdf:first ; rdf:rest _:2e5089 . _:2e5089 rdf:first _:2e5079; rdf:rest rdf:nil . _:2e5079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "elemental reagent"@en; owl:equivalentClass _:2e50a9; rdfs:subClassOf , , _:2e50e9; "an elemental molecular entity that bears a reagent role"; rdfs:comment "elemental reagents include stand-alone atomic reagents (e.g. P32) and molecules comprised of only one type of atom (e.g. O2, N2, Fe2)" . _:2e50a9 a owl:Class; owl:intersectionOf _:2e50b9 . _:2e50b9 rdf:first ; rdf:rest _:2e50d9 . _:2e50d9 rdf:first _:2e50c9; rdf:rest rdf:nil . _:2e50c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e50e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_bioactive small molecule"@en; rdfs:subClassOf ; "an organic molecule of low molecular weight, which is by definition not a polymer, and can interact with and affect the function or activity of one or more biological molecules in the context of a cell, tissue, or organism."; rdfs:comment "The conventional upper molecular weight limit for a small molecule is approximately 800 Daltons. The term small molecule is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or polysaccharide and alters the activity or function of the biopolymer. "; "http://en.wikipedia.org/wiki/Small_molecule"; """decided not needed - merged with organic small moelcule class former eq class axiom : 'molecular entity' and ('has quality' some 'low molecular weight') and (has_disposition some bioactive)""" . a owl:Class; rdfs:label "obsolete_bioactive small molecule reagent"@en; rdfs:subClassOf ; """decided no longer needed as i merged with organic small molecule reagent former eq class def : 'molecular entity' and ('has quality' some 'low molecular weight') and ('has role' some 'reagent role') and (has_disposition some bioactive)""" . a owl:Class; rdfs:label "obsolete_molecular label"@en; rdfs:subClassOf ; "a molecular entity bearing a reagent role that is realized in a detection of label assay, where the molecular label associates directly or indirectly with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of label assay. A label may associate covalently or non-covalently with its target, and may or may not yield some detectable signal. In the latter case, the label is capable of binding to some moelcular entity bearing a reporter that is able to yield some detectable signal." . a owl:Class; rdfs:label "activity reporter role"@en; rdfs:subClassOf , _:2e50f9; rdfs:comment "an 'activity reporter' is different from a 'molecular reporter' in that the former is used to measure the rate of some biological process or activity (eg promoter activity or mRNA translation), as opposed to the presence or abundance of some molecular analyte."; "Examples include a luciferase reporter whose promoter element is activated by the presence of a transcriptional activator, or horse-radish peroxidase coonjugated to some secondary antibody which catalyzes the conversion of an ECL substrate to produce light."; "a reagent role inhereing in a molecular entity (typically a gene or enzyme) that is activated to produce some detectable output (i.e. an indicator) in response to some biomolecular event, in order to indicate the presence, amount, or location of some entity of interest. The output of this reporter will either directly elicit some detectable signal that is measurable in a biological assay (eg luciferase in a luciferase assay), or be 'recognized' by an analyte reporter that elicits such a signal (eg beta-galactosidase which is recognized by its colorimetric substrate X-gal)."; . _:2e50f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5109 . _:2e5109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5119 . _:2e5119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_molecular probe"@en; rdfs:subClassOf ; """replaced witih two tiered, principled naming approach using moelculr label sub roles: axioms that were here: has_disposition some 'molecular binding disposition' not (has_disposition some 'detectable disposition')"""; """a molecular label capable of targeted, non-covalent binding to some moelcular entity of interest, to facilitate the target's association with a reporter and allow its detection. Molecular probes contain some structural element that targets them to associate non-covalently with an analyte (or with a label associated with an analyte). As probes themselves do no produce a signal, they must recruit some molecular reporter in order to be detected."""; "targeted, non-signal producing label" . a owl:Class; rdfs:label "obsolete_molecular reporter"@en; rdfs:subClassOf ; "non-targeted, signal producing label"; """replaced witih two tiered, principled naming approach using moelculr label sub roles: axioms that were here: has_disposition some 'detectable disposition' not (has_disposition some 'molecular binding disposition')""" . a owl:Class; rdfs:label "obsolete_fluorescent reporter role"@en; rdfs:subClassOf ; "fluorochrome role"; "ChEBI: fluorochrome"; "a molecular reporter role inhering in a molecular entity that has a disposition to fluoresce, and is used to impart fluorescence to a target analyte allowing its detection in an assay"; "implemented new approach for moelcular label modeling (using the molec label role for defining molec label and targeted and reporter axes based children, but not for defining colorimetric, fluorescent, radioactive label children . . .will use dispositions here. " . a owl:Class; rdfs:label "bovine serum albumin"@en; rdfs:subClassOf ; "BSA"; . a owl:Class; rdfs:label "obsolete_radioactive reporter role"@en; rdfs:subClassOf ; "implemented new approach for moelcular label modeling (using the molec label role for defining molec label and targeted and reporter axes based children, but not for defining colorimetric, fluorescent, radioactive label children . . .will use dispositions here. "; "a molecular reporter role inhering in a radioactive molecular entity, and is used to impart radioactivity to a target analyte allowing its detection in an assay." . a owl:Class; rdfs:label "cytokine"@en; owl:equivalentClass _:2e5129; rdfs:subClassOf , _:2e5169; "FMA cytokine? "; "a small cell-signaling molecule of a type secreted by numerous cell types and used as signaling molecules in intercellular communication. Cytokines can be classified as proteins, peptides, or glycoproteins; the term \"cytokine\" encompasses a large and diverse family of regulators produced throughout the body by cells of diverse embryological origin"; "http://en.wikipedia.org/wiki/Cytokine"; . _:2e5129 a owl:Class; owl:intersectionOf _:2e5139 . _:2e5139 rdf:first ; rdf:rest _:2e5159 . _:2e5159 rdf:first _:2e5149; rdf:rest rdf:nil . _:2e5149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5169 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "interleukin-3 reagent"@en; rdfs:subClassOf , _:2e5179; "IL-3 reagent", "IL3 reagent"; . _:2e5179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "tunicamycin"@en; rdfs:subClassOf , _:2e5189; "an organic small molecule that derives from Streptomyces lysosuperificus, and which blocks the reaction of UDP-GlcNAc and Dol-P in the first step of glycoprotein synthesis, thus inhibiting the synthesis of all N-linked glycoproteins"; "http://tunicamycin.noneto.com/"; "a ChEBI:tunicamycin class"; . _:2e5189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "investigation objective"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_fluorescent reporter "@en; rdfs:subClassOf ; "fluorochrome" . a owl:Class; rdfs:label "reagent solution"@en; owl:equivalentClass _:2e5199; rdfs:subClassOf , , _:2e51d9; "a chemical solution that bears a reagent role, realized through its participation in a scientific experiment or technique"; "chemical solution reagent" . _:2e5199 a owl:Class; owl:intersectionOf _:2e51a9 . _:2e51a9 rdf:first ; rdf:rest _:2e51c9 . _:2e51c9 rdf:first _:2e51b9; rdf:rest rdf:nil . _:2e51b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e51d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular target role"; rdfs:subClassOf , _:2e51e9; "a role inhereing in a molecular entity that is specifically bound by some molecular probe (e.g. a molecular label, a chemical inhibitor) in the process of some assay or material processing technique."; "experimental molecular target role"; rdfs:comment "This association of a molecule with its target is typically through a non-covalent binding interaction. However in some cases such as that of a covalent molecular label, the association is mediated through creation of a direct covalent bond (e.g. incorporation of P33 into an oligonucleotide probe, or conjugation of Cy3 to a secondary antibody)" . _:2e51e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_material collection technique"; rdfs:subClassOf ; "Collection can include collecting whole material entities (e.g. collecting a frog or a bone), collecting parts of material entities (e.g. breaking off a piece of a rock, a leaf from a tree), collecting all or a portion of some collection (e.g. a portion of sand from a streambed, or all water from a puddle) or, similarly, collecting individuals from populations or their environments (e.g. a bee from a colony, a woodchuck from the woods)."; """Def 1: a material processing technique in which an agent physically obtains and stores some material entity or entities of interest, and in doing so separates them from other like entities or from their environment. Def 2: a material processing technique in which some material entity representing a part of some whole, or a portion of some population or group, is obtained and stored."""; """merged with specimen collection, because we determined that the targets of all collections in our domain are likely to qualify as specimens former logical definition: 'material processing technique' and (achieves_objective_specification some 'obsolete_material collection objective')""" . a owl:Class; rdfs:label "artificial environment"; rdfs:subClassOf ; "an environment in which an object is found as a consequence of being processed / re-located by some intentional agent out of its natural environment" . a owl:Class; rdfs:label "obsolete_material preparation technique"; rdfs:subClassOf ; "a technique in which a material entity is prepared in some way (synthesized, collected, purified, etc) to be used in an experiment or technique as part of an investigation."; """in light of re-interpretation of 'material processing' and 'material processing technique' as being more broadly considered to cover cases of collection and material separation, and to have output some material that is intended for use in an investigation (ie research material), 'material preparation technique' was deemed unnecessary and was obsoleted. As a result, the label of 'prepared material' was changed to 'research material', and this was used in an axiom on 'research material role' (inheres_in some 'research material'). In addition, material collection was moved to be a child of technique.""" . a owl:Class; rdfs:label "obsolete_research material"; rdfs:subClassOf ; "TO GET MATERIALS THAT ARE RESEARCH MATERIALS TO INFER AS SUCH, CONVENTION SHOULD BE TO ASSERT THAT THEY HAVE A RESEARCH MATERIAL ROLE, OR, WHENEVER POSSIBLE, CREATE AN AXIOM SAYING THAT A MATERIAL ENTITY IS OUTPUT FROM SOME MATERIAL PROCESSING TECHNIQUE (BECAUSE MATERIAL PROCESSING TECHNIQUES ARE ASSERTED TO HAVE ONLY RESEARCH MATERIALS AS OUTPUT, AND THEREFORE WILL HAVE A RESEARCH MATERIAL ROLE AND BE INFERRED TO BE RESEARCH MATERIALS). ALTERNATIVELY, IF NO WANT TO HAVE AN AXIOM STATING THAT THE MATERIAL IS OUTPUT FROM SOME MATERIAL PROCESSING TECHNIQUE, YOU CAN SAY USE AN AXIOM TO SAY IT HAS A RESEARCH MATERIAL ROLE . . . SO USE OF AN AXIOM STATING A MATERIAL HAS A 'RESEARCH MATERIAL ROLE' IS A BACKUP, TO BE USED ONLY IF THERE IS NO AXIOM THAT IT IS OUTPUT FROM SOME TECHNIQUE."; "a material entity that is intended to be used or studied in a research investigation, as either specified input directly into an assay or a material processing technique, or that is produced through a material processing technique"; "Note that while most research materials are processed, this is not always/neccessarily true, and thus 'research material' is asserted only as children of material entity and not processed material. An example of a research material that is not necessarily processed is a specimen (although the vast majority of specimens are processed). Thus, the specimen class classifies as a research material but not a processed material. Since the scope of ReO (and OBI) covers primarily research materials, and the vast majority of research materials are processed, there is likely to be few if any other differences between the classified research material and processed material hierarchies."; """decided to elim research material and research material role - was not necessary - esp after not needing it ti define technique becasue decided this would not be a defined class, and all techniques would be asserted as such Previous eq class axiom: material_entity and (('has role' some 'obsolete_research material role') or (has_part some ('has role' some 'obsolete_research material role'))) Previous superclass axiom : participates_in some 'material processing technique' (or spec output of some mat processing tech?)""" . a owl:Class; rdfs:label "obsolete_experiment"; rdfs:subClassOf ; "a set of planned processes that has the objective to generate data about some material entity in order to test or generate one or more hypotheses. An experiment consists of planning, execution of one or more assays, data analysis, and drawing conclusions. But any material processing techniques perfomed to generate input materials for the experiment are not considered part of the experiment (rather, these are part of a larger investigation of which the experiment is a part). "; """APPROACH #1: Clarificaiton of the distinctions between investigation, experiment, and assay : Investigation vs Experiment: An investigation consists necessarily of planning (in which objectives are set), execution (in which assays and techniques are performed), documentation (in which process and results are recorded) and analysis (in which data is interpreted). Like an investigation, an experiment consists of planning, execution, documentation, and analysis. Furthermore, investigations or experiments can aim to generate hypotheses in addition to testing them. However, ther are two key distinctions we would like to make in modeling investigations vs experiments: (1) unlike investigations, the execution phase of an experiment does not include material processing or preparation techniques - only assays that generate data. So, a given experiment may be equivalent to an investigation when its execution consists only of an assay or set of assays. (2) the objectives of an experiment are more limited in scope, aiming to generated data about some INSTANCE of an evaluant and thereby test some hypothesis. By contrast, the objectives of investigations can reach farther to seek knowledge about CLASSES of natural materials and phenomenon even when INSTANCES of these classes are not directly used in the execution of an investigation (ie when cancer cell lines are used as 'proxies' for seeking knowledge about a particular class of tumor). Experiment vs Assay: Unlike an investigation or experiment, an assay consists only of an execution stage. An assay is a self-contained planned process, which does not include related planning or analysis processes. So, while a given experiment may consist of only a single assay, the experment also comprehends planning and analysis processes. """, """APPROACH #2: Clarificaiton of the distinctions between investigation, experiment, and assay : Investigation vs Experiment: An investigation consists necessarily of planning (in which objectives are set), execution (in which assays and techniques are performed), documentation (in which process and results are recorded) and analysis (in which data is interpreted). Like an investigation, an experiment consists of planning, execution, documentation, and analysis. Furthermore, investigations or experiments can aim to generate hypotheses in addition to testing them. However, the key distinction we would like to make in modeling investigations vs experiments is that, unlike investigations, the execution phase of an experiment does not include material processing or preparation techniques - only assays that generate data. So, a given experiment may be equivalent to an investigation when its execution consists only of an assay or set of assays. Experiment vs Assay: Unlike an investigation or experiment, an assay consists ONLY of an execution stage. An assay is a self-contained planned process, which does not include related planning or analysis processes. So, while a given experiment may consist of only a single assay, the experment also comprehends planning and analysis processes. Investigation and Experiment vs Assay: The objectives of an assay are more limited in scope, aiming to generated data about some INSTANCE of an evaluant. By contrast, the objectives of experiments or investigations can reach farther to seek knowledge about CLASSES of natural materials and phenomenon. This can be true even when INSTANCES of these CLASSES about which knowledge is sought are not directly used in the execution of an investigation (ie when cancer cell lines are used as 'proxies' for seeking knowledge about a particular class of tumor). So, in justifying that a cell line is a reagent, we can it is permissible for reagents to bear an evaluant role in an assay ONLY as a 'proxy specimen' about which DATA is generated, but it is not true that a reagent can be an instance of the class specified as the thing about which knowledege is sought/conclusoins are made (recall, drawing a conclusion is a part of an investigation, but not an assay)."""; """5-3-12 - DONT LIKE THE NOTION THAT EXPERIMENTS ARE LIKE INVESTIGATIONS BUT DONT INCLUDE MATERIAL PROCESSING TECHNIQUES - SEEMS ARBITRARY DISTINCTION AND NOT A SHARED OR INTUITIVE ONE. former axioms: 'planned process' 'has component part' exactly 0 'material processing technique' achieves_objective_specification some 'experimental objective' has_part some 'interpreting data' has_part some assay has_part some documenting has_part some planning part_of some investigation""" . a owl:Class; rdfs:label "data analysis technique"; rdfs:subClassOf ; """a data processing technique that involves inspecting, cleaning, transforming, or modeling data with the objective of highlighting useful information, suggesting conclusions, and supporting decision making. Data analysis aims to clarify, explain, interpret, or predict scientific phenomenon to support the generation of conculsions or hypotheses."""; "http://en.wikipedia.org/wiki/Data_analysis" . a owl:Class; rdfs:label "obsolete_planning"; rdfs:subClassOf ; "replaced by OBI:planning"; "discuss with OBI whether planning is a planned process, and whether it has a specified output, and whether its output should more generally be a directive information entity (OBI says it has_participant some 'plan specification . . . but it seems liek a specification could only be an output of a planning process, and couldnt a planning process have outputs that are not plan specifications (ie could have output that is an action specification?)." . a owl:Class; rdfs:label "obsolete_specimen collection"; rdfs:subClassOf ; "replaced with OBI:specimen creation class (editor preferred label changed to specimen collection). If we decide that specimens can be created as well as collected, then re-implement this class as a child of specimen creation."; "a material collection technique in which some material is obtained form its natural environment as an example of some class of material entity. Specimens are often used as input into some assay or material processing technique as part of an investigation." . a owl:Class; rdfs:label "obsolete_specimen"; rdfs:subClassOf ; "replaced with OBI:specimen class"; rdfs:comment "a 'specimen' is considered as a single instance of a class of entities, and unlike a 'sample', is not necessarily considered as representative of some larger population" . a owl:Class; rdfs:label "obsolete_specimen creation"; rdfs:subClassOf ; "may bring back as an equivalent class to group specimen collectiona nd specimen production, if we decide that specimens can be 'manufactured' in addition to being collected" . a owl:Class; rdfs:label "obsolete_molecular_ stain"; rdfs:subClassOf ; "targeted, signal producing label", "labeled molecular probe", "molecular indicator"; """replaced witih two tiered, principled naming approach using moelculr label sub roles: axioms that were here: has_disposition some 'detectable disposition' has_disposition some 'molecular binding disposition' """ . a owl:Class; rdfs:label "experimental objective"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_goat serum albumin"; rdfs:subClassOf . a owl:Class; rdfs:label "bovine serum albumin reagent"; owl:equivalentClass _:2e51f9; rdfs:subClassOf , , _:2e5239, _:2e5289, _:2e5299, _:2e52a9; "BSA reagent"; """BSA is an example of a protein that is commonly used as a regent in biomedical experimentation. BSA is typically purified from some biological source, but can also be recombinantly expressed. BSA is used in a variety of ways (ie can bear a number of reagent sub-roles), including as a blocking agent, a stabilizing agent, and a protein standard. Note that we take the liberty of assigning several roles to a class such as BSA, despite the fact that in paractice a givne instnace of BSA might only ever bear or realize one of these roles. This is done for practical reasons, to allow modeling ot the various ways in which reagents have the potential to be used (an alternate approach is to use dispositions or some other form of dependent continuant to model such attributes in this way, whihc would not require intent to be applied for using a given instance in a specified way, in order to be borne by that instance)"""; . _:2e51f9 a owl:Class; owl:intersectionOf _:2e5209 . _:2e5209 rdf:first ; rdf:rest _:2e5229 . _:2e5229 rdf:first _:2e5219; rdf:rest rdf:nil . _:2e5219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5249 . _:2e5249 a owl:Class; owl:intersectionOf _:2e5259 . _:2e5259 rdf:first ; rdf:rest _:2e5279 . _:2e5279 rdf:first _:2e5269; rdf:rest rdf:nil . _:2e5269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5299 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e52a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_material collection objective"; rdfs:subClassOf ; "merged with specimen collection objective, because we determined that the targets of all collections in our domain are likely to qualify as specimens"; "a material component separation objective to physically obtain and stores some material entity or entities of interest, and in doing so separate them from other like entities or from their environment. " . a owl:Class; rdfs:label "obsolete_cytokine role"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_radioactive reporter"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_non-incorporant input role"; rdfs:subClassOf ; """In a buffered reaction that is part of some technique to generate a macromolecular output, any buffers or other chemicals that may exhange atoms or ions with participants make only minor contributions at the atomic level of composition. The output cannot be said to derive from these buffers/chemicals, which therefore play non-incorporant roles. For example, In a material labeling technique where a small molecule fluorochrome is conjugated to an antibody, the incorporants include an antibody and a fluorochrome. However any buffers or other chemicals that may exhange atoms, ions, or small molecular moieties with the antibody or fluorochrome and thereby contribute minimally to the composition of the specified output, at an atomic level of granularity, play only a non-incorporant roles. Similarly, in the case where a cell line is used to produce a recombinant protein: (1) any macromolecular building blocks (e.g. amino acids, nucleic acids, etc) that are provided by a cell line and incorporated into the specified output material are significant incorporants; (2) the cell line itself is considered a non-incorporant, as it exits at a coarser level of granularity than these molecular building blocks and the output protein, and as such the specified output cannot be said to derive from the cell line."""; rdfs:comment """Any specified input into a material processing that merely facilitates the transfer of matter from incorporants to specified output, and does not contribute material of its own to the specified output, will bear a non-incorporant role that is realized in this material procesing event. Also, any specified input that make material contributions only at a finer level of granularity that that at which it exists (e.g. a buffer contributing atomic or ionic moities, or a cell contributing amino acids), will bear a non-incorporant role in a materiall processing."""; "processing facilitator role"; """a specified input role inhering in a material entity and realized by the bearer's participation in a material processing where the specified output does not derive from the bearer of the incorporant role (ie the bearer contributes no significant material to the composition of the specified output material). Can be considered as a reagent role realized in a material processing technique"""; """former superclass axioms: 'inheres in' some (material_entity and (is_specified_input_of some 'material processing'))""" . a owl:Class; rdfs:label "obsolete_DAPI"; rdfs:subClassOf ; "replaced by CHEBI_51231 DAPI" . a owl:Class; rdfs:label "coomassie blue"; rdfs:subClassOf , , _:2e52b9, _:2e52c9, _:2e52d9; . _:2e52b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e52c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e52d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "covalent tracker role"; rdfs:subClassOf ; "molecular tracker role (according to old naming scheme)"; "a molecular tracker role inhering in a molecular entity that is not capable of producing a detectable signal, and not capable of autonomous non-covalent association with a molecular target (such that it must be covalenly attached to an analyte of interest, or to a targeted molecular label that can direct it to an analyte)."; "Examples include biotin incorporated into a oligonucleotide probe, or a FLAG epitope tag incorporated into a recombinant protein.", """Case 1: Nucleotides synthesized with the incorporation of biotin were used to synthesize a cDNA probe, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. Here, biotin bears a tracker role, the fluorochrome bears a reporter role, and the antibody bears a probe role. Case 2 : An oligonucleotide synthesized with radioactive P33 and used to detect the presence of complementary sequence on a southern blot. Here, P33 bears a reporter role, and the oligo bears a probe role. Case 3: a protein labeling assay involving the detection of S35-labeled methionine incorporated into newly synthesized proteins in a cell culture cells. Here, S35 bears a reporter role, and there is no probe role realized. Case 4: Covalent attachment of an fluorochrome into a primary antibody to detect a specific cellular protein in an immunocytochemistry assay. Here, the fluorochrome bears a reporter role, and the antibody bears the probe role. Case 5: Immunosytochemical detection of a FLAG epitope tag in an overexpressed protein in cell culture cells, using a fluorochrome conjugated anti-FLAG antibody. Here, as in Case 4, the fluorochrome bears a reporter role and the antibody bears the probe role. In addition, the FLAG tag also bears a tracker role. Case 6: Phalloidin molecules (a fungal toxin that binds F-actin) are conjugated to rhodamine fluorochrome and applied to a slide of fixed cells to detect actin fibers by fluorescent microscopy. Here, phalloidin bears a probe role (it binds non-covalently to actin), and rhodamine bears a reporter role.""" . a owl:Class; rdfs:label "obsolete_molecular tracker"; rdfs:subClassOf ; "non-targeted, non-signal producing label"; """replaced witih two tiered, principled naming approach using moelculr label sub roles: axioms that were here: and (not (has_disposition some 'molecular binding disposition')) and (not (has_disposition some 'detectable disposition'))""" . a owl:Class; rdfs:label "intentional agent"; owl:equivalentClass _:2e52e9; rdfs:subClassOf , _:2e5359, _:2e5369; "FOAF:agent, or wait to see how ISF/ARG handles this?"; "any person or organization capable of intentional action (an entity that perceives and acts). Agents are bearers of an 'achieved role' that results from self-motivated action or intention that reflect the agent's skills, abilities, or efforts"; "may be labeled as 'intentional agent' to distinguish from the use of 'agent' in the relations agent_in and has_agent, in which the 'agent' referred to plays a causative role in some process, but is not necessarily an intentional being." . _:2e52e9 a owl:Class; owl:intersectionOf _:2e5309 . _:2e5309 rdf:first _:2e52f9; rdf:rest _:2e5349 . _:2e52f9 a owl:Class; owl:unionOf _:2e5319 . _:2e5319 rdf:first ; rdf:rest _:2e5329 . _:2e5329 rdf:first ; rdf:rest rdf:nil . _:2e5349 rdf:first _:2e5339; rdf:rest rdf:nil . _:2e5339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5359 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "chemical reaction"; rdfs:subClassOf ; """http://bioinformatics.oxfordjournals.org/content/19/4/524.long, http://edtech2.boisestate.edu/millerc/edtech573/biochemglossary.htm"""; "class from some appropriate ontology - SIO has a chemical reaction class, but is not under the OBO Foundry umbrella"; rdfs:comment "Note that this view of a chemical reacion covers molecular binding/interaction events, such as the recognition of an epitope by an antibody."; "a process in which chemical entities under go some transformation, transport or binding event whereby chemical bonds between atoms are rearranged." . a owl:Class; rdfs:label "obsolete_specified input role"; rdfs:subClassOf ; "a role inhering in a material entity gained through an agent's intention for it to be specified input into some technique, and realized through the bearer's participation in this technique"; """no longer needed/used. former eq class axioms: 'ascribed role' and ('is realized by' some 'inputting of a material participant') former superclass axioms: 'inheres in' only (is_specified_input_of some (technique or (part_of some technique))) 'inheres in' some (is_specified_input_of some (technique or (part_of some technique))) """; . a owl:Class; rdfs:label "incorporant role"; rdfs:subClassOf , _:2e5379, _:2e5389; """Examples illustrating incorporant vs non-incorporant roles: In a buffered reaction that is part of some technique to generate a macromolecular output, any buffers or other chemicals that may exhange atoms or ions with participants make only minor contributions at the atomic level of composition. The output cannot be said to derive from these buffers/chemicals, which therefore play non-incorporant roles. For example, In a material labeling technique where a small molecule fluorochrome is conjugated to an antibody, the incorporants include an antibody and a fluorochrome. However any buffers or other chemicals that may exhange atoms, ions, or small molecular moieties with the antibody or fluorochrome and thereby contribute minimally to the composition of the specified output, at an atomic level of granularity, play only a non-incorporant roles. Similarly, in the case where a cell line is used to produce a recombinant protein: (1) any macromolecular building blocks (e.g. amino acids, nucleic acids, etc) that are provided by a cell line and incorporated into the specified output material are significant incorporants; (2) the cell line itself is considered a non-incorporant, as it exits at a coarser level of granularity than these molecular building blocks and the output protein, and as such the specified output cannot be said to derive from the cell line.""", """Two material labeling techniques are described below to illustrate the use of incorporant role and its subtypes: Example 1: In a material labeling technique where a small molecule fluorochrome is conjugated to an antibody, the incorporants include an antibody and a fluorochrome. A primary incorporant role is realized by the antibody, and a secondary incorporant role is realized by the fluorochrome, because the specified output is an 'antibody' which is labeled by a fluorochrome. Both the antibody and fluorochrome realize significant incorporant roles. However any buffers or other chemicals that may exhange atoms, ions, or small molecular moieties with the antibody or fluorochrome and thereby contribute minimally to the composition of the specified output do not play significant incorporant roles (and may play non- incorporant roles?). Furthermore, the antibody realizes a major incorporant role, and the fluorochrome realizes a minor incorporant role, as the antibody contributes a significantly greater proportion of the material in the specified output compared to the fluorochrome Example 2 : In a material labeleing technique where a large GFP protein is attached to a small 10-amino acid peptide representing a protein degradation signal (a 'degron'), the incorporants include the GFP protein and the degron. A primary incorporant role is realized by the degron, and a secondary incorporant role is realized by the GFP protein, because the specified output is a 'degron' that i is labeled by GFP. Both the GFP protein and the degron play significant incorporant roles. However any buffers or other chemicals that may exhange atoms, ions, or small molecular moieties with incorporants and thereby contribute minimally to the composition of the specified output do not play significant incorporant roles (and may play non-incorporant roles). Here, the degron realizes the minor incorporant role and the GFP protein realizes the major incorporant role, as the GFP contributes a significantly greater proportion of material in the specified output compared to the degron."""; "a role inhering in a material entity, that is gained through an agent's intention for it to be specified input into some material processing in which the specified output material derives from the bearer of the incorporant role (ie the bearer contributes significant material to the composition of the specified output material), and realized by the execution of this material processing event"; rdfs:comment "alt def: a specified input role inhering in a material entity and realized by the bearer's participation in a material processing where the specified output derives from the bearer of the incorporant role (ie the bearer contributes significant material to the composition of the specified output material)" . _:2e5379 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5399 . _:2e5399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_primary incorporant role"; rdfs:subClassOf ; "an incorporant role inhering in a material entity, that is gained through an agent's intention for it to be specified input into some material processing where it will be modified by attachment of some secondary incorporant, and realized by the execution of this material processing event"; rdfs:comment "a primary incorporant role inheres in the input material whose identity is retained in the specified output material (ie in an antibody labeling technique, the primary incorporant role is realized by the antibody because the specified output is a 'labeled antibody' (and not an 'antibodies label)" . a owl:Class; rdfs:label "obsolete_secondary incorporant role"; rdfs:subClassOf ; "an incorporant role inhering in a material entity, that is gained through an agent's intention for it to be specified input into some material processing where it will modify some primary incorporant, and realized by the execution of this material processing event" . a owl:Class; rdfs:label "obsolete_major incorporant role"; rdfs:subClassOf ; "an incorporant role inhering in an input material entity gained through an agent's intention for it be input into some material processing where it will contribute the most significant amount of material to the composition of the specified output relative to other incorporants, and realized in the exection of such a material processing event" . a owl:Class; rdfs:label "obsolete_minor incorporant role"; rdfs:subClassOf ; "an incorporant role inhering in an input material entity gained through an agent's intention for it be input into some material processing where it will not contribute the most significant amount of material to the composition of the specified output relative to other incorporants, and realized in the exection of such a material processing event" . a owl:Class; rdfs:label "obsolete_significant incorporant"; rdfs:subClassOf ; rdfs:comment """To bear a significant incorporant role, (1) an input material entity must contribute material to the composition of the specified material output; and (2) this contributed material must represent a significant part of the input material entity itself (ie be necessary to its 'existence', such that its loss results in a change of identity or type). In this way, any buffers or other chemicals that may exhange atoms, ions, or small molecular moieties with incorporants and thereby contribute minimally to the composition of the specified output do not play significant incorporant roles. Similarly, in the case where a cell line is used to produce a virus or recombinant protein, while any macromolecular building blocks (e.g. amino acids, nucleic acids, etc) that are provided by a cell line and incorporated into the specified output material are significant incorporants, the cell line itself is not considered a significant incorporant. This is because these 'building blocks' are not necessary to the identity of the cell line of which they are a part (ie they can be lost without changing the identity or type of the cell line)."""; "an incorporant role inhering in an input material entity, that is (1) GAINED through an agent's intention for it be input into some material processing where it will contribute a significant amount of material to the composition of the specified output, and where this contributed material represents a significant part of the input material entity; and (2) REALIZED in the execution of such a material processing event." . a owl:Class; rdfs:label "obsoelte_significant incorporant 2"; rdfs:subClassOf ; """an incorporant role inhering in a material entity that is realized by the bearer's participation in a material processing where it contributes material to the composition of the specified output, and this contributed material exists at the same level of granularity as the bearer and the specified output. In this way, any buffers or other chemicals that may exhange atoms or ions with process participants, and thereby make minor contributions at the atomic level of composition, do not play significant incorporant roles when the specified output is some larger macromolecular entity. Similarly, in the case where a cell line is used to produce a virus or recombinant protein: (1) any macromolecular building blocks (e.g. amino acids, nucleic acids, etc) that are provided by a cell line and incorporated into the specified output material are significant incorporants; (2) the cell line itself is not considered a significant incorporant, as these molecular building blocks exist at a finer level of granularity as the cell line does.""" . a owl:Class; rdfs:label "obsolete_instrument role"; rdfs:subClassOf ; "research instrument role"; "a research material role that inheres in some processed material that is gained upon some agent's intent to use it's bearer in some technique, and realized through its use in this technique."; "4-10-12 - decided not to use this notion of an instrument role for now" . a owl:Class; rdfs:label "obsolete_facilitator role"; rdfs:subClassOf ; "technique facilitator role"; "a research material role inhering in a material entiity and realized by the bearer's specified input into some assay or material processing technique, such that : (1) in the case of an assay, the bearer is not the evaluant about which data is generated, but rather facililtates the generation of such data; and (2) in the case of a material processing technique, the bearer does not contribute 'significant' material to the specified output material, but rather facilitates conditions necessary for the generation of this output material." . a owl:Class; rdfs:label "molecular reagent"; owl:equivalentClass _:2e53a9; rdfs:subClassOf , , _:2e53e9, _:2e53f9; "a molecular entity that bears a reagent role in virtue of its being intended for application in a scientific technique to participate in a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material output."; . _:2e53a9 a owl:Class; owl:intersectionOf _:2e53b9 . _:2e53b9 rdf:first ; rdf:rest _:2e53d9 . _:2e53d9 rdf:first _:2e53c9; rdf:rest rdf:nil . _:2e53c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e53e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e53f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_material processing technique input role"; rdfs:subClassOf ; """no longer needed/used former superclass axioms: 'inheres in' some (material_entity and (is_specified_input_of some 'material processing technique')) 'is realized by' only ('material processing' or (part_of some 'material processing technique'))""" . a owl:Class; rdfs:label "obsolete_assay input role"; rdfs:subClassOf ; """former superclass axioms: 'obsolete_specified input role'' inheres in' some (material_entity and (is_specified_input_of some assay)) 'is realized by' only (assay or (part_of some assay))""" . a owl:Class; rdfs:label "obsolete_non-evaluant input role"; rdfs:subClassOf ; "a role that inheres in an entity that is gained upon an agent’s intent to study the entity in some assay, and realized in the execution of an assay which the bearer facilitates the generation of data about some other entity " . a owl:Class; rdfs:label "reagent specification"; rdfs:subClassOf , _:2e5409, _:2e5419, _:2e5469; """an action specification indicating an agent's intent to use a material entity as a reagent in some technique. It is through the planning process that generates an action specification that reagent role is gained by a material entity, and it is through the execution of the actions specified in a reagent specification that the reagent role is realized.""" . _:2e5409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5429 . _:2e5429 a owl:Class; owl:intersectionOf _:2e5439 . _:2e5439 rdf:first ; rdf:rest _:2e5459 . _:2e5459 rdf:first _:2e5449; rdf:rest rdf:nil . _:2e5449 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5469 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5479 . _:2e5479 a owl:Class; owl:intersectionOf _:2e5489 . _:2e5489 rdf:first ; rdf:rest _:2e54a9 . _:2e54a9 rdf:first _:2e5499; rdf:rest rdf:nil . _:2e5499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_instrument"; rdfs:subClassOf ; "PERSON:Melissa Haendel"; """OBI (align/replace with OBI:device) eagle-i"""; "instrument class form ERO or OBI"; "replaced by ERO:instument"; "Material entity that is designed to have a function and play a role in scientific investigation."; "device"; "http://en.wikipedia.org/wiki/Scientific_instrument" . a owl:Class; rdfs:label "ascribed role"; rdfs:subClassOf , _:2e54b9; "note that this role is stated to be realized by 'part of' some planned process, because in some cases the role is realized by a biological process that is performed as part of a planned process. And because 'part of' is reflexive, this single axiom accounts for the other (majority of) cases where the role is realized directly by a planned process."; "assigned role", "specified role"; "http://en.wikipedia.org/wiki/Role"; "a role assigned unilaterally by an intentional agent to an entity that plays no active part in its bearing of the role (ie it is not earned or chosen by the bearer). This role is conferred through some planning process which specifies some intended use by the agent, and is realized through the bearer's participation in a process achieving this intended use."; rdfs:comment "An ascribed role is gained based on the unilateral intention of some agent, conferring the role on a bearer that plays no active part in its gaining the role" . _:2e54b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biological role"; owl:equivalentClass _:2e54c9; rdfs:subClassOf , _:2e5509; "a role inhering in some biological entity that is realized through a biological process" . _:2e54c9 a owl:Class; owl:intersectionOf _:2e54d9 . _:2e54d9 rdf:first ; rdf:rest _:2e54f9 . _:2e54f9 rdf:first _:2e54e9; rdf:rest rdf:nil . _:2e54e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_artifactual function"; rdfs:subClassOf ; "splitting functions into artifactual and biological was too complicated - may revisit this later"; rdfs:comment """superclass axiom: inheres_in some (material_entity and (is_specified_output_of some 'material processing'))""" . a owl:Class; rdfs:label "obsolete_biological function"; rdfs:subClassOf . a owl:Class; rdfs:label "research material specification"; rdfs:subClassOf ; "an action specification indicating an agent's intent to use a material entity as a research material in some technique as part of an investigation" . a owl:Class; rdfs:label "molecular label detection assay"; owl:equivalentClass _:2e5519; rdfs:subClassOf , _:2e55b9 . _:2e5519 a owl:Class; owl:intersectionOf _:2e5529 . _:2e5529 rdf:first ; rdf:rest _:2e5549 . _:2e5549 rdf:first _:2e5539; rdf:rest _:2e5569 . _:2e5539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5569 rdf:first _:2e5559; rdf:rest rdf:nil . _:2e5559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5579 . _:2e5579 a owl:Class; owl:intersectionOf _:2e5589 . _:2e5589 rdf:first ; rdf:rest _:2e55a9 . _:2e55a9 rdf:first _:2e5599; rdf:rest rdf:nil . _:2e5599 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e55b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf _:2e55c9, _:2e5619, _:2e5629; rdfs:comment "Alt def: an assay which detects a signal produced by a molecular label that is associated with some target analyte, where the molecular label serves as a proxy for the presence, abundance, or location of the analyte. The detected (signal-producing) label may associate with the this analyte directly (e.g a molecular stain incorporated directly into an analyte), or indirectly (e.g. a molecular reporter which associates through a molecular probe or tracker that binds the analyte directly)."; "OBI:detection of molecular tracer assay, once implemented in OBI"; "an assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached" . _:2e55c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e55d9 . _:2e55d9 a owl:Class; owl:intersectionOf _:2e55e9 . _:2e55e9 rdf:first ; rdf:rest _:2e5609 . _:2e5609 rdf:first _:2e55f9; rdf:rest rdf:nil . _:2e55f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5639 . _:2e5639 a owl:Class; owl:intersectionOf _:2e5649 . _:2e5649 rdf:first ; rdf:rest _:2e5669 . _:2e5669 rdf:first _:2e5659; rdf:rest rdf:nil . _:2e5659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_molecular target binding role"; rdfs:subClassOf ; "merged with parent 'molecular probe/effector role'"; "a reagent role inhering in a molecular entity that is applied in a technique to form a non-covalent chemical bond with a specified molecular target or targets under defined experimental conditions." . a owl:Class; rdfs:label "detectable disposition"; rdfs:subClassOf ; rdfs:comment "this is not a intentional role becasue there is no requirement that this dispostion be exploited in a particular way to meet some agents specified need."; "a disposition inhering in some material entity to be detected by a laboratory instrument during the execution of some assay, in virtue of the bearers ability to emit a detectable signal "; "disposition to be detected by detection instrument", "disposition to produce detectable signal" . a owl:Class; rdfs:label "chemical interaction"; owl:equivalentClass _:2e5679; rdfs:subClassOf , _:2e5689, _:2e56d9; "class from some appropriate ontology (GRO has a molecular interaction class that might work?) (SIO has a chemical interaction class, but is not under the OBO Foundry umbrella)"; "http://ww2.chemistry.gatech.edu/~lw26/structure/molecular_interactions/mol_int.html, and the 'chemical interaction' class from Semanticscience Integrated Ontology (SIO)"; "molecular interaction", "non-covalent interaction"; "a chemical interaction that occurs between two or more distinct molecular entities, or two or more groups within a single molecule, in which chemical entities interact through some set of attractive forces. All molecular interactions are fundamentally electrostatic in nature and can described by Coulombs Law. They typically fall into one of the following categories: ion-dipole interaction, dipole-dipole interaction, dipole-induced dipole interaction, induced dipole-induced dipole interaction, and hydrogen bonding."; rdfs:comment "Note that we call this a 'chemical' or 'molecular' interaction because it occurs between molecular entities or groups at a chemical level (ie exploiting only the 'chemical' properties of the interactors, and not emergent 'physical' properties that result from some structured or coordinated organization of these molecules in space). Even in the cases where compounds or solutions are mixed to promote an interaction, the interaction occurs fundamentally at a chemical level and depends only on the chemical properties of the molecular entities that comprise the interactors."; . _:2e5679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5689 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e5699 . _:2e5699 a owl:Class; owl:unionOf _:2e56a9 . _:2e56a9 rdf:first ; rdf:rest _:2e56c9 . _:2e56c9 rdf:first _:2e56b9; rdf:rest rdf:nil . _:2e56b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e56d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e56e9 . _:2e56e9 a owl:Class; owl:unionOf _:2e56f9 . _:2e56f9 rdf:first ; rdf:rest _:2e5719 . _:2e5719 rdf:first _:2e5709; rdf:rest rdf:nil . _:2e5709 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "Alexa Fluor"; rdfs:subClassOf , , _:2e5729, _:2e5739, _:2e5749; . _:2e5729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_mortal cell culture cell"; rdfs:subClassOf ; "CL:primary cell line cell"; """We recommend avoiding use of the term 'primary', as to some this means 'yet to be passaged' and for others it means 'not immortalized'. Thus we recommend the label 'mortal cell culture cell' rather than ‘primary cell line cell’. Note also that in ReO we view the term 'culture' as more general than 'line', where culture covers all types of cultures (mortal and immortal), while ‘line’ is used in labels only for cell cultures that are immortalized. This is because, as with the term ‘primary’, there is varied use of the term ‘line’. To some it means ‘any cell culture that has been passaged’, and to others it means ‘any cell culture that can be propagated long term (ie immortalized)’. So, while there may be disagreement that a passaged but mortal culture is a cell line, all would agree that an immortalized culture is a cell line. Thus our use of the labels ‘mortal cell culture cell’ and ‘immortal cell line cell’."""; "primary cell culture cell"; "replaced by CL primary cell culture cell"; "a cultured multicellular organism cell that is part of a mortal cell culture that does not have the capacity to proliferate indefinitely" . a owl:Class; rdfs:label "fluorescent molecular reporter"; owl:equivalentClass _:2e5759; rdfs:subClassOf , _:2e5799; "a molecular label that is capable of producing a fluorescent detectable signal"; . _:2e5759 a owl:Class; owl:intersectionOf _:2e5769 . _:2e5769 rdf:first ; rdf:rest _:2e5789 . _:2e5789 rdf:first _:2e5779; rdf:rest rdf:nil . _:2e5779 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5799 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_reporter-tracker conjugate"; rdfs:subClassOf ; """decided not needed, esp since: any axiom on classes (fluorochrome conj ab, radiolabled DNA/RNA probe, and reporter tracker conjugate) saying that a targeted tracker was part of or proper part of the class prevented classification of the targeted tracker role as a type of molecular probe role - could not figure out why so scrapped all of these usages and obsoleted reporter tracker conjugate. previous logical def : 'targeted reporter' and (has_part some 'targeted tracker') and (has_part some 'covalent reporter')"""; "reporter-probe conjugate"; . a owl:Class; rdfs:label "conjugated antibody reagent"; owl:equivalentClass _:2e57a9; rdfs:subClassOf , _:2e57e9; "an antibody reagent that has been covalently modified to contain some additional moiety, typically to enable its detection in an assay or to facilitate targeted delivery of the conjugated species to some precise molecular target."; "labeled antibody"; "Cy5-conjugated antibody, biotin-conjugated antibody"; . _:2e57a9 a owl:Class; owl:intersectionOf _:2e57b9 . _:2e57b9 rdf:first ; rdf:rest _:2e57d9 . _:2e57d9 rdf:first _:2e57c9; rdf:rest rdf:nil . _:2e57c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e57e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "fluorochrome-conjugated antibody"; rdfs:subClassOf , , _:2e57f9, _:2e5809, _:2e58d9; "an antibody reagent that has been conjugated to some fluorescent reporter molecule" . _:2e57f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5809 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5819 . _:2e5819 a owl:Class; owl:intersectionOf _:2e5829 . _:2e5829 rdf:first ; rdf:rest _:2e5849 . _:2e5849 rdf:first _:2e5839; rdf:rest rdf:nil . _:2e5839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5859 . _:2e5859 a owl:Class; owl:intersectionOf _:2e5869 . _:2e5869 rdf:first ; rdf:rest _:2e5889 . _:2e5889 rdf:first _:2e5879; rdf:rest rdf:nil . _:2e5879 a owl:Class; owl:intersectionOf _:2e58a9 . _:2e58a9 rdf:first _:2e5899; rdf:rest _:2e58c9 . _:2e5899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e58c9 rdf:first _:2e58b9; rdf:rest rdf:nil . _:2e58b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e58d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_immortalized cell line cell"; rdfs:subClassOf ; "a cultured multicellular organism cell that is part of an immortal cell culture having the capacity to proliferate indefinitely if given appropriate space and nutrients"; "permanent cell line cell (as in CLO), immortalized cell line cell (similar to OBI 'immortalized cell culture')"; "replaced by CL:permanent cell line cell" . a owl:Class; rdfs:label "obsolete_experimental modification"; rdfs:subClassOf ; "3-24-12: merged/replaced with ??? (experimental modification technique (REO_0000548)??? - no because the notion of experimental modification is now considered to involve the input of a material and the output of a modified version of this input material)"; "a material modification technique with the objective to make structural alterations to some input material or materials to produce some output that represents a structurally modified version of some specified reference material."; "material modification technique" . a owl:Class; rdfs:label "unconjugated antibody reagent"; owl:equivalentClass _:2e58e9; rdfs:subClassOf , _:2e5929; "typical primary antibodies used in immunoblots, where a conjugated secondary antibody must be used to detect the presece of this unconjugated primary antibody"; "unlabeled antibody"; "an antibody reagent that has not been modified to contain any additional tag or label."; . _:2e58e9 a owl:Class; owl:intersectionOf _:2e58f9 . _:2e58f9 rdf:first ; rdf:rest _:2e5919 . _:2e5919 rdf:first _:2e5909; rdf:rest rdf:nil . _:2e5909 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2e5929 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "phosphorus-32 reagent"; owl:equivalentClass _:2e5939; rdfs:subClassOf , _:2e5999, _:2e59a9, _:2e59b9; "a molecular reagent that is engineered to contain P32, so as to experimentally exploit its radioactive properties (typically for labeling some target molecule or tracing some substance of interest)"; "ATP Alpha 32P, disodium (P32)phosphate"; . _:2e5939 a owl:Class; owl:intersectionOf _:2e5949 . _:2e5949 rdf:first ; rdf:rest _:2e5969 . _:2e5969 rdf:first _:2e5959; rdf:rest _:2e5989 . _:2e5959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5989 rdf:first _:2e5979; rdf:rest rdf:nil . _:2e5979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e59a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e59b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "radioactive molecular reporter"; owl:equivalentClass _:2e59c9; rdfs:subClassOf , , _:2e5a09; "a molecular label that is capable of producing a detectable signal that is radioactive in nature"; . _:2e59c9 a owl:Class; owl:intersectionOf _:2e59d9 . _:2e59d9 rdf:first ; rdf:rest _:2e59f9 . _:2e59f9 rdf:first _:2e59e9; rdf:rest rdf:nil . _:2e59e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5a09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unlabeled DNA probe"; rdfs:subClassOf , _:2e5a19, _:2e5a39; "a DNA oligonucleotide reagent that is a single-stranded DNA molecule that has not been labeled in some way to allow detection of a complementary sequence among a mixture of other nucleic acid molecules." . _:2e5a19 a owl:Class; owl:complementOf _:2e5a29 . _:2e5a29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5a39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "labeled DNA probe"; rdfs:subClassOf , , , _:2e5a49, _:2e5a59, _:2e5a69; "http://www.everythingbio.com/glos/definition.php?word=DNA+probe"; "a DNA oligonucleotide reagent that is a single-stranded DNA molecule that is labeled in some way to allow detection of a complementary sequence among a mixture of other nucleic acid molecules." . _:2e5a49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5a59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5a69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5a79 . _:2e5a79 a owl:Class; owl:intersectionOf _:2e5a89 . _:2e5a89 rdf:first ; rdf:rest _:2e5aa9 . _:2e5aa9 rdf:first _:2e5a99; rdf:rest rdf:nil . _:2e5a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5ab9 . _:2e5ab9 a owl:Class; owl:intersectionOf _:2e5ac9 . _:2e5ac9 rdf:first ; rdf:rest _:2e5ae9 . _:2e5ae9 rdf:first _:2e5ad9; rdf:rest rdf:nil . _:2e5ad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "radiolabeled DNA probe"; owl:equivalentClass _:2e5af9; rdfs:subClassOf , , _:2e5bb9, _:2e5c49, _:2e5c59; "a DNA probe that contains at least one atom that is a radioactive isotope, such as P-32 or P-33, that emits a radioactive signal to allow detection of the probe and target DNA with which it hybridizes" . _:2e5af9 a owl:Class; owl:intersectionOf _:2e5b09 . _:2e5b09 rdf:first ; rdf:rest _:2e5b29 . _:2e5b29 rdf:first _:2e5b19; rdf:rest rdf:nil . _:2e5b19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5b39 . _:2e5b39 a owl:Class; owl:intersectionOf _:2e5b49 . _:2e5b49 rdf:first ; rdf:rest _:2e5b69 . _:2e5b69 rdf:first _:2e5b59; rdf:rest rdf:nil . _:2e5b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5b79 . _:2e5b79 a owl:Class; owl:intersectionOf _:2e5b89 . _:2e5b89 rdf:first ; rdf:rest _:2e5ba9 . _:2e5ba9 rdf:first _:2e5b99; rdf:rest rdf:nil . _:2e5b99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5bb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5bc9 . _:2e5bc9 a owl:Class; owl:intersectionOf _:2e5bd9 . _:2e5bd9 rdf:first ; rdf:rest _:2e5bf9 . _:2e5bf9 rdf:first _:2e5be9; rdf:rest rdf:nil . _:2e5be9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5c09 . _:2e5c09 a owl:Class; owl:intersectionOf _:2e5c19 . _:2e5c19 rdf:first ; rdf:rest _:2e5c39 . _:2e5c39 rdf:first _:2e5c29; rdf:rest rdf:nil . _:2e5c29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5c49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5c59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "oligonucleotide label"; owl:equivalentClass _:2e5c69; rdfs:subClassOf , , _:2e5ca9, _:2e5cb9, _:2e5cc9; . _:2e5c69 a owl:Class; owl:intersectionOf _:2e5c79 . _:2e5c79 rdf:first ; rdf:rest _:2e5c99 . _:2e5c99 rdf:first _:2e5c89; rdf:rest rdf:nil . _:2e5c89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5ca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5cc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "labeled RNA probe"; rdfs:subClassOf , , , _:2e5cd9, _:2e5d69, _:2e5d79; "an RNA oligonucleotide reagent that is a single-stranded RNA molecule that is labeled in some way to allow detection of a complementary sequence among a mixture of other nucleic acid molecule"; "http://www.everythingbio.com/glos/definition.php?word=DNA+probe" . _:2e5cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5ce9 . _:2e5ce9 a owl:Class; owl:intersectionOf _:2e5cf9 . _:2e5cf9 rdf:first ; rdf:rest _:2e5d19 . _:2e5d19 rdf:first _:2e5d09; rdf:rest rdf:nil . _:2e5d09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5d29 . _:2e5d29 a owl:Class; owl:intersectionOf _:2e5d39 . _:2e5d39 rdf:first ; rdf:rest _:2e5d59 . _:2e5d59 rdf:first _:2e5d49; rdf:rest rdf:nil . _:2e5d49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5d69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5d79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unlabeled RNA probe"; rdfs:subClassOf , _:2e5d89, _:2e5da9 . _:2e5d89 a owl:Class; owl:complementOf _:2e5d99 . _:2e5d99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5da9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "radiolabeled RNA probe"; owl:equivalentClass _:2e5db9; rdfs:subClassOf , , _:2e5e79, _:2e5e89, _:2e5e99, _:2e5ea9; "an RNA probe that contains at least one atom that is a radioactive isotope, such as P-32 or P-33, that emits a radioactive signal to allow detection of the probe and target nucelic acid with which it hybridizes" . _:2e5db9 a owl:Class; owl:intersectionOf _:2e5dc9 . _:2e5dc9 rdf:first ; rdf:rest _:2e5de9 . _:2e5de9 rdf:first _:2e5dd9; rdf:rest rdf:nil . _:2e5dd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5df9 . _:2e5df9 a owl:Class; owl:intersectionOf _:2e5e09 . _:2e5e09 rdf:first ; rdf:rest _:2e5e29 . _:2e5e29 rdf:first _:2e5e19; rdf:rest rdf:nil . _:2e5e19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5e39 . _:2e5e39 a owl:Class; owl:intersectionOf _:2e5e49 . _:2e5e49 rdf:first ; rdf:rest _:2e5e69 . _:2e5e69 rdf:first _:2e5e59; rdf:rest rdf:nil . _:2e5e59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5e79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5e89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5ea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5eb9 . _:2e5eb9 a owl:Class; owl:intersectionOf _:2e5ec9 . _:2e5ec9 rdf:first ; rdf:rest _:2e5ee9 . _:2e5ee9 rdf:first _:2e5ed9; rdf:rest rdf:nil . _:2e5ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5ef9 . _:2e5ef9 a owl:Class; owl:intersectionOf _:2e5f09 . _:2e5f09 rdf:first ; rdf:rest _:2e5f29 . _:2e5f29 rdf:first _:2e5f19; rdf:rest rdf:nil . _:2e5f19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_unconjugated antibody tracker"; rdfs:subClassOf ; "an antibody reagent that has not been conjugated to some molecular moiety, and is applied as a targeted tracker to facilitate the detection of some target analyte"; """uneccessary class. previous eq class axiom: 'unconjugated antibody reagent' and ('has role' some 'targeted tracker role')"""; . a owl:Class; rdfs:label "fluorescent stain"; rdfs:subClassOf . a owl:Class; rdfs:label "colorimetric stain"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_colorimetric reporter"; rdfs:subClassOf . a owl:Class; rdfs:label "molecular label"; owl:equivalentClass _:2e5f39; rdfs:subClassOf , _:2e5f79; """The following use cases illustrate how the four primary subtypes of molecular reporter ( targeted tracker, targeted reporter, covalent tracker, and covalent reporter) apply. Case 1: Nucleotides synthesized to contain a biotin moiety were used to synthesize a cDNA probe, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. Here, biotin is a covalent tracker, the biotin-labeld probe is a targeted tracker (targets some nucelic acid that is the analyte of interest), and the fluorochrome-conjugated antibody is a targeted reporter (it targets the biotin-labled probe). Case 2 : An oligonucleotide synthesized with radioactive dATP[P33] and used to detect the presence of complementary sequence on a southern blot. Here, dATP[P33] is a covalent reporter, and the P33-containing oligo is a targeted reporter. Case 3: a protein labeling assay involving the detection of S35-labeled methionine incorporated into newly synthesized proteins in a cell culture cells. Here, Methionine[S35] is a covalent reporter. The label is incorporated directly into the analyte in this example, so no additional label is needed. Case 4: An immunocytochemistry assay where a fluorochrome-labeled primary antibody is used to detect a specific cellular protein on a fixed slide. Here, the fluorochrome alone is a covalent reporter, the antibody alone is a targeted tracker, and the fluorochrome-antibody conjugate is a targeted reporter. Case 5: Immunocytochemical detection of a FLAG epitope tag in an overexpressed protein in cell culture cells, using a fluorochrome conjugated anti-FLAG antibody. Here, as in Case 4, the fluorochrome alone is a covalent reporter, the antibody alone is a targeted tracker, and the fluorochrome-antibody conjugate is a targeted reporter. In addition, the FLAG tag is a covalent tracker. Case 6: Phalloidin molecules (a fungal toxin that binds F-actin) are conjugated to rhodamine fluorochrome and applied to a slide of fixed cells to detect actin fibers by fluorescent microscopy. Here, phalloidin is a targeted tracker, the rhodamine is a covalent reporter, and the rhodamine-phalloidin conjugate is a targeted reporter."""; """Axes of Classification: The top level primary/asserted axis for molecular label classification distinguishes 'reporters' from 'trackers', based on the 'detectablility' of the molecular entity bearing the molecular label role. At the next level in the hierarchy, a distinciton is made between 'covalent' and 'targeted' labels, based on the mechanism of binding that the label uses in associating with its intended target. Logical Definitions: Pursued this approach for logical defs of molecular label subclasses using molecular label subroles (rather than dispositions) because: (1) according to our interpretation of a BFO:role, we believe it to be ontologically correct to create and apply these roles in this way, as the application of molecular entities as reporters or trackers reflects a role they bear and not some more fundamental disposition or quality shared by all members of a molecular label subclass; (2) practically speaking, the use of dispositions can lead to complex axiomatization and high burden for getting classes/instances to qualify for subsumption as labels, and (3) the assignment of such molecular dispositions may be out of scope for ReO/OBI. Rather, we used molecular label role subtypes, and 'hid' dispositions required for these roles in the definition of the role. However, because bearing such dispositions is not always neccessary and sufficient to 'define' a subclass of molecular lables, we use the roles for defining our molecular label equivalent classes. """; "molecular tracer"; "a molecular reagent intended to associate with some molecular target to allow its detection in a molecular label detection technique, wherein the bearer serves as a proxy for the presence, abundance, or location of this molecular target."; ; . _:2e5f39 a owl:Class; owl:intersectionOf _:2e5f49 . _:2e5f49 rdf:first ; rdf:rest _:2e5f69 . _:2e5f69 rdf:first _:2e5f59; rdf:rest rdf:nil . _:2e5f59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e5f79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "oligonucleotide"; owl:equivalentClass _:2e5f89; rdfs:subClassOf , _:2e5fb9, _:2e6069; "a nucleic acid polymer consisting of a short, linear, single strand of typically 100 or fewer nucleotides" . _:2e5f89 a owl:Class; owl:unionOf _:2e5f99 . _:2e5f99 rdf:first ; rdf:rest _:2e5fa9 . _:2e5fa9 rdf:first ; rdf:rest rdf:nil . _:2e5fb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e5fc9 . _:2e5fc9 a owl:Class; owl:intersectionOf _:2e5fd9 . _:2e5fd9 rdf:first ; rdf:rest _:2e5ff9 . _:2e5ff9 rdf:first _:2e5fe9; rdf:rest rdf:nil . _:2e5fe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6009 . _:2e6009 a owl:Class; owl:intersectionOf _:2e6019 . _:2e6019 rdf:first ; rdf:rest _:2e6039 . _:2e6039 rdf:first _:2e6029; rdf:rest _:2e6059 . _:2e6029 a owl:Restriction; owl:onProperty ; owl:hasValue . _:2e6059 rdf:first _:2e6049; rdf:rest rdf:nil . _:2e6049 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . _:2e6069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6079 . _:2e6079 a owl:Class; owl:intersectionOf _:2e6089 . _:2e6089 rdf:first ; rdf:rest _:2e60a9 . _:2e60a9 rdf:first _:2e6099; rdf:rest rdf:nil . _:2e6099 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "targeted reporter"; owl:equivalentClass _:2e60b9; rdfs:subClassOf , , _:2e60f9; "a molecular reporter that is capable of autonomous, non-covalent association with a molecular target"; "molecular dye", "molecular stain"; "coomassie blue, DAPI, a fluorochrome-conjugated antibody"; . _:2e60b9 a owl:Class; owl:intersectionOf _:2e60c9 . _:2e60c9 rdf:first ; rdf:rest _:2e60e9 . _:2e60e9 rdf:first _:2e60d9; rdf:rest rdf:nil . _:2e60d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e60f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "targeted tracker"; owl:equivalentClass _:2e6109; rdfs:subClassOf , , _:2e6149; "biotin-labeled oligonucleotide probe, digoxygenin-labeled antibody"; "a molecular tracker that is capable of autonomous non-covalent association with a molecular target."; . _:2e6109 a owl:Class; owl:intersectionOf _:2e6119 . _:2e6119 rdf:first ; rdf:rest _:2e6139 . _:2e6139 rdf:first _:2e6129; rdf:rest rdf:nil . _:2e6129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "atomic reagent"; owl:equivalentClass _:2e6159; rdfs:subClassOf , , _:2e6199; rdfs:comment "atomic reagents are single, independently existing atoms bearing a reagent role, such as radioactive P32"; "an atomic molecular entity that bears a reagent role"; "P32, S35, C14 (although as reagents these typically come as salts or incorporated into some larger molecule such as a nucleotide phosphate or amino acid) " . _:2e6159 a owl:Class; owl:intersectionOf _:2e6169 . _:2e6169 rdf:first ; rdf:rest _:2e6189 . _:2e6189 rdf:first _:2e6179; rdf:rest rdf:nil . _:2e6179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "covalent reporter"; owl:equivalentClass _:2e61a9; rdfs:subClassOf , , _:2e61e9; "methionine[S35], Alexafluor 555, Cy5"; "a molecular reporter that is not capable of autonomous non-covalent association with a molecular target, such that it must be covalenly attached to an analyte of interest, or to a targeted molecular label that can direct it to an analyte"; . _:2e61a9 a owl:Class; owl:intersectionOf _:2e61b9 . _:2e61b9 rdf:first ; rdf:rest _:2e61d9 . _:2e61d9 rdf:first _:2e61c9; rdf:rest rdf:nil . _:2e61c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e61e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "covalent tracker"; owl:equivalentClass _:2e61f9; rdfs:subClassOf , , _:2e6239; "biotin, digoxygenin"; "a molecular tracker that is not capable of autonomous non-covalent association with a molecular target, such that it must be covalenly attached to an analyte of interest, or to a targeted molecular label that can direct it to an analyte"; . _:2e61f9 a owl:Class; owl:intersectionOf _:2e6209 . _:2e6209 rdf:first ; rdf:rest _:2e6229 . _:2e6229 rdf:first _:2e6219; rdf:rest rdf:nil . _:2e6219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "colorimetric targeted reporter"; owl:equivalentClass _:2e6249; rdfs:subClassOf , _:2e6289; "chromogenic targeted reporter"; "a targeted reporter that is detectable in virtue of its emiting light in the visible human-visible range of colors along the electromagnetic spectrum" . _:2e6249 a owl:Class; owl:intersectionOf _:2e6259 . _:2e6259 rdf:first ; rdf:rest _:2e6279 . _:2e6279 rdf:first _:2e6269; rdf:rest rdf:nil . _:2e6269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "fluorescent targeted reporter"; owl:equivalentClass _:2e6299; rdfs:subClassOf , , _:2e62d9; "a targeted reporter that is detectable in virtue of its exhibiting fluorescence" . _:2e6299 a owl:Class; owl:intersectionOf _:2e62a9 . _:2e62a9 rdf:first ; rdf:rest _:2e62c9 . _:2e62c9 rdf:first _:2e62b9; rdf:rest rdf:nil . _:2e62b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e62d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "radioactive targeted reporter"; owl:equivalentClass _:2e62e9; rdfs:subClassOf , , _:2e6329; "a targeted reporter that is detectable in virtue of its exhibiting radioactivity" . _:2e62e9 a owl:Class; owl:intersectionOf _:2e62f9 . _:2e62f9 rdf:first ; rdf:rest _:2e6319 . _:2e6319 rdf:first _:2e6309; rdf:rest rdf:nil . _:2e6309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "colorimetric covalent reporter"; owl:equivalentClass _:2e6339; rdfs:subClassOf , _:2e6379; "chromogenic covalent reporter", "colorigenic covalent reporter" . _:2e6339 a owl:Class; owl:intersectionOf _:2e6349 . _:2e6349 rdf:first ; rdf:rest _:2e6369 . _:2e6369 rdf:first _:2e6359; rdf:rest rdf:nil . _:2e6359 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6379 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "fluorescent covalent reporter"; owl:equivalentClass _:2e6389; rdfs:subClassOf , , _:2e63c9 . _:2e6389 a owl:Class; owl:intersectionOf _:2e6399 . _:2e6399 rdf:first ; rdf:rest _:2e63b9 . _:2e63b9 rdf:first _:2e63a9; rdf:rest rdf:nil . _:2e63a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e63c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "radioactive covalent reporter"; owl:equivalentClass _:2e63d9; rdfs:subClassOf , , _:2e6419 . _:2e63d9 a owl:Class; owl:intersectionOf _:2e63e9 . _:2e63e9 rdf:first ; rdf:rest _:2e6409 . _:2e6409 rdf:first _:2e63f9; rdf:rest rdf:nil . _:2e63f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "buffer solution"; owl:equivalentClass _:2e6429; rdfs:subClassOf , _:2e64e9, _:2e6539, _:2e6549; "a chemical solution (typically aqueous) that resists change in pH upon addition of small amounts of acid or base."; """Note here that while a buffer is defined logically as a molecular entity that has a reagent role and a buffer disposition, a buffer solution cannot be defined as: \"'chemical solution' and ('has role' some 'reagent role') and (has_grain some buffer)\", because there will be some solutions that have a chemical with a buffereing disposition as a part but the buffering disposition might not be exploited in a reagent/buffereing capacity in the solution (perhaps because it is not present at high enough levels to buffer the solution, but is nonetheless an important component of the solution for other specified reasons). Therefore we use a buffer reagent role in the logical definition here - """; . _:2e6429 a owl:Class; owl:intersectionOf _:2e6439 . _:2e6439 rdf:first ; rdf:rest _:2e6459 . _:2e6459 rdf:first _:2e6449; rdf:rest rdf:nil . _:2e6449 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6469 . _:2e6469 a owl:Class; owl:intersectionOf _:2e6479 . _:2e6479 rdf:first ; rdf:rest _:2e6499 . _:2e6499 rdf:first _:2e6489; rdf:rest rdf:nil . _:2e6489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e64a9 . _:2e64a9 a owl:Class; owl:intersectionOf _:2e64b9 . _:2e64b9 rdf:first ; rdf:rest _:2e64d9 . _:2e64d9 rdf:first _:2e64c9; rdf:rest rdf:nil . _:2e64c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e64e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e64f9 . _:2e64f9 a owl:Class; owl:intersectionOf _:2e6509 . _:2e6509 rdf:first ; rdf:rest _:2e6529 . _:2e6529 rdf:first _:2e6519; rdf:rest rdf:nil . _:2e6519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6549 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6559 . _:2e6559 a owl:Class; owl:intersectionOf _:2e6569 . _:2e6569 rdf:first ; rdf:rest _:2e6589 . _:2e6589 rdf:first _:2e6579; rdf:rest rdf:nil . _:2e6579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6599 . _:2e6599 a owl:Class; owl:intersectionOf _:2e65a9 . _:2e65a9 rdf:first ; rdf:rest _:2e65c9 . _:2e65c9 rdf:first _:2e65b9; rdf:rest rdf:nil . _:2e65b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "buffering disposition"; rdfs:subClassOf , _:2e65d9; "a disposition inhering in a weak acid or base to resist changes in pH within a certain buffered pH range when in aqueous solution, and realized through some buffering process"; "ChEBI (discuss whether buffer should be a role or a disposition in ChEBI)" . _:2e65d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "buffer"; owl:equivalentClass _:2e65e9; rdfs:subClassOf , _:2e6629, _:2e6639; "Note here that we define buffers as those chemical entities that are actually applied as reagents (and thus bear a reagent role>buffer role) - not chemicals that merely have a 'buffering disposition'"; "sodium phosphate, HEPES (4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid N-(2-Hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid)), PIPES (1,4-Piperazinediethanesulfonic acid Piperazine-1,4-bis(2-ethanesulfonic acid) Piperazine-N,N′-bis(2-ethanesulfonic acid) )"; rdfs:comment "Most typical biological buffer agents are small molecules or salts (chemical reagents in ReO, ie non-information macromolecule reagents). However, because information macromolecules such as proteins and short peptides CAN serve as buffers (e.g. a common buffer is the diglycine peptide (Gly-Gly) which qualifies as an information macromolecule in ReO), buffer is classified here as a molecular reagent and not more specifically as a chemical reagent."; "A molecular reagent which is added to an acidic or basic solution in order to modify or maintain its pH value in a specified range"; . _:2e65e9 a owl:Class; owl:intersectionOf _:2e65f9 . _:2e65f9 rdf:first ; rdf:rest _:2e6619 . _:2e6619 rdf:first _:2e6609; rdf:rest rdf:nil . _:2e6609 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6639 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_creating a mixture of molecules in solution"; rdfs:subClassOf ; "replaced by OBI class" . a owl:Class; rdfs:label "obsolete_cell in vitro"; rdfs:subClassOf ; "http://dictionary.reference.com/browse/in+vitro"; "a cell that has been removed from a natural environment, and placed in a controlled artificial environment for use in some investigation. Includes multicellular organism cells removed from an organism, and unicellular organisms removed from a natural environment."; rdfs:comment """'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. Note here that' in vitro' is not simply the union of 'ex vivo' and 'ex environemnt', as cell culture cells are also considered in vitro, but are not ex vivo or ex environemnt."""; "replaced by CL cell in vitro" . a owl:Class; rdfs:label "experimentally modified multicellular organism cell ex vivo"; rdfs:subClassOf ; "experimentally modified cell ex vivo"; rdfs:comment "cells ex environment differ from cells in vitro in that cells ex environment are formerly part of a natural environment, but removed and placed in a controlled artificial environment for use in some investigation. cells in vitro were not necessarily once part of a natural environment (e.g. cultured cells)"; "an experimentally modified multicellular organism cell that has been removed from an organism, and placed in a controlled artificial environment for use in some investigation." . a owl:Class; rdfs:label "experimentally modified multicellular organism cell in vivo"; owl:equivalentClass _:2e6649; rdfs:subClassOf , , _:2e66a9 . _:2e6649 a owl:Class; owl:intersectionOf _:2e6659 . _:2e6659 rdf:first ; rdf:rest _:2e6679 . _:2e6679 rdf:first _:2e6669; rdf:rest _:2e6699 . _:2e6669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6699 rdf:first _:2e6689; rdf:rest rdf:nil . _:2e6689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e66a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf _:2e66b9; "an experimentally modified multicellular organism cell that is part of an organism (and not re-located by some intentional agent to a controlled artificial setting for use in some investigation or study)" . _:2e66b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_microarray"; rdfs:subClassOf ; "PERSON: Melissa Haendel"; "http://en.wikipedia.org/wiki/Microarray"; "a material entity that is a 2D array on a solid substrate (usually a glass slide or silicon thin-film cell) that allows assay of a large number of biological samples using high-throughput screening methods"; "replaced with OBI microarray" . a owl:Class; rdfs:label "obsolete_experimental modification objective"; rdfs:subClassOf ; """physical material processing objective?, structural processing objective?, compositional processing objective?, material modification objective?"""; rdfs:comment "The 'physical changes' refered to in the definition alter the structural makeup of the input material by adding/removing material or re-arranging their internal structure. These are changes beyond simple 'contextual changes' such those resulting from, for example, collecting a specimen, or selecting a subpopulation of cells."; """8-2-12 no longer needed after implementing new 'role-based' approach for modeling experimental modification former eq class def: 'obsolete_physical material component separation objective' or 'obsolete_physical material combination with target objective' former superclass axiom: 'material processing objective'"""; "the objective of a material processing to make physical changes to a specified input material (whereby structural or compositional alterations are made), to produce some output that represents a modified version of the specified input material." . a owl:Class; rdfs:label "obsolete_contextual re-location objective"; rdfs:subClassOf ; """contextual material processing objective, contextual modification objective, contextual transformation objective"""; """the objective for a material processing technique to yield a specified output that has undergone a change in context or location, but to which no internal physical changes have been made (ie no material added or removed, and/or structural rearrangements) Alt: an objective for a material processing technique to yield a specified output that has undergone a change in context or location, but to which no changes have been made affecting its inherent physical structure (ie no material added or removed, and/or structural rearrangements)"""; """8-2-12 no longer needed after implementing new 'role-based' approach for modeling experimental modification former eq class def: 'material portioning objective' or 'obsolete_contextual material component separation objective' or 'obsolete_contextual material combination with target objective' former superclass axiom: 'material processing objective'""" . a owl:Class; rdfs:label "specimen collection objective"; rdfs:subClassOf , , _:2e66c9; """Specimen Creation vs Specimen Collection:: As we will model things in ReO, a specimen creation is not a material processing, as specimens can be created purely through observation (for ex, identification of monkeys in a population through observation of distinguishing features) and certainly can be achieved without a collection process (tagging monkeys with a colored dart fired from a dart gun to identify/track the tagged specimen) . Specimen collection is a type of specimen creation in which the specimen of interest is physically removed from its environment into a lab environment for study. The specimen creation objective will thus fall outside the material processing/transformation objective branch, while the specimen collection objective class will reside within this branch, under contextual processing objective > material separation objective> material collection objective. As for the related processes that achieve these objectives, specimen creation will be a planned process (and inferred to be a technique), and specimen collection a material collection process (inferred to be a material processing technique)"""; "a material component separation objective to physically obtain and store some material entity or entities of interest, and in doing so separate them from other like entities or from their environment, so that it may be applied in a scientific technique as part of an investigation" . _:2e66c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e66d9 . _:2e66d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "specimen collection"; owl:equivalentClass _:2e66e9; rdfs:subClassOf , , _:2e6729, _:2e6779; "Specimen collection is asserted as a subclass of material processing technique, and inferred as a child of material colllection, and has one (inferred) child (sample collection). "; "a material collection process in which the object of colleciton bears a specimen role (ie is intended to be studied in some investigation as an example of its kind)."; rdfs:comment """Relation to Specimen Creation : Specimen creation typically (but not always) involves physical collection of a material of interest to be studied or used in an investigation. A specimen collection class was created to cover the typical case, which is subsumed by the specimen creation class that should be used when the specimen role is gained without physical collection of the material entiy(ies) of interest. Examples of 'collected specimens' include blood collected from an organism, or soil samples collected from some environment. Specimens can also be created without collection, for example by tagging animals to track them in the wild, o rmy merely observing the intended specimen and noting distinguishing features that will allow subsequent identification and study. Finally, specimens can also be processed from other specimens, for example the extraction of nuclear material from a cell specimen to generate a nuclear extract specimen.""" . _:2e66e9 a owl:Class; owl:intersectionOf _:2e66f9 . _:2e66f9 rdf:first ; rdf:rest _:2e6719 . _:2e6719 rdf:first _:2e6709; rdf:rest rdf:nil . _:2e6709 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6739 . _:2e6739 a owl:Class; owl:intersectionOf _:2e6749 . _:2e6749 rdf:first ; rdf:rest _:2e6769 . _:2e6769 rdf:first _:2e6759; rdf:rest rdf:nil . _:2e6759 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6779 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6789 a owl:Axiom; "note here that it is more precise to say this rather than simple has output some specimen (as not all specimens are processed materials)"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e6799 . _:2e6799 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e67a9 . _:2e67a9 a owl:Class; owl:intersectionOf _:2e67b9 . _:2e67b9 rdf:first ; rdf:rest _:2e67d9 . _:2e67d9 rdf:first _:2e67c9; rdf:rest rdf:nil . _:2e67c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material sampling objective"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_reagent"; rdfs:subClassOf ; """this class was created as an obsolete class to hold annotations on the original reagent class that we replaced on 11-21-11 with a new reagent class according to the Oct '11 OBI workshop - where we define reagent as a union of molecular reagent and non molecular reagent (because we could not come up with a single reagent definition that worked to cover both, but wished them to reside under the same reagent parent. but we wanted to keep the URI of the reagent class to be REO:0000000, so we could obsolete that original class. therefore we just transferred all annotations from this class to this new obsolete_reagent class"""; rdfs:comment """A reagent is a material entity bearing a reagent role that is : (1) GAINED by virtue of its bearer being intended as input into either (a) an assay, where it contributes to the detection, measurement, or examination of some other substance or process, or (b) a material processing technique aimed at producing materials to be used in such an assay (2) REALIZABLE only through its bearer participating in (or having parts that participate in) some chemical reaction during the execution of some assay or material processing technique, such that(a) in the case of an assay, data is not generated about the bearer, and (b) in the case of a material processing technique, the bearer does not contribute significant material to the specified output material. Reagents are therefore distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents necessarily are chemically altered or consumed (or have parts that are) when they participate in some technique. By contrast, instruments are not consumed or have parts that are chemically altered or consumed in a chemical reaction during the technique. Reagents are distinguished from evaluants only in the sense that, while a type of material entity can bear both of these roles, a given instance of the material cannot realize both in the same process. For example, taq polymerase can bear both a reagent and evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated."""; "a material entity that bears a reagent role"; """As input into an assay, a reagent is not that which data is generated about, but rather facilitates the generation of data about an evaluant. For example, in a DNA sequenceing assay, buffers, labeled nucleotides, and polymerase enzyme are reagents, and the input template DNA to be sequenced is the evaluant. As input into a material processing technique, a reagent does not contribute significant material to the specified output object, but rather facilitates the creation or modification of the input material that does contribute matter to this output object. For example, in a PCR reaction to amplify a DNA insert for subcloning, the buffer and polymerase enzyme serve as reagents, while the template and nucleotides that are incorporated into the output material do not play a reagent role. These two examples illustrate how the same type of material (e.g nucelotides) can serve as reagents in one context (a sequenceing assay) but not in another (a PCR reaction to generate subcloning intermediates). Similarly, different instances of the same class of material entity can bear a reagent or an evaluant role that are realized in different processes. For example, taq polymerase can play a reagent role in a PCR technique, but studied as an evaluant in a biochemical structure-function assay. Thus, in the context of a given assay or technique, an instance of a material entity is EITHER a reagent OR and evaluant, but not both."""; "The reagent hierachy contains a core, disjoint set of reagent classes that includes 'antibody reagent', 'chemical reagent', 'cell line', 'nucleic acid reagent', 'protein reagent', and 'reagent library'. Each instance of a reagent or reagent class will fall under only one of these core categories. In addition, several equivalent classes of reagents are defined (e.g. molecular label, moleculr probe, gene knockdown reagent), based on logically defined attributes exhibited by reagents exhibit (e.g. roles, functions, processes participating in, etc). In addition to in addition to classifying under one of the core reagent classes listed above, a given reagents or reagent class might also classify as one or more of these equivalent classes (as inferred by the reasoner). For example, a plasmid expressing an siRNA molecule targeted against a cellular gene product will classify as a nucleic acid reagent > DNA construct > siRNA construct, as well as a gene knockdown reagent (based on the function of the siRNA product of this plasmid)"; "a material entity generated to participate in a planned process aimed at producing, detecting, measuring, or examining some biological, chemical, or physical substance or process. A reagent necessarily participates in some chemical reaction whereby it is altered or consumed (or has parts that are) during the execution of the planned process." . a owl:Class; rdfs:label "obsolete_reagent_role"; rdfs:subClassOf ; """a role inhering in a material entity generated to participate in a planned process aimed at producing, detecting, measuring, or examining some biological, chemical, or physical substance or process. A reagent necessarily participates in some chemical reaction whereby it is altered or consumed (or has parts that are) during the execution of the planned process. a role inhering in a material entity intended to be input into an assay aimed at detecting, measuring, or examining some other material or process, or input into a material processing technique as a participant that does not contribute significant material to the specified output. Realization of a reagent role requires participation in a chemical reaction as part of an assay or material processing technique. a role inhering in a material entity intended to be input into an assay as a participant that facilitates the generation of data about some other material serving as an evaluant, or into a material processing technique as a participant that does not contribute significant material to the specified output. Realization of a reagent role requires participation in a chemical reaction as part of an assay or material processing technique. a role inhering in a material entity intended to be input into an assay where it participates in some chemical reaction to facilitate the generation of data about some other material serving as an evaluant, or a material processing technique where it participates in a chemical reaction to facilitate the generation of some specified output to which it does not contribute significant material."""; rdfs:comment "BP exmaple : even in the same exact process (addition of a fluorescent labeled antibody to an ELISA plate to measure binding to some fixed protein), the identity of the evaluant and the reagent(s) are in the eye of the experimentalist. For instance, if the goal of the assay is to confirm that the antibody probe works by comparing binding to positive and negative control proteins on the ELISA, then it is the evaluant and the proteins on the ELISA plate are the reagents. If the goal of the assay is to identify a protein target from some panel of samples using a known/validated fluorochrome-linked antibody probe, then the antibody probe and fluorocrome are reagents, and the protein samples on the ELISA plate are the evaluants.", "a material entity being a reagent (bearing a reagent role) does not mean that data cannot be generated in about that material in an assay, only that the reagent role of that material entity is not realized in such an assay (rather, an evaluant role also inhering in this material entity is realized in this case)."; """Explanation of Roles Realized Through Three Squential Techniques: 1. A Material Processing Technique (Generation of a Labeled Antibody) In a antibody labeling technique, the antibody and fluorochrome play incorporant roles (primary and secondary incorporant roles, respectively), and any coupling or elution buffers used play reagent roles. 2. An Assay (Determining Degree of Labeling) In an assay to determine the efficiency of labeling of the antibody, the labeled antibody plays an evaluant role, the fluorochrome plays an analyte role, and any buffers used in the assay play reagent roles 3. An Assay (Detecting Expression Level and Location of a Protein of Interest) In a immunocytochemicsty assay, the cells play an evaluant role, the endogenous protein of interest plays an analyte role, and the molecular labels (labeled antibody probe, fluorescent reporter), as well as any buffers, fixatives, and detergents used, play reagent roles. This example illustrates how a given material entity (an antibody or fluorochrome) can bear many different research material roles (an incorporant role, an evaluant role, a reagent role), and how these roles are realized in different processes.""", """As input into an assay, the reagent is not that which data is generated about, but rather facilitates the generation of data about an evaluant. For example, in a DNA sequenceing assay, the input template DNA to be sequenced plays an evaluant role, and the buffers, labeled nucleotides, and polymerase enzyme play reagent roles. As input into a material processing technique, a reagent does not contribute significant material to the specified output object, but rather facilitates the creation or modification of input material that does contribute matter to this output object. For example, in a PCR reaction to amplify a DNA insert for subcloning, the buffer and polymerase enzyme serve reagent roles, while the template and nucleotides that are incorporated into the output material do not play a reagent role (rather, these play incorporant roles). These examples illustrate how the same type of material (e.g nucelotides) can serve as reagents in one context (a sequenceing assay) but not in another (a PCR reaction to generate subcloning intermediates). Similarly, different instances of the same class of material entity can bear a reagent or an evaluant role that are realized in different processes. For example, taq polymerase can be used as a reagent in a PCR technique, but studied as an evaluant in a biochemical assay of taq structure and function. Thus, in the context of a given assay or technique, an instance of a material entity that can BEAR a reagent or evanualnt role, can PLAY only one of these roles but not both. """; """a role inhering in a processed material that is gained through a planning process which specifies its intended use as input into some technique, in which it will participate in some chemical reaction as part of either (1) an assay in which data is not generated about the bearer; or (2) a material processing technique in which the specified output does not derive from the bearer of the reagent role (ie the bearer does not contribute significant material to the composition of the specified output). The reagent role is realized through the bearer's participation in such a process. or a role inhering in a processed material that is gained through a planning process which specifies its intended use in assay or material processing technique, and is realized through the bearer's participation in or having parts that participate in some chemical reaction during: (1) an assay in which data is not generated about the bearer; or (2) a material processing technique in which the specified output does not derive from the bearer of the reagent role (ie the bearer does not contribute significant material to the composition of the specified output)"""; """this class was created as an obsolete class to hold annotations on the original reagent role class that we replaced on 11-21-11 with a new reagent class according to the Oct '11 OBI workshop - where we define reagent role as a union of molecular reagent and non molecular reagent roles (because we could not come up with a single reagent role definition that worked to cover both, but wished them to reside under the same reagent role parent. but we wanted to keep the URI of the reagent role class to be REO:0000001, so we could obsolete that original class. therefore we just transferred all annotations from this class to this new obsolete_reagent_role class"""; "OBI (need to have discussions with OBI to clearly define the reagent role, and adopt a common representation in ReO and OBI)"; """Reagents vs Instruments/Devices: Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents neccessarily are chemically altered or consumed (or have parts that are) during the technique. By contrast, instruments are not consumed or have parts that are chemically altered or consumed in a chemical reaction during the technique.""" . a owl:Class; rdfs:label "obsolete_reagent role 2"; rdfs:subClassOf ; "failed test class"; """v4 def (newest, 12-10-11): a role inhering in a material entity that is (1) intended to be input into some scientific technique to facilitate the generation of data about some other entity, or the production of a material output that does not derive from the bearer of the reagent role unless the output is itself a reagent, and (2) comprised (only) of molecular-scale parts intended to participate in a chemical reaction or interaction during this technique Note that if we say a reagent now consists only of the components of a material intended to participate in some reaction . . . we may now be able to say that a reagent is: a role inhereing in a molecular entity (single or multi-chain entiteis or mixtures), or in the combined molecular parts of some larger material entity, that are intended to participate in a chemical reaction or interaction as part of a scientific technique to generate data about some other entity, or produce some material output that does not derive from the bearer unless the output is itself a reagent. This last part assures that things like dNTPs and P32 incorporated into an oligo probe bear reagent roles, as they are not used on their own in a reagent capacity, but rather are always incorported into some other molecular entity which has a reagent role. So this means that ANY input into a material processing technique with a reagent creation objective (be it an incorporant or non-incorporant) realizes a reagent role in this process? Or is the reagent role of dNTPs realized only when the reagent role of the resulting PCR product (ie probe, construct/insert etc) is realized? Same goes for construct inserts - are these reagents? So may say something like : \". . . and realized in a scientific technique whereby the bearer (or a larger reagent of which it is a part) . . . \""""; rdfs:comment """Note that if we go with newest approach for defining reagent role, we may not need the clause 'immediately consumed or inactivated'. In the definition for this class, this clause implies that a molecular reagent or molecular part of a non-molecular reagent is either physically altered or destroyed in a chemical reaction, or sequestered or otherwise indisposed by some molecular interaction, such that any potential re-use of the reagent would require material processing to restore it to a usable state (e.g. uncoupling and re-purifying an antibody, washing of bound probes and contaminants from a microarray plate, washing and re-culturing a cell line)""" . a owl:Class; rdfs:label "obsolete_molecular reagent role 2"; rdfs:subClassOf ; "a reagent role inhering in a processed molecular entity (includes single-chain, multi-chain complexes, and mixtures) that is intended to participate in a chemical reaction or interaction as part of some scientific technique to facilitate the generation of data about some other entity, or the production of some material that does not derive from the bearer of the reagent role unless the output is itself a reagent." . a owl:Class; rdfs:label "obsolete_non-molecular reagent role 2"; rdfs:subClassOf ; """a role inhering in a processed non-molecular entity (includes objects, aggregates, and mixtures, collections) that has as parts (winston component_parts or stuff_parts?) only molecular entities intended to be immediately consumed in a chemical reaction as part of some scientific technique, where it facilitates the generation of data about some other entity, or facilitates the production of some material entity that does not derive from the bearer of the reagent role. 'Immediate consumption' requires that the bearer's molecular parts are 'significantly altered' during the execution of a single experiment, such that any re-use would require some processing to restore them to a usable state (e.g. washing of bound probes and contaminants from a microarray plate, washing and re-culturing of a cell line)"""; rdfs:comment """A key issue here is distinguishing non-molecular reagents (ie microarrays, cell lines) from instruments, which also are input into experiments and facilitate the generation of data about other entities or the production of other materials. However, entiteis we consider to be instruments typically do not have parts that participate in chemical reactions. For example, pipettes, tissue culture dishes, or microscopes, while often specified as inputs for tecniques that generate data about other entities or generated other material outputs, bear no components that participate in a chemical reaction or interaction during execution of this technique. In a few cases, however, instuments DO have parts that participate in chemical reactions - for example the case of gel running boxes, which contain wires/electrodes that necessarily (ie as specified) exchange electrons and metal ions into the running buffer during an experiment. It is to account for these cases that language was included in the 'reagent role' definition that stipulates the 'immediate consumption or inactivation' of reagents during execution of a technique. This excludes instruments that have parts which participate in chemical reactions (e.g. gel running boxes, pH meter probes), as their components (typically metal wires/electrodes) are chemically altered but not to the extent that they require restoration before running additional experiments."""; "material reagent role, macroscopic reagent role" . a owl:Class; rdfs:label "obsolete_physical characteristic"; rdfs:subClassOf ; """exploratory class - not needed. previous eq class definition was 'disposition or function or quality'"""; rdfs:comment """just testing the idea that all dependent continuants excpet roles are innately tied to the physical make-up of their bearers (ie a natural consequence of their material structure), whereas roles are socially or contextually ascribed and not a necessary consequecne of the physical make-up of their bearers. See http://precedings.nature.com/documents/1941/version/1/files/npre20081941-1.pdf"""; . a owl:Class; rdfs:label "reagent creation objective"; rdfs:subClassOf , _:2e67e9; "This class would seem to be analogous to specimen creation objective, as both the role of specimen and the role of reagent are 'in the eye of the beholder' (ie are a result of the intent of the researcher who designs an experiment, such that almost any material entity has potential to bear a specimen role or a reagent in some experiment somewhere). For this reason, specimen roles or reagent roles are not applied to universal classes (cell, organism, nucleic acid, etc), but rather, universal classes are subclassed to delineate those universals that bear a specimen or reagent role (ie cell>cell specimen, nucleic acid > nucleic acid reagent). Because applying these roles to the universal class would indicate that ALL instances of cells or nucleic acids bear a specimen or reagent role, and this is not the case. It may be the case, however, for some material entities that are manufactured with the intent of serving a reagent role (for ex, alexafluor dyes, microarrays, synthetic oligos, cell lines?, etc)"; """an objective realized by some agents intent to apply some processed material as a reagent in some technique/ investigation. In some cases this objective is realized at the same time a material is processed or created (ie when it is processed/created for the express purpose of being used as a reagent). In other cases this objective is realized after a material has been processed for some other purpose, and some agent decides to apply it in a technique/investigation as a reagent. For these reasons, this objective is not a material processing objective - as it can be realized in 'intentional' / 'cognitive' processes that are not material processings.""" . _:2e67e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_autonomous role"; rdfs:subClassOf ; "earned role"; "a role that is borne/earned by an agent in virtue of the bearer's own intentional actions, which does not require recognition by some external/authoratative agent"; "author role" . a owl:Class; rdfs:label "obsolete_non-molecular entity"; rdfs:subClassOf ; . a owl:Class; rdfs:label "obsolete_proxy role"; rdfs:subClassOf ; "a role inhering in a material entity that is intended to be measured in some assay as a surrogate for some other material entity bearing an evaluant role realilzed in the assay" . a owl:Class; rdfs:label "molecular reporter"; owl:equivalentClass _:2e67f9; rdfs:subClassOf , _:2e6839, _:2e6849; "a molecular label that is capable of producing a detectable signal"; . _:2e67f9 a owl:Class; owl:intersectionOf _:2e6809 . _:2e6809 rdf:first ; rdf:rest _:2e6829 . _:2e6829 rdf:first _:2e6819; rdf:rest rdf:nil . _:2e6819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_indicator reagent"; rdfs:subClassOf ; """deceded not needed for now as we have the associated role - but may want ti re-implement in future former eq class axiom: 'molecular entity' and ('has role' some 'indicator reagent role') superclass axiom: 'is bearer of' some 'detectable disposition'"""; "reporter reagent"; "a molecular entity that is able to generate a detectable signal, and is intended to be used as a proxy for measuring some relative characteristic of an analyte in an analyte assay (e.g. its presence in, abundance in, location in, or processing by some evaluant), or for the activity of an evaluant in an activity assay."; . a owl:Class; rdfs:label "obsolete_molecular effector reagent role"; rdfs:subClassOf ; "was meant to account for moleuclar effectors that may not neccessarily interact with their targets, but will wait to implement this if/when if is needed"; rdfs:comment """Created as a complement the molecular target role, and represent the molecular entity that seeks out and interacts with some molecular target of interest (according to some intentional agents specification, or some biological agents intent). Here we consider only effectors used as reagents (wherease the molecular target is often not a reagent, and thus 'molecular target role' is a research material role) Molecular effector role is broadly conceived to cover targeted labels meant to facilitate detection of their targets, as well bioactive/pharmacological agents such as drugs, inhibitors, etc that are meant to effect the biological activity of their targets as a tool in some investigation. Is always paried with some moleuclar target as another participant in the scientific technique, which is the more passive subject in this context. The effector participant can be said to be the one that is intended to seek out or recognizes the target."""; "molecular agent role, molecular probe role, molecular binding role"; "a reagent role that inheres in a molecular entity applied in a scientific technique to effect (ie activate, inhibit, react with, enzymatically process, etc) some moelcular target of interest" . a owl:Class; rdfs:label "indicator reagent role"; rdfs:subClassOf , _:2e6859; rdfs:comment "this is essentially a reagent role inhering in a bearer with a detectable dispostion, and realized in an assay that exploits this detectable disposition. Will cover (1) MOLECULAR REPORTERS that physically associate with some analyte of interest (e.g. Cy5, DAPI stain); (2) the products of ACTIVITY REPORTERS (e.g. luciferase, x-gal, ECL); AND (3) MATERIAL TRACERS (e.g. barium tracers in stool)"; "reporter role"; "a reagent role inihering in a molecular entity that is intended to be detected in an assay as a proxy to yield information about some analyte or evaluant of interest"; . _:2e6859 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6869 . _:2e6869 a owl:Class; owl:intersectionOf _:2e6879 . _:2e6879 rdf:first ; rdf:rest _:2e6899 . _:2e6899 rdf:first _:2e6889; rdf:rest rdf:nil . _:2e6889 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_fluorescent stain role"; rdfs:subClassOf ; "implemented new approach for moelcular label modeling (using the molec label role for defining molec label and targeted and reporter axes based children, but not for defining colorimetric, fluorescent, radioactive label children . . .will use dispositions here. " . a owl:Class; rdfs:label "obsolete_colorimetric stain role"; rdfs:subClassOf ; "implemented new approach for moelcular label modeling (using the molec label role for defining molec label and targeted and reporter axes based children, but not for defining colorimetric, fluorescent, radioactive label children . . .will use dispositions here. " . a owl:Class; rdfs:label "molecular tracker"; owl:equivalentClass _:2e68a9; rdfs:subClassOf , _:2e68e9, _:2e6939; "a molecular label that is not capable of producing a detectable signal"; "biotin, digoxygenin, biotin-labeled oligonucleotide probes, digoxygenin-conjugated antibodies"; "molecular probe"; rdfs:comment "as trackers are not capable of producing a detectable signal, they must be detected through use of some secondary label that is detectable."; . _:2e68a9 a owl:Class; owl:intersectionOf _:2e68b9 . _:2e68b9 rdf:first ; rdf:rest _:2e68d9 . _:2e68d9 rdf:first _:2e68c9; rdf:rest rdf:nil . _:2e68c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e68e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e68f9 . _:2e68f9 a owl:Class; owl:intersectionOf _:2e6909 . _:2e6909 rdf:first ; rdf:rest _:2e6929 . _:2e6929 rdf:first _:2e6919; rdf:rest rdf:nil . _:2e6919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6939 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular tracker role"; rdfs:subClassOf , _:2e6949; "a molecular label role inhering in a molecular entity that is not capable of producing a detectable signal (such that to allow detection of some target analyte, it must associate with some molecular reporter that does produce a detectable signel)" . _:2e6949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6959 . _:2e6959 a owl:Class; owl:intersectionOf _:2e6969 . _:2e6969 rdf:first ; rdf:rest _:2e6989 . _:2e6989 rdf:first _:2e6979; rdf:rest rdf:nil . _:2e6979 a owl:Class; owl:complementOf _:2e6999 . _:2e6999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular reporter role"; rdfs:subClassOf , _:2e69a9; rdfs:comment "Detectable signals are typically colorimetric, fluorescent, or radioactive in nature"; "a molecular label role inhering in a molecular entity that is capable of producing a detectable signal"; "molecular detector role" . _:2e69a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e69b9 . _:2e69b9 a owl:Class; owl:intersectionOf _:2e69c9 . _:2e69c9 rdf:first ; rdf:rest _:2e69e9 . _:2e69e9 rdf:first _:2e69d9; rdf:rest rdf:nil . _:2e69d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biotin-labeled DNA probe"; owl:equivalentClass _:2e69f9; rdfs:subClassOf , , _:2e6ab9, _:2e6ac9, _:2e6ad9; . _:2e69f9 a owl:Class; owl:intersectionOf _:2e6a09 . _:2e6a09 rdf:first ; rdf:rest _:2e6a29 . _:2e6a29 rdf:first _:2e6a19; rdf:rest rdf:nil . _:2e6a19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6a39 . _:2e6a39 a owl:Class; owl:intersectionOf _:2e6a49 . _:2e6a49 rdf:first ; rdf:rest _:2e6a69 . _:2e6a69 rdf:first _:2e6a59; rdf:rest rdf:nil . _:2e6a59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6a79 . _:2e6a79 a owl:Class; owl:intersectionOf _:2e6a89 . _:2e6a89 rdf:first ; rdf:rest _:2e6aa9 . _:2e6aa9 rdf:first _:2e6a99; rdf:rest rdf:nil . _:2e6a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6ab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6ac9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6ad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6ae9 . _:2e6ae9 a owl:Class; owl:intersectionOf _:2e6af9 . _:2e6af9 rdf:first ; rdf:rest _:2e6b19 . _:2e6b19 rdf:first _:2e6b09; rdf:rest rdf:nil . _:2e6b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6b29 . _:2e6b29 a owl:Class; owl:intersectionOf _:2e6b39 . _:2e6b39 rdf:first ; rdf:rest _:2e6b59 . _:2e6b59 rdf:first _:2e6b49; rdf:rest rdf:nil . _:2e6b49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biotin-labeled RNA probe"; owl:equivalentClass _:2e6b69; rdfs:subClassOf , , _:2e6c29, _:2e6c39, _:2e6c49; . _:2e6b69 a owl:Class; owl:intersectionOf _:2e6b79 . _:2e6b79 rdf:first ; rdf:rest _:2e6b99 . _:2e6b99 rdf:first _:2e6b89; rdf:rest rdf:nil . _:2e6b89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6ba9 . _:2e6ba9 a owl:Class; owl:intersectionOf _:2e6bb9 . _:2e6bb9 rdf:first ; rdf:rest _:2e6bd9 . _:2e6bd9 rdf:first _:2e6bc9; rdf:rest rdf:nil . _:2e6bc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6be9 . _:2e6be9 a owl:Class; owl:intersectionOf _:2e6bf9 . _:2e6bf9 rdf:first ; rdf:rest _:2e6c19 . _:2e6c19 rdf:first _:2e6c09; rdf:rest rdf:nil . _:2e6c09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6c29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6c39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6c49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6c59 . _:2e6c59 a owl:Class; owl:intersectionOf _:2e6c69 . _:2e6c69 rdf:first ; rdf:rest _:2e6c89 . _:2e6c89 rdf:first _:2e6c79; rdf:rest rdf:nil . _:2e6c79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6c99 . _:2e6c99 a owl:Class; owl:intersectionOf _:2e6ca9 . _:2e6ca9 rdf:first ; rdf:rest _:2e6cc9 . _:2e6cc9 rdf:first _:2e6cb9; rdf:rest rdf:nil . _:2e6cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "microarray DNA probe"; rdfs:subClassOf , , _:2e6cd9, _:2e6ce9; "microarray DNA reporter"; "a DNA oligonucleotide that is immobilized on the surface of a microarray support substrate, to sequester and allow for the quantification of complementary target oligonucleotides from some nucleic acid sample under investigation" . _:2e6cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6ce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "microarray RNA probe"; rdfs:subClassOf , , _:2e6cf9, _:2e6d09; "an RNA oligonucleotide that is immobilized on the surface of a microarray support substrate, to sequester and allow for the quantification of complementary target oligonucleotides from some nucleic acid sample under investigation"; "microarray RNA reporter" . _:2e6cf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6d09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell culture transfection"; owl:equivalentClass _:2e6d19; rdfs:subClassOf , , _:2e6db9, _:2e6dc9 . _:2e6d19 a owl:Class; owl:intersectionOf _:2e6d29 . _:2e6d29 rdf:first ; rdf:rest _:2e6d49 . _:2e6d49 rdf:first _:2e6d39; rdf:rest _:2e6da9 . _:2e6d39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6d59 . _:2e6d59 a owl:Class; owl:intersectionOf _:2e6d69 . _:2e6d69 rdf:first ; rdf:rest _:2e6d89 . _:2e6d89 rdf:first _:2e6d79; rdf:rest rdf:nil . _:2e6d79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6da9 rdf:first _:2e6d99; rdf:rest rdf:nil . _:2e6d99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6dc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6dd9 . _:2e6dd9 a owl:Class; owl:intersectionOf _:2e6de9 . _:2e6de9 rdf:first ; rdf:rest _:2e6e09 . _:2e6e09 rdf:first _:2e6df9; rdf:rest rdf:nil . _:2e6df9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsoleted_RNA microarray"; rdfs:subClassOf . a owl:Class; rdfs:label "nucleic acid microarray"; rdfs:subClassOf , _:2e6e19; "a microarray that is comprised of numerous collections of like oligonucleotides, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed oligonucleotide 'probes' are used to determine the identity or quantity of 'target' nucleic acid molecules (or nucleic acid-associated molecules) in some biological specimen of interest, based on quantification of hybridization between specimen nucleic acid targets and immobilized microarray nucleic acid molecules. " . _:2e6e19 a owl:Class; owl:intersectionOf _:2e6e29 . _:2e6e29 rdf:first ; rdf:rest _:2e6e49 . _:2e6e49 rdf:first _:2e6e39; rdf:rest rdf:nil . _:2e6e39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6e59 . _:2e6e59 a owl:Class; owl:intersectionOf _:2e6e69 . _:2e6e69 rdf:first ; rdf:rest _:2e6e89 . _:2e6e89 rdf:first _:2e6e79; rdf:rest rdf:nil . _:2e6e79 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e6e99 . _:2e6e99 a owl:Class; owl:intersectionOf _:2e6ea9 . _:2e6ea9 rdf:first ; rdf:rest _:2e6ec9 . _:2e6ec9 rdf:first _:2e6eb9; rdf:rest rdf:nil . _:2e6eb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e6ed9 a owl:Axiom; "here and elsewhere, should we say has aggregate part some and only nucleic acid?"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e6ee9 . _:2e6ee9 a owl:Class; owl:intersectionOf _:2e6ef9 . _:2e6ef9 rdf:first ; rdf:rest _:2e6f19 . _:2e6f19 rdf:first _:2e6f09; rdf:rest rdf:nil . _:2e6f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6f29 . _:2e6f29 a owl:Class; owl:intersectionOf _:2e6f39 . _:2e6f39 rdf:first ; rdf:rest _:2e6f59 . _:2e6f59 rdf:first _:2e6f49; rdf:rest rdf:nil . _:2e6f49 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e6f69 . _:2e6f69 a owl:Class; owl:intersectionOf _:2e6f79 . _:2e6f79 rdf:first ; rdf:rest _:2e6f99 . _:2e6f99 rdf:first _:2e6f89; rdf:rest rdf:nil . _:2e6f89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular microarray"; owl:equivalentClass _:2e6fa9; rdfs:subClassOf , _:2e70a9; "a microarray that is comprised of numerous collections of like molecular entities, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed molecule 'probes' are used to determine the identity or quantity of some 'target' molecule(s) in a biological specimen of interest, based on quantification of binding between specimen molecular targets and immobilized microarray probes. " . _:2e6fa9 a owl:Class; owl:intersectionOf _:2e6fb9 . _:2e6fb9 rdf:first ; rdf:rest _:2e6fd9 . _:2e6fd9 rdf:first _:2e6fc9; rdf:rest rdf:nil . _:2e6fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e6fe9 . _:2e6fe9 a owl:Class; owl:intersectionOf _:2e6ff9 . _:2e6ff9 rdf:first ; rdf:rest _:2e7019 . _:2e7019 rdf:first _:2e7009; rdf:rest rdf:nil . _:2e7009 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e7029 . _:2e7029 a owl:Class; owl:intersectionOf _:2e7039 . _:2e7039 rdf:first ; rdf:rest _:2e7059 . _:2e7059 rdf:first _:2e7049; rdf:rest rdf:nil . _:2e7049 a owl:Class; owl:intersectionOf _:2e7079 . _:2e7079 rdf:first _:2e7069; rdf:rest _:2e7099 . _:2e7069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7099 rdf:first _:2e7089; rdf:rest rdf:nil . _:2e7089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e70a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e70b9 . _:2e70b9 a owl:Class; owl:intersectionOf _:2e70c9 . _:2e70c9 rdf:first ; rdf:rest _:2e70e9 . _:2e70e9 rdf:first _:2e70d9; rdf:rest rdf:nil . _:2e70d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e70f9 . _:2e70f9 a owl:Class; owl:intersectionOf _:2e7109 . _:2e7109 rdf:first ; rdf:rest _:2e7129 . _:2e7129 rdf:first _:2e7119; rdf:rest rdf:nil . _:2e7119 a owl:Class; owl:intersectionOf _:2e7149 . _:2e7149 rdf:first _:2e7139; rdf:rest _:2e7169 . _:2e7139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7169 rdf:first _:2e7159; rdf:rest rdf:nil . _:2e7159 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_cDNA microarray"; rdfs:subClassOf . a owl:Class; rdfs:label "synthesis objective"; rdfs:subClassOf , , _:2e7179; "material assembly objective"; "a material combination objective to physically assemble more than one simpler input component into some larger product that bears some function, and wherein the autonomous identify of none of the specified inputs is retained (ie the specified output is distinct in identity from any of the specified inputs)" . _:2e7179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7189 . _:2e7189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7199 . _:2e7199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_protein microarray"; rdfs:subClassOf ; "http://en.wikipedia.org/wiki/Protein_microarray"; "a molecular microarray that is used to measure protein abundance in a specimen of interest, which consists of fixed substrate (typically glass or silicon) onto which different molecules of protein (typically antibodies) have been affixed at separate locations in an ordered manner thus forming a microscopic array. Alternatively, an array of non-protein molecules, such as DNA promoter sequences, can be fixed to the array as capture probes for a protein mixture that is incubated with the array. "; "replaced with OBI protein microarray"; "protein-binding array" . a owl:Class; rdfs:label "carbohydrate microarray"; rdfs:subClassOf , _:2e71a9; "a molecular microarray that is comprised of numerous collections of like carbohydrate or carbohydrate-containing molecules, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed carbohydrate 'probes' are used to determine the identity or quantity of some 'target' molecule(s) in a biological specimen of interest, based on quantification of binding between specimen molecular targets and immobilized carbohydrate probes. "; "glycoarray"; rdfs:comment "Carbohydrates arrays comprise arrays of mono- and oligosaccharides, complex polysaccharides, glycoconjugates, glycoproteins " . _:2e71a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e71b9 . _:2e71b9 a owl:Class; owl:intersectionOf _:2e71c9 . _:2e71c9 rdf:first ; rdf:rest _:2e71e9 . _:2e71e9 rdf:first _:2e71d9; rdf:rest rdf:nil . _:2e71d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e71f9 . _:2e71f9 a owl:Class; owl:intersectionOf _:2e7209 . _:2e7209 rdf:first ; rdf:rest _:2e7229 . _:2e7229 rdf:first _:2e7219; rdf:rest rdf:nil . _:2e7219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7239 . _:2e7239 a owl:Class; owl:intersectionOf _:2e7259 . _:2e7259 rdf:first _:2e7249; rdf:rest _:2e72b9 . _:2e7249 a owl:Class; owl:intersectionOf _:2e7279 . _:2e7279 rdf:first _:2e7269; rdf:rest _:2e7299 . _:2e7269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7299 rdf:first _:2e7289; rdf:rest rdf:nil . _:2e7289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e72b9 rdf:first _:2e72a9; rdf:rest rdf:nil . _:2e72a9 a owl:Class; owl:unionOf _:2e72c9 . _:2e72c9 rdf:first ; rdf:rest _:2e72d9 . _:2e72d9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "chemical compound microarray"; rdfs:subClassOf , _:2e72e9; "chemical microarray", "small molecule microarray"; rdfs:comment "Chemical compund microarrays are routinely used for screening molecules such as proteins that bind with specific chemical compounds. In general drug discovery research, they provide a multiplex way to search potential drugs for therapeutic targets."; "a microarray that is comprised of numerous collections of like chemical entities, typically organic small molecules, which are spotted in a two-dimensional array onto a solid support matrix. The arrayed chemical 'probes' are used to determine the identity or quantity of some 'target' molecule(s) in a biological specimen of interest, based on quantification of binding between specimen molecular targets and immobilized microarray probes. "; "http://en.wikipedia.org/wiki/Chemical_compound_microarray" . _:2e72e9 a owl:Class; owl:intersectionOf _:2e72f9 . _:2e72f9 rdf:first ; rdf:rest _:2e7319 . _:2e7319 rdf:first _:2e7309; rdf:rest rdf:nil . _:2e7309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7329 . _:2e7329 a owl:Class; owl:intersectionOf _:2e7339 . _:2e7339 rdf:first ; rdf:rest _:2e7359 . _:2e7359 rdf:first _:2e7349; rdf:rest rdf:nil . _:2e7349 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e7369 . _:2e7369 a owl:Class; owl:intersectionOf _:2e7379 . _:2e7379 rdf:first ; rdf:rest _:2e7399 . _:2e7399 rdf:first _:2e7389; rdf:rest rdf:nil . _:2e7389 a owl:Class; owl:intersectionOf _:2e73b9 . _:2e73b9 rdf:first _:2e73a9; rdf:rest _:2e73d9 . _:2e73a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e73d9 rdf:first _:2e73c9; rdf:rest rdf:nil . _:2e73c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cellular microarray"; rdfs:subClassOf , _:2e73e9; "a microarray that is comprised of numerous collections of like varying materials (e.g. antibodies, proteins, or chemical compunds), which are spotted in a two-dimensional array onto a solid support 'chip' matrix, typically made of glass or silicon. These arrayed molecule 'probes' can interact with cells cultured on the chip, allowing multiplexed interrogation of the impact of the spotted materials on cell growth or function."; "http://en.wikipedia.org/wiki/Cellular_microarray" . _:2e73e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e73f9 . _:2e73f9 a owl:Class; owl:intersectionOf _:2e7409 . _:2e7409 rdf:first ; rdf:rest _:2e7429 . _:2e7429 rdf:first _:2e7419; rdf:rest rdf:nil . _:2e7419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7439 . _:2e7439 a owl:Class; owl:intersectionOf _:2e7449 . _:2e7449 rdf:first ; rdf:rest _:2e7469 . _:2e7469 rdf:first _:2e7459; rdf:rest rdf:nil . _:2e7459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7479 . _:2e7479 a owl:Class; owl:intersectionOf _:2e7489 . _:2e7489 rdf:first ; rdf:rest _:2e74a9 . _:2e74a9 rdf:first _:2e7499; rdf:rest rdf:nil . _:2e7499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e74b9 . _:2e74b9 a owl:Class; owl:unionOf _:2e74c9 . _:2e74c9 rdf:first ; rdf:rest _:2e74e9 . _:2e74e9 rdf:first _:2e74d9; rdf:rest rdf:nil . _:2e74d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e74f9 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e7509 . _:2e7509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7519 . _:2e7519 a owl:Class; owl:intersectionOf _:2e7529 . _:2e7529 rdf:first ; rdf:rest _:2e7549 . _:2e7549 rdf:first _:2e7539; rdf:rest rdf:nil . _:2e7539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7559 . _:2e7559 a owl:Class; owl:intersectionOf _:2e7569 . _:2e7569 rdf:first ; rdf:rest _:2e7589 . _:2e7589 rdf:first _:2e7579; rdf:rest rdf:nil . _:2e7579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7599 . _:2e7599 a owl:Class; owl:intersectionOf _:2e75a9 . _:2e75a9 rdf:first ; rdf:rest _:2e75c9 . _:2e75c9 rdf:first _:2e75b9; rdf:rest rdf:nil . _:2e75b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e75d9 . _:2e75d9 a owl:Class; owl:unionOf _:2e75e9 . _:2e75e9 rdf:first ; rdf:rest _:2e7609 . _:2e7609 rdf:first _:2e75f9; rdf:rest rdf:nil . _:2e75f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "tissue microarray"; rdfs:subClassOf , _:2e7619; "http://en.wikipedia.org/wiki/Tissue_microarray"; "a microarray that consists of paraffin blocks in which up to multiple separate tissue cores are assembled in array fashion to allow multiplex histological analysis" . _:2e7619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7629 . _:2e7629 a owl:Class; owl:intersectionOf _:2e7639 . _:2e7639 rdf:first ; rdf:rest _:2e7659 . _:2e7659 rdf:first _:2e7649; rdf:rest rdf:nil . _:2e7649 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "antibody microarray"; rdfs:subClassOf , _:2e7669; "a protein microarray that is comprised of numerous collections of like antibodies, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed antibody 'probes' are used to determine the identity or quantity of some recognized antigen(s) in a biological specimen of interest, based on quantification of binding between these antigens in the specimen and immobilized antibody probes. "; "http://en.wikipedia.org/wiki/Antibody_microarray"; rdfs:comment "Antibody microarray is often used for detecting protein expressions from cell lysates in general research and special biomarkers from serum or urine for diagnostic applications." . _:2e7669 a owl:Class; owl:intersectionOf _:2e7679 . _:2e7679 rdf:first ; rdf:rest _:2e7699 . _:2e7699 rdf:first _:2e7689; rdf:rest rdf:nil . _:2e7689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e76a9 . _:2e76a9 a owl:Class; owl:intersectionOf _:2e76b9 . _:2e76b9 rdf:first ; rdf:rest _:2e76d9 . _:2e76d9 rdf:first _:2e76c9; rdf:rest rdf:nil . _:2e76c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2e76e9 . _:2e76e9 a owl:Class; owl:intersectionOf _:2e76f9 . _:2e76f9 rdf:first ; rdf:rest _:2e7719 . _:2e7719 rdf:first _:2e7709; rdf:rest rdf:nil . _:2e7709 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_buffer role"; rdfs:subClassOf ; """a reagent role that exploits some buffering disposition in its realization through the process of buffering"""; "replaced by OBI: buffer role" . a owl:Class; rdfs:label "metal elemental molecule"; rdfs:subClassOf ; "http://en.wikipedia.org/wiki/Metal"; "a molecule comprised only of a single type of metal atom"; "Fe2, Zn2" . a owl:Class; rdfs:label "non-metal elemental molecule"; rdfs:subClassOf ; "a molecule comprised only of a single type of non-metal atom"; "http://en.wikipedia.org/wiki/Non-metal" . a owl:Class; rdfs:label "natural environment"; rdfs:subClassOf ; "an environment in which an object is naturally found (ie independent of planned processing/re-location by some intentional agent)." . a owl:Class; rdfs:label "obsolete_phosphorus-33 reagent"; rdfs:subClassOf ; "didnt need both P32 and P33 as examples" . a owl:Class; rdfs:label "cultured unicellular organism"; owl:equivalentClass _:2e7729; rdfs:subClassOf , , _:2e7769, _:2e7779; owl:disjointWith ; rdfs:comment "cultured unicellular organisms are not considered to be 'ex environment', since we define 'ex environment' as 'having once been part of a natural environment', and a given unicellular organism that is cultured in a lab was never part of some environment at any point in its existence."; "cultured single cell organism"; "a unicellular organism that is maintained (propagated or held metabolically active) in vitro as part of a cell culture" . _:2e7729 a owl:Class; owl:intersectionOf _:2e7739 . _:2e7739 rdf:first ; rdf:rest _:2e7759 . _:2e7759 rdf:first _:2e7749; rdf:rest rdf:nil . _:2e7749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7779 a owl:Class; owl:complementOf _:2e7789 . _:2e7789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7799 . _:2e7799 a owl:Class; owl:unionOf _:2e77a9 . _:2e77a9 rdf:first ; rdf:rest _:2e77b9 . _:2e77b9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "experimentally modified unicellular organism"; owl:equivalentClass _:2e77c9; rdfs:subClassOf , , _:2e7809; owl:disjointWith ; "a unicelllular organism that is the specified output of an experimental modification technique that introduces physical changes to the cell (ie changes in composition and/or internal structural arrangement)"; "experimentally modified single cell organism" . _:2e77c9 a owl:Class; owl:intersectionOf _:2e77d9 . _:2e77d9 rdf:first ; rdf:rest _:2e77f9 . _:2e77f9 rdf:first _:2e77e9; rdf:rest rdf:nil . _:2e77e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7809 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetic material vector function"; rdfs:subClassOf ; "genetic material delivery function"; rdfs:comment "As a point of terminological clarification, 'genetic material' refers specifically to a nucleic acid that is capable of being replicated and inherited by offspring cells or organisms. However, we indicated here that the 'genetic material vector function' can be realized by any transfection or transformation process where there is the potental for the delivered nucleic acid to be stably replicated, even though in many cases the goal is merely for transient vector propagation or gene expression."; "a function that inheres in a piece of DNA that is constructed to contain functional elements that facilitate the incorporation, replication, and often the expression of specific DNA sequences in a host cell of orgnaism." . a owl:Class; rdfs:label "obsolete_cell modification objective"; rdfs:subClassOf ; "decided to define cell modification techniques (used to define exp mod cell) as achieve obj some material mod obj, and also having ouput some cell or has grain some cell . . . should work well since all techniques should have axioms stating their outputs anyway, and thus can just use the material mod obj rather than needed a more specific cell mod obj." . a owl:Class; rdfs:label "cell modification technique"; owl:equivalentClass _:2e7819 . _:2e7819 a owl:Class; owl:intersectionOf _:2e7829 . _:2e7829 rdf:first ; rdf:rest _:2e7849 . _:2e7849 rdf:first _:2e7839 . _:2e7839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7859 . _:2e7859 a owl:Class; owl:intersectionOf _:2e7879 . _:2e7879 rdf:first _:2e7869; rdf:rest _:2e78c9 . _:2e7869 a owl:Class; owl:unionOf _:2e7889 . _:2e7889 rdf:first ; rdf:rest _:2e78a9 . _:2e78a9 rdf:first _:2e7899; rdf:rest rdf:nil . _:2e7899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e78c9 rdf:first _:2e78b9; rdf:rest rdf:nil . _:2e78b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7849 rdf:rest _:2e78e9 . _:2e78e9 rdf:first _:2e78d9; rdf:rest rdf:nil . _:2e78d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf , _:2e78f9, _:2e7949, _:2e79d9; rdfs:comment "The 'physical changes' described in the definition alter the structural makeup of the input cells by adding/removing material or re-arranging their internal structure. These are changes beyond simple 'contextual changes' such those resulting from collecting a specimen, or selecting a subpopulation of cells."; "labeling the surface of a cell with biotin, transfection of a cell with plasmid DNA, infecting a cell with a retrovirus, establishing a cell culture in media"; "a material processing technique intended to introduce physical changes to a cell or cell culture" . _:2e78f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7909 . _:2e7909 a owl:Class; owl:intersectionOf _:2e7919 . _:2e7919 rdf:first ; rdf:rest _:2e7939 . _:2e7939 rdf:first _:2e7929; rdf:rest rdf:nil . _:2e7929 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7959 . _:2e7959 a owl:Class; owl:intersectionOf _:2e7979 . _:2e7979 rdf:first _:2e7969; rdf:rest _:2e79c9 . _:2e7969 a owl:Class; owl:unionOf _:2e7989 . _:2e7989 rdf:first ; rdf:rest _:2e79a9 . _:2e79a9 rdf:first _:2e7999; rdf:rest rdf:nil . _:2e7999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e79c9 rdf:first _:2e79b9; rdf:rest rdf:nil . _:2e79b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e79d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e79e9 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e79f9 . _:2e79f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7a09 . _:2e7a09 a owl:Class; owl:intersectionOf _:2e7a19 . _:2e7a19 rdf:first ; rdf:rest _:2e7a39 . _:2e7a39 rdf:first _:2e7a29; rdf:rest rdf:nil . _:2e7a29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "clonal unicellular organism culture"; owl:equivalentClass _:2e7a49; rdfs:subClassOf , , _:2e7a89; "a unicellular organism culture that derives from a single unicellular organism that is isolated from some population of cells and propagated to create a new culture"; . _:2e7a49 a owl:Class; owl:intersectionOf _:2e7a59 . _:2e7a59 rdf:first ; rdf:rest _:2e7a79 . _:2e7a79 rdf:first _:2e7a69; rdf:rest rdf:nil . _:2e7a69 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2e7a89 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "biotin-labeled cell"; rdfs:subClassOf , , _:2e7a99, _:2e7aa9; . _:2e7a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7aa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7ab9 . _:2e7ab9 a owl:Class; owl:intersectionOf _:2e7ac9 . _:2e7ac9 rdf:first ; rdf:rest _:2e7ae9 . _:2e7ae9 rdf:first _:2e7ad9; rdf:rest rdf:nil . _:2e7ad9 a owl:Class; owl:intersectionOf _:2e7b09 . _:2e7b09 rdf:first _:2e7af9; rdf:rest _:2e7b69 . _:2e7af9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7b19 . _:2e7b19 a owl:Class; owl:intersectionOf _:2e7b29 . _:2e7b29 rdf:first ; rdf:rest _:2e7b49 . _:2e7b49 rdf:first _:2e7b39; rdf:rest rdf:nil . _:2e7b39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7b69 rdf:first _:2e7b59; rdf:rest rdf:nil . _:2e7b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7b79 . _:2e7b79 a owl:Class; owl:intersectionOf _:2e7b89 . _:2e7b89 rdf:first ; rdf:rest _:2e7ba9 . _:2e7ba9 rdf:first _:2e7b99; rdf:rest rdf:nil . _:2e7b99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "chemically fixed cell"; owl:equivalentClass _:2e7bb9; rdfs:subClassOf , _:2e7bf9; """CARO, CL, OBI? : Need to decide if CARO, CL, others would consider a dead cell still a cell? MH: i am a little concerned about classes like this one, which are not alive but are experimentally modified. not sure if the cell modification objective or cell modification techniques should apply to live only, or all cells? i think it really depends on how we define the \"modification\"- eg. material, physical, etc. does it matter if it is alive or dead? not sure."""; . _:2e7bb9 a owl:Class; owl:intersectionOf _:2e7bc9 . _:2e7bc9 rdf:first ; rdf:rest _:2e7be9 . _:2e7be9 rdf:first _:2e7bd9; rdf:rest rdf:nil . _:2e7bd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7bf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "multicellular organism cell"; owl:equivalentClass _:2e7c09; rdfs:subClassOf ; "a cell that is part of or derives from a multicellular organism"; . _:2e7c09 a owl:Class; owl:intersectionOf _:2e7c19 . _:2e7c19 rdf:first ; rdf:rest _:2e7c39 . _:2e7c39 rdf:first _:2e7c29; rdf:rest rdf:nil . _:2e7c29 a owl:Class; owl:unionOf _:2e7c59 . _:2e7c59 rdf:first _:2e7c49; rdf:rest _:2e7c79 . _:2e7c49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7c79 rdf:first _:2e7c69; rdf:rest rdf:nil . _:2e7c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_cultured multicellular organism cell"; rdfs:subClassOf ; "a multicellular organism cell that is maintained (propagated or held metabolically active) in vitro as part of a cell culture"; "CL, OBI : not clear whether the 'cell line cell' and 'cell line culture' classes in these two ontologies, respectively, are intended to refer to only cultured multicellular organism cells, or ALL cultured cells. So unclear how to xref this class (or where it might be imported from)"; "replaced by C::cell culutre cell (we assumed that CL cell culture cells refer only to those from multicellular organisms, but if not we can reinstate this REO class)"; "while cultured multicellular organism cells are considered to be experimentally modfied, they are not considered to be cells ex vivo, as 'ex vivo' is conceived of as 'having once been part of an organism', and a given cell culture cell has not at any point in its existence been a part of some organism. Thus, cultured cells stand outside the in vivo/ex vivo split, and are inferred to be experimentally modified cells." . a owl:Class; rdfs:label "experimentally modified multicellular organism cell"; owl:equivalentClass _:2e7c89; rdfs:subClassOf , , _:2e7cc9; owl:disjointWith ; "a multicellular organism cell that is the specified output of an experimental modification technique that introduces physical changes to the cell (ie changes in composition and/or internal structural arrangement)"; "Note in this hierarchy that cultured cells stand outside the in vivo/ex vivo split. This is because, while cell culture cells ARE considered to be experimentally modfied, they ARE NOT considered to be cells ex vivo, as 'ex vivo' is conceived of as 'having once been part of an organism', and a given cell culture cell has not at any point in its existence been a part of some organism." . _:2e7c89 a owl:Class; owl:intersectionOf _:2e7c99 . _:2e7c99 rdf:first ; rdf:rest _:2e7cb9 . _:2e7cb9 rdf:first _:2e7ca9; rdf:rest rdf:nil . _:2e7ca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7cc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "selected multicellular organism cell ex vivo"; rdfs:subClassOf , _:2e7cd9, _:2e7ce9, _:2e7d39, _:2e7d49; "a multicellular organism cell that is output from some in vitro cell selection technique, whereby a subset of cells is separated from some total population of input cells, based on a specified attribute or set of attributes they bear "; rdfs:comment """selection alone is not an experimental modification - it is a contextual change, not a structural change, and thus selected cells need not be experimentally modified. However, some selection processes can involve experimental modification of the input cell population. Thus, selected cell stands outside the modified/unmodified split. Furthermore, while most selection processes occur in vitro, some may occur in vivo or in environment. """ . _:2e7cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7ce9 a owl:Class; owl:complementOf _:2e7cf9 . _:2e7cf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7d09 . _:2e7d09 a owl:Class; owl:unionOf _:2e7d19 . _:2e7d19 rdf:first ; rdf:rest _:2e7d29 . _:2e7d29 rdf:first ; rdf:rest rdf:nil . _:2e7d39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e7d49 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "cell selection technique"; owl:equivalentClass _:2e7d59; rdfs:subClassOf ; rdfs:comment "a material processing technique in which a subset of cells is separated from some total population of input cells, based on a specified attribute or set of attributes they bear " . _:2e7d59 a owl:Class; owl:intersectionOf _:2e7d69 . _:2e7d69 rdf:first ; rdf:rest _:2e7d89 . _:2e7d89 rdf:first _:2e7d79; rdf:rest rdf:nil . _:2e7d79 a owl:Class; owl:intersectionOf _:2e7da9 . _:2e7da9 rdf:first _:2e7d99; rdf:rest _:2e7dc9 . _:2e7d99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7dc9 rdf:first _:2e7db9; rdf:rest rdf:nil . _:2e7db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material selection objective"; rdfs:subClassOf ; "a material processing objective to separate a subset of some collection of material entities away from some total input collection, based on a specified attribute or set of attributes borne by the selected entities, and such that only the selected entities will be used for some subsequent planned process" . a owl:Class; rdfs:label "obsolete_cell selection objective"; rdfs:subClassOf ; "a selection objective to separate a subset of cells from some larger population, based on a specified attribute or set of attributes borne by the selected cells, and such that only the selected cells will be used for some subsequent planned process" . a owl:Class; rdfs:label "selection technique"; owl:equivalentClass _:2e7dd9; rdfs:subClassOf , _:2e7e19; "a material processing technique with the objective to separate a subset of some collection of material entities away from some total input collection, based on a specified attribute or set of attributes borne by the selected entities, and such that only the selected entities will be used for some subsequent planned process" . _:2e7dd9 a owl:Class; owl:intersectionOf _:2e7de9 . _:2e7de9 rdf:first ; rdf:rest _:2e7e09 . _:2e7e09 rdf:first _:2e7df9; rdf:rest rdf:nil . _:2e7df9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7e19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unmodified multicellular organism cell ex vivo"; owl:equivalentClass _:2e7e29; rdfs:subClassOf , ; "unmodified multicellular organism cell in vitro", "direct ex vivo multicellular organism cell"; "while this class is defined based on properties it does not have (an OBO foundry no-no), it does represent a class of cells that researchers are interested in talking about and discovering, and thus we need to implement a class here."; "an unmodified multicellular organism cell that is not part of an organism, but instead part of some controlled artificial environment for use in some investigation." . _:2e7e29 a owl:Class; owl:intersectionOf _:2e7e39 . _:2e7e39 rdf:first ; rdf:rest _:2e7e59 . _:2e7e59 rdf:first _:2e7e49; rdf:rest rdf:nil . _:2e7e49 a owl:Class; owl:complementOf _:2e7e69 . _:2e7e69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e7e79 . _:2e7e79 a owl:Class; owl:unionOf _:2e7e89 . _:2e7e89 rdf:first ; rdf:rest _:2e7e99 . _:2e7e99 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "CD4+ T-cell ex vivo"; rdfs:subClassOf ; . a owl:Class; rdfs:label "transfected cell in vivo"; rdfs:subClassOf , _:2e7ea9, _:2e7eb9; . _:2e7ea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7eb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "passaged unicellular organism culture"; owl:equivalentClass _:2e7ec9; rdfs:subClassOf , , _:2e7f09; "unicellular organism line"; "a unicellular cell culture that has been passaged"; . _:2e7ec9 a owl:Class; owl:intersectionOf _:2e7ed9 . _:2e7ed9 rdf:first ; rdf:rest _:2e7ef9 . _:2e7ef9 rdf:first _:2e7ee9; rdf:rest rdf:nil . _:2e7ee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cancer cell in vivo"; owl:equivalentClass _:2e7f19; rdfs:subClassOf , , , _:2e7f99, _:2e7fa9; "a cell that is the output of some malignant cell transformation process whereby a cell in vivo becomes capable of causing cancer in an organism. Such cells are typically able to proliferate indefinitely if cultured in vitro."; rdfs:comment "Cancer cells are by definition in vivo, as diseases inhere only in the context of an organism. Transfomred cells' include such in vivo cancer cells, as well as in vitro cells that have the characteristics of cancer (such as transformed cell line cells)."; "malignant cell" . _:2e7f19 a owl:Class; owl:intersectionOf _:2e7f29 . _:2e7f29 rdf:first ; rdf:rest _:2e7f49 . _:2e7f49 rdf:first _:2e7f39; rdf:rest rdf:nil . _:2e7f39 a owl:Class; owl:intersectionOf _:2e7f69 . _:2e7f69 rdf:first _:2e7f59; rdf:rest _:2e7f89 . _:2e7f59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7f89 rdf:first _:2e7f79; rdf:rest rdf:nil . _:2e7f79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7f99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e7fa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transformed"; rdfs:subClassOf ; "a cellular quality characterized by the capacity to cause cancer in vivo and proliferate indefinitely and in an uncontrolled/unregulated manner in vitro"; . a owl:Class; rdfs:label "experimentally modified unicellular organism ex environment"; rdfs:subClassOf ; "an experimentally modified unicellular organism that has been removed from its natural environment, and placed in a controlled artificial environment for use in some investigation."; rdfs:comment "cells ex environment differ from cells in vitro in that cells ex environment are formerly part of a natural environment, but removed and placed in a controlled artificial environment for use in some investigation. cells in vitro were not necessarily once part of a natural environment (e.g. cultured cells)"; "experimentally modified single cell organism ex environment" . a owl:Class; rdfs:label "unmodified unicellular organism ex environment"; owl:equivalentClass _:2e7fb9; rdfs:subClassOf , ; "unmodified single cell organism ex environment", "unmodified single cell organism in vitro", "unmodified unicellular organism in vitro", "direct ex environment unicellular organism"; "an unmodified unicellular organism that is not part of a natural environment, but instead part of some controlled artificial environment for use in some investigation." . _:2e7fb9 a owl:Class; owl:intersectionOf _:2e7fc9 . _:2e7fc9 rdf:first ; rdf:rest _:2e7fe9 . _:2e7fe9 rdf:first _:2e7fd9; rdf:rest rdf:nil . _:2e7fd9 a owl:Class; owl:complementOf _:2e7ff9 . _:2e7ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8009 . _:2e8009 a owl:Class; owl:unionOf _:2e8019 . _:2e8019 rdf:first ; rdf:rest _:2e8029 . _:2e8029 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "experimentally modified unicellular organism in environment"; owl:equivalentClass _:2e8039; rdfs:subClassOf , , _:2e8079; "an experimentally modified unicellular organism that is found in a native setting (i.e. in a natural environment, and not re-located by some intentional agent to a controlled artificial setting for use in some investigation or study)"; "experimentally modified single cell organism in environment" . _:2e8039 a owl:Class; owl:intersectionOf _:2e8049 . _:2e8049 rdf:first ; rdf:rest _:2e8069 . _:2e8069 rdf:first _:2e8059; rdf:rest rdf:nil . _:2e8059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cultured biomaterial"; rdfs:subClassOf , _:2e8089; rdfs:comment "Biomaterial cultures include cell, tissue, organ and virus/organism cultures. Culturing cell cultures maintains cellular metabolism, and in most cases growth and proliferation. Tissue/organ culturing maintains core biological processes in the tissue or organ, and in some cases tissue proliferation. Virus and organism culturing maintains whole organism metabolism, and in most cases growth and reproduction."; "a material entity of biological origin (or collection of such entities) that is maintained in vitro in a metabolically active state (ie to ensure maintenance of biological processes typical of the given type of culture)." . _:2e8089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biomaterial culture maintenance"; rdfs:subClassOf , _:2e8099; "a material processing technique that is the collection of all techniques directly involved in maintenance of biomaterial culture in a metabolically active state (ie maintenance of biological processes typical of the given type of culture)."; rdfs:comment "Biomaterial cultures include cell, tissue, organ and virus/organism cultures. Culturing cell cultures maintains cellular metabolism, and in most cases growth and proliferation. Tissue/organ culturing maintains core biological processes in the tissue or organ, and in some cases tissue proliferation. Virus and organism culturing maintains whole organism metabolism, and in most cases growth and reproduction." . _:2e8099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "tissue culture maintenance"; rdfs:subClassOf . a owl:Class; rdfs:label "organism culture maintenance"; rdfs:subClassOf . a owl:Class; rdfs:label "tissue culture"; rdfs:subClassOf . a owl:Class; rdfs:label "virus culture"; rdfs:subClassOf . a owl:Class; rdfs:label "selected passaged unicellular organism culture"; owl:equivalentClass _:2e80a9; rdfs:subClassOf , , _:2e8139, _:2e8179; "a unicellular organism culture that has been passaged, and is the output of some cell culture cell selection technique whereby a specified subset of cells from an input cell culture is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; "selected unicellular organism line"; . _:2e80a9 a owl:Class; owl:intersectionOf _:2e80b9 . _:2e80b9 rdf:first ; rdf:rest _:2e80d9 . _:2e80d9 rdf:first _:2e80c9; rdf:rest _:2e80f9 . _:2e80c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e80f9 rdf:first _:2e80e9; rdf:rest rdf:nil . _:2e80e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8109 . _:2e8109 a owl:Class; owl:unionOf _:2e8119 . _:2e8119 rdf:first ; rdf:rest _:2e8129 . _:2e8129 rdf:first ; rdf:rest rdf:nil . _:2e8139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8149 . _:2e8149 a owl:Class; owl:unionOf _:2e8159 . _:2e8159 rdf:first ; rdf:rest _:2e8169 . _:2e8169 rdf:first ; rdf:rest rdf:nil . _:2e8179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organ culture"; rdfs:subClassOf . a owl:Class; rdfs:label "multicellular organism cell culture"; owl:equivalentClass _:2e8189; rdfs:subClassOf , _:2e8209, _:2e8219; "a cell culture consisting of a population of cells isolated from some multicellular organism, that is maintained over a period of time by culturing in vitro"; """CL, regarding their intended meaning of CL:cell line (CL:0000001), and suitability as a import to replace this ReO class? OBI, regarding their intended meaning of cell line culture and relation to this 'multicellular organism cell culture' ReO class"""; . _:2e8189 a owl:Class; owl:intersectionOf _:2e8199 . _:2e8199 rdf:first ; rdf:rest _:2e81b9 . _:2e81b9 rdf:first _:2e81a9; rdf:rest rdf:nil . _:2e81a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e81c9 . _:2e81c9 a owl:Class; owl:intersectionOf _:2e81d9 . _:2e81d9 rdf:first ; rdf:rest _:2e81f9 . _:2e81f9 rdf:first _:2e81e9; rdf:rest rdf:nil . _:2e81e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8229 . _:2e8229 a owl:Class; owl:intersectionOf _:2e8239 . _:2e8239 rdf:first ; rdf:rest _:2e8259 . _:2e8259 rdf:first _:2e8249; rdf:rest rdf:nil . _:2e8249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "clonal cell line"; owl:equivalentClass _:2e8269; rdfs:subClassOf , , _:2e82a9; "an immortal cell line that derives from a single multicellular organism cell that is isolated from some population of cells, propagated, and immortalized to create a new immortal cell line"; "OBI:clonal cell line"; . _:2e8269 a owl:Class; owl:intersectionOf _:2e8279 . _:2e8279 rdf:first ; rdf:rest _:2e8299 . _:2e8299 rdf:first _:2e8289; rdf:rest rdf:nil . _:2e8289 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2e82a9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "selected cell line"; owl:equivalentClass _:2e82b9; rdfs:subClassOf , , _:2e8329; "an immortal cell line that is the output of some selective cell subculturing or establishing selected cell culture technique, whereby a specified subset of cells from an input immortal cell line or transformed cell collection is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; "Decision at OBI philly workshop - define/model 'selection' such that cloning does not qualitfy as a type of selection . . .. selection implies that some quality or feature is desired in the cells from which the new cell line will form. Cloning does not - but rather specifies only that the new cell line will form from only one cell."; "selected immortal cell line"; . _:2e82b9 a owl:Class; owl:intersectionOf _:2e82c9 . _:2e82c9 rdf:first ; rdf:rest _:2e82e9 . _:2e82e9 rdf:first _:2e82d9; rdf:rest rdf:nil . _:2e82d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e82f9 . _:2e82f9 a owl:Class; owl:unionOf _:2e8309 . _:2e8309 rdf:first ; rdf:rest _:2e8319 . _:2e8319 rdf:first ; rdf:rest rdf:nil . _:2e8329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8339 . _:2e8339 a owl:Class; owl:unionOf _:2e8349 . _:2e8349 rdf:first ; rdf:rest _:2e8359 . _:2e8359 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "passaged mortal cell culture"; owl:equivalentClass _:2e8369; rdfs:subClassOf , , _:2e83a9; owl:disjointWith ; rdfs:comment "note that the alternative term 'cell line' applies only in some communities, where this term is synonymous with any cell culture that has been passaged (as opposed to the more common usage to refer to any cell culture that has been immortalized to grow continuously)"; "secondary cell culture", " cell line"; "a mortal cell culture that has been passaged"; . _:2e8369 a owl:Class; owl:intersectionOf _:2e8379 . _:2e8379 rdf:first ; rdf:rest _:2e8399 . _:2e8399 rdf:first _:2e8389; rdf:rest rdf:nil . _:2e8389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e83a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "selected mortal cell culture"; owl:equivalentClass _:2e83b9; rdfs:subClassOf , , _:2e8429; "a mortal cell culture that is the output of some selective cell subculturing or establishing selected cell culture technique, whereby a specified subset of cells from an input mortal cell culture or biological specimen is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; . _:2e83b9 a owl:Class; owl:intersectionOf _:2e83c9 . _:2e83c9 rdf:first ; rdf:rest _:2e83e9 . _:2e83e9 rdf:first _:2e83d9; rdf:rest rdf:nil . _:2e83d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e83f9 . _:2e83f9 a owl:Class; owl:unionOf _:2e8409 . _:2e8409 rdf:first ; rdf:rest _:2e8419 . _:2e8419 rdf:first ; rdf:rest rdf:nil . _:2e8429 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8439 . _:2e8439 a owl:Class; owl:unionOf _:2e8449 . _:2e8449 rdf:first ; rdf:rest _:2e8459 . _:2e8459 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "selected passaged mortal cell culture"; owl:equivalentClass _:2e8469; rdfs:subClassOf , , _:2e84f9, _:2e8539; "a mortal cell culture that has been both passaged and output from some cell culture cell selection process whereby a specified subset of cells from an input cell culture is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; . _:2e8469 a owl:Class; owl:intersectionOf _:2e8479 . _:2e8479 rdf:first ; rdf:rest _:2e8499 . _:2e8499 rdf:first _:2e8489; rdf:rest _:2e84b9 . _:2e8489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e84b9 rdf:first _:2e84a9; rdf:rest rdf:nil . _:2e84a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e84c9 . _:2e84c9 a owl:Class; owl:unionOf _:2e84d9 . _:2e84d9 rdf:first ; rdf:rest _:2e84e9 . _:2e84e9 rdf:first ; rdf:rest rdf:nil . _:2e84f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8509 . _:2e8509 a owl:Class; owl:unionOf _:2e8519 . _:2e8519 rdf:first ; rdf:rest _:2e8529 . _:2e8529 rdf:first ; rdf:rest rdf:nil . _:2e8539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unpassaged mortal cell culture"; owl:equivalentClass _:2e8549; rdfs:subClassOf , , _:2e8589; "Note that it is possible to have an unpassaged immortal cell line, only in cases where the culture is established from cells transformed in vivo that are immediately capable of long term propagation (ie without undergoing some immortalization technique). "; "primary cell culture"; "a mortal cell culture that has not been passaged"; "OBI and CLO: clarify intended meaning of the classes 'primary cell culture' in OBI and 'primary cell line' and CLO, to see which can be re-used or xrefed here. E.g OBI:primary cell culture may be a xref here, assuming OBI intendes this class to refer to cell cultures that aredirectly taken from a tissue source and not yet passaged."; . _:2e8549 a owl:Class; owl:intersectionOf _:2e8559 . _:2e8559 rdf:first ; rdf:rest _:2e8579 . _:2e8579 rdf:first _:2e8569; rdf:rest rdf:nil . _:2e8569 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2e8589 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "selected cell culture"; owl:equivalentClass _:2e8599; rdfs:subClassOf , _:2e8609; "A drug-resistant HeLa cell line generated through a drug treatment based selection. CD4+ T-cells isolated from a blood specimen through FACS-based selection."; "a cell culture that is the output of some selective cell subculturing or establishing selected cell culture technique, whereby a specified subset of cells from an input cell culture or biological specimen is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; "Example defined class based on a cells having endured a selection process whereby a subpopulation of interest is selectivley propagated. This can include cell cultures deriving from established cultures through a selection process, and also 'de novo' cell culutres whereby freshly isolated cells are selected to seed a 'new' culture. For example, using flow cytometry to select freshly isolated CD4+ T-cells for culture."; . _:2e8599 a owl:Class; owl:intersectionOf _:2e85a9 . _:2e85a9 rdf:first ; rdf:rest _:2e85c9 . _:2e85c9 rdf:first _:2e85b9; rdf:rest rdf:nil . _:2e85b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e85d9 . _:2e85d9 a owl:Class; owl:unionOf _:2e85e9 . _:2e85e9 rdf:first ; rdf:rest _:2e85f9 . _:2e85f9 rdf:first ; rdf:rest rdf:nil . _:2e8609 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8619 . _:2e8619 a owl:Class; owl:unionOf _:2e8629 . _:2e8629 rdf:first ; rdf:rest _:2e8639 . _:2e8639 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "passaged cell culture"; owl:equivalentClass _:2e8649; rdfs:subClassOf , _:2e86c9; "a cell culture that has been passaged"; "cell line"; "Example defined class based on a cell culture having been passaged. In some communities, this constitutes creation of a 'cell line' (where a line is defined as any culture that has been passaged). In other communities however, a 'line' is not considered without some immortalization process to ensure long-term propagation. We provide here the term 'cell line' as an alternative term here for use in those communities considering a passaged culture to be a 'line', but do not advocate the broad use of 'cell line' as a class name given its alternate meanings (a cell culutre that has been passaged, vs a cell culutre that is immortal)"; . _:2e8649 a owl:Class; owl:intersectionOf _:2e8659 . _:2e8659 rdf:first ; rdf:rest _:2e8679 . _:2e8679 rdf:first _:2e8669; rdf:rest rdf:nil . _:2e8669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8689 . _:2e8689 a owl:Class; owl:unionOf _:2e8699 . _:2e8699 rdf:first ; rdf:rest _:2e86b9 . _:2e86b9 rdf:first _:2e86a9; rdf:rest rdf:nil . _:2e86a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e86c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e86d9 . _:2e86d9 a owl:Class; owl:unionOf _:2e86e9 . _:2e86e9 rdf:first ; rdf:rest _:2e8709 . _:2e8709 rdf:first _:2e86f9; rdf:rest rdf:nil . _:2e86f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "selected unicellular organism culture"; owl:equivalentClass _:2e8719; rdfs:subClassOf , , _:2e8789; "a unicellular orgnism culture that is the output of some selective cell subculturing or establishing selected cell culture technique, whereby a specified subset of cells from an input cell culture or biological specimen is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; . _:2e8719 a owl:Class; owl:intersectionOf _:2e8729 . _:2e8729 rdf:first ; rdf:rest _:2e8749 . _:2e8749 rdf:first _:2e8739; rdf:rest rdf:nil . _:2e8739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8759 . _:2e8759 a owl:Class; owl:unionOf _:2e8769 . _:2e8769 rdf:first ; rdf:rest _:2e8779 . _:2e8779 rdf:first ; rdf:rest rdf:nil . _:2e8789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8799 . _:2e8799 a owl:Class; owl:unionOf _:2e87a9 . _:2e87a9 rdf:first ; rdf:rest _:2e87b9 . _:2e87b9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "unpassaged unicellular organism culture"; owl:equivalentClass _:2e87c9; rdfs:subClassOf , , _:2e8809; "Note here that we take unpassaged to be disjoint from passaged and also from selected cells, as the process of cell culture cell selection generally requires paggasing to allow outgrowth of the selected cells into a culture of its own"; "a unicellular organism culture that has not been passaged"; . _:2e87c9 a owl:Class; owl:intersectionOf _:2e87d9 . _:2e87d9 rdf:first ; rdf:rest _:2e87f9 . _:2e87f9 rdf:first _:2e87e9; rdf:rest rdf:nil . _:2e87e9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2e8809 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "information template role"; rdfs:subClassOf , _:2e8819; "a role inhereing in some material information bearer or information macromolecule that is realized through a process in which the information or sequence content of the bearer is copied and becomes encoded in a new material information bearer"; "role inhering in a gene and realized through its trancription to mRNA, or the translation of this mRNA to a protein" . _:2e8819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8829 . _:2e8829 a owl:Class; owl:unionOf _:2e8839 . _:2e8839 rdf:first ; rdf:rest _:2e8849 . _:2e8849 rdf:first ; rdf:rest _:2e8859 . _:2e8859 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "nucleic acid analog"; owl:equivalentClass _:2e8869; rdfs:subClassOf , , _:2e88e9, _:2e88f9, _:2e8909, _:2e8959, _:2e8969; "morpholinos, locked nucleic acids, peptide nucleic acids"; """1. This class is tagged as a primary classification axis because it is necessarily disjoint from DNA and RNA reagents (ie analogs of these nucleic acids are thenselves not considered to be DNA or RNA molecules) 2. Note that nucleic acid analogs are considered to be information macromolecules, as their sequences typically map in a precise way to the sequences of natural nucleic acids. For example, a morpholino is a synthetic oligo that is not a nucleic acid, but it carries sequence information that relates each monomer to some specific nucleic acid or set of nucleic acids, allowing it to bind a nucleic acid an a sequence specific manner."""; "a DNA reagent that is engineered to exhibit structurally similarity to naturally-occurring nucleic acids, such that it maintains some similar chemical properties and activity, while its structural differences allow probing or manipulation of the biochemical environment of the analog"; . _:2e8869 a owl:Class; owl:intersectionOf _:2e8879 . _:2e8879 rdf:first ; rdf:rest _:2e8899 . _:2e8899 rdf:first _:2e8889; rdf:rest rdf:nil . _:2e8889 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e88a9 . _:2e88a9 a owl:Class; owl:intersectionOf _:2e88b9 . _:2e88b9 rdf:first ; rdf:rest _:2e88d9 . _:2e88d9 rdf:first _:2e88c9; rdf:rest rdf:nil . _:2e88c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e88e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e88f9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e8909 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8919 . _:2e8919 a owl:Class; owl:intersectionOf _:2e8929 . _:2e8929 rdf:first ; rdf:rest _:2e8949 . _:2e8949 rdf:first _:2e8939; rdf:rest rdf:nil . _:2e8939 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_information biomacromolecule"; rdfs:subClassOf ; """ChEBI - what is definition here - any sequence molecule is an information molecule? or must it be genetic/genetically derived? or would synthetic molecules like morpholinos qualify? There is no definition for this term in ChEBI, but alt label is 'genetically encoded biomacromolecule/biopolymer', suggesting that such molecules must have actually represent a gene or a gene product that was encoded by a gene. """; "genetic sequence biopolymer/macromolecule, information biopolymer"; """decided not to consider biological origin of these molecules for now, given ambiguity of ChEBI here, and the complexity this brings to the ontology. previous logical definition : 'organic biomacromolecule' and (bearer_of some (is_concretization_of some 'genetic sequence region')))"""; "ChEBI information biomacromolecule? . . . hard to say because there is no definition in ChEBI (see ReO developer note)"; rdfs:comment """This class represents natural or artificial polymers that carry sequence information of a genetic nature (ie, information that is translatale to a nucleic acid sequence in a defined way - such that it can be aligned with or related to or translated into a sequence of nucleic acids). In this sense, in encompasses a broader set of instances than ChEBI 'information biomacromolecule', which could be imported as a subclass of ReO:information macromolecule. So, for ex, a morpholino is a synthetic oligo that is not made of nucleic acids, but it carries sequence information that relates each monomer to some specific nucleic acid or set of nucleic acids, allowing it to bind a nucleic acid an a sequence specific manner. Other examples of 'genetic sequence macromolecules' are other nucleic acid analogs such as locked nucleic acids or peptide nucleic acids, and synthetic primers or peptides, etc.""" . a owl:Class; rdfs:label "obsolete_information molecular entity"; rdfs:subClassOf ; "reworked heirarchy (1-6-12)"; "organic genetic sequence molecular entity, information organic molecular entity? genetic-information organic molecular entity ('information' here is taken to mean genetically encoded information)" . a owl:Class; rdfs:label "information macromolecular complex"; rdfs:subClassOf , _:2e8979; "genetic sequence macromolecular complex, information macromolecular complex?" . _:2e8979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_non-information organic molecular entity"; rdfs:subClassOf ; "reworked heirarchy (1-6-12)" . a owl:Class; rdfs:label "molecular mass"; rdfs:subClassOf , , _:2e8989 . _:2e8989 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "low molecular weight"; rdfs:subClassOf ; rdfs:comment "used to define the 'organic small molecule' class in ReO, whose weight cut off is at 800 daltons or less"; "a chemical mass quality inhereing in a molecular entity with a molecular weight of less than 800 daltons."; . a owl:Class; rdfs:label "obsolete_organic large molecule"; rdfs:subClassOf ; """Not sure if I want to have size based classes as a primary axis for organic molecular entities, as this would require ontology developers and data annotators/curators to know the molecular weight of a given molecular entity before creating a class or annotation, respectively. Also, this seems an arbitray way to classify a hierarchy of molecular entities. Additionally, this could cause a problem if weight is unknown or borderline, and class is placed under the parent class of 'organic molecular entity' . . . because then it wouldn’t classify as a chemical reagent, which would be defined as ('inorganic molecular entity' or 'organic small molecule' or 'non-information organic macromolecule') and has_role some 'reagent role' Consider removing this level and just having information and non-information molecular entities as direct children of 'organic molecular entity', along with 'nucleic acid reagent' and 'organic small molecule' defined classes. Then could change the definition of 'chemical reagent' to ('inorganic molecular entity or non-information molecular entity and (has_role some reagent role))"""; "An organic compound with a large relative molecular mass, including those created by some form of polymerization. " . a owl:Class; rdfs:label "high molecular weight"; rdfs:subClassOf ; rdfs:comment "used to define the 'organic macromolecule' class in ReO, whose weight cut off is at 800 daltons or higher"; "a chemical mass quality inhereing in a molecular entity with a molecular weight of greater than 800 daltons." . a owl:Class; rdfs:label "deoxyribonucleoside triphosphate reagent"; owl:equivalentClass _:2e8999; rdfs:subClassOf , , _:2e89d9; "a nucleoside triphosphate reagent containing three phosphate groups bound to a 2'-deoxyribo- sugar ring"; "dNTP reagent", "dNTPs" . _:2e8999 a owl:Class; owl:intersectionOf _:2e89a9 . _:2e89a9 rdf:first ; rdf:rest _:2e89c9 . _:2e89c9 rdf:first _:2e89b9; rdf:rest rdf:nil . _:2e89b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e89d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_organic large molecule chemical reagent"; rdfs:subClassOf ; "An organic macromolecule that bears a reagent role " . a owl:Class; rdfs:label "metalloid elemental molecule"; rdfs:subClassOf ; "http://en.wikipedia.org/wiki/Metalloid"; "a molecule comprised only of a single type of metalloid atom" . a owl:Class; rdfs:label "DNA oligonucleotide reagent"; owl:equivalentClass _:2e89e9; rdfs:subClassOf , , _:2e8a29, _:2e8ad9; "a DNA reagent consisting of a short, linear string of typically 100 or fewer nucleotides"; "synthetic DNA oligo", "DNA oligo reagent"; "http://en.wikipedia.org/wiki/Oligonucleotide, http://www.operon.com/products/custom_oligos/glossary.aspx" . _:2e89e9 a owl:Class; owl:intersectionOf _:2e89f9 . _:2e89f9 rdf:first ; rdf:rest _:2e8a19 . _:2e8a19 rdf:first _:2e8a09; rdf:rest rdf:nil . _:2e8a09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8a29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8a39 . _:2e8a39 a owl:Class; owl:intersectionOf _:2e8a49 . _:2e8a49 rdf:first ; rdf:rest _:2e8a69 . _:2e8a69 rdf:first _:2e8a59; rdf:rest rdf:nil . _:2e8a59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8a79 . _:2e8a79 a owl:Class; owl:intersectionOf _:2e8a89 . _:2e8a89 rdf:first ; rdf:rest _:2e8aa9 . _:2e8aa9 rdf:first _:2e8a99; rdf:rest _:2e8ac9 . _:2e8a99 a owl:Restriction; owl:onProperty ; owl:hasValue . _:2e8ac9 rdf:first _:2e8ab9; rdf:rest rdf:nil . _:2e8ab9 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . _:2e8ad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA primer reagent"; owl:equivalentClass _:2e8ae9; rdfs:subClassOf , , , _:2e8b29, _:2e8b39; "http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29"; "a DNA oligonucleotide reagent that is applied in a technique (typically PCR) to bind to some complementary nucleic acid template and serve as a starting point for nucleic acid synthesis" . _:2e8ae9 a owl:Class; owl:intersectionOf _:2e8af9 . _:2e8af9 rdf:first ; rdf:rest _:2e8b19 . _:2e8b19 rdf:first _:2e8b09; rdf:rest rdf:nil . _:2e8b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8b29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8b39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA oligonucleotide reagent"; owl:equivalentClass _:2e8b49; rdfs:subClassOf , , _:2e8b89, _:2e8c39; "RNA oligo reagent", "synthetic RNA oligo"; "an RNA reagent consisting of a short, linear string of typically 100 or fewer nucleotides" . _:2e8b49 a owl:Class; owl:intersectionOf _:2e8b59 . _:2e8b59 rdf:first ; rdf:rest _:2e8b79 . _:2e8b79 rdf:first _:2e8b69; rdf:rest rdf:nil . _:2e8b69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8b89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8b99 . _:2e8b99 a owl:Class; owl:intersectionOf _:2e8ba9 . _:2e8ba9 rdf:first ; rdf:rest _:2e8bc9 . _:2e8bc9 rdf:first _:2e8bb9; rdf:rest rdf:nil . _:2e8bb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8bd9 . _:2e8bd9 a owl:Class; owl:intersectionOf _:2e8be9 . _:2e8be9 rdf:first ; rdf:rest _:2e8c09 . _:2e8c09 rdf:first _:2e8bf9; rdf:rest _:2e8c29 . _:2e8bf9 a owl:Restriction; owl:onProperty ; owl:hasValue . _:2e8c29 rdf:first _:2e8c19; rdf:rest rdf:nil . _:2e8c19 a owl:Restriction; owl:onProperty ; owl:cardinality "1"^^xsd:nonNegativeInteger . _:2e8c39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "metalloid elemental molecule reagent"; owl:equivalentClass _:2e8c49; rdfs:subClassOf , , _:2e8c89; "an elemental molecule that is comprised only of a single type of metalloid atom and that bears a reagent role" . _:2e8c49 a owl:Class; owl:intersectionOf _:2e8c59 . _:2e8c59 rdf:first ; rdf:rest _:2e8c79 . _:2e8c79 rdf:first _:2e8c69; rdf:rest rdf:nil . _:2e8c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8c89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "non-metal elemental molecule reagent"; owl:equivalentClass _:2e8c99; rdfs:subClassOf , , _:2e8cd9; "an elemental molecule that is comprised only of a single type of non-metal atom and that bears a reagent role" . _:2e8c99 a owl:Class; owl:intersectionOf _:2e8ca9 . _:2e8ca9 rdf:first ; rdf:rest _:2e8cc9 . _:2e8cc9 rdf:first _:2e8cb9; rdf:rest rdf:nil . _:2e8cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "metal elemental molecule reagent"; owl:equivalentClass _:2e8ce9; rdfs:subClassOf , , _:2e8d29; "an elemental molecule that is comprised only of a single type of metal atom and that bears a reagent role" . _:2e8ce9 a owl:Class; owl:intersectionOf _:2e8cf9 . _:2e8cf9 rdf:first ; rdf:rest _:2e8d19 . _:2e8d19 rdf:first _:2e8d09; rdf:rest rdf:nil . _:2e8d09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8d29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_metal atom"; rdfs:subClassOf ; "replaced by ChEBI metal atom" . a owl:Class; rdfs:label "obsolete_non-metal atom"; rdfs:subClassOf ; "replaced by ChEBI nonmetal atom" . a owl:Class; rdfs:label "metalloid atom"; rdfs:subClassOf . a owl:Class; rdfs:label "metal atomic reagent"; owl:equivalentClass _:2e8d39; rdfs:subClassOf , , _:2e8d79; "a metal atomic molecular entity that bears a reagent role" . _:2e8d39 a owl:Class; owl:intersectionOf _:2e8d49 . _:2e8d49 rdf:first ; rdf:rest _:2e8d69 . _:2e8d69 rdf:first _:2e8d59; rdf:rest rdf:nil . _:2e8d59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8d79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "non-metal atomic reagent"; owl:equivalentClass _:2e8d89; rdfs:subClassOf , , _:2e8dc9; "a non-metal atomic molecular entitu that bears a reagent role" . _:2e8d89 a owl:Class; owl:intersectionOf _:2e8d99 . _:2e8d99 rdf:first ; rdf:rest _:2e8db9 . _:2e8db9 rdf:first _:2e8da9; rdf:rest rdf:nil . _:2e8da9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8dc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "metalloid atomic reagent"; owl:equivalentClass _:2e8dd9; rdfs:subClassOf , , _:2e8e19; "a metalloid atomic molecular entity that bears a reagent role" . _:2e8dd9 a owl:Class; owl:intersectionOf _:2e8de9 . _:2e8de9 rdf:first ; rdf:rest _:2e8e09 . _:2e8e09 rdf:first _:2e8df9; rdf:rest rdf:nil . _:2e8df9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8e19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_polynucleotide"; rdfs:subClassOf ; "molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain"; "http://en.wikipedia.org/wiki/Polynucleotide" . a owl:Class; rdfs:label "obsolete_peptide nucleic acid"; rdfs:subClassOf ; "http://en.wikipedia.org/wiki/Peptide_nucleic_acid"; "a nucleic acid analog wherein the ribose-sugar backbone of DNA and RNA is replaced by a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The various purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds."; "replaced with chEBI class"; rdfs:comment "The name is somewhat of a misnomer as PNA is not an acid. Synthetic peptide nucleic acid oligomers have been used in recent years in molecular biology procedures, diagnostic assays and antisense therapies. Due to their higher binding strength it is not necessary to design long PNA oligomers for use in these roles, which usually require oligonucleotide probes of 20–25 bases"; "PNA" . a owl:Class; rdfs:label "LNA nucleotide"; rdfs:subClassOf ; rdfs:comment "These monomers are used to chemically synthesize complete LNA oligomers wherein the locked ribose conformation enhances base stacking and backbone pre-organization. This significantly increases the hybridization properties (melting temperature) of oligonucleotides. LNA nucleotides can also be mixed with natural DNA or RNA monomers wihtin a single oligonucleotide."; "locked nucleic acid nucleotide"; "http://en.wikipedia.org/wiki/Locked_nucleic_acid"; "a modified RNA nucleotide wherein ribose moiety is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge \"locks\" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. LNA nucleotides can be mixed with DNA or RNA residues in the oligonucleotide whenever desired." . a owl:Class; rdfs:label "bioactive"; rdfs:subClassOf ; rdfs:comment "a disposition to interact with, be processed by, or affect the function or activity of one or more biological molecules in the context of a cell, tissue, or organism" . a owl:Class; rdfs:label "bioactive molecular entity"; owl:equivalentClass _:2e8e29; rdfs:subClassOf , _:2e8e69; "a molecular entity thatbears a disposition to interact with, be processed by, or affect the function or activity of one or more biological molecules in the context of a cell, tissue, or organism" . _:2e8e29 a owl:Class; owl:intersectionOf _:2e8e39 . _:2e8e39 rdf:first ; rdf:rest _:2e8e59 . _:2e8e59 rdf:first _:2e8e49; rdf:rest rdf:nil . _:2e8e49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8e69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_polysaccharide"; rdfs:subClassOf ; "replaced with ChEBI:polysaccharide" . a owl:Class; rdfs:label "polysaccharide reagent"; owl:equivalentClass _:2e8e79; rdfs:subClassOf , , _:2e8eb9; rdfs:comment "This term is commonly used only for those containing more than ten monosaccharide residues, but here we include even di- or tri-saccharides as polysaccharides so as not to have to enforce some arbitrary cutoff."; "An organic macromolecule chemical reagent that is a polysaccharide consisting of monosaccharide residues linked glycosidically. " . _:2e8e79 a owl:Class; owl:intersectionOf _:2e8e89 . _:2e8e89 rdf:first ; rdf:rest _:2e8ea9 . _:2e8ea9 rdf:first _:2e8e99; rdf:rest rdf:nil . _:2e8e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8eb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_lipid small molecule"; rdfs:subClassOf ; """decided to forgo the lipid small vs macromolecule classification scheme, and use the hydrocarbon vs simple vs complex subclassing approach. But can always revert to the other way of doing it). note that one consequence of this is that lipid and lipid reagent become organic small molecules and organic small molecule reagents, respectively, which may not be intuitive to consider larger lipids to be small molecules."""; "a lipid that does not contain a long hydrocarbon chain comprised primarily of a repeating carbon backbone saturted with bonds to hydrogen, or unsaturated and containing C=C double bonds. Examples include steroids such as cholesterol."; . a owl:Class; rdfs:label "protein enzyme"; owl:equivalentClass _:2e8ec9; rdfs:subClassOf , _:2e8f09; "protein enzyme class from appropriate ontology (PRO?, chebi?)"; . _:2e8ec9 a owl:Class; owl:intersectionOf _:2e8ed9 . _:2e8ed9 rdf:first ; rdf:rest _:2e8ef9 . _:2e8ef9 rdf:first _:2e8ee9; rdf:rest rdf:nil . _:2e8ee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organic small molecule"; rdfs:subClassOf , , _:2e8f19, _:2e8f59, _:2e8f69; "http://en.wikipedia.org/wiki/Small_molecule"; "An organic small molecule is an organic molecule of low molecular weight, which is by definition not a polymer, and can interact with and affect the function or activity of one or more biological molecules in the context of a cell, tissue, or organism."; rdfs:comment "In ReO, we consider the concept of 'small molecules' broadly to include all organic molecules that are not macromolecules (ie not polypeptides, polynucleotides, or carbohydrates). Conventionally, the term 'small molecule' is usually restricted to a molecule that interact in some way with biological macromolecules - ie binds with high affinity a biopolymer such as protein, nucleic acid, or polysaccharide and alters the activity or function of the biopolymer. The conventional upper molecular weight limit for a small molecule is approximately 800 Daltons."; "organic bioactive small molecule" . _:2e8f19 a owl:Class; owl:complementOf _:2e8f29 . _:2e8f29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8f39 . _:2e8f39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e8f49 . _:2e8f49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8f59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8f69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organic small molecule reagent"; owl:equivalentClass _:2e8f79; rdfs:subClassOf , , _:2e8fb9; "small molecule reagent", "organic bioactive small molecule reagent", "organic small molecule chemical reagent", "bioactive small molecule reagent"; """1. In ReO, we consider the concept of 'small molecules' broadly to include all organic molecules that are not macromolecules (ie not polypeptides, polynucleotides, or carbohydrates). Conventionally, the term 'small molecule' is usually restricted to a molecule that interact in some way with biological macromolecules (ie. are 'bioactive'), binding with high affinity a biopolymer such as protein, nucleic acid, or polysaccharide, often in such a way as to alter the activity or function of the biopolymer. The conventional upper molecular weight limit for a small molecule is approximately 800 Daltons, although no such restriction is made in ReO. 2. While most definitions of 'small molecule' state that they are 'not polymers', allowance is often made for very short peptides or nucleic acids (e.g. dinucleotides or short peptides such as glutathione). However, in ReO we prioritize a clear distinction between macro- and small molecuese, and between molecules that carry genetic information and those that do not. Thus we consider small peptides or oligos to be macromolecules and NOT small molecule reagents (this includes examples such as the tri-peptide glutathione, which is technically not encoded in the genome, but synthesized chemically/directly from its constituent amino acids)."""; "Alexafluors, DAPI stain, biotin, acetone, cycloheximide, genticin, dNTPs, amino acids, cholesterol, phospholipids"; "http://en.wikipedia.org/wiki/Small_molecule"; "an organic molecular reagent of low molecular weight, which is by definition not a polymer, and can interact with and affect the function or activity of one or more biological molecules in the context of a cell, tissue, or organism."; . _:2e8f79 a owl:Class; owl:intersectionOf _:2e8f89 . _:2e8f89 rdf:first ; rdf:rest _:2e8fa9 . _:2e8fa9 rdf:first _:2e8f99; rdf:rest rdf:nil . _:2e8f99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e8fb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA primer reagent"; owl:equivalentClass _:2e8fc9; rdfs:subClassOf , , , _:2e9009, _:2e9019; "an RNA oligonucleotide reagent that is applied in a technique (typically PCR) to bind to some complementary nucleic acid template and serve as a starting point for nucleic acid synthesiss." . _:2e8fc9 a owl:Class; owl:intersectionOf _:2e8fd9 . _:2e8fd9 rdf:first ; rdf:rest _:2e8ff9 . _:2e8ff9 rdf:first _:2e8fe9; rdf:rest rdf:nil . _:2e8fe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_primer role"; rdfs:subClassOf ; "replaced by OBI primer role"; rdfs:comment "a role palyed by oligonucleotides that seed the polymerase-driven replication of a nucleic acid molecule." . a owl:Class; rdfs:label "obsolete_chemical entity"; rdfs:subClassOf ; "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances."; "replaced by ChEBI:chemical entity" . a owl:Class; rdfs:label "obsolete_chemical substance"; rdfs:subClassOf ; "A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types" . a owl:Class; rdfs:label "obsolete_group"; rdfs:subClassOf ; "obsolete_chemical group"; "A defined linked collection of atoms or a single atom within a molecular entity" . a owl:Class; rdfs:subClassOf ; "obsolete_chemical mixture"; "A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind." . a owl:Class; rdfs:subClassOf ; "obsolete_pure chemical substance"; "A pure substance is a chemical substance composed of multiple molecules, which are all of the same kind" . a owl:Class; rdfs:subClassOf ; "replaced by ChEBI:organic group"; "obsolete_organic chemical group" . a owl:Class; rdfs:subClassOf ; "obsolte_inorganic chemical group"; "replaced by ChEBI:inorganic group" . a owl:Class; rdfs:label "monomeric residue"; owl:equivalentClass _:2e9029; rdfs:subClassOf , _:2e9069; "macromolecule residue", "polymer residue"; "An alanine residue is a monomeric residue that is a monomeric part of a polypeptide, and derives_from/ is_substituent_group_from an alanine molecular entity (monomer)"; "a organic chemical group that represents a monomeric subunit of some organic macromolecule (nucleic acid, polypeptide, or polysaccharide), and derives from (ChEBI:is_substituent_group_from) some molecular entity representing a free-standing monomer." . _:2e9029 a owl:Class; owl:intersectionOf _:2e9039 . _:2e9039 rdf:first ; rdf:rest _:2e9059 . _:2e9059 rdf:first _:2e9049; rdf:rest rdf:nil . _:2e9049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "ribonucleoside triphosphate reagent"; owl:equivalentClass _:2e9079; rdfs:subClassOf , , _:2e90b9; "a nucleoside triphosphate reagent containing three phosphate groups bound to a ribose sugar ring"; "NTP reagent" . _:2e9079 a owl:Class; owl:intersectionOf _:2e9089 . _:2e9089 rdf:first ; rdf:rest _:2e90a9 . _:2e90a9 rdf:first _:2e9099; rdf:rest rdf:nil . _:2e9099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e90b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleoside triphosphate reagent"; owl:equivalentClass _:2e90c9; rdfs:subClassOf , , , _:2e9109; "NTP reagent"; "a nucleobasic reagent that is a nucleoside containing three phosphate groups bound to its sugar ring" . _:2e90c9 a owl:Class; owl:intersectionOf _:2e90d9 . _:2e90d9 rdf:first ; rdf:rest _:2e90f9 . _:2e90f9 rdf:first _:2e90e9; rdf:rest rdf:nil . _:2e90e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_modified amino acid residue"; rdfs:subClassOf . a owl:Class; rdfs:label "unmodified amino acid residue"; rdfs:subClassOf . a owl:Class; rdfs:label "organic macromolecule"; owl:equivalentClass _:2e9119; rdfs:subClassOf , _:2e9179, _:2e9189; """ChEBI: 4-11-12 Note that for now we are leaving out the notion of bio____. (e.g. biomacromolecule), as the current definition of biomacromolecule in ChEBI is vague, reading 'any macromolecule formed by a living organism' - but it is not clear if this means literally produced in an organism, or 'of a type' that is produced in an organism. Need to ask ChEBI about this. Esp since they have things like 'locked nucleic acid' and 'peptide nucleic acid' as children - and these are artificial/synthetic moelcules. For now, I can create a qualities 'biological' (of a type produced in a living organism) and 'biologically produced'/endogenously-derived' (literally produced by a living organism), ans use these in axioms to capture this aspect/dimension of molecules or other materials."""; rdfs:comment "Note that key to the definition here is being comprised or repetition of some monomeric building block, and not any specific size constraint. As a result, ReO would consider even a di-peptide or di-nucleotide to be a macromolecule."; "An organic molecular entity whose structure essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass (ie polymerization). As a result, macromolecules typically display a high molecular mass (relative to small molecules)."; "IUPAC - http://goldbook.iupac.org/M03667.html"; "organic polymer"; "DNA, RNA, proteins, peptides, polysaccharides. Long chain lipids with repeating hydrocarbon moieties are not considered macromolecules in ReO." . _:2e9119 a owl:Class; owl:intersectionOf _:2e9129 . _:2e9129 rdf:first ; rdf:rest _:2e9149 . _:2e9149 rdf:first _:2e9139; rdf:rest _:2e9169 . _:2e9139 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2e9169 rdf:first _:2e9159; rdf:rest rdf:nil . _:2e9159 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e9179 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2e9189 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "obsolete_bioactive organic small molecule"; rdfs:subClassOf ; "merged with orgaic small molecule" . a owl:Class; rdfs:label "antibody production"; rdfs:subClassOf , _:2e9199, _:2e91a9, _:2e91b9, _:2e9209; "antibody creation", "antibody manufacturing"; "a material processing technique with the goal of generating antibody reagents for applicaiton in some scientific technique. This is a multi-step process that requires immunization of some organism to activate the adaptive immune response, and collection of antibodies either from the immunized organism directly, of from hybridoma cells that are generated by fusing activated B-cells from the immunized organism with myeloma cells" . _:2e9199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e91a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e91b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e91c9 . _:2e91c9 a owl:Class; owl:intersectionOf _:2e91d9 . _:2e91d9 rdf:first ; rdf:rest _:2e91f9 . _:2e91f9 rdf:first _:2e91e9; rdf:rest rdf:nil . _:2e91e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_organic polymer"; rdfs:subClassOf ; "decided that macromolecule would be synonymous with polymer - according to ChEBI and IUPAC defs. " . a owl:Class; rdfs:label "obsolete_organic biomacromolecule"; rdfs:subClassOf ; "organic biopolymer, biomacromolecule, biopolymer"; "ChEBI (it is unclear what ChEBI means by 'biomacromolecule' - def is 'a macromolecule formed by a living organism' - but we want to interpret this as 'a macromolecule OF A TYPE formed in a living organism' - so that things like synthetic peptides and PCR products will qualify. Need to ask ChEBI about this. Esp since they have things like 'locked nucleic acid' and 'peptide nucleic acid' as children - and these are artificial/synthetic moelcules.)"; "an organic macromolecule that is of a type formed in a living organism (includes polynucleotides such as nucelic acids, amino acid chains such as proteins and peptides, carbohydrates, and lipid macromolecules such as fatty acids). "; """decided not to consider biological origin of these molecules for now, given ambiguity of ChEBI here, and the complexity this brings to the ontology. previous logical definition : 'organic macromolecule' and (has_quality some biological)"""; rdfs:comment "includes polynucleotides formed in vivo, by PCR, through synthetic chemistry, and likewise includes polypeptides fromed in vivo thruogh ribosomal translation, or in vitro through techniques like chemical peptide synthesis)" . a owl:Class; rdfs:label "obsolete_organic non-biological polymer"; rdfs:subClassOf ; "organic non-biological macromolecule"; "decided to remove the bioological vs non biological distinction"; rdfs:comment """synthetic, non-biological polymers include synthetic rubber, Bakelite, neoprene, nylon, PVC, polystyrene, polyethylene, polypropylene, polyacrylonitrile, PVB, silicone, and many more. Certain synthetic organic polymers are of interest in biological research because they are associated with carcinogenic additives, such as BPA.""" . a owl:Class; rdfs:label "organic molecular complex"; rdfs:subClassOf . a owl:Class; rdfs:label "organic macromolecular complex"; rdfs:subClassOf . a owl:Class; rdfs:label "monoclonal antibody production"; rdfs:subClassOf , , _:2e9219, _:2e9229, _:2e92b9 . _:2e9219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9229 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9239 . _:2e9239 a owl:Class; owl:intersectionOf _:2e9249 . _:2e9249 rdf:first ; rdf:rest _:2e9269 . _:2e9269 rdf:first _:2e9259; rdf:rest rdf:nil . _:2e9259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9279 . _:2e9279 a owl:Class; owl:intersectionOf _:2e9289 . _:2e9289 rdf:first ; rdf:rest _:2e92a9 . _:2e92a9 rdf:first _:2e9299; rdf:rest rdf:nil . _:2e9299 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e92b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e92c9 . _:2e92c9 a owl:Class; owl:intersectionOf _:2e92d9 . _:2e92d9 rdf:first ; rdf:rest _:2e92f9 . _:2e92f9 rdf:first _:2e92e9; rdf:rest rdf:nil . _:2e92e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_non-information biomacromolecule"; rdfs:subClassOf ; """decided not to consider biological origin of these molecules for now, given ambiguity of ChEBI here, and the complexity this brings to the ontology. previous logical definition : 'organic biomacromolecule' and (not (bearer_of some (is_concretization_of some 'genetic sequence region')))"""; "non-information biopolymer" . a owl:Class; rdfs:label "non-information macromolecular complex"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_lipid macromolecule"; rdfs:subClassOf ; """decided to forgo the lipid small vs macromolecule classification scheme, and use the hydrocarbon vs simple vs complex subclassing approach. But can always revert to the other way of doing it). note that one consequence of this is that lipid and lipid reagent become organic small molecules and organic small molecule reagents, respectively, which may not be intuitive to consider larger lipids to be small molecules."""; "a lipid that contains one or more long hydrocarbon chains, comprised primarily of a repeating carbon backbone saturted with bonds to hydrogen, or unsaturated and containing C=C double bonds. While technincally not macromolecules in the sense that they are not polymers comprised of repeating monomeric subunits, the repeating structure in the hydrocarbon chain resembles this feature of macromolecules."; . a owl:Class; rdfs:label "ontology class role"; owl:equivalentClass _:2e9309; rdfs:subClassOf ; "replaced with OBI/IAO curation status specification (ie used the has curation status annotation property to link classes and axioms to the individuals I defined to indicate class purpose or curation specification . . . ie the status of a class or axiom and/or what shoulld be done with it (upon release)"; "data about an ontology class that indicates the role of a given class from an ontological perspective, as representing the primary or secondary axis of classification, or its reason for inclusion in the ontology, as an example of the types of defined classes that ReO can be used to create, or an example of a more granular class that ReO can accommodate." . _:2e9309 a owl:Class; owl:oneOf _:2e9319 . _:2e9319 rdf:first ; rdf:rest _:2e9329 . _:2e9329 rdf:first ; rdf:rest _:2e9339 . _:2e9339 rdf:first ; rdf:rest _:2e9349 . _:2e9349 rdf:first ; rdf:rest _:2e9359 . _:2e9359 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "obsoelte_cell specimen collection"; rdfs:subClassOf ; "OBI (clarify that they intend their cell specimen class to refer to a collection of cells, and only multicellular orgnism cells)"; """not needed. had eq class axiom: material_entity and ('has grain' some (cell and ('has role' some 'specimen role')))"""; "OBI:cell specimen? (although the def of this OBI class seems to be specific for multicellular organism cells)"; . a owl:Class; rdfs:label "unpassaged cell culture"; owl:equivalentClass _:2e9369; rdfs:subClassOf , _:2e93a9; "a cell culture that is freshly isolated and yet to be passaged"; "Here we provide 'primary cell culture' as an alternative term, as in some communities 'primary' is associated with cultures that have not been passaged. However in other circles, 'primary' refers to mortal cell cultures that can be passaged but are not immortal. Thus, we recommend avoiding broad use of the label 'primary' for cell cultures. "; "primary cell culture"; "OBI and CLO: clarify intended meaning of the classes 'primary cell culture' in OBI and 'primary cell line' and CLO, to see which can be re-used or xrefed here. E.g OBI:primary cell culture may be a xref here, assuming OBI intendes this class to refer to cell cultures that are directly taken from a tissue source and not yet passaged."; ; . _:2e9369 a owl:Class; owl:intersectionOf _:2e9379 . _:2e9379 rdf:first ; rdf:rest _:2e9399 . _:2e9399 rdf:first _:2e9389; rdf:rest rdf:nil . _:2e9389 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2e93a9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "hybridization function"; rdfs:subClassOf , _:2e93b9; "a molecular binding function inhereing in a nucleic acid and realized in the non-covalent, sequence-specific interaction between the bearer and a complementary strands of nucleic acid to form a single hybrid, which in the case of two strands is referred to as a duplex."; rdfs:comment "this function is used in ReO as inhering in chemically synthesized oligonucleotides that are used in experimetnal applicaitons such as PCR and DNA sequencing" . _:2e93b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e93c9 a owl:Axiom; "testing this design pattern for relating functions to dispositions they exploit"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e93d9 . _:2e93d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleic acid synthesis"; owl:equivalentClass _:2e93e9; rdfs:subClassOf , _:2e9429, _:2e9439; "a molecular synthesis technique whereby a nucleic acid is constructed from simpler chemical entities, typically individual nucleotide monomers" . _:2e93e9 a owl:Class; owl:intersectionOf _:2e93f9 . _:2e93f9 rdf:first ; rdf:rest _:2e9419 . _:2e9419 rdf:first _:2e9409; rdf:rest rdf:nil . _:2e9409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9429 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9449 a owl:Axiom; "not sure this is required - if fusing two oligos qualifies as nucleic acid synthesis, then this axiom is not valid"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e9459 . _:2e9459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "target of structural rearrangement role"; rdfs:subClassOf , _:2e9469; "a role realized by a planned process in which the bearer is physically modified through the structural re-arrangement of its existing components. No new material is physically associated with the bearer, and no material is removed from the bearer in this process (ie no net gain or loss of matter)."; "One example might be a point mutation sequence alteration - where the target cell (or perhaps its material genome) that is intended to undergo a directed point mutation of one or more residues would bear a 'target of structural rearrangement role' realized by some 'genetic modification technique'." . _:2e9469 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9479 . _:2e9479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_synthesis"; rdfs:subClassOf ; "decided not needed for now"; "should ultimtely live in OBI?"; "a manufacturing process whereby an output material entity is constructed from a set of simpler input material entities" . a owl:Class; rdfs:label "chemical nucleic acid synthesis"; rdfs:subClassOf . a owl:Class; rdfs:label "amino acid analog"; owl:equivalentClass _:2e9489; rdfs:subClassOf , , , _:2e9529, _:2e9579, _:2e9589; rdfs:comment "Note that such molecules are not always amino acids themselves, in cases where the structural modifications made in creating the analog disrupt the amine or carboxyl functional groups that are required to be amino acids. Most alterations, however, target the amino acid side chain, and thus most amino acid analogs qualify as amino acids."; "This class is tagged as a secondary classificaiton axis because it is not necessarily disjoint from non-canonical amino acid reagent (ie amino acid analogs can include molecules that cornform to the definition of an amino acid but are artificially engineered to serve as analogs, and also molecules that are not amino acids at all but are designed to mimic them as analogs)"; "L-Photo-Leucine and L-Photo-Methionine are analogs of L-Leucine and L-Methionine amino acids that can be endogenously incorporated into the primary sequence of proteins during synthesis and then ultraviolet light (UV)-activated to covalently crosslink proteins within protein-protein interaction domains in their native environment within live cells. (http://www.piercenet.com/browse.cfm?fldID=65A33F64-3AE8-4C6F-BA56-B791075902B7)"; "an amino acid reagent that is an artificial organic small molecule designed to exhibit structural similarity to some other (typically naturally occurring) amino acid, but exhibit functional differences such that it can be applied to mimic this natural amino acid and facilitate probing of its surrounding biochemical environment."; . _:2e9489 a owl:Class; owl:intersectionOf _:2e9499 . _:2e9499 rdf:first ; rdf:rest _:2e94b9 . _:2e94b9 rdf:first _:2e94a9; rdf:rest _:2e9519 . _:2e94a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e94c9 . _:2e94c9 a owl:Class; owl:intersectionOf _:2e94d9 . _:2e94d9 rdf:first ; rdf:rest _:2e94f9 . _:2e94f9 rdf:first _:2e94e9; rdf:rest rdf:nil . _:2e94e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9519 rdf:first _:2e9509; rdf:rest rdf:nil . _:2e9509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9539 . _:2e9539 a owl:Class; owl:intersectionOf _:2e9549 . _:2e9549 rdf:first ; rdf:rest _:2e9569 . _:2e9569 rdf:first _:2e9559; rdf:rest rdf:nil . _:2e9559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleotide analog"; owl:equivalentClass _:2e9599; rdfs:subClassOf , , _:2e9639, _:2e9689; "an organic small molecule reagent that is engineered to exhibit structurally similarity to some natural nucleotide, such that it maintains some similar chemical properties and activity, while its structural differences allow probing or manipulation of the biochemical environment of the analog"; "unnatural nucleotide"; . _:2e9599 a owl:Class; owl:intersectionOf _:2e95a9 . _:2e95a9 rdf:first ; rdf:rest _:2e95c9 . _:2e95c9 rdf:first _:2e95b9; rdf:rest _:2e9629 . _:2e95b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e95d9 . _:2e95d9 a owl:Class; owl:intersectionOf _:2e95e9 . _:2e95e9 rdf:first ; rdf:rest _:2e9609 . _:2e9609 rdf:first _:2e95f9; rdf:rest rdf:nil . _:2e95f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9629 rdf:first _:2e9619; rdf:rest rdf:nil . _:2e9619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9639 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9649 . _:2e9649 a owl:Class; owl:intersectionOf _:2e9659 . _:2e9659 rdf:first ; rdf:rest _:2e9679 . _:2e9679 rdf:first _:2e9669; rdf:rest rdf:nil . _:2e9669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleoside analog"; owl:equivalentClass _:2e9699; rdfs:subClassOf , , _:2e9739, _:2e9789; "unnatural nucleoside"; "an organic small molecule reagent that is engineered to exhibit structurally similarity to some natural nucleoside, such that it maintains some similar chemical properties and activity, while its structural differences allow probing or manipulation of the biochemical environment of the analog"; . _:2e9699 a owl:Class; owl:intersectionOf _:2e96a9 . _:2e96a9 rdf:first ; rdf:rest _:2e96c9 . _:2e96c9 rdf:first _:2e96b9; rdf:rest _:2e9729 . _:2e96b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e96d9 . _:2e96d9 a owl:Class; owl:intersectionOf _:2e96e9 . _:2e96e9 rdf:first ; rdf:rest _:2e9709 . _:2e9709 rdf:first _:2e96f9; rdf:rest rdf:nil . _:2e96f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9729 rdf:first _:2e9719; rdf:rest rdf:nil . _:2e9719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9749 . _:2e9749 a owl:Class; owl:intersectionOf _:2e9759 . _:2e9759 rdf:first ; rdf:rest _:2e9779 . _:2e9779 rdf:first _:2e9769; rdf:rest rdf:nil . _:2e9769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "modified nucleotide"; rdfs:subClassOf ; "nucleotide derivative, nucleotide natural derivative" . a owl:Class; rdfs:label "modified nucleoside"; rdfs:subClassOf ; "nucleoside derivative" . a owl:Class; rdfs:label "enzymatic nucleic acid synthesis"; rdfs:subClassOf ; "OBI:enzymatic amplification (confirm first that this class has intended meaning - although its def and subclasses suggest it does refer to nucelic acid synthetic processes)" . a owl:Class; rdfs:label "polymerase chain reaction"; rdfs:subClassOf , _:2e9799; "OBI:polymerase chain reaction"; "PCR" . _:2e9799 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "value specification"; rdfs:subClassOf ; """OBI (discuss distinction I am making (with unit labels and with value specification vs measurement data ICEs and with related object properties as well) between measured and specified data) (and consider if this could be a sibling of setting datum, under data item, rather than a directive ICE. If so, could change label to specified value data?)"""; . a owl:Class; rdfs:label "scalar value specification"; rdfs:subClassOf ; . a owl:Class; rdfs:label "protein enzyme reagent"; owl:equivalentClass _:2e97a9; rdfs:subClassOf , , _:2e97e9; "An example protein reagent class defined by bearing a molecular function (catalytic activity)."; "a protein reagent that bears catalytic activity, and is used to catalyze a chemical reaction as part of some scientific technique "; . _:2e97a9 a owl:Class; owl:intersectionOf _:2e97b9 . _:2e97b9 rdf:first ; rdf:rest _:2e97d9 . _:2e97d9 rdf:first _:2e97c9; rdf:rest rdf:nil . _:2e97c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e97e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polyclonal antibody production"; rdfs:subClassOf , , _:2e97f9, _:2e9849 . _:2e97f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9809 . _:2e9809 a owl:Class; owl:intersectionOf _:2e9819 . _:2e9819 rdf:first ; rdf:rest _:2e9839 . _:2e9839 rdf:first _:2e9829; rdf:rest rdf:nil . _:2e9829 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9859 . _:2e9859 a owl:Class; owl:intersectionOf _:2e9869 . _:2e9869 rdf:first ; rdf:rest _:2e9889 . _:2e9889 rdf:first _:2e9879; rdf:rest rdf:nil . _:2e9879 a owl:Class; owl:intersectionOf _:2e98a9 . _:2e98a9 rdf:first _:2e9899; rdf:rest _:2e9909 . _:2e9899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e98b9 . _:2e98b9 a owl:Class; owl:intersectionOf _:2e98c9 . _:2e98c9 rdf:first ; rdf:rest _:2e98e9 . _:2e98e9 rdf:first _:2e98d9; rdf:rest rdf:nil . _:2e98d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9909 rdf:first _:2e98f9; rdf:rest rdf:nil . _:2e98f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9919 . _:2e9919 a owl:Class; owl:intersectionOf _:2e9929 . _:2e9929 rdf:first ; rdf:rest _:2e9949 . _:2e9949 rdf:first _:2e9939; rdf:rest rdf:nil . _:2e9939 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9959 a owl:Axiom; """previos axiom: has_proper_part some ('specimen collection from organism' and (has_specified_output some ('portion of organism substance' and (has_proper_part some 'polyclonal antibody'))))"""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e9969 . _:2e9969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9979 . _:2e9979 a owl:Class; owl:intersectionOf _:2e9989 . _:2e9989 rdf:first ; rdf:rest _:2e99a9 . _:2e99a9 rdf:first _:2e9999; rdf:rest rdf:nil . _:2e9999 a owl:Class; owl:intersectionOf _:2e99c9 . _:2e99c9 rdf:first _:2e99b9; rdf:rest _:2e9a29 . _:2e99b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e99d9 . _:2e99d9 a owl:Class; owl:intersectionOf _:2e99e9 . _:2e99e9 rdf:first ; rdf:rest _:2e9a09 . _:2e9a09 rdf:first _:2e99f9; rdf:rest rdf:nil . _:2e99f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9a29 rdf:first _:2e9a19; rdf:rest rdf:nil . _:2e9a19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9a39 . _:2e9a39 a owl:Class; owl:intersectionOf _:2e9a49 . _:2e9a49 rdf:first ; rdf:rest _:2e9a69 . _:2e9a69 rdf:first _:2e9a59; rdf:rest rdf:nil . _:2e9a59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "monoclonal antibody"; owl:equivalentClass _:2e9a79; rdfs:subClassOf , , _:2e9ab9, _:2e9ac9, _:2e9ad9, _:2e9ae9; "Note that because I consider this reagent to be a molecular entity, it bears no intrinsic quality or attribute that sets it apart from a polyclonal antibody reagent. The difference is one of origination/process used to create the antibody. If the reagent was considered to be the collection of antibodies in a tube (as ERO has done), then we could say that the difference between monoclonal and polyclonal was that the former has_grain only one type of molecule, vs the latter consisting of many different types of antibodies."; "An mouse anti-human Mad4 antibody."; rdfs:comment "In practice, the notion of a monoclonal antibody is considered from the perspective of a collection of individual antibody complexes, each of which recognizes the same epitope, such that this colleciton is considered 'monospecific'. This feature results from the mode of their production using hybridoma cells, which derive from a single B-cell that produces one species of antibody that is specific to a single immunogenic epitope. However at the structural level of an individual molecule, there is no physical distinction between an individual monoclonal antibody and an individual polyclonal antibody."; "An antibody reagent produced by clonal hybridoma cells deriving from the fusion of a single activasted B-cell with a neoplastic cell, such that antibodies isolated from such cells are monospecific for a single epitope. A collection of such antibodies has specificity for a single epitopes on its target antigen - versus a collection of 'polyclonal antibodies', which recognize various different epitopes. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies."; "monoclonal antibody reagent" . _:2e9a79 a owl:Class; owl:intersectionOf _:2e9a89 . _:2e9a89 rdf:first ; rdf:rest _:2e9aa9 . _:2e9aa9 rdf:first _:2e9a99; rdf:rest rdf:nil . _:2e9a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ac9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ae9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9af9 a owl:Axiom; "note that this axiom will allow for reasoner to infer that a monoclonal antibody derives from some organism (because derives from is transitive, and I made a property chain that says derives_from o part_of -> derives_from)"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e9b09 . _:2e9b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polyclonal antibody"; rdfs:subClassOf , _:2e9b19, _:2e9b59, _:2e9b69; "A rabbit anti-human SHH antibody."; "Note that because I consider this reagent to be a molecular entity, it bears no intrinsic quality or attribute that sets it apart from a monoclonal antibody reagent. The difference is one of origination/process used to create the antibody. If the reagent was considered to be the collection of antibodies in a tube (as ERO has done), then we could say that the difference between monoclonal and polyclonal was that the former has_grain only one type of molecule, vs the latter consisting of many different types of antibodies."; "polyclonal antibody reagent"; "an antibody reagent that is output from an antibody production process that yields a heterogenous collection of antibodies that are not mono-specific (ie individual antibodies in the collection may recognize different epitopes becasue they arise from more than one clone of B-lymphocyte cells). Polyclonal antibodies are typically manufactured through an antibody production technique in which a host organism is immunized with a specific immunogen and antibodies purified from serum collected following the induced immune response. A collection of such antibodies has specificity for various different epitopes on its target antigen - versus a collection of 'monoclonal antibodies', which all recognize a single epitope. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies."; rdfs:comment """In practice, the notion of a polyclonal antibody is considered from the perspective of a collection of individual antibody complexes, where different antibodies in this collection may recognize distinct epitopes that are part of the same immunogen used in the generation of these antibodies. This feature results from the mode of their production whereby serum is collected directly from an immunized animal and antobodies purified for experimetnal use. However at the structural level of the individual antibody molecule (which is considered here to be the antibody reagent), there is no physical distinction between an individual polyclonal antibody and an individual monoclonal antibody. The difference derives from thier distinct modes of production, and the uniformity of molecules when they are collected and stored in solution. Polyclonal antibody reagents are typically generated through a polyclonal antibody production technique in which antibodies are 'manufactured' by artificially inducing an immune response in some organism and harvesting the antibodies produced as a result. However, in some cases, antibodies existing 'naturally' in some organism are characterized and found to be applicable as reagents. Thus, we say that polyclonal antibody reagents can be output from an 'polyclonal antibody production', or from an 'specimen collection from an organism'.""" . _:2e9b19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9b29 . _:2e9b29 a owl:Class; owl:unionOf _:2e9b39 . _:2e9b39 rdf:first ; rdf:rest _:2e9b49 . _:2e9b49 rdf:first ; rdf:rest rdf:nil . _:2e9b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9b69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9b79 . _:2e9b79 a owl:Class; owl:unionOf _:2e9b89 . _:2e9b89 rdf:first ; rdf:rest _:2e9b99 . _:2e9b99 rdf:first ; rdf:rest rdf:nil . _:2e9ba9 a owl:Axiom; "axiom applied so this will qualify as a biomaterial (note that not all polyclonal antibodies are bioengineered outputs of an antibody produciton technique - as some might be extracted from organisms that naturally produce the antibody and then applied as reagents - this is an outlier case, but we choose to model it here)"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e9bb9 . _:2e9bb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9bc9 . _:2e9bc9 a owl:Class; owl:unionOf _:2e9bd9 . _:2e9bd9 rdf:first ; rdf:rest _:2e9be9 . _:2e9be9 rdf:first ; rdf:rest rdf:nil . _:2e9bf9 a owl:Axiom; """note that not all polyclonal antibodies are bioengineered outputs of an antibody production technique - as some might be extracted from organisms that naturally produce the antibody and then applied as reagents - this is an outlier case, but we choose to model it here. previous axiom: is_specified_output_of some (('polyclonal antibody production') or ('specimen collection from organism' and (has_specified_output some 'polyclonal antibody'))) """; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e9c09 . _:2e9c09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9c19 . _:2e9c19 a owl:Class; owl:unionOf _:2e9c29 . _:2e9c29 rdf:first ; rdf:rest _:2e9c39 . _:2e9c39 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "immunization technique"; rdfs:subClassOf , _:2e9c49, _:2e9c59, _:2e9ce9, _:2e9d39; "OBI - clarify meaning/usage of OBI:immunization in vitro and OBI:immunization in vivo) and determine how relate to ReO:immunizaitn technique"; "a material processing technique whereby some immunogenic material is administered to some organism or cell line or other immune-competent biological system, in order to initiate an adaptive immune response" . _:2e9c49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9c59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9c69 . _:2e9c69 a owl:Class; owl:intersectionOf _:2e9c79 . _:2e9c79 rdf:first ; rdf:rest _:2e9c99 . _:2e9c99 rdf:first _:2e9c89; rdf:rest rdf:nil . _:2e9c89 a owl:Class; owl:intersectionOf _:2e9cb9 . _:2e9cb9 rdf:first _:2e9ca9; rdf:rest _:2e9cd9 . _:2e9ca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9cd9 rdf:first _:2e9cc9; rdf:rest rdf:nil . _:2e9cc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9cf9 . _:2e9cf9 a owl:Class; owl:intersectionOf _:2e9d09 . _:2e9d09 rdf:first ; rdf:rest _:2e9d29 . _:2e9d29 rdf:first _:2e9d19; rdf:rest rdf:nil . _:2e9d19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9d39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_immunization"; rdfs:subClassOf ; "replaced by OBI immunization"; "The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope." . a owl:Class; rdfs:label "immunogen role"; rdfs:subClassOf , _:2e9d49; "a role inhering in any entity capable of eliciting an adaptive immune response when introduced to components of the immune system."; "'OBI:immunogen role? (assuming we can clarify their definition)" . _:2e9d49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9d59 . _:2e9d59 a owl:Class; owl:intersectionOf _:2e9d69 . _:2e9d69 rdf:first ; rdf:rest _:2e9d89 . _:2e9d89 rdf:first _:2e9d79; rdf:rest rdf:nil . _:2e9d79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "immunogen"; owl:equivalentClass _:2e9d99; rdfs:subClassOf , , _:2e9dd9, _:2e9de9, _:2e9e29; "molecular immunogen"; rdfs:comment "immunogens are different from immunogenic materials in that they are fundamentally chemical or molecular entities, while immunogenic materials can include larger, more complex materials such as cells or organisms that contain as part some chemical immunogen."; "a chemical entity (typically a molecule) bearing an immunogen role, and containing an epitope whose recognition by an immune receptor in an immune-competent system initiates an adpative immune response that realizes the immunogen role." . _:2e9d99 a owl:Class; owl:intersectionOf _:2e9da9 . _:2e9da9 rdf:first ; rdf:rest _:2e9dc9 . _:2e9dc9 rdf:first _:2e9db9; rdf:rest rdf:nil . _:2e9db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9dd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9de9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9df9 . _:2e9df9 a owl:Class; owl:unionOf _:2e9e09 . _:2e9e09 rdf:first ; rdf:rest _:2e9e19 . _:2e9e19 rdf:first ; rdf:rest rdf:nil . _:2e9e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular inhibitor role"; rdfs:subClassOf . a owl:Class; rdfs:label "molecular activator role"; rdfs:subClassOf ; "molecular inducer role"; rdfs:comment "note that many bearers of such a role will also have an activator function, becasue it was created/designed for the purpose of being an activator (e.g. ATP, or a ligant such as insulin). However, in the context of biomedical experimentation, many chemicals are applied as activators that do not bear such a function (ie they were not created/designed to serve as activators, but are used to do so). Consider, for example, a calcium salt used to activate some ion channel in a mitochondrial prep to trigger the release apoptotic proteins. Here, calcium bears an activator role, but no an activator function. So we conceive of this as a reagent role realized in the context of an experiment or technique. " . a owl:Class; rdfs:label "molecular probe role"; owl:equivalentClass _:2e9e39; rdfs:subClassOf , _:2e9ec9, _:2e9ed9, _:2e9f39; "re-use or align with/xref ChEBI:'probe'?"; "molecular effector role", "molecular agent role"; "a reagent role that inheres in a molecular entity applied in a scientific technique in order to target and interact with some molecular target of interest, typically with the goal of labeling the target for detection, purifying it, or altering its structure or behavior."; rdfs:comment """This role is broadly conceived to cover: (1)'targeted' molecular labels (ie targeted trackers and targeted reporters) used to facilitate detection of some molecular target of interest (2) bioactive/pharmacological agents such as drugs, inhibitors, etc that are used to alter the biological activity of their targets in some investigation (3) molecular entities used as 'captors' to purify target molecules from a complex mixture, such as antibodies used in immunoprecipitations, or chemicals affixed to resins to isolate some interaction target""" . _:2e9e39 a owl:Class; owl:intersectionOf _:2e9e49 . _:2e9e49 rdf:first ; rdf:rest _:2e9e69 . _:2e9e69 rdf:first _:2e9e59; rdf:rest rdf:nil . _:2e9e59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9e79 . _:2e9e79 a owl:Class; owl:intersectionOf _:2e9e89 . _:2e9e89 rdf:first ; rdf:rest _:2e9ea9 . _:2e9ea9 rdf:first _:2e9e99; rdf:rest rdf:nil . _:2e9e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9eb9 . _:2e9eb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9ee9 . _:2e9ee9 a owl:Class; owl:intersectionOf _:2e9ef9 . _:2e9ef9 rdf:first ; rdf:rest _:2e9f19 . _:2e9f19 rdf:first _:2e9f09; rdf:rest rdf:nil . _:2e9f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9f29 . _:2e9f29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9f39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9f49 . _:2e9f49 a owl:Class; owl:intersectionOf _:2e9f59 . _:2e9f59 rdf:first ; rdf:rest _:2e9f79 . _:2e9f79 rdf:first _:2e9f69; rdf:rest rdf:nil . _:2e9f69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9f89 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2e9f99 . _:2e9f99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2e9fa9 . _:2e9fa9 a owl:Class; owl:intersectionOf _:2e9fb9 . _:2e9fb9 rdf:first ; rdf:rest _:2e9fd9 . _:2e9fd9 rdf:first _:2e9fc9; rdf:rest rdf:nil . _:2e9fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "monosaccharide residue"; rdfs:subClassOf , , _:2e9fe9, _:2e9ff9, _:2ea009 . _:2e9fe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2e9ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "primer reagent"; owl:equivalentClass _:2ea019; rdfs:subClassOf , , _:2ea059, _:2ea0b9, _:2ea0c9; "an oligonucleotide reagent that is applied in a technique (typically PCR) to bind to some complementary nucleic acid template and serve as a starting point for nucleic acid synthesis"; . _:2ea019 a owl:Class; owl:intersectionOf _:2ea029 . _:2ea029 rdf:first ; rdf:rest _:2ea049 . _:2ea049 rdf:first _:2ea039; rdf:rest rdf:nil . _:2ea039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea069 . _:2ea069 a owl:Class; owl:intersectionOf _:2ea079 . _:2ea079 rdf:first ; rdf:rest _:2ea099 . _:2ea099 rdf:first _:2ea089; rdf:rest rdf:nil . _:2ea089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea0a9 . _:2ea0a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea0b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea0c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA interference oligonucleotide"; rdfs:subClassOf , _:2ea0d9, _:2ea0e9; "An RNA oligonucleiotide capable of sillencing expression of a target gene through the RNA interference pathway." . _:2ea0d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea0e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA oligonucleotide"; rdfs:subClassOf ; "An RNA interference oligonucleotide that includes gene-specific targeting sequences intended to silence expression of a target gene through the RNAi pathway, and also contains flanking miRNA sequence elements that allow for processing by cellular microRNA processing machinery into active miRNA molecules. " . a owl:Class; rdfs:label "siRNA oligonucleotide"; rdfs:subClassOf ; "an RNA interference oligonucleotide capable of silencing expression of a target gene through the RNAi pathway. siRNAs are synthesized as single-stranded molecules, typically 19-25 nucleotides in length, and paired with complementary sequences to form duplexes that serve as substrates for cellular RNAi processing machinery." . a owl:Class; rdfs:label "dsRNA oligonucleotide"; rdfs:subClassOf ; "an RNA interference oligonucleotide comprised of complementary strands of RNA that form double-stranded duplexes, and can be processed through the RNAi pathway into short interfering RNA (siRNA) molecules used to silence target gene expression." . a owl:Class; rdfs:label "obsolete_native cell"; rdfs:subClassOf ; "A cell that is found in a natural setting, and not re-located by some intentional agent to a controlled artificial setting for use in some investigation or study. Covers multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)."; rdfs:comment "Note that 'native' here bears significance only in relation to the location of a cell as part of an environment or organism, and not to the internal state of the cell. Thus, native cells can display altered physical structure or internal biochemical processes/metabolism, as a result of some experimental modification."; "replaced by CL: native cell" . a owl:Class; rdfs:label "unmodified multicellular organism cell in vivo"; owl:equivalentClass _:2ea0f9; rdfs:subClassOf , , _:2ea139; "an unmodified multicellular organism cell that is part of an organism"; "native unmodified multicellular organism cell" . _:2ea0f9 a owl:Class; owl:intersectionOf _:2ea109 . _:2ea109 rdf:first ; rdf:rest _:2ea129 . _:2ea129 rdf:first _:2ea119; rdf:rest rdf:nil . _:2ea119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "experimentally modified native cell"; owl:equivalentClass _:2ea149; rdfs:subClassOf , , _:2ea189; owl:disjointWith ; "a native cell that is the specified output of an experimental modification technique that introduces physical changes to the cell (ie changes in composition and/or internal structural arrangement)" . _:2ea149 a owl:Class; owl:intersectionOf _:2ea159 . _:2ea159 rdf:first ; rdf:rest _:2ea179 . _:2ea179 rdf:first _:2ea169; rdf:rest rdf:nil . _:2ea169 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unmodified cell in vitro"; owl:equivalentClass _:2ea199; rdfs:subClassOf , _:2ea1d9; rdfs:comment "a cell that has only been 'contextually' modified through their removal from an organism or from their natural environment, but not physically modified through some experimental modification (such as labeling, culturing, or fixing)" . _:2ea199 a owl:Class; owl:intersectionOf _:2ea1a9 . _:2ea1a9 rdf:first ; rdf:rest _:2ea1c9 . _:2ea1c9 rdf:first _:2ea1b9; rdf:rest rdf:nil . _:2ea1b9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2ea1d9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "obsolete_experimentally modified cell in vitro"; rdfs:subClassOf ; "replaced by CL: exp mod cell in vitro"; "a cell in vitro that is output from a cell modification technique that introduces physical changes to the cell" . a owl:Class; rdfs:label "organic small molecule complex"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_CL:cell by organism/class"; rdfs:subClassOf ; "was jsut a temp/test class to illustrate where this CL class would go (under ReO:unmodified native cell'"; . a owl:Class; rdfs:label "experimentally modified unicellular organism in vitro"; owl:equivalentClass _:2ea1e9; rdfs:subClassOf , ; "an experimentally modified unicellular organism that is not part of its natural environment, but rather is part of a controlled artificial environment for use in some investigation." . _:2ea1e9 a owl:Class; owl:intersectionOf _:2ea1f9 . _:2ea1f9 rdf:first ; rdf:rest _:2ea219 . _:2ea219 rdf:first _:2ea209; rdf:rest rdf:nil . _:2ea209 a owl:Class; owl:complementOf _:2ea229 . _:2ea229 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea239 . _:2ea239 a owl:Class; owl:unionOf _:2ea249 . _:2ea249 rdf:first ; rdf:rest _:2ea259 . _:2ea259 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "experimentally modified multicellular organsim cell in vitro"; owl:equivalentClass _:2ea269; rdfs:subClassOf , , _:2ea309; "an experimentally modified multicellular organism cell that is not part of some organism, but rather is part of a controlled artificial environment for use in some investigation." . _:2ea269 a owl:Class; owl:intersectionOf _:2ea279 . _:2ea279 rdf:first ; rdf:rest _:2ea299 . _:2ea299 rdf:first _:2ea289; rdf:rest _:2ea2f9 . _:2ea289 a owl:Class; owl:complementOf _:2ea2a9 . _:2ea2a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea2b9 . _:2ea2b9 a owl:Class; owl:unionOf _:2ea2c9 . _:2ea2c9 rdf:first ; rdf:rest _:2ea2d9 . _:2ea2d9 rdf:first ; rdf:rest rdf:nil . _:2ea2f9 rdf:first _:2ea2e9; rdf:rest rdf:nil . _:2ea2e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unmodified unicellular organism in environment"; owl:equivalentClass _:2ea319; rdfs:subClassOf , , _:2ea379, _:2ea389; "native unmodified unicellular organism"; "an unmodified unicellular organism that is part of a native setting (i.e. in a natural environment, and not re-located by some intentional agent to a controlled artificial setting for use in some investigation or study)" . _:2ea319 a owl:Class; owl:intersectionOf _:2ea329 . _:2ea329 rdf:first ; rdf:rest _:2ea349 . _:2ea349 rdf:first _:2ea339; rdf:rest _:2ea369 . _:2ea339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea369 rdf:first _:2ea359; rdf:rest rdf:nil . _:2ea359 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2ea379 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea389 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "naturally occurring"; rdfs:subClassOf ; owl:disjointWith ; "a quality inhereing in any material entity that is OF A TYPE existing in nature (ie represents a type or structural arrangement that exists without human intent or interventions, although a given bearer does not necessarily need to be produced naturally - see comment)."; "natural"; rdfs:comment """ 'Natural' and 'biological' molecules can be synthetically manufactured, so long as they conform to the structural (for small molecules) or definitional (for macromolecules) requirements for some class of molecule that exists in nature ('natural') or is endogenously produced by a living organism ('biological'). Note here that, requirements for synthetically-produced molecues to be considered 'natural' or 'biological' are different for small molecules vs macromolecules. A synthetic small molecules must exhibit structural identity (ie have the same molecular formula and structure) as some naturally-occurring molecule to be considered 'natural'. By contrast, we apply a looser qualifying standard for a syntheitc macromolcule to be considered 'natural' or 'biological'. A macromolecules is here considered to be 'natural' or 'biological' if it meets the structural requirements defining a type of macromolecule that is biologically produced (polypeptides, polynucleotides, or carbohydrates) - regardless of whether the molecule is actually produced naturally or synthetically, and regardless of wheter the sequence is actually found in nature. So a synthetic peptide is a type of natural, bioligical macromolecule, because its structural make-up conforms to the definition of a naturally-occurring biological macromolecule type (a protein), in that it is comprised of a linear chain of amino acids joined through peptide bonds. But agian, the sequence of the peptide does not need to represent a sequence found naturally. For macromolecules then, 'natural' does not require precise molecular structure or sequence identity with a macromolecule found in nature (ie does not need to represent a sequence of monomeric units found naturally). Rather, 'natural' implies that the macromolecule conforms to the definitional requirements for a type found in nature, and 'biological' further restricts this to types produced by living organisms.""" . a owl:Class; rdfs:label "unmodified unicellular organism"; owl:equivalentClass _:2ea399; rdfs:subClassOf , _:2ea3d9; "a unicellular organism that has not been experimentally modified through some cell modification technique, and thus exhibits a physical structure and internal biochemical metabolism that are the result of natural processes" . _:2ea399 a owl:Class; owl:intersectionOf _:2ea3a9 . _:2ea3a9 rdf:first ; rdf:rest _:2ea3c9 . _:2ea3c9 rdf:first _:2ea3b9; rdf:rest rdf:nil . _:2ea3b9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2ea3d9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "unmodified multicellular organism cell"; owl:equivalentClass _:2ea3e9; rdfs:subClassOf , _:2ea429; "a multicellular organism cell that has not been experimentally modified through some cell modification technique, and thus exhibits a physical structure and internal biochemical metabolism that are the result of natural processes" . _:2ea3e9 a owl:Class; owl:intersectionOf _:2ea3f9 . _:2ea3f9 rdf:first ; rdf:rest _:2ea419 . _:2ea419 rdf:first _:2ea409; rdf:rest rdf:nil . _:2ea409 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2ea429 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "biologically occurring"; rdfs:subClassOf ; "a quality inhering in any material entity that is OF A TYPE that is naturally created by some biological entity (organism or virus)."; "biological"; rdfs:comment """'Naturally occurring' and 'biologically occurring' molecules can be synthetically manufactured, so long as they conform to the definitional requirements for some class of molecules that exists in nature or is endogenously produced by a living organism, respectively. For example, 'biologically occurring' macromolecules include any macromolecule that meets the structural requirements defining a type of macromolecule that is biologically produced (polypeptides, polynucleotides, or polysaccharides) - regardless of whether the molecule is actually produced endogenously or synthetically, and regardless of whether the sequence of the molecule is one found in nature. So a synthetic peptide is a type of organic biomacromolecule, because its structural make-up conforms to the definition of a biological type (protein), in that it is comprised of a linear chain of amino acids joined through peptide bonds. However, the sequence of the peptide does not need to represent a sequence found naturally. For macromolecules then, 'naturally occurring' does not require precise molecular structure or sequence identity with a macromolecule found in nature (ie does not need to represent a sequence of monomeric units found naturally). Rather, 'naturally occurring' implies that the macromolecule conforms to the definitional requirements for a type found in nature, and 'biological' further restricts this to types produced by living organisms. By contrast, for small molecules, ''biologically occurring requires exact structural equality with some molecular entity created naturally by some organism."""; """Examples of biologically occurring materials: - organisms and their parts - biological specimens such as blood samples or tissue samples - any DNA oligonucleotide, whether endogenously produced in some cell, enymatically generated through a PCR reaction, or chemically synthesized (regardless of whether its sequence matches some naturally ocurring DNA sequence) - any polypeptide, whether endogenously produced by some organsim, produced in a bacterial cell from some recombinant plasmid, or chemically synthesized de novo (regardless of whether its sequence matches some naturally ocurring protein sequence) Examples materials that are NOT biologically occurring: - a cell line (and other materials manufactured from biological inputs - although cell line cells are biologically occurring?) - analog nucleic acids such as morpholinos""" . a owl:Class; rdfs:label "length value specification"; rdfs:subClassOf ; . a owl:Class; rdfs:label "obsolete_molecular quality"; rdfs:subClassOf ; "this and child molecular quality terms replaced by equivalents from PATO"; "A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc." . a owl:Class; rdfs:label "obsolete_solubility"; rdfs:subClassOf ; "replaced by PATO:solubility" . a owl:Class; rdfs:label "obsolete_soluble"; rdfs:subClassOf ; "A solubility quality inhering in a substance by virtue of the bearer's disposition to dissolve in a liquid." . a owl:Class; rdfs:label "obsolete_polarity"; rdfs:subClassOf ; rdfs:comment "Polarity refers to a separation of electric charge leading to a molecule or its chemical groups having an electric dipole or multipole moment. Molecular polarity is dependent on the difference in electronegativity between atoms in a compound and the asymmetry of the compound's structure. Polarity underlies a number of physical properties including surface tension, solubility, and melting- and boiling-points."; "A molecular quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole."; "PATO:polarity" . a owl:Class; rdfs:label "obsolete_non-polar polarity"; rdfs:subClassOf ; "A molecular quality that inheres in a molecular entity by virtue of the bearer not exhibiting sufficient separation of electric charge such that it does not exhibit an electric dipole moment." . a owl:Class; rdfs:label "obsoelte_polar polarity"; rdfs:subClassOf ; "A molecular quality that inheres in a molecular entity by virtue of the bearer exhibiting a separation of electric charge which leads to the it having an electric dipole." . a owl:Class; rdfs:label "obsolete_lipid"; rdfs:subClassOf ; "http://goldbook.iupac.org/L03571.html"; "an organic small molecule of biological origin that is soluble in nonpolar solvents, and is comprised primarily of carbon and hydrogen atoms. Lipids include saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. "; "ChEBI lipid"; rdfs:comment """Opinions and authorities vary as to whether some lipids can be considered to be macromolecules. Here, we consider lipids to be small molecules, despite the fact that many can be quite large, since they are not true macromolecules in the sense that they are not comprised of repeating monomeric subunits. The term 'lipid' covers a wide range of substances which contain moieties belonging chemically to hydrocarbons, alcohols, aldehydes, acids, amines or glucides. Accordingly, lipids cannot be defined structurally, but are rather defined by their chemical proeprties (ie their solubility in non-polar solvents). The majority of lipid molecules are waxes, triacylglycerols, phospholipids and glycolipids. Other substances are also considered as lipids while belonging to other classes of molecules, e.g. fat soluble vitamins (A, D, E and K), coenzymes (ubiquinones), pigments (carotenoids), terpenes, phenolics and sterols. (http://www.cyberlipid.org/cyberlip/home0001.htm)""" . a owl:Class; rdfs:label "solvent"; owl:equivalentClass _:2ea439; rdfs:subClassOf , , _:2ea479; "http://en.wikipedia.org/wiki/Solvent"; """Solvent and Solute Examples \"One of the most common examples that confuses many students is to identify solvent and solute in vinegar. In vinegar solution, water is the solvent; whereas acetic acid is the solute. To be more precise, a liquid solute is dissolved in a liquid solvent in vinegar. Similarly, other solvent and solute examples are soda water (gas is solute and water is solvent) and steel (solid carbon dissolved in solvent iron).\" http://www.buzzle.com/articles/solvent-and-solute.html"""; "a liquid, solid, or gas that is used to dissolve a solid, liquid, or gaseous solute, resulting in a solution"; . _:2ea439 a owl:Class; owl:intersectionOf _:2ea449 . _:2ea449 rdf:first ; rdf:rest _:2ea469 . _:2ea469 rdf:first _:2ea459; rdf:rest rdf:nil . _:2ea459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polar solvent"; owl:equivalentClass _:2ea489; rdfs:subClassOf , _:2ea509 . _:2ea489 a owl:Class; owl:intersectionOf _:2ea499 . _:2ea499 rdf:first ; rdf:rest _:2ea4b9 . _:2ea4b9 rdf:first _:2ea4a9; rdf:rest rdf:nil . _:2ea4a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ea4c9 . _:2ea4c9 a owl:Class; owl:intersectionOf _:2ea4d9 . _:2ea4d9 rdf:first ; rdf:rest _:2ea4f9 . _:2ea4f9 rdf:first _:2ea4e9; rdf:rest rdf:nil . _:2ea4e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea509 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ea519 . _:2ea519 a owl:Class; owl:intersectionOf _:2ea529 . _:2ea529 rdf:first ; rdf:rest _:2ea549 . _:2ea549 rdf:first _:2ea539; rdf:rest rdf:nil . _:2ea539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "non-polar solvent"; owl:equivalentClass _:2ea559; rdfs:subClassOf , _:2ea5d9 . _:2ea559 a owl:Class; owl:intersectionOf _:2ea569 . _:2ea569 rdf:first ; rdf:rest _:2ea589 . _:2ea589 rdf:first _:2ea579; rdf:rest rdf:nil . _:2ea579 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ea599 . _:2ea599 a owl:Class; owl:intersectionOf _:2ea5a9 . _:2ea5a9 rdf:first ; rdf:rest _:2ea5c9 . _:2ea5c9 rdf:first _:2ea5b9; rdf:rest rdf:nil . _:2ea5b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea5d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ea5e9 . _:2ea5e9 a owl:Class; owl:intersectionOf _:2ea5f9 . _:2ea5f9 rdf:first ; rdf:rest _:2ea619 . _:2ea619 rdf:first _:2ea609; rdf:rest rdf:nil . _:2ea609 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "canonical amino acid"; rdfs:subClassOf , , _:2ea629, _:2ea679; owl:disjointWith ; "Here we have imported under this class all L-isomer amino acid classes corresponding to the 21 children of ChEBI:canonical aa residue, and also L-pyrrolisine. The fact we are making a canonicity distinction implies that we are talking about alpha aa residues, as this distinction is not relevant to non-alpha aa residues. This, we omit 'alpha' from the label of this class."; "canonical alpha-amino acid", "proteinogenic amino acid", "natural amino acid"; "http://en.wikipedia.org/wiki/Proteinogenic"; "an alpha amino acid that is one of the set of all alpha-amino acids that naturally are incorporated into protein chains by the ribosome."; "ChEBI may be a good place to host such a class (they have canonical amino acid residue, but not canonical amino acid - it is unclear why there is no canonical amino acid class implemented in ChEBI)"; rdfs:comment """There are 22 canonical amino acids (Isoleucine, Alanine, Leucine, Arginine, Lysine, Aspartate, Methionine, Cysteine, Phenylalanine, Glutamate, Threonine. Glutamine, Tryptophan, Glycine, Valine, Proline, Histidine, Serine, Tyrosine, Asparagine, Selenocysteine, and Pyrrolysine.), including those corresponding to the 21 L-isomer residues enumerated in ChEBI:canonical amino acid residue, plus L-pyrrolysine, the most recently discovered amino acid that is naturally incorporated into proteins: This class is limited to only those molecules exhibiting the exact structures of these 22 canonical amino acids, and does not include any modified versions or isomers of these moelcules. Thus they are 'unmodified' by definition.""" . _:2ea629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea639 . _:2ea639 a owl:Class; owl:intersectionOf _:2ea649 . _:2ea649 rdf:first ; rdf:rest _:2ea669 . _:2ea669 rdf:first _:2ea659; rdf:rest rdf:nil . _:2ea659 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ea679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea689 a owl:Axiom; ""; "Also, the axiom here may not quite work - esp since we may not want to rely on an incorporant role. Could we use the capable_of relation somehow? capable of input into some translation? participates_in some (translation and (bearer_of some natural)) does not work, because partifipation in translation is not required for being a canonical aa, just the capacity to do so."; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2ea699 . _:2ea699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea6a9 . _:2ea6a9 a owl:Class; owl:intersectionOf _:2ea6b9 . _:2ea6b9 rdf:first ; rdf:rest _:2ea6d9 . _:2ea6d9 rdf:first _:2ea6c9; rdf:rest rdf:nil . _:2ea6c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "obsolete_translation"; rdfs:subClassOf ; "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. "; "replaced by GO:trnaslation" . a owl:Class; rdfs:label "incorporant disposition"; rdfs:subClassOf ; "a disposition to be incorporated into the output of some synthetic process (be it an endogenous biological process or a planned process), such that the output derives some significant portion of material from the bearer of the incorporant role." . a owl:Class; rdfs:label "obsolete_modified amino acid"; rdfs:subClassOf ; "O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine, O-phospho-L-carnitine, N-acetly-D-ornithine, biotin-conjugated citrullene"; "This class includes all amino acids, natural or unnatural, that are functional derivatives of some as of yet undefiend set of foundational, 'unmodified' amino acids (which includes at minimum the set of canonical amino acids). We acknowledge this definition is vague and imprecise, and are working with ChEBI and others to address this. However, we implement this class now with the expectation that users will apply common sense to determine if a given amino acid is modified or not. As a point of reference, see the Sigma catalog entries for 'amino acids' (http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16181993) vs 'modified amino acids' (http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16360557) "; "ChEBI:modified amino acid"; rdfs:comment """As canonical amino acids are defined strictly by their molecular structures, any modifications will result in a non-canonical amino acid (e.g. even a natural modification such as a phosphorylation). Examples include any naturally-occurring or artificial modifications of amino acids that result in structures not represented in the set of canonical amino acids, such as O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine."""; "a non-canonical amino acid that is functionally derived from some other amino acid"; "amino acid derivative" . a owl:Class; rdfs:label "experimentally modified amino acid reagent"; rdfs:subClassOf ; rdfs:comment "Note that two key differences here between experimentally modified aa and aa analog are that being an analog requires additionally that (1) the modified material is not natural (ie not of a natural type), and (2) there is some intent to apply the bearer to mimic the reference material in some way. For example, experimental phosphorylation of an amino acid is a material modification, but does not necessarily output an aa analog."; "35S labeled methionine"; "an experimentally modified amino acid (ie an amino acid that is output from some technique intended to introduce some specified structural modification), that bears a reagent role"; """decided not needed/too complilcated. former logical definition: ('amino acid analog' or 'modified amino acid') and ('has role' some 'reagent role')""" . a owl:Class; rdfs:label "obsolete_molecular analog function"; rdfs:subClassOf ; "a function inhering in a synthetic molecule that is designed to exhibit structural similarity to some other (typically naturally occurring) molecule, and realized in a process in which the bearer mimics/stands in for this other molecule. The specified structural similarity is such that the bearer can mimic some chemical or biological activity of this molecular entity, while also exhibiting specified structural differences that serve some specified purpose (e.g. that allow it to probe or alter the biochemical environment of the bearer in some way). "; "Instead of subclassing the analog function/role into things like 'molecular analog function' and 'amino acid analog function', I have used the toward relation with the base/parent 'analog function' to indicate the type of material entity that a bearer of the analog role is intended to mimic. For example, a molecular analog function/role would not be a class, but an axiom : bearer_of some (analog function/role and (towards some molecular entity)). However, not sure if the towards relation applies to functions and roles (definition says that it applies only to relational qualities and dispositions)."; . a owl:Class; rdfs:label "unnatural"; rdfs:subClassOf ; rdfs:comment "For small molecules, this is defined at the level of molecular structure, such that unnatural molecules are those exhibiting a molecular structure that is not found naturally without human intervention."; "artificial"; "of a type not existing in nature" . a owl:Class; rdfs:label "obsolete_analog reagent role"; rdfs:subClassOf ; "decided to use the analog function to define analog eq classes instead, but may ultimately re-instate this role if needed"; "a reagent role inhering in a synthetic material entity that is designed to exhibit structural similarity to a naturally occurring material. This similarity is such that the bearer can mimic some attributes or activity activity of this material entity, while also exhibiting specified structural differences that allow it to probe or alter the environment of the bearer in some way."; rdfs:comment "The molecular analog role exploits a more fundamental molecular analog function, for the purpose of probing or affecting it molecular environment in some scientific technique." . a owl:Class; rdfs:label "non-information macromolecule"; owl:equivalentClass _:2ea6e9; rdfs:subClassOf ; "an organic macromolecule that does not carry genetic sequence information (ie is not part of or encoded by a genome, or a macromolecule that is engineered or synthesized to mimic such molecules and carry sequence information that maps to a nucleic acid or protein sequence)"; "non-information organic macromolecule" . _:2ea6e9 a owl:Class; owl:intersectionOf _:2ea6f9 . _:2ea6f9 rdf:first ; rdf:rest _:2ea719 . _:2ea719 rdf:first _:2ea709; rdf:rest rdf:nil . _:2ea709 a owl:Class; owl:complementOf _:2ea729 . _:2ea729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea739 . _:2ea739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea749 . _:2ea749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_amino acid analog function"; rdfs:subClassOf ; "Instead of subclassing the analog function/role into things like 'molecular analog function' and 'amino acid analog function', I have used the toward relation with the base/parent 'analog function' to indicate the type of material entity that a bearer of the analog role is intended to mimic. For example, a molecular analog function/role would not be a class, but an axiom : bearer_of some (analog function/role and (towards some molecular entity)). However, not sure if the towards relation applies to functions and roles (definition says that it applies only to relational qualities and dispositions)."; "a molecular analog function inhering in a synthetic small molecule that is designed to exhibit structural similarity to some other (typically naturally occurring) amino acid, and realized in a process in which the bearer mimics/stands in for this amino acid"; . a owl:Class; rdfs:label "obsolete_amino acid analog reagent"; rdfs:subClassOf ; "a synthetic and unnatural organic small molecule that is designed to exhibit structural similarity to some other (typically naturally occurring) amino acid, and applied in some scientific technique as a reagent"; rdfs:comment "Note that two key differences here between experimentally modified aa and aa analog are that being an analog requires additionally that (1) the modified material is not natural (ie not of a natural type), and (2) there is some intent to apply the bearer to mimic the reference material in some way. For example, experimental phosphorylation of an amino acid is a material modification, but does not necessarily output an aa analog."; "IAO/OBI/PATO? (the towards relation is defined as having a relational quality or a disposition as a domain, but I use it here to have a role as a domain. Is this OK?) "; "decided that all analogs will be reagents for now, since they are created with the intent to substitue for a real molecule in an experiment"; "L-Photo-Leucine and L-Photo-Methionine are analogs of L-Leucine and L-Methionine amino acids that can be endogenously incorporated into the primary sequence of proteins during synthesis and then ultraviolet light (UV)-activated to covalently crosslink proteins within protein-protein interaction domains in their native environment within live cells. (http://www.piercenet.com/browse.cfm?fldID=65A33F64-3AE8-4C6F-BA56-B791075902B7)" . a owl:Class; rdfs:label "canonical amino acid reagent"; owl:equivalentClass _:2ea759; rdfs:subClassOf , , , _:2ea799 . _:2ea759 a owl:Class; owl:intersectionOf _:2ea769 . _:2ea769 rdf:first ; rdf:rest _:2ea789 . _:2ea789 rdf:first _:2ea779; rdf:rest rdf:nil . _:2ea779 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea799 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:comment "There are 22 canonical amino acids (Isoleucine, Alanine, Leucine, Arginine, Lysine, Aspartate, Methionine, Cysteine, Phenylalanine, Glutamate, Threonine. Glutamine, Tryptophan, Glycine, Valine, Proline, Histidine, Serine, Tyrosine, Asparagine, Selenocysteine, and Pyrrolysine.), including those corresponding to the 21 L-isomer residues enumerated in ChEBI:canonical amino acid residue, plus L-pyrrolysine, the most recently discovered amino acid that is naturally incorporated into proteins. This class is limited to only those molecular reagents exhibiting the exact structures of these 22 canonical amino acids, and does not include any modified versions or isomers of these moelcules."; "canonical alpha-amino acid reagent", "proteinogenic amino acid reagent", "natural amino acid reagent"; "a canonical amino acid that bears a reagent role. The canonical amino acids are L-isomers of alpha-amino acids that are naturally incorporated into protein chains during ribosomal protein translation"; . a owl:Class; rdfs:label "amino acid reagent"; owl:equivalentClass _:2ea7a9; rdfs:subClassOf , _:2ea819; "an organic small molecule reagent that is a carboxylic acid containing one or more amino groups, or an chemical analog engineered to mimic such an amino acid"; . _:2ea7a9 a owl:Class; owl:intersectionOf _:2ea7c9 . _:2ea7c9 rdf:first _:2ea7b9; rdf:rest _:2ea809 . _:2ea7b9 a owl:Class; owl:unionOf _:2ea7d9 . _:2ea7d9 rdf:first ; rdf:rest _:2ea7e9 . _:2ea7e9 rdf:first ; rdf:rest rdf:nil . _:2ea809 rdf:first _:2ea7f9; rdf:rest rdf:nil . _:2ea7f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_lipid macromolecule reagent"; rdfs:subClassOf ; "a lipid reagent that contains one or more long hydrocarbon chains, comprised primarily of a repeating carbon backbone saturted with bonds to hydrogen, or unsaturated and containing C=C double bonds. While technincally not macromolecules in the sense that they are not polymers comprised of repeating monomeric subunits, the repeating structure in the hydrocarbon chain resembles this feature of macromolecules."; """decided to forgo the lipid small vs macromolecule classification scheme, and use the hydrocarbon vs simple vs complex subclassing approach. But can always revert to the other way of doing it). note that one consequence of this is that lipid and lipid reagent become organic small molecules and organic small molecule reagents, respectively, which may not be intuitive to consider larger lipids to be small molecules."""; . a owl:Class; rdfs:label "lipid reagent"; owl:equivalentClass _:2ea829; rdfs:subClassOf , , _:2ea869; rdfs:comment """The term 'lipid' covers a wide range of substances which contain moieties belonging chemically to hydrocarbons, alcohols, aldehydes, acids, amines or glucides. Accordingly, lipids cannot be defined structurally, but are rather defined by their chemical proeprties (ie their solubility in non-polar solvents). The majority of lipid molecules are waxes, triacylglycerols, phospholipids and glycolipids. Other substances are also considered as lipids while belonging to other classes of molecules, e.g. fat soluble vitamins (A, D, E and K), coenzymes (ubiquinones), pigments (carotenoids), terpenes, phenolics and sterols (adapted from http://www.cyberlipid.org/cyberlip/home0001.htm) Opinions and authorities vary as to whether some lipids can be considered to be macromolecules (as opposed to orgnaic small molecules). Here, we consider lipids to be small molecules, despite the fact that many can be quite large, since they are not true macromolecules in the sense that they are not comprised of repeating monomeric subunits. """; "an organic small molecule reagent that is soluble in nonpolar solvents, and is comprised primarily of carbon and hydrogen atoms. Lipids consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. "; . _:2ea829 a owl:Class; owl:intersectionOf _:2ea839 . _:2ea839 rdf:first ; rdf:rest _:2ea859 . _:2ea859 rdf:first _:2ea849; rdf:rest rdf:nil . _:2ea849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_lipid small molecule reagent"; rdfs:subClassOf ; "a lipid reagent that does not contain a long hydrocarbon chain comprised primarily of a repeating carbon backbone saturted with bonds to hydrogen, or unsaturated and containing C=C double bonds."; """decided to forgo the lipid small vs macromolecule classification scheme, and use the hydrocarbon vs simple vs complex subclassing approach. But can always revert to the other way of doing it). note that one consequence of this is that lipid and lipid reagent become organic small molecules and organic small molecule reagents, respectively, which may not be intuitive to consider larger lipids to be small molecules."""; . a owl:Class; rdfs:label "information macromolecule"; owl:equivalentClass _:2ea879; rdfs:subClassOf , _:2ea8c9; """ChEBI: This class encompasses a broader set of instances than ChEBI 'information biomacromolecule' (ie analog macromolecules such as morpholinos), so we are likely not able to import and re-use the ChEBI:information biomacromolecule class here. This class has no definition in ChEBI, but biomacromolecule is defined as 'formed in a living organism', which is not a requirement for our 'information macromolecule' class. We may at some point wish, however, to import this ChEBI class as a subclass of ReO:information macromolecule. Note that the ChEBI class does include things like 'locked nucleic acid' and 'peptide nucleic acid' as children - and these are artificial/synthetic moelcules. This is inconsistent with their textual definition. Note that the ChEBI:information biomacromolcule class does include things like 'locked nucleic acid' and 'peptide nucleic acid' as children - and these are artificial/synthetic molecules. This is inconsistent with their textual definition for biological macromolecule. Need to determine what the relationship is between my placeholder term here and ChEBI:information biomacromolecule."""; "genetic information biopolymer", "sequence macromolecule", "information biopolymer", "sequence biopolymer", "genetic sequence biopolymer", "genetic sequence macromolecule"; rdfs:comment "This class represents macromolecules that are natrually produced, bioengineered, or synthetically manufactured. For example, a morpholino is a synthetic oligo that is not a nucleic acid, but it carries sequence information that relates each monomer to some specific nucleic acid or set of nucleic acids, allowing it to bind a nucleic acid an a sequence specific manner. Other examples of 'genetic sequence macromolecules' are other nucleic acid analogs such as peptide nucleic acids, and synthetic primers or peptides."; "This class represents natural or artificial polymers that carry sequence information of a genetic nature (ie, information that is translatable to a nucleic acid or protein sequence in some defined way). This includes sequence information naturally part of or encoded by the genomes of organisms, as well as artificially designed and synthesized nucleic acid or polypeptide modleules, and nucleic acid/protein 'analogs', whose sequences map to genetic information carried in natural nucleic acids and proteins." . _:2ea879 a owl:Class; owl:intersectionOf _:2ea889 . _:2ea889 rdf:first ; rdf:rest _:2ea8a9 . _:2ea8a9 rdf:first _:2ea899; rdf:rest rdf:nil . _:2ea899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea8b9 . _:2ea8b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea8c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea8d9 . _:2ea8d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_endogenously-produced"; rdfs:subClassOf ; "a quality inhering in a biolgocial material that is output of a naturally occuring biological process (ie one that occurs in nature without human intention)"; rdfs:comment "unlike 'biological', which describes materials that need only be OF A TYPE of some object produced in an organism, 'endogenously-produced' requires that the bearer was actually produced in an organism (or biologically derived system), AND produced without human intervension (e.g. bioengineered proteins do not qualify)" . a owl:Class; rdfs:label "naturally created"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "unlike 'naturally-occurring', which describes materials that need only be OF A TYPE of some object produced in nature, 'naturally-created' requires that the bearer was actually produced through some natural process, and is structure not designed in any way by some human or computational agent."; "a quality inhering in a material whose structural composition and design is entirely the result of natural processes (ie not engineered in any way by some intentional agent), and is produced as part of some natural process which evolved and can occur in the absense of human intervention (but which may or may not be part of some planned process)." . a owl:Class; rdfs:label "biologically created"; rdfs:subClassOf , , _:2ea8e9; owl:disjointWith ; "Used the term 'biologically created' rather than 'biologically produced', as 'created' implies the bearer's design and production was driven by some organism (even if its actual synthesis by some is part of a planned process)"; "a quality inhering in a material whose structural composition and design is entirely the result of natural biological processes (ie not engineered in any way by some intentional agent), and which is produced in an organism or organism-derived system through a biological process (which may or may not be part of some planned process)"; rdfs:comment "unlike 'biologically occurring', which describes materials that need only be OF A TYPE of some object produced in an organism, 'biologically-created' requires that the bearer was actually produced in an organism (or biologically derived system), AND produced without human intent or intervention (e.g. bioengineered proteins do not qualify)"; """Examples of biologically created materials*: - organisms and their parts - biological specimens such as blood samples or tissue samples - a DNA oligonucleotide endogenously produced in some cell, - a protein endogenously produced by some organism from its genomic DNA - an antibody produced by an organism as a result of natural (ie not 'planned') exposure to some immunogen Examples materials that are NOT biologically created: - a cell line (and other materials manufactured from biological inputs) - analog nucleic acids such as morpholinos - a DNA oligonucleotide enymatically generated through a PCR reaction, or chemically synthesized - a protein produced in a bacterial cell from some recombinant plasmid, or a polypeptide chemically synthesized de novo - an antibody produced by an organism as a result of somoe experimental exposure to some immunogen See explanation of 'bioengineered', which is disjoint with 'biologically created', for further clarification and examples. *note that all examples of biologically created materials must not derive from a bioengineered organism (?)""" . _:2ea8e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea8f9 . _:2ea8f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea909 . _:2ea909 a owl:Class; owl:intersectionOf _:2ea919 . _:2ea919 rdf:first ; rdf:rest _:2ea939 . _:2ea939 rdf:first _:2ea929; rdf:rest rdf:nil . _:2ea929 a owl:Class; owl:complementOf _:2ea949 . _:2ea949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleotide analog residue"; rdfs:subClassOf , _:2ea959, _:2ea969 . _:2ea959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea979 . _:2ea979 a owl:Class; owl:unionOf _:2ea989 . _:2ea989 rdf:first ; rdf:rest _:2ea999 . _:2ea999 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "obsolete_solvent reagent"; rdfs:subClassOf ; """dcided to view all solvents as reagents, and made solvent a reagent role. former eq class def: solvent and ('has role' some 'reagent role')"""; "a solvent that bears a reagent role" . a owl:Class; rdfs:label "obsolete_non-polar solvent reagent"; rdfs:subClassOf ; "a non-polar solvent that bears a reagent role" . a owl:Class; rdfs:label "obsolete_polar solvent reagent"; rdfs:subClassOf ; "a polar solvent that bears a reagent role" . a owl:Class; rdfs:label "obsolete_unmodified amino acid"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_unmodified amino acid reagent"; rdfs:subClassOf ; "an amino acid reagent that has not been experimentally modified, and exhibits a chemical structure/formula found in nature"; rdfs:comment "can be naturally-produced or synthetic" . a owl:Class; rdfs:label "analog function"; rdfs:subClassOf , _:2ea9a9, _:2ea9b9; rdfs:comment """Key features of these analogs is that (1) they exhibit some novel, unnatural function or role relative to some natural molecule which they are applied to mimic/stand in for, and (2) they are not naturally occurring themselves, either as independent molecular entities or as residues/components of larger macromolecules. For example, a biotin-conjugated serine molecule would be considered an amio acid analog, as this chemical structure is not found in nature but could be used to replace natural serine in a polypeptide (and allow, for example, its purification using a streptavidin column). By contrast, phosphate-conjugated serine molecule (O-phospho-L-serine) represents a chemical structure found in nature (as part of a serine-phosphorylated polypeptide) - and thusdoes not introduce some novel, unnatural function or role when applied in place of serine. The presumption here is that there is a core set of natural/biological that biomedical researchers are interested in, which are afforded a special/conferred status (these are things like nucleotides, amino acids, monosaccharides, etc). Accordingly, biochemists and chemical reagent manufacturers often synthesize artificial and unnatural 'analogs' of them, which can be used to probe or alter the function of biological systems. Thus, we see in ReO classes such as 'nucleotide analog' and 'amino acid analog'."""; "a function inhering in a synthetic material entity that is designed to exhibit structural similarity to some other (typically naturally occurring) material entity, and realized in a process in which the bearer mimics/stands in for this other material. The specified structural similarity is such that the bearer can mimic some attributes or activity of the analogous natural material entity, while also exhibiting specified structural differences that confer some novel activity which allows it to probe or alter the environment of the bearer" . _:2ea9a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ea9b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ea9c9 . _:2ea9c9 a owl:Class; owl:intersectionOf _:2ea9d9 . _:2ea9d9 rdf:first ; rdf:rest _:2ea9f9 . _:2ea9f9 rdf:first _:2ea9e9; rdf:rest rdf:nil . _:2ea9e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_experimental modification objective"; rdfs:subClassOf ; "3-23-12: merged/relaced by 'physical material processing objective' (REO_0000302), and label of 0000320 changed to 'experimental modification objective' (previously was a child of 0000302"; "the objective to makephysical/ structural alterations to some input material or materials, to produce some output that represents a modified version of some specified input material" . a owl:Class; rdfs:label "experimental modification"; owl:equivalentClass _:2eaa09; rdfs:subClassOf , _:2eaa89, _:2eaad9; "physical modification"; """8-24-12 Many (inferred) children of this class represent categories of experimental modifications, that are distinguished based on various classification criteria: 1. Type of material that is modified (e.g. cell modification technique, antibody conjugation technique) 2. Type of modification made (e.g. genetic modification technique, molecular labeling technique, imm8nization) Design pattern for each mode of classification/type of defined class can be extended and consistently applied to create new defined classes as they may be needed in the future. Design patterns: 1. Based on type of material modified: a. 'material processing technique' and (has_specified_input some ('X' and ('has role' some 'target of physical modification role'))) and (has_specified_output some 'X') 2. Based on type of modification made: a. indicate the specified inputs and the roles they have (e.g. molecular label with a material to be added, and material entity with a target of material addition) b. document some attribute of the specified output that reflects the modification made (e.g. has specified output some cell and has proper part some (material genome and (bears concretization of some sequence alteration) c. use a more specific target of modification role (e.g. target of stable genetic modification role, target of transgenic modification role) Use a or b when possible, and resort to c if necessary."""; """The purpose of modeling the notion of physical/experimental modification in this way is to be able to record that a given material has been experimentally modified - as this represents an important concept/distinction for researchers considering the nature of a given resource when they are interpreting data, looking for resources, or planning experiments. The founding use case for this was the need to logically model the CL class 'experimentally modified cell' - where it was decided that 'experimental modification' here was meant to imply some physical change to the cell (addition or removal or structural re-arrangement of material). This is contrasted with the notion of 'contextually modified' - whereby a material entity undergoes a change in context/location, but no physical change is made to its internal, self-contained structure. For example, an appendix surgically removed from an organism is contextually modified, and the organism itself is physically/experimentally modified. This organizational class ('experimental modification') collects all material processing techniques considered to 'physically modify' some specified input material. We use 'target of physical modification' roles inhering in the SPECIFIED inputs of material processing techniques to record the intent of the researcher to physically modify some input material. These roles inhere in a specified input material that an agent intends to modify and thereby produce a specified output representing a modified version of this target (ie there is a preservation of identity between the specified input bearing the 'target of physical modification role' and the specified output of the process in which this role is realized). To define an experimentally modified material, we can indicate that it is output from some experimental modification that has_specified_output some entity X that bears a 'target of physical modification role', and that the specified output is also of type X (ie the specified output is that input which was the target of modification). For example, a 'cell modification technique' is defined as any experimental modification where the specified output is a cell that bears a 'target of physical modification role', and the specified output is also a cell. An 'experimentally modified cell' can then be defined as any cell that is output of such a technique. Using this pattern, we are able to infer that a given class of material entities is 'experimentally modified' based on their being output from a material processing technique that meets the criteria for experimental modification. Note that not every specified output of an experimental modification qualifies as 'experimentally modified' (e.g. an appendix output from an appendix removal). Only those output from experimental modification techniques where the specified output is the same as the specified input that bears a 'target of physical modification role' (e.g. the organism from which the appendix was removed). Thus, we create experimental modification technique subclasses of 'experimental modification' to specify this (ie that the specified output of a 'cell modfiication technique' is of the same type as the specified input that is to be modified - ie a cell), and use these in our definitions of specific types of experimentally modified entities (e.g. experimentally modified cell).""", """A key concept here is that an 'experimental modification' is any technique that has some specified input that is intended to be modified. But to be 'experimentally modified', a material must not only be output from such an experimental modification, but it must also bear a 'target of physical modification role' as input, which is realized in the technique. This means that in techniques that can have specified outputs that are contextually modified or physically modified (for example an appendix removal that may have as specified output a contextually modified appendix or a physically modified organism), we can use the deisgn patterns in ReO to be precise as to which output is experimentally modified - the one that as input bore a 'target of physical modification role')."""; "a material processing technique whereby physical alterations (ie structural or compositional changes) are made to a specified input material, to produce some output that represents a modified version of the specified input material."; """Experimental modifications are those that ADD material, REMOVE material, or REARRANGE material: Adding Material: labeling a cell with biotin, conjugating an antibody with a fluorochrome, transfecting cells in culture, fixation of a tissue specimen, ubiquitination of a recombinant protein, immunization of an organism Removing Material: surgical removal of an anatomical entity or tumor form an organism, enzymatic digestion of cell surface proteins on a cell, dephosphorylation of a recombinant protein Rearranging Material - homogenization of a tissue sample, introducing a point mutation into the genome of some cell"""; rdfs:comment "An experimental modification makes physical changes to some input material representing a 'target of physical modification', and a modified version of this same material entity is specified as output ( (ie shares identity with the input target of modification). The 'physical' changes refered to in the definition alter the structural makeup of the input material by adding/removing material or re-arranging their internal structure. These are changes beyond simple 'contextual changes' such those resulting from, for example, collecting a specimen, or selecting a subpopulation of cells." . _:2eaa09 a owl:Class; owl:intersectionOf _:2eaa19 . _:2eaa19 rdf:first ; rdf:rest _:2eaa39 . _:2eaa39 rdf:first _:2eaa29; rdf:rest rdf:nil . _:2eaa29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eaa49 . _:2eaa49 a owl:Class; owl:intersectionOf _:2eaa59 . _:2eaa59 rdf:first ; rdf:rest _:2eaa79 . _:2eaa79 rdf:first _:2eaa69; rdf:rest rdf:nil . _:2eaa69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaa89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eaa99 . _:2eaa99 a owl:Class; owl:intersectionOf _:2eaaa9 . _:2eaaa9 rdf:first ; rdf:rest _:2eaac9 . _:2eaac9 rdf:first _:2eaab9; rdf:rest rdf:nil . _:2eaab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eaae9 . _:2eaae9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaaf9 a owl:Axiom; "need to consider more what the meaning of 'transforms' is . . . and if it applies to all children of experimental modification (ie doe sa genetic modification technique transform some unmodified cell?) I would say yes. So this could be a nice way to modl the notion of the specified output of an experimentla modification being a physically altered versio0n of the specified input (ie identity retained)"; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2eab09 . _:2eab09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eab19 . _:2eab19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "non-canonical amino acid"; rdfs:subClassOf ; "any amino acid that is not in the set of 22 canonical amino acids that are naturally incorporated into proteins during translation"; " Includes naturally occurring amino acids such as carnitine or ornithine, and any naturally or artificially 'modified' versions of amino acids that result in structures not represented in the set of canonical amino acids (e.g. O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine)." . a owl:Class; rdfs:label "non-canonical amino acid reagent"; owl:equivalentClass _:2eab29; rdfs:subClassOf , , _:2eab69; "Includes naturally occurring amino acids such as carnitine, and any naturally or artificially modified versions of amino acids that result in structures not represented in the set of canonical amino acids (e.g. O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine, O-phospho-L-carnitine, N-acetly-D-carbamic acid, biotin-conjugated GABA)."; "an amino acid reagent exhibiting a molecular structure that does not correspond to one of the 22 canonical amino acids that are naturally incorporated into proteins during translation. This class of non-canonical amino acids includes 'canonical amino acids' that have been structurally 'modified' (for example by phosphorylation or biotinylation)."; . _:2eab29 a owl:Class; owl:intersectionOf _:2eab39 . _:2eab39 rdf:first ; rdf:rest _:2eab59 . _:2eab59 rdf:first _:2eab49; rdf:rest rdf:nil . _:2eab49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eab69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "endogenous antigen role"; rdfs:subClassOf , _:2eab79, _:2eab89; rdfs:comment "Note that the endogneous antigen role can be realized in the context of an experimental technique, where the antigen is applied to initiate an immune response in an immune-competent system as part of the experiment. So andogenous antigen and experimental antigen classes are not disjoint, as a given instance could belong to both classes.", """Note that a bearer of this role can also bear an experimental antigen role. For example, if a protocol specifies an antigen to stimulate an immune response is as part of some experiment (e.g. in studying the immune response itself, or its byproducts), the antigen is an endogenous antigen and an experimental antigen. However, in the majority of cases, the experimental antigen is recognized simply to allow for its detection in some fixed/prepared specimen - and not to applied to trigger an immune response. Note malso another important distinction : any molecule interacting with an adaptive immune receptor (to allow for its detection or to trigger a GENERAL immune response) bears an antigen role. If the interaction triggers an ADAPTIVE immune response, then the molecule additionally bears an immunogen role."""; "OBI: antigen role? (assuming we clarify the definition here)"; "a role that inheres in a chemical entity, that is realized in the context of some immune-competent organism or biological system through the interaction of the bearer with an adaptive immune receptor complex, in such a way as to trigger an immune response." . _:2eab79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eab89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eab99 . _:2eab99 a owl:Class; owl:intersectionOf _:2eaba9 . _:2eaba9 rdf:first ; rdf:rest _:2eabc9 . _:2eabc9 rdf:first _:2eabb9; rdf:rest rdf:nil . _:2eabb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_immunogen role"; rdfs:subClassOf ; "accidentally must have duplicated the immunogen role, because ended up with this extra one. "; "a role inhering in any entity capable of eliciting an immune response when introduced to components of the immune system" . a owl:Class; rdfs:label "experimental antigen role"; rdfs:subClassOf , , _:2eabd9, _:2eac29; "a role that inheres in some chemical or molecular entity, and is realized by the recognition of the bearer by an adaptive immune receptor complex during the course of some scientific technique. This interaction is specified by some plan specification, and is used to probe or affect some molecular target in the experimental system."; "For example, the use of antibody reagents to recognize experimental antigens can allow for localization or abundance of an antigen analyte to be tracked, or can be used to effect some biological response by the antigen (e.g. activation of some membrane receptor activity borne by the antigen, or inhibition of some enzymatic function borne by the antigen)"; "OBI:assay antigen role? Need to sort out their meaning here first, before deciding on an import strategy"; rdfs:comment "Note that a bearer of this role can also bear an endogenous antigen role, for example in cases where an immune response is stimulated by an antigen as part of some experiment (e.g. in studying the immune response itself, or its byproducts), the antigen is an endogenous antigen and an experimental antigen." . _:2eabd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eabe9 . _:2eabe9 a owl:Class; owl:intersectionOf _:2eabf9 . _:2eabf9 rdf:first ; rdf:rest _:2eac19 . _:2eac19 rdf:first _:2eac09; rdf:rest rdf:nil . _:2eac09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eac29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_adaptive immune response"; rdfs:subClassOf ; "replaced by GO:adaptive immune response" . a owl:Class; rdfs:label "obsolete_epitope binding by adaptive immune receptor"; rdfs:subClassOf ; "OBI : 'significant enough to trigger an immune response' does not necessarily mean an 'adaptive immune response', right? (otherwise this process would apply only for immunogens, and not more generally to any antigen)"; "is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding."; "replaced by OBI epitope binding by adaptive immune receptor" . a owl:Class; rdfs:label "obsolete_antigen binding function"; rdfs:subClassOf ; "adapted from GO:antigen binding (MF)"; "a molecular binding function inhereing in an adaptive immune receptor complex that was produced to bind selectively and non-covalently with an antigen - any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen."; "replaced by GO: antigen binding function" . a owl:Class; rdfs:label "obsolete_molecular binding function"; rdfs:subClassOf ; "a function inhereing in some molecular entity that was generated for the purpose of selectively and non-covalently associating with some other molecular entity."; "replaced by GO:binding (relabeled as moelcular binding function)" . a owl:Class; rdfs:label "obsolete_immune response"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_T cell receptor complex"; rdfs:subClassOf ; "replaced with GO:T cell receptor complex" . a owl:Class; rdfs:label "obsolete_B cell receptor complex"; rdfs:subClassOf ; "replaced with GO:B cell receptor complex" . a owl:Class; rdfs:label "antigen"; owl:equivalentClass _:2eac39; rdfs:subClassOf , , _:2eac79, _:2eac89, _:2eac99; "any chemical entity that is recognized by an adaptive immune receptor, be it in the context of a functional immune response in some organism or biological system (endogenous antigen), or in the context of some experimental technique where this interaction is used to generate data or effect some response in the system being studied (experimental antigen)." . _:2eac39 a owl:Class; owl:intersectionOf _:2eac49 . _:2eac49 rdf:first ; rdf:rest _:2eac69 . _:2eac69 rdf:first _:2eac59; rdf:rest rdf:nil . _:2eac59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eac79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eac89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eac99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaca9 a owl:Axiom; "noet that beacause all antigens have_part some epitope, and an epitope 'is recognized by' some 'adaptive immune receptor complex, this axiom should be inferred using the proeprty chain: has_part o 'is recognized by' -> 'is recognized by'"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2eacb9 . _:2eacb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_epitope"; rdfs:subClassOf . a owl:Class; rdfs:label "experimental antibody target"; owl:equivalentClass _:2eacc9; rdfs:subClassOf , _:2ead49, _:2ead99; "material antibody target"; "a material which represents an intended target of some antibody reagent in some scientific technique"; rdfs:comment """This class allows us to talk about the material entity which an antibody is used to target in an experiment, even in cases where the actual antigen is not known (e.g. antibodies known to recognize a certain cell or organelle type, for example, but where the actual molecular antigen associated with these targets is not known). To qualify as an experimental antibody target, a material needs to have been demonstrated (or hypothesized based on structural homology) to be recognized by some antibody reagent. Note that, because the part_of relation is reflexive, it is acceptible for molecular or chemical antigens themselves to be experimental antibody targets (ie they are still part_of some experimental antigen, in that they are part_of themselves).""" . _:2eacc9 a owl:Class; owl:intersectionOf _:2eacd9 . _:2eacd9 rdf:first ; rdf:rest _:2eacf9 . _:2eacf9 rdf:first _:2eace9; rdf:rest rdf:nil . _:2eace9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ead09 . _:2ead09 a owl:Class; owl:intersectionOf _:2ead19 . _:2ead19 rdf:first ; rdf:rest _:2ead39 . _:2ead39 rdf:first _:2ead29; rdf:rest rdf:nil . _:2ead29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ead49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ead59 . _:2ead59 a owl:Class; owl:intersectionOf _:2ead69 . _:2ead69 rdf:first ; rdf:rest _:2ead89 . _:2ead89 rdf:first _:2ead79; rdf:rest rdf:nil . _:2ead79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ead99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_disposition to be bound by an adaptive immune receptor"; rdfs:subClassOf ; "replaced by OBI term" . a owl:Class; rdfs:label "obsolete_experimental antigen"; rdfs:subClassOf ; "OBI - same as assay antigen? (this is a class in OBI)"; rdfs:comment "Note that this class is not disjoint from endognous antigen. In cases where an immune response is stimulated by an antigen as part of some experiment (for example, in studying the immune response itself, or its byproducts), the antigen is an endogenous antigen and an experimental antigen."; "an antigen that is recognized by some antibody reagent in the context of some experimental technique, where this interaction allows probing or effecting of the molecular environment in the experimental system."; "For example, experimental antigen recognition can allow for localization or abundance of the analyte to be tracked, or can be used to effect some biological response on the part of the antigen (e.g. activation of some membrane receptor activity borne by the antigen, or inhibition of some enzymatic function borne by the antigen). Additionally, experimental antigen recognition can trigger an adaptive immune response, in cases where this process is studied or exploited as part of a technique."; """decided that the roles were sufficeint, and we could refer to such a class as experimental antigen with the class expression (antigen and has role some experimentsl antigen role). Also, this class was not inferring correctly as an antigen from some reason. prev axioms: 'has role' some 'experimental antigen role' and part_of some 'experimental antibody target'""" . a owl:Class; rdfs:label "obsolete_endogenous antigen"; rdfs:subClassOf ; """decided that the roles were sufficeint, and we could refer to such a class s endogneous antigen with the class expression (antigen and has role some endogneous antigen role) prev axoims: has role some endogenous antigen role"""; rdfs:comment "Note that this class is not disjoint from experimental antigen. In cases where an immune response is stimulated by an antigen as part of some experiment, the antigen is an endogenous antigen and an experimental antigen."; "OBI:antigen? - need to sort out their meaning of antigen vs assay antigen, and refine our modeling as well, before deciding on proper import strategy here"; "an antigen that is recognized by an adaptive immune receptor in the context of a functional immune system such that this interaction triggers an immune response" . a owl:Class; rdfs:label "obsolete_adaptive immune receptor complex"; rdfs:subClassOf ; "replaced by OBI:adaptive immune receptor"; "GO (this class should eventually come from GO, not OBI)" . a owl:Class; rdfs:label "immunotechnique"; owl:equivalentClass _:2eada9; rdfs:subClassOf , _:2eae29, _:2eae49; "a technique in which an antibody reagent is applied (typically to detect some target analyte and report on its presence, abundance, or location, however antibody reagents can also be used as effectors - for example to inhibit some moelcular activity, or stimulate some receptor)"; . _:2eada9 a owl:Class; owl:intersectionOf _:2eadb9 . _:2eadb9 rdf:first ; rdf:rest _:2eadd9 . _:2eadd9 rdf:first _:2eadc9; rdf:rest rdf:nil . _:2eadc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eade9 . _:2eade9 a owl:Class; owl:intersectionOf _:2eadf9 . _:2eadf9 rdf:first ; rdf:rest _:2eae19 . _:2eae19 rdf:first _:2eae09; rdf:rest rdf:nil . _:2eae09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eae29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eae39 . _:2eae39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eae49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eae59 . _:2eae59 a owl:Class; owl:intersectionOf _:2eae69 . _:2eae69 rdf:first ; rdf:rest _:2eae89 . _:2eae89 rdf:first _:2eae79; rdf:rest rdf:nil . _:2eae79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_experimental antibody target role"; rdfs:subClassOf ; "material antibody target role"; """decided this class was not necessary, and would define experimental antibody targets as has_part some (has_role some experimental antigen role). axioms: inheres_in some (material_entity and (has_part some 'experimental antigen')) is_realized_by some ('epitope binding by adaptive immune receptor' and (part_of some immunotechnique))"""; rdfs:comment """This class allows us to talk about the material entity which an antibody is used to target in an experiment, even in cases where the actual antigen is not known (e.g. antibodies known to recognize a certain cell or organelle type, for example, but where the actual molecular antigen associated with these targets is not known). As the part_of relation is reflexive, it is acceptible for antigens themselves to bear a material antibody target role, and thus be material antibody targets.""" . a owl:Class; rdfs:label "IgG immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG antibody" . a owl:Class; rdfs:label "IgG1 immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG1 antibody" . a owl:Class; rdfs:label "IgG2a immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG2a antibody" . a owl:Class; rdfs:label "IgG2b immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG2b antibody" . a owl:Class; rdfs:label "IgG2c immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG2c antibody" . a owl:Class; rdfs:label "IgG3 immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG3 antibody" . a owl:Class; rdfs:label "IgG4 immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgG4 antibody" . a owl:Class; rdfs:label "IgA immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgA antibody" . a owl:Class; rdfs:label "IgD immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgD antibody" . a owl:Class; rdfs:label "IgE immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgE antibody" . a owl:Class; rdfs:label "IgM immunoglobulin complex, circulating"; rdfs:subClassOf ; "IgM antibody" . a owl:Class; rdfs:label "IgG monoclonal antibody reagent"; rdfs:subClassOf , , _:2eae99, _:2eaea9 . _:2eae99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgG1 polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgG1 monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaeb9, _:2eaec9 . _:2eaeb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG2a monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaed9, _:2eaee9 . _:2eaed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG2a polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgG2b monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaef9, _:2eaf09 . _:2eaef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaf09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG2b polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgG2c monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaf19, _:2eaf29 . _:2eaf19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaf29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG2c polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgG3 monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaf39, _:2eaf49 . _:2eaf39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaf49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG3 polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgG4 monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaf59, _:2eaf69 . _:2eaf59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaf69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgG4 polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgA monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaf79, _:2eaf89 . _:2eaf79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eaf89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgA polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgD monoclonal antibody reagent"; rdfs:subClassOf , , _:2eaf99, _:2eafa9 . _:2eaf99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eafa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgD polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgE monoclonal antibody reagent"; rdfs:subClassOf , , _:2eafb9, _:2eafc9 . _:2eafb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eafc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgE polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "IgM monoclonal antibody reagent"; rdfs:subClassOf , , _:2eafd9, _:2eafe9 . _:2eafd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eafe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "IgM polyclonal antibody reagent"; rdfs:subClassOf ; """Isotypes of polyclonal antibody reagents are never specified (because are heterogenous, but are predominantly IgG) Was a child of its relevantantibody> Ig_ antibody class, and had superclass axioms: has_role some reagent role and is_specified_output_of some ('polyclonal antibody production' or 'antibody collection technique')""" . a owl:Class; rdfs:label "obsolete_antibody collection technique"; rdfs:subClassOf ; "any material processing technique with the objective to collect from input material some material containing antibodies for use in an experimental context (ie as a specimen or reagent). This can include collection of serum from some organism, which can be further processed to yield a purified preparation of antibodies."; """replaced with OBI: collecting specimen from organism / specimen collection from organism former subclass axioms: 'material processing technique' achieves_objective_specification some 'specimen collection objective' has_specified_output some 'antibody reagent'""" . a owl:Class; rdfs:label "obsolete_immunogenic reagent"; rdfs:subClassOf ; """Decided was not absolutely necessary for now (only usage was in immunization technique), and was looking out of sorts in the inferred regent hierarchy. Former eq class axiom: 'immunogenic material' and ('has role' some ('reagent role' and ('is realized by' only 'immunization technique'))) Former superclass axioms: 'has role' some ('immunogen role' and ('is realized by' some (proper_part_of some technique))) and 'has role' some 'material to be added role' and is_specified_output_of some 'material processing'"""; rdfs:comment "an immunogenic reagent is an immunogenic material that is applied in an investigation. Its reagent role is most often realized in an antibody production technique, where the imunogenic reagent is used to immunize an organism which will produce an antibody reagent. However, its reagent role can also be realized in an assay to study immune system function, where the immunogenic reagent is applied to trigger an immune response that is under investigation"; "an immunogenic material that is applied as a reagent in some immunization technique to facilitate the controlled production of an antibody, or the study of some immunological process triggered by the immunogen. "; . a owl:Class; rdfs:label "antigen role"; owl:equivalentClass _:2eaff9; rdfs:subClassOf , _:2eb039, _:2eb049; "would appear to be a biological role, as it is realilzed in a biological process . . . even for experimental antigens, this role is realized by a biological process that occurs as part of an experimental technique (in as much as recognition of a protein on a W blot can be considered a biological process? It does realize a biological function - so this could be criteria for it being a biological role)" . _:2eaff9 a owl:Class; owl:intersectionOf _:2eb009 . _:2eb009 rdf:first ; rdf:rest _:2eb029 . _:2eb029 rdf:first _:2eb019; rdf:rest rdf:nil . _:2eb019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "antigenic material"; owl:equivalentClass _:2eb059; rdfs:subClassOf , _:2eb099; "any material entity that has as part some chemical/molecular component that is recognized by an adaptive immune receptor (ie has as part some antigen)" . _:2eb059 a owl:Class; owl:intersectionOf _:2eb069 . _:2eb069 rdf:first ; rdf:rest _:2eb089 . _:2eb089 rdf:first _:2eb079; rdf:rest rdf:nil . _:2eb079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb099 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "immunogenic material"; owl:equivalentClass _:2eb0a9; rdfs:subClassOf , _:2eb0e9, _:2eb0f9, _:2eb149; "a material entity that has part some immunogen. The immunogen bears an immunogen role which is realized in the process of its epitope recognition by an immune receptor initiating an adpative immune response."; rdfs:comment "immunogens are different from immunogenic materials in that they are fundamentally chemical or molecular entities, while immunogenic materials can include larger, more complex materials such as cells or organisms that contain as part some molecular immunogen." . _:2eb0a9 a owl:Class; owl:intersectionOf _:2eb0b9 . _:2eb0b9 rdf:first ; rdf:rest _:2eb0d9 . _:2eb0d9 rdf:first _:2eb0c9; rdf:rest rdf:nil . _:2eb0c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb0e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb0f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb109 . _:2eb109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb119 . _:2eb119 a owl:Class; owl:unionOf _:2eb129 . _:2eb129 rdf:first ; rdf:rest _:2eb139 . _:2eb139 rdf:first ; rdf:rest rdf:nil . _:2eb149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_immunogenic study subject"; rdfs:subClassOf ; rdfs:comment "Imunogenic study subjects/specimens bear both an immunogen role and a study subject role, and as such are the subject of study in some investigation where their immunogenic properties are examined (e.g a study of immunogen processing by the lysosome, or epitope-immune receptor binding affinity)."; "an immunogen or immunogenic material that is studied in an investigation."; """Obsoleted immunogenic reagent, so obsoleted this one too for now. Former eq class axiom: 'immunogenic material' and ('has role' some 'study subject role') Former superclass axiom: 'has role' some ('immunogen role' and ('is realized by' some (part_of some investigation)))"""; . a owl:Class; rdfs:label "clonal cell culture"; owl:equivalentClass _:2eb159; rdfs:subClassOf , _:2eb199, _:2eb1a9; "OBI:clonal cell culture"; "an cell culture that derives from a single cell that is isolated from some population of cells and expanded in culture."; . _:2eb159 a owl:Class; owl:intersectionOf _:2eb169 . _:2eb169 rdf:first ; rdf:rest _:2eb189 . _:2eb189 rdf:first _:2eb179; rdf:rest rdf:nil . _:2eb179 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2eb199 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb1a9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "obsolete_immunogenic research material"; rdfs:subClassOf ; "an immunogen that is applied as a reagent in an antibody production technique, or that is studied as the subject of an investigation or assay"; """decided not needed for now, but can bring back later if I want had eq class axiom: material_entity and ('has role' some 'research material role') and (has_part some immunogen) and superclass axiom: has_part some (immunogen and ('has role' some ('immunogen role' and ('is realized by' some (part_of some technique)))))""" . a owl:Class; rdfs:label "obsolete_contextual material component separation objective"; rdfs:subClassOf ; "an objective to obtain an appendix specimen, through separating the appendix from an organism (by contrast, an objective to obtain an organism missing its appendix through this same separation process achieves a 'physical material component separation objective')"; """an objective to obtain 'separated material', representing specified component(s) removed from some target of material component separation, in such a way that the separated material has undergone a change in context or location, but remains unaltered in its self-contained physical structure and composition. (ie it has been 're-located' from being 'part of' or 'contained in' some larger material) (for clearer understanding here, contrast with the definition and examples of 'physical material compoennt separation objective')"""; """8-2-12 - no longer needed after implementing new approach for modeling experimental modification former superclass axioms : 'material component separation objective' part_of some ('plan specification' and (has_part some ('action specification' and (specifies_occurrence_of some (has_specified_output some ('has role' some 'obsolete_separated material role'))))))""" . a owl:Class; rdfs:label "obsolete_separated material role"; rdfs:subClassOf ; "a role inhering in a material entity that is realized through the separation of the bearer from some greater target of material component separation"; "8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles"; "compliments the 'target of material component separation role' in modeling the outputs of a material component separation process" . a owl:Class; rdfs:label "obsolete_material extraction objective"; rdfs:subClassOf ; "decided not needed - merge with mateiral component separation? "; "material isolation objective"; "A material component separation objective to separate a desired component of an input material from the remainder"; rdfs:comment "Note that this differs from a purification, where the objective is simply to obtain a more pure/concentrated output with respect to some desired components. Extraction attempts to obtain only some specified components of the input material (ie a pure material - however in practice the output extract is rarely pure)."; "OBI:extraction" . a owl:Class; rdfs:label "target of material removal role"; rdfs:subClassOf , _:2eb1b9; "a target of modification role that inheres in an entity from which material is removed in a material component separation process. This component separation process is 'asymmetric', in that the separated material exhibits a differential composition from the target from which it was removed (ie one or more specified parts of the target become discriminately and differentially segregated between the outputs of this separation process)"; "target of material component separation role" . _:2eb1b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb1c9 . _:2eb1c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_collected material role"; rdfs:subClassOf ; "8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles" . a owl:Class; rdfs:label "obsolete_purified material role"; rdfs:subClassOf ; "8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles" . a owl:Class; rdfs:label "obsolete_portioned material role"; rdfs:subClassOf ; "8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles" . a owl:Class; rdfs:label "obsolete_selected material role"; rdfs:subClassOf ; "8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles" . a owl:Class; rdfs:label "obsolete_physical material component separation objective"; rdfs:subClassOf ; "an objective to obtain an organism missing its appendix, through separating the appendix from the organism (by contrast, an objective to obtain an appendix specimen through this same separation process achieves a contextual material component separation objective)"; """an objective to modify some 'target of material component separation' by removing some specified portion of its physical material (ie to obtain a physically modified version of some input material through a discriminating/asymmetric separation of specified components from the 'unmodified' input material) (for clearer understanding here, contrast with the definition and examples of 'contextual material compoennt separation objective') --- (objective to obtain a physically modified version of some input material, in virtue of its having lost material through some asymmetric material component separation process)"""; """8-2-12 - no longer needed after implementing new approach for modeling experimental modification repv superclass axioms: 'material component separation objective' part_of some ('plan specification' and (has_part some ('action specification' and (specifies_occurrence_of some (has_specified_output some ('has role' some 'target of material removal role')))))) . . . (very experimental axiom here - relies on the assumption that we can say a material still bears the target of material separation role after this role is realized.)""" . a owl:Class; rdfs:label "obsolete_specified output role"; rdfs:subClassOf ; """8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles former eq class axiom: 'ascribed role' and ('is realized by' some 'outputting of a material participant') former superclass axiom: 'inheres in' only (is_specified_output_of some (technique or (part_of some technique))) 'inheres in' some (is_specified_output_of some (technique or (part_of some technique)))"""; . a owl:Class; rdfs:label "obsolete_combined material role"; rdfs:subClassOf ; "a role inhering in a material entity that is realized through the combination of the bearer with some target of material combination"; "relocated material role?"; "replaced with new combined material class" . a owl:Class; rdfs:label "obsolete_delivered material role"; rdfs:subClassOf ; """8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles 'inheres in' some (is_specified_output_of some (achieves_objective_specification some 'material delivery objective')) 'is realized by' some (achieves_objective_specification some 'material delivery objective')"""; "relocated material role?" . a owl:Class; rdfs:label "obsolete_pooled material role"; rdfs:subClassOf ; """8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles 'inheres in' some (is_specified_output_of some (achieves_objective_specification some 'material pooling objective')) 'is realized by' some (achieves_objective_specification some 'material pooling objective')""" . a owl:Class; rdfs:label "obsolete_combined material role"; rdfs:subClassOf ; "a role inhering in a material entity that is realized through its being specified output from a material combiantion process"; """8-2-12 - Implemented new approach for modeling experimentally modified entities that does not and will not require these roles former superclass axiom: 'is realized by' some ('outputting of a material participant' and (part_of some (achieves_objective_specification some 'material combination objective')))""" . a owl:Class; rdfs:label "obsolete_contextual material separation technique"; rdfs:subClassOf ; """3-24-12: was a test class that is no longer wanted had necc axioms: achieves_objective_specification some 'contextual material component separation objective' and has_specified_output some (has_role some 'separated material role')""" . a owl:Class; rdfs:label "material pooling objective"; rdfs:subClassOf ; rdfs:comment """material poolings do not have an input 'target of material addition' that becomes modified through the pooling process. Rather, inputs are combined in such a way that they loose their identity as independent entities, and become part of a new entity created through the pooling process. For this reason, we are not able to consider the relative fates of a 'target of material addition' and a 'material to be added', and thus unable to subclass the material pooling objective into 'contextual' vs 'physical' children as is done for it sibling 'material component combination objective'."""; "a material combination objective to combine more than one input material, typically of similar composition or origin, to obtain a new entity (ie the specified output is distinct in identity from any of the specified inputs) ." . a owl:Class; rdfs:label "obsolete_contextual material combination with target objective"; rdfs:subClassOf ; "an objective to modify the context in which a pathogen is found, through injection of a pathogen into a model organism's blood stream (thus allowing study of the pathogen's response to being inside a host)"; "an objective to place some 'material to be added' in a new context or location within or as part of a 'target of material addition', in such a way that no physical modifications are made to its internal, self-contained structure or composition."; rdfs:comment "The key to distinguishing a 'physical' from 'contextual' combination objective is to consider what the specified output is of the material combination process (ie what is the output of interest for study or use by the investigator?). If this output is the target of material addition that is now modified in virtue of containing more material, then the combination process achieves a 'physical' combination objective. Rather, if the output of interest is the material to be added that is now in to be studied or used in some new context or location, then the material combination achieves a 'contextual' combination objective." . a owl:Class; rdfs:label "obsolete_physical material combination with target objective"; rdfs:subClassOf ; "an objective to modifiy a model orgnaism through injection of a pathogen into the organism's blood stream (allowing study of the organism's response to infection)"; rdfs:comment "The key to distinguishing a 'physical' from 'contextual' combination objective is to consider what the specified output is of the material combination process (ie what is the output of interest for study or use by the investigator?). If this output is the target of material addition that is now modified in virtue of containing more material, then the combination process achieves a 'physical' combination objective. Rather, if the output of interest is the material to be added that is now in to be studied or used in some new context or location, then the material combination achieves a 'contextual' combination objective."; "an objective to modify some 'target of material addition'' by adding material to its physical make-up (ie to obtain a physically modified version of the input target, in virtue of its containing new material)." . a owl:Class; rdfs:label "obsolete_material decontamination objective"; rdfs:subClassOf . a owl:Class; rdfs:label "material fractionation objective"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_material delivery objective"; rdfs:subClassOf ; "a contextual material combination with target objective to deliver some material to be combined to a new location within some target of material combination (such that this material can be studied or used based on its new context)"; "material re-location objective" . a owl:Class; rdfs:label "obsolete_material addition objective"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_material attachment objective"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_separant role"; rdfs:subClassOf ; """former superclass axiom: 'is realized by' some ('material processing' and (achieves_objective_specification some 'material separation objective'))"""; "material to be separated role" . a owl:Class; rdfs:label "test class 1"; rdfs:subClassOf . a owl:Class; rdfs:label "test class 2"; rdfs:subClassOf . a owl:Class; rdfs:label "test class 3"; rdfs:subClassOf . a owl:Class; rdfs:label "specimen preparation objective"; rdfs:subClassOf ; "NIF has a 'specimen preparation' class, but it is not defined"; "a material processing objective to prepare a material entity for input into an assay in which it will serve as a specimen about which data will be generated" . a owl:Class; rdfs:label "specimen preparation technique"; owl:equivalentClass _:2eb1d9; rdfs:subClassOf , _:2eb219; "NIF has a 'specimen preparation' class, but it is not defined" . _:2eb1d9 a owl:Class; owl:intersectionOf _:2eb1e9 . _:2eb1e9 rdf:first ; rdf:rest _:2eb209 . _:2eb209 rdf:first _:2eb1f9; rdf:rest rdf:nil . _:2eb1f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_material genetic sequence bearer"; rdfs:subClassOf ; "a material_entity in which a concretization of some genetic sequence region inheres"; rdfs:comment "Can be nucleic acid or protein encoding a genetic sequence region, or a reagent such as a primer or expresison construct or recombinant protein that encodesa genetic sequence region. This genetic sequence may or may not represent that of a naturally occuring gene."; """merged with information macromolecule had eq class axiom : material_entity and ('is bearer of' some (concretizes some 'genetic sequence region'))""" . a owl:Class; rdfs:label "engineered"; rdfs:subClassOf , _:2eb229; rdfs:comment "The key feature here is that some aspect of the structure of any bearer of this quality was designed or specified in some way by an intentional agent."; """Bearers of this quality can include artificial molecules with no naturally-occurring counterpart (e.g. syntheitic drugs such as methotrexate), and molecules designed to exactly reproduce naturally-occurring molecules (e.g. chemically synthesized amino acids, chemically synthesized natural products). Several additional examples are provided below relating to bioengineered proteins (as this is the most common application for the 'engineered' quality): 1. A recombinant protein is considered bioengineered, as its sequence is precisely and completely specified through the engineering of a recombinant DNA construct, which serves as the genetic template for transcription and translation processes used to generate the recombinant protein 2. An antibody reagent produced through an antibody production technique where an organism is exposed to an immunogen with the intent of exploiting the adaptive immune response to produce an antibody that will bear a sequence in its paratope which recognizes the immunogen designed and used in its production 3. A non-example is insulin generated through the stimulation of a pancreatic beta cell line with glucose in order to stimulate its secretion. Here, the insulin produced is not considered 'bioengineered', because despite being output from some planned process, its sequence was not designed or engineered in any way by an intentional agent. Cell lines are also non-examples, as the production of the line itself is not through a biological process, but through some 'establishing cell culture'. (cell culture cells, on the other hand, might be considered bioengineered)"""; "engineered"; "a quality inhering in a material whose structural composition is at least partially designed or engineered by some intentional agent, and produced as part of some planned process" . _:2eb229 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb239 . _:2eb239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb249 . _:2eb249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "synthetic"; rdfs:subClassOf . a owl:Class; rdfs:label "bioengineered"; rdfs:subClassOf , , _:2eb259; "a quality inhereing in some material entity whose structual composition is in some way designed or engineered by some agent, and which is produced through some biological process that is co-opted as part of a material processing technique to produce this designed product of interest"; """Several examples are provided below relating to bioengineered proteins (as this is the most common application for the 'bioengineered' quality): A recombinant protein is considered bioengineered, as its sequence is precisely and completely specified through the engineering of a recombinant DNA construct, which serves as the genetic template for transcription and translation processes used to generate the recombinant protein An antibody reagent produced through an antibody production technique where an organism is exposed to an immunogen with the intent of exploiting the adaptive immune response to produce an antibody that will bear a sequence in its paratope which recognizes the immunogen designed and used in its production A non-example is insulin generated through the stimulation of a pancreatic beta cell line with glucose in order to stimulate its secretion. Here, the insulin produced is not considered 'bioengineered', because despite being output from some planned process, its sequence was not designed or engineered in any way by an intentional agent. Another non-example is a cell line, as this is not generated through a biological process (despite having only biologically occurring materials as parts) . . . as 'establishing a cell line' is not a biological process""" . _:2eb259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb269 . _:2eb269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb279 . _:2eb279 a owl:Class; owl:intersectionOf _:2eb289 . _:2eb289 rdf:first ; rdf:rest _:2eb2a9 . _:2eb2a9 rdf:first _:2eb299; rdf:rest rdf:nil . _:2eb299 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "synthetic oligopeptide"; rdfs:subClassOf ; "synthetic peptide"; "a synthetic polypeptide of relatively low molecular weight, typically consisting of 50 or fewer amino acid residues" . a owl:Class; rdfs:label "synthetic polyamino acid"; rdfs:subClassOf ; "http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/general-polyamino-acids-faq.html#1"; "a synthetic peptide that is of relative high molecular weight (typically more than 50 amino acid residues long)" . a owl:Class; rdfs:label "synthetic homo-polyamino acid"; rdfs:subClassOf ; "http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/general-polyamino-acids-faq.html#1"; "a synthetic polyamino acid made up of a single amino acid residue as the repeating unit" . a owl:Class; rdfs:label "manufacturing objective"; owl:equivalentClass _:2eb2b9; rdfs:subClassOf , _:2eb319; "this 'manufacturing objective' class is distinct from OBI:device creation objective in that not all 'manufactured' materials must be devices. For example, chemicals synthesis can be considered a moelcular-scale manufacturing process that does not prodcue a device. May want to consider a different label (engineering objective, material production objective?), as manufacturing has connotations associates with large scale mass-production, and connotations associated with production devices or instruments as opposed to chemicals."; "the objective to produce some processed material output according to some design specification describing its structure, composition, and function"; """OBI: why is OBI:device creation objective not a child of OBI:manufacturing objective? Can i use the OBI:manufacturing objective class here (is already in Obsolete classes in ReO)? does it cover things like molecular synthesis, or ornly larger scale production efforts?"""; rdfs:comment "manufactured objects can result from material combinations or separations." . _:2eb2b9 a owl:Class; owl:intersectionOf _:2eb2c9 . _:2eb2c9 rdf:first ; rdf:rest _:2eb2e9 . _:2eb2e9 rdf:first _:2eb2d9; rdf:rest rdf:nil . _:2eb2d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb2f9 . _:2eb2f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb309 . _:2eb309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb319 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb329 . _:2eb329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb339 . _:2eb339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "naturally-produced protein reagent"; owl:equivalentClass _:2eb349; rdfs:subClassOf , , _:2eb3b9, _:2eb3c9; owl:disjointWith ; "testing this as a primary axis of classification, disjoint form 'bioengineered protein reagent'"; "a protein whose structural composition and design is entirely the result of natural processes, and not engineered in any way by some intentional agent."; . _:2eb349 a owl:Class; owl:intersectionOf _:2eb359 . _:2eb359 rdf:first ; rdf:rest _:2eb379 . _:2eb379 rdf:first _:2eb369; rdf:rest _:2eb3a9 . _:2eb369 a owl:Class; owl:complementOf _:2eb389 . _:2eb389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb3a9 rdf:first _:2eb399; rdf:rest rdf:nil . _:2eb399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb3b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb3c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb3d9 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2eb3e9 . _:2eb3e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "bioengineered protein reagent"; owl:equivalentClass _:2eb3f9; rdfs:subClassOf , _:2eb489, _:2eb4d9, _:2eb4e9, _:2eb4f9; "a polypeptide reagent (protein or protein complex) that is produced through some bioengineering technique, in which some biological protein synthesis is intentionally and manipulated by an agent in such a way as to determine or impact the sequence of the specified protein output from this process", "testing this as a primary axis of classification, disjoint form 'naturally-produced protein reagent'", "Note that 'polyclonal andtibody does not classify here because unlike monoclonal antibodies, they are not necessarily output from an 'antibody production' bioengineering technique (ie in some cases, they are collected from natural sources and then applied experimentally as reagents)"; . _:2eb3f9 a owl:Class; owl:intersectionOf _:2eb419 . _:2eb419 rdf:first _:2eb409; rdf:rest _:2eb459 . _:2eb409 a owl:Class; owl:unionOf _:2eb429 . _:2eb429 rdf:first ; rdf:rest _:2eb439 . _:2eb439 rdf:first ; rdf:rest rdf:nil . _:2eb459 rdf:first _:2eb449; rdf:rest _:2eb479 . _:2eb449 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb479 rdf:first _:2eb469; rdf:rest rdf:nil . _:2eb469 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb499 . _:2eb499 a owl:Class; owl:unionOf _:2eb4a9 . _:2eb4a9 rdf:first ; rdf:rest _:2eb4c9 . _:2eb4c9 rdf:first _:2eb4b9; rdf:rest rdf:nil . _:2eb4b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb4d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb4e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb4f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb509 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2eb519 . _:2eb519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant protein reagent"; owl:equivalentClass _:2eb529; rdfs:subClassOf , _:2eb569, _:2eb579, _:2eb589; "a bioengineered protein that is translated from a recombinant DNA construct" . _:2eb529 a owl:Class; owl:intersectionOf _:2eb539 . _:2eb539 rdf:first ; rdf:rest _:2eb559 . _:2eb559 rdf:first _:2eb549; rdf:rest rdf:nil . _:2eb549 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb569 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb599 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2eb5a9 . _:2eb5a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant"; rdfs:subClassOf ; rdfs:comment "typically inheres in a protein that is produced in cultured cells or tissue using a recombinant protein expression construct " . a owl:Class; rdfs:label "obsolete_enzymatically manufactured"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_bioengineering technique"; rdfs:subClassOf ; """an antibody production technique where an organism is immunized and its serum collected. Here, some intentional agent directly manipulates the natural process of an 'adaptive immune response' by introducing a immunogenic material, to trigger the biological production of antibodies according to the specifications of a planned process. a recombinant protein production technique whereby the source genetic material used in the biological process of protein translation is artificially engineered to generate a specifiec protein of interest"""; "a material processing technique whereby a natural biological process is intentionally and specifically triggered or manipulated by some agent to produce some specified product that is output from this biological process"; "decided not needed yet, and tricky to define - so jsut going with bioengineered protein production for now" . a owl:Class; rdfs:label "social role"; rdfs:subClassOf ; "student role, employee role, reagent role "; "a role that inheres in a bearer in virtue of its context in a social order or set of conventions, that is conferred through the intentions of one or more social agents. A social role can be gained 'actively' by an agent through the agents own actions or intentions (an 'achieved role'), or 'passively' by an entity as a result of the bearer being assigned the role by some external agent or social convention that specifies some intended use by the agent or some status conferred by the agent (an 'ascribed role')."; "http://en.wikipedia.org/wiki/Role"; "intentional role" . a owl:Class; rdfs:label "contractual role"; rdfs:subClassOf ; "an achieved role that inheres in a bearer as the result of a bilateral agreement or social contract between parties/agents" . a owl:Class; rdfs:label "unmodified native cell"; owl:equivalentClass _:2eb5b9; rdfs:subClassOf , _:2eb5f9; "a native cell that has not been experimentally modified, and thus exhibits a physical structure and internal biochemical metabolism that are the result of natural processes"; "CL - confirm that this would be the parent of their 'cell by organism' and 'cell by class' organizational classes" . _:2eb5b9 a owl:Class; owl:intersectionOf _:2eb5c9 . _:2eb5c9 rdf:first ; rdf:rest _:2eb5e9 . _:2eb5e9 rdf:first _:2eb5d9; rdf:rest rdf:nil . _:2eb5d9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . _:2eb5f9 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "unit label"; rdfs:subClassOf ; . a owl:Class; rdfs:label "value specification unit label"; owl:equivalentClass _:2eb609; rdfs:subClassOf , _:2eb689; "OBI (discuss distinction I am making (with unit labels and with value specification vs measurement data ICEs and with related object properties as well) between measured and specified data)"; . _:2eb609 a owl:Class; owl:intersectionOf _:2eb619 . _:2eb619 rdf:first ; rdf:rest _:2eb639 . _:2eb639 rdf:first _:2eb629; rdf:rest rdf:nil . _:2eb629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb649 . _:2eb649 a owl:Class; owl:intersectionOf _:2eb659 . _:2eb659 rdf:first ; rdf:rest _:2eb679 . _:2eb679 rdf:first _:2eb669; rdf:rest rdf:nil . _:2eb669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb699 . _:2eb699 a owl:Class; owl:intersectionOf _:2eb6a9 . _:2eb6a9 rdf:first ; rdf:rest _:2eb6c9 . _:2eb6c9 rdf:first _:2eb6b9; rdf:rest rdf:nil . _:2eb6b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_inputting of a material participant"; rdfs:subClassOf . a owl:Class; rdfs:label "macromolecule length unit"; owl:equivalentClass _:2eb6d9; rdfs:subClassOf ; . _:2eb6d9 a owl:Class; owl:oneOf _:2eb6e9 . _:2eb6e9 rdf:first ; rdf:rest _:2eb6f9 . _:2eb6f9 rdf:first ; rdf:rest _:2eb709 . _:2eb709 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "nucleic acid sequence region"; owl:equivalentClass _:2eb719; rdfs:subClassOf , _:2eb789; "a genetic sequence region that is encoded in a nucleic acid molecule" . _:2eb719 a owl:Class; owl:intersectionOf _:2eb729 . _:2eb729 rdf:first ; rdf:rest _:2eb749 . _:2eb749 rdf:first _:2eb739; rdf:rest rdf:nil . _:2eb739 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eb759 . _:2eb759 a owl:Class; owl:unionOf _:2eb769 . _:2eb769 rdf:first ; rdf:rest _:2eb779 . _:2eb779 rdf:first ; rdf:rest rdf:nil . _:2eb789 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eb799 . _:2eb799 a owl:Class; owl:unionOf _:2eb7a9 . _:2eb7a9 rdf:first ; rdf:rest _:2eb7b9 . _:2eb7b9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "polypeptide sequence region"; owl:equivalentClass _:2eb7c9; rdfs:subClassOf , _:2eb839; "amino acid sequence region"; "a genetic sequence region that is determined by the order of amino acids in a polypeptide molecule"; "SO:polypeptide? (not SO:polypeptide region, becasue this is defined as part_of some polypeptide)" . _:2eb7c9 a owl:Class; owl:intersectionOf _:2eb7d9 . _:2eb7d9 rdf:first ; rdf:rest _:2eb7f9 . _:2eb7f9 rdf:first _:2eb7e9; rdf:rest rdf:nil . _:2eb7e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eb809 . _:2eb809 a owl:Class; owl:unionOf _:2eb819 . _:2eb819 rdf:first ; rdf:rest _:2eb829 . _:2eb829 rdf:first ; rdf:rest rdf:nil . _:2eb839 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eb849 . _:2eb849 a owl:Class; owl:unionOf _:2eb859 . _:2eb859 rdf:first ; rdf:rest _:2eb869 . _:2eb869 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "experimentally modified cell"; owl:equivalentClass _:2eb879; rdfs:subClassOf , , _:2eb8b9, _:2eb8c9; "a cell that is the specified output of an experimental modification technique that introduces physical changes to the cell (ie changes in composition and/or internal structural arrangement)"; . _:2eb879 a owl:Class; owl:intersectionOf _:2eb889 . _:2eb889 rdf:first ; rdf:rest _:2eb8a9 . _:2eb8a9 rdf:first _:2eb899; rdf:rest rdf:nil . _:2eb899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb8b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb8c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb8d9 . _:2eb8d9 a owl:Class; owl:intersectionOf _:2eb8e9 . _:2eb8e9 rdf:first ; rdf:rest _:2eb909 . _:2eb909 rdf:first _:2eb8f9; rdf:rest rdf:nil . _:2eb8f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb919 . _:2eb919 a owl:Class; owl:intersectionOf _:2eb929 . _:2eb929 rdf:first ; rdf:rest _:2eb949 . _:2eb949 rdf:first _:2eb939; rdf:rest rdf:nil . _:2eb939 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eb959 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2eb969 . _:2eb969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb979 . _:2eb979 a owl:Class; owl:intersectionOf _:2eb989 . _:2eb989 rdf:first ; rdf:rest _:2eb9a9 . _:2eb9a9 rdf:first _:2eb999; rdf:rest rdf:nil . _:2eb999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eb9b9 . _:2eb9b9 a owl:Class; owl:intersectionOf _:2eb9c9 . _:2eb9c9 rdf:first ; rdf:rest _:2eb9e9 . _:2eb9e9 rdf:first _:2eb9d9; rdf:rest rdf:nil . _:2eb9d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "simple lipid"; rdfs:subClassOf , _:2eb9f9, _:2eba49, _:2eba59, _:2eba69, _:2eba79; "fatty acids, waxes, triglycerides, and sterols"; "a lipid with a relatively simple structure comprised of only carbon, hydrogen, and oxygen atoms"; "http://www.mmeade.com/cheat/lipids.html" . _:2eb9f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eba09 . _:2eba09 a owl:Class; owl:intersectionOf _:2eba19 . _:2eba19 rdf:first ; rdf:rest _:2eba39 . _:2eba39 rdf:first _:2eba29; rdf:rest rdf:nil . _:2eba29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eba49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eba59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eba69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eba79 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eba89 . _:2eba89 a owl:Class; owl:intersectionOf _:2eba99 . _:2eba99 rdf:first ; rdf:rest _:2ebaa9 . _:2ebaa9 rdf:first ; rdf:rest _:2ebab9 . _:2ebab9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "hydrocarbon"; rdfs:subClassOf , _:2ebac9, _:2ebad9, _:2ebb19, _:2ebb69; "alkanes, alkenes, cycloalkanes "; "hydrocarbon lipid"; "an organic small molecule comprised only of carbon and hydrogen atoms"; "http://www.mmeade.com/cheat/lipids.html" . _:2ebac9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebad9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ebae9 . _:2ebae9 a owl:Class; owl:intersectionOf _:2ebaf9 . _:2ebaf9 rdf:first ; rdf:rest _:2ebb09 . _:2ebb09 rdf:first ; rdf:rest rdf:nil . _:2ebb19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ebb29 . _:2ebb29 a owl:Class; owl:intersectionOf _:2ebb39 . _:2ebb39 rdf:first ; rdf:rest _:2ebb59 . _:2ebb59 rdf:first _:2ebb49; rdf:rest rdf:nil . _:2ebb49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebb69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "complex lipid"; rdfs:subClassOf , _:2ebb79, _:2ebbc9, _:2ebbd9, _:2ebbe9; "http://www.mmeade.com/cheat/lipids.html"; "phosphoglycerides, phosphosphingolipids, and glycolipids"; "a lipid with a relatively complex structure comprised of carbon, hydrogen, oxygen, and at least one more type of atom (nitrogen, phosphorus, sulfur, etc) or containing some complex moiety such as a sugar or protein." . _:2ebb79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ebb89 . _:2ebb89 a owl:Class; owl:intersectionOf _:2ebb99 . _:2ebb99 rdf:first ; rdf:rest _:2ebbb9 . _:2ebbb9 rdf:first _:2ebba9; rdf:rest rdf:nil . _:2ebba9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebbc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebbd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebbe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "complex lipid reagent"; owl:equivalentClass _:2ebbf9; rdfs:subClassOf , , _:2ebc39; owl:disjointWith , ; "a lipid reagent comprised of carbon, hydrogen, oxygen, and at least one more type of atom (nitrogen, phosphorus, sulfur, etc) or containing some complex moiety such as a sugar or protein."; "phosphoglycerides, phosphosphingolipids, and glycolipids and derived reagents" . _:2ebbf9 a owl:Class; owl:intersectionOf _:2ebc09 . _:2ebc09 rdf:first ; rdf:rest _:2ebc29 . _:2ebc29 rdf:first _:2ebc19; rdf:rest rdf:nil . _:2ebc19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebc39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "hydrocarbon reagent"; owl:equivalentClass _:2ebc49; rdfs:subClassOf , , _:2ebc89; owl:disjointWith ; "an organic small molecule reagent comprised only of carbon and hydrogen atoms. Hydrocarbons classify as lipids as they are soluble in non-polar solvents."; "alkane, alkene, cycloalkane based reagents" . _:2ebc49 a owl:Class; owl:intersectionOf _:2ebc59 . _:2ebc59 rdf:first ; rdf:rest _:2ebc79 . _:2ebc79 rdf:first _:2ebc69; rdf:rest rdf:nil . _:2ebc69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebc89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "simple lipid reagent"; owl:equivalentClass _:2ebc99; rdfs:subClassOf , , _:2ebcd9; "a lipid reagent with a relatively simple structure comprised of only carbon, hydrogen, and oxygen atoms"; "fatty acids, triglycerides, sterols and derved reagents" . _:2ebc99 a owl:Class; owl:intersectionOf _:2ebca9 . _:2ebca9 rdf:first ; rdf:rest _:2ebcc9 . _:2ebcc9 rdf:first _:2ebcb9; rdf:rest rdf:nil . _:2ebcb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebcd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular library"; owl:equivalentClass _:2ebce9; rdfs:subClassOf , _:2ebdc9, _:2ebe19, _:2ebe29; rdfs:comment "a reagent library that is a collection of stored molecular entities. Each molecular entity has associated information stored in some kind of database with information such as its structure, purity, quantity, and physiochemical characteristics." . _:2ebce9 a owl:Class; owl:intersectionOf _:2ebcf9 . _:2ebcf9 rdf:first ; rdf:rest _:2ebd19 . _:2ebd19 rdf:first _:2ebd09; rdf:rest _:2ebd79 . _:2ebd09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ebd29 . _:2ebd29 a owl:Class; owl:intersectionOf _:2ebd39 . _:2ebd39 rdf:first ; rdf:rest _:2ebd59 . _:2ebd59 rdf:first _:2ebd49; rdf:rest rdf:nil . _:2ebd49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebd79 rdf:first _:2ebd69; rdf:rest rdf:nil . _:2ebd69 a owl:Restriction; owl:onProperty ; owl:onClass _:2ebd89; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ebd89 a owl:Class; owl:intersectionOf _:2ebd99 . _:2ebd99 rdf:first ; rdf:rest _:2ebdb9 . _:2ebdb9 rdf:first _:2ebda9; rdf:rest rdf:nil . _:2ebda9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebdc9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ebdd9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ebdd9 a owl:Class; owl:intersectionOf _:2ebde9 . _:2ebde9 rdf:first ; rdf:rest _:2ebe09 . _:2ebe09 rdf:first _:2ebdf9; rdf:rest rdf:nil . _:2ebdf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebe19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebe29 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ebe39 . _:2ebe39 a owl:Class; owl:intersectionOf _:2ebe49 . _:2ebe49 rdf:first ; rdf:rest _:2ebe69 . _:2ebe69 rdf:first _:2ebe59; rdf:rest rdf:nil . _:2ebe59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "chemical library"; owl:equivalentClass _:2ebe79; rdfs:subClassOf , _:2ebf79, _:2ebfc9, _:2ebfd9; "A library of kinase inhibitors."; "a reagent library that is a collection of stored chemical reagents. Each chemical has associated information stored in some kind of database with information such as the chemical structure, purity, quantity, and physiochemical characteristics of the compound."; "http://en.wikipedia.org/wiki/Chemical_library" . _:2ebe79 a owl:Class; owl:intersectionOf _:2ebe89 . _:2ebe89 rdf:first ; rdf:rest _:2ebea9 . _:2ebea9 rdf:first _:2ebe99; rdf:rest _:2ebec9 . _:2ebe99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebec9 rdf:first _:2ebeb9; rdf:rest _:2ebf29 . _:2ebeb9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ebed9 . _:2ebed9 a owl:Class; owl:intersectionOf _:2ebee9 . _:2ebee9 rdf:first ; rdf:rest _:2ebf09 . _:2ebf09 rdf:first _:2ebef9; rdf:rest rdf:nil . _:2ebef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebf29 rdf:first _:2ebf19; rdf:rest rdf:nil . _:2ebf19 a owl:Restriction; owl:onProperty ; owl:onClass _:2ebf39; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ebf39 a owl:Class; owl:intersectionOf _:2ebf49 . _:2ebf49 rdf:first ; rdf:rest _:2ebf69 . _:2ebf69 rdf:first _:2ebf59; rdf:rest rdf:nil . _:2ebf59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebf79 a owl:Restriction; owl:onProperty ; owl:onClass _:2ebf89; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ebf89 a owl:Class; owl:intersectionOf _:2ebf99 . _:2ebf99 rdf:first ; rdf:rest _:2ebfb9 . _:2ebfb9 rdf:first _:2ebfa9; rdf:rest rdf:nil . _:2ebfa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebfc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ebfd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ebfe9 . _:2ebfe9 a owl:Class; owl:intersectionOf _:2ebff9 . _:2ebff9 rdf:first ; rdf:rest _:2ec019 . _:2ec019 rdf:first _:2ec009; rdf:rest rdf:nil . _:2ec009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "organism library"; owl:equivalentClass _:2ec029; rdfs:subClassOf , _:2ec109, _:2ec159, _:2ec1a9; "A reagent library consisting of a collection of organism reagents" . _:2ec029 a owl:Class; owl:intersectionOf _:2ec039 . _:2ec039 rdf:first ; rdf:rest _:2ec059 . _:2ec059 rdf:first _:2ec049; rdf:rest _:2ec0b9 . _:2ec049 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec069 . _:2ec069 a owl:Class; owl:intersectionOf _:2ec079 . _:2ec079 rdf:first ; rdf:rest _:2ec099 . _:2ec099 rdf:first _:2ec089; rdf:rest rdf:nil . _:2ec089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec0b9 rdf:first _:2ec0a9; rdf:rest rdf:nil . _:2ec0a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec0c9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec0c9 a owl:Class; owl:intersectionOf _:2ec0d9 . _:2ec0d9 rdf:first ; rdf:rest _:2ec0f9 . _:2ec0f9 rdf:first _:2ec0e9; rdf:rest rdf:nil . _:2ec0e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec109 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec119; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec119 a owl:Class; owl:intersectionOf _:2ec129 . _:2ec129 rdf:first ; rdf:rest _:2ec149 . _:2ec149 rdf:first _:2ec139; rdf:rest rdf:nil . _:2ec139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec159 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec169 . _:2ec169 a owl:Class; owl:intersectionOf _:2ec179 . _:2ec179 rdf:first ; rdf:rest _:2ec199 . _:2ec199 rdf:first _:2ec189; rdf:rest rdf:nil . _:2ec189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec1a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_organism reagent"; rdfs:subClassOf ; """for now, dont need this - because only use case for reagent library, and just say libraries can have components that are reagents or organisms previous logical def was : organism and has role some reagent role previous alt term was model organism"""; . a owl:Class; rdfs:label "obsolete_outputting of a material participant"; rdfs:subClassOf . a owl:Class; rdfs:label "multicellular organism cell in situ"; rdfs:subClassOf , _:2ec1b9; "a hepatocyte studied as part of a cultured liver tissue specimen. A leukocyte studied in the context of a whole blood sample."; "http://en.wikipedia.org/wiki/In_situ"; rdfs:comment """In biology, in situ means to examine the phenomenon exactly in place where it occurs (i.e. without moving it to some special medium). This phrase in situ when used in laboratory science such as cell science can mean something intermediate between in vivo and in vitro. For example, examining a cell within a whole organ intact and under perfusion may be in situ investigation. This would not be in vivo as the donor is sacrificed before experimentation, but it would not be the same as working with the cell alone (a common scenario for in vitro experiments)."""; "a multicellular organism cell that is located in its natural anatomical context, but the anatomical material supplying this context is no longer part of a living organism."; . _:2ec1b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec1c9 . _:2ec1c9 a owl:Class; owl:intersectionOf _:2ec1d9 . _:2ec1d9 rdf:first ; rdf:rest _:2ec1f9 . _:2ec1f9 rdf:first _:2ec1e9; rdf:rest rdf:nil . _:2ec1e9 a owl:Class; owl:complementOf _:2ec209 . _:2ec209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biological specimen"; owl:equivalentClass _:2ec219; rdfs:subClassOf , _:2ec279, _:2ec289, _:2ec299; "ERO:biological specimen (but may want to wait until ERO and OBI agree on a meaning for specimen, and I decide how I need/want it defined here)"; "anatomical specimen" . _:2ec219 a owl:Class; owl:intersectionOf _:2ec229 . _:2ec229 rdf:first ; rdf:rest _:2ec249 . _:2ec249 rdf:first _:2ec239; rdf:rest _:2ec269 . _:2ec239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec269 rdf:first _:2ec259; rdf:rest rdf:nil . _:2ec259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec279 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec289 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec299 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transfection agent role"; rdfs:subClassOf , _:2ec2a9, _:2ec2b9; "a reagent role inhereing in some molecular entity that is used to deliver foreign material (typically DNA) into a cell or organism." . _:2ec2a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ec2b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_foreign genomic sequence"; rdfs:subClassOf ; """Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class. former axiom : encoded in matterial bearer soem genetic material"""; rdfs:comment "This class essentially represents sequence encoded by any nucleic acid molecule or nucleic acid span that is experimentally introduced as genetic material into a cell or organism. This sequence is typically not represented in the reference genome of the host cell, and often it is trans-genomic - i.e. its sequence content is represented in the refernce genome of some organism other than that into which it is introduced. However, this sequence CAN represent a duplicaiton of sequence existing in the host cell's natural genome (ie the introduced nucleic acid encodes an additional copy of a sequence that IS part of a reference genome for the host cell's source organism) "; "experimental genomic sequence", "modified genomic sequence", "extra-genomic sequence"; "Note that the nucleic acid bearer of this sequence contained in a cell or organism in such a way as to be stably replicated in its host (and is therefore considered heritable 'genetic material'). Note also that we consider here only foreign genomic sequence that is the result of an experimental procedure (ie this class does not cover naturally occuring cases of genetic material transfered between organisms)"; "a genomic sequence region that is encoded by genetic material that is experimentally introduced into a cell or organism. Note that the bearer of such sequence is experimentally introduced 'genetic material', and therefore is necessarily: (1) a proper_part_of some host cell or organism; (2) heritable by the progeny of this host, such that the sequence content it encodes is stably propagated in subsequent generations of cells; and (3) not a 'natural' part of the host's physical genome."; """sequence information carreid by a exogneous transposon element introduced into the genomic DNA of some host cell. Regardless of whether this introduced material represented seqence found in the host cells genome or not, if is still considered to to carry extra-genomic information. For example, sequence found in a recombinant plasmid that represent an endogenous human gene and is stably overexpressed in a human cell line would represent extra-genomic sequence but not trans-genomic sequence. """ . a owl:Class; rdfs:label "obsolete_DNA analog"; rdfs:subClassOf ; "a DNA reagent that is engineered to exhibit structurally similarity to naturally-occurring DNA, such that it maintains some similar chemical properties and activity, while its structural differences allow probing or manipulation of the biochemical environment of the analog"; "deoxyribonucleic acid analog"; rdfs:comment "DNA analogs are comprised entirely of nucleotide analog residues. Polymers that contain only selected analog residues are still considered to be DNA nucleic acid molecules"; "locked nucleic acids (LNA), peptide nucleic acids (PNA)"; """decided was unnecessary for now, as most nucelic acid analogs arent indicated as being more specifically analogs of DNA vs RNA former eq class axiom : 'nucleic acid analog' and ('information macromolecule' and ('is bearer of' some ('analog function' and (towards some 'deoxyribonucleic acid'))))""" . a owl:Class; rdfs:label "obsolete_RNA analog"; rdfs:subClassOf ; "a DNA reagent that is engineered to exhibit structurally similarity to naturally-occurring RNA, such that it maintains some similar chemical properties and activity, while its structural differences allow probing or manipulation of the biochemical environment of the analog"; """decided was unnecessary for now, as most nucelic acid analogs arent indicated as being more specifically analogs of DNA vs RNA former eq class axiom: 'nucleic acid analog' and ('information macromolecule' and ('is bearer of' some ('analog function' and (towards some 'ribonucleic acid'))))"""; "ribonucleic acid analog" . a owl:Class; rdfs:label "known bioactives collection chemical library"; owl:equivalentClass _:2ec2c9 . _:2ec2c9 a owl:Class; owl:intersectionOf _:2ec2d9 . _:2ec2d9 rdf:first ; rdf:rest _:2ec2f9 . _:2ec2f9 rdf:first _:2ec2e9 . _:2ec2e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec309 . _:2ec309 a owl:Class; owl:intersectionOf _:2ec319 . _:2ec319 rdf:first ; rdf:rest _:2ec339 . _:2ec339 rdf:first _:2ec329 . _:2ec329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec349 . _:2ec349 a owl:Class; owl:intersectionOf _:2ec359 . _:2ec359 rdf:first ; rdf:rest _:2ec379 . _:2ec379 rdf:first _:2ec369; rdf:rest rdf:nil . _:2ec369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec339 rdf:rest rdf:nil . _:2ec2f9 rdf:rest _:2ec399 . _:2ec399 rdf:first _:2ec389; rdf:rest rdf:nil . _:2ec389 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec3a9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec3a9 a owl:Class; owl:intersectionOf _:2ec3b9 . _:2ec3b9 rdf:first ; rdf:rest _:2ec3d9 . _:2ec3d9 rdf:first _:2ec3c9; rdf:rest rdf:nil . _:2ec3c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec3e9 . _:2ec3e9 a owl:Class; owl:intersectionOf _:2ec3f9 . _:2ec3f9 rdf:first ; rdf:rest _:2ec419 . _:2ec419 rdf:first _:2ec409; rdf:rest rdf:nil . _:2ec409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf , _:2ec429, _:2ec4b9; "A chemical library that consists of chemicals known to exert a biological effect in living organisms or cells."; "PERSON: Matthew Brush"; "PERSON: Matthew Brush" . _:2ec429 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec439; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec439 a owl:Class; owl:intersectionOf _:2ec449 . _:2ec449 rdf:first ; rdf:rest _:2ec469 . _:2ec469 rdf:first _:2ec459; rdf:rest rdf:nil . _:2ec459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec479 . _:2ec479 a owl:Class; owl:intersectionOf _:2ec489 . _:2ec489 rdf:first ; rdf:rest _:2ec4a9 . _:2ec4a9 rdf:first _:2ec499; rdf:rest rdf:nil . _:2ec499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec4b9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec4c9 . _:2ec4c9 a owl:Class; owl:intersectionOf _:2ec4d9 . _:2ec4d9 rdf:first ; rdf:rest _:2ec4f9 . _:2ec4f9 rdf:first _:2ec4e9; rdf:rest rdf:nil . _:2ec4e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec509 . _:2ec509 a owl:Class; owl:intersectionOf _:2ec519 . _:2ec519 rdf:first ; rdf:rest _:2ec539 . _:2ec539 rdf:first _:2ec529; rdf:rest rdf:nil . _:2ec529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "natural product extracts chemical library"; owl:equivalentClass _:2ec549; rdfs:subClassOf , _:2ec6a9, _:2ec739; "A chemical library that consists of chemicals produced by and extracted from living organisms."; rdfs:comment "A natural products extracts chemical library can be used to screen for drug targets."; "PERSON: Matthew Brush"; "PERSON: Matthew Brush" . _:2ec549 a owl:Class; owl:intersectionOf _:2ec559 . _:2ec559 rdf:first ; rdf:rest _:2ec579 . _:2ec579 rdf:first _:2ec569; rdf:rest _:2ec619 . _:2ec569 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec589 . _:2ec589 a owl:Class; owl:intersectionOf _:2ec599 . _:2ec599 rdf:first ; rdf:rest _:2ec5b9 . _:2ec5b9 rdf:first _:2ec5a9; rdf:rest rdf:nil . _:2ec5a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec5c9 . _:2ec5c9 a owl:Class; owl:intersectionOf _:2ec5d9 . _:2ec5d9 rdf:first ; rdf:rest _:2ec5f9 . _:2ec5f9 rdf:first _:2ec5e9; rdf:rest rdf:nil . _:2ec5e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec619 rdf:first _:2ec609; rdf:rest rdf:nil . _:2ec609 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec629; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec629 a owl:Class; owl:intersectionOf _:2ec639 . _:2ec639 rdf:first ; rdf:rest _:2ec659 . _:2ec659 rdf:first _:2ec649; rdf:rest rdf:nil . _:2ec649 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec669 . _:2ec669 a owl:Class; owl:intersectionOf _:2ec679 . _:2ec679 rdf:first ; rdf:rest _:2ec699 . _:2ec699 rdf:first _:2ec689; rdf:rest rdf:nil . _:2ec689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec6a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec6b9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec6b9 a owl:Class; owl:intersectionOf _:2ec6c9 . _:2ec6c9 rdf:first ; rdf:rest _:2ec6e9 . _:2ec6e9 rdf:first _:2ec6d9; rdf:rest rdf:nil . _:2ec6d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec6f9 . _:2ec6f9 a owl:Class; owl:intersectionOf _:2ec709 . _:2ec709 rdf:first ; rdf:rest _:2ec729 . _:2ec729 rdf:first _:2ec719; rdf:rest rdf:nil . _:2ec719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec739 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec749 . _:2ec749 a owl:Class; owl:intersectionOf _:2ec759 . _:2ec759 rdf:first ; rdf:rest _:2ec779 . _:2ec779 rdf:first _:2ec769; rdf:rest rdf:nil . _:2ec769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec789 . _:2ec789 a owl:Class; owl:intersectionOf _:2ec799 . _:2ec799 rdf:first ; rdf:rest _:2ec7b9 . _:2ec7b9 rdf:first _:2ec7a9; rdf:rest rdf:nil . _:2ec7a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "synthetic chemical library"; owl:equivalentClass _:2ec7c9; rdfs:subClassOf , _:2ec929, _:2ec9b9; "A chemical library that consists solely of synthetic chemicals."; "PERSON: Matthew Brush"; "PERSON: Matthew Brush" . _:2ec7c9 a owl:Class; owl:intersectionOf _:2ec7d9 . _:2ec7d9 rdf:first ; rdf:rest _:2ec7f9 . _:2ec7f9 rdf:first _:2ec7e9; rdf:rest _:2ec899 . _:2ec7e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec809 . _:2ec809 a owl:Class; owl:intersectionOf _:2ec819 . _:2ec819 rdf:first ; rdf:rest _:2ec839 . _:2ec839 rdf:first _:2ec829; rdf:rest rdf:nil . _:2ec829 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec849 . _:2ec849 a owl:Class; owl:intersectionOf _:2ec859 . _:2ec859 rdf:first ; rdf:rest _:2ec879 . _:2ec879 rdf:first _:2ec869; rdf:rest rdf:nil . _:2ec869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec899 rdf:first _:2ec889; rdf:rest rdf:nil . _:2ec889 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec8a9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec8a9 a owl:Class; owl:intersectionOf _:2ec8b9 . _:2ec8b9 rdf:first ; rdf:rest _:2ec8d9 . _:2ec8d9 rdf:first _:2ec8c9; rdf:rest rdf:nil . _:2ec8c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec8e9 . _:2ec8e9 a owl:Class; owl:intersectionOf _:2ec8f9 . _:2ec8f9 rdf:first ; rdf:rest _:2ec919 . _:2ec919 rdf:first _:2ec909; rdf:rest rdf:nil . _:2ec909 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec929 a owl:Restriction; owl:onProperty ; owl:onClass _:2ec939; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ec939 a owl:Class; owl:intersectionOf _:2ec949 . _:2ec949 rdf:first ; rdf:rest _:2ec969 . _:2ec969 rdf:first _:2ec959; rdf:rest rdf:nil . _:2ec959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ec979 . _:2ec979 a owl:Class; owl:intersectionOf _:2ec989 . _:2ec989 rdf:first ; rdf:rest _:2ec9a9 . _:2ec9a9 rdf:first _:2ec999; rdf:rest rdf:nil . _:2ec999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ec9b9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ec9c9 . _:2ec9c9 a owl:Class; owl:intersectionOf _:2ec9d9 . _:2ec9d9 rdf:first ; rdf:rest _:2ec9f9 . _:2ec9f9 rdf:first _:2ec9e9; rdf:rest rdf:nil . _:2ec9e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eca09 . _:2eca09 a owl:Class; owl:intersectionOf _:2eca19 . _:2eca19 rdf:first ; rdf:rest _:2eca39 . _:2eca39 rdf:first _:2eca29; rdf:rest rdf:nil . _:2eca29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_transgenomic sequence 2"; rdfs:subClassOf ; "a nucleic acid sequence that is encoded by a 'foreign', heritable nucleic acid (ie the physical nucleic acid bearing this sequence is experimentally added to a host cell), where the sequence of this nucleic acid is not represented in a reference genome of the host cell's source organism."; "sequence of a mouse gene that is overexpressed in a human cell line. loxP sequence inserted to surrpound a gene to be excised in a knockout mouse. "; "Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class." . a owl:Class; rdfs:label "antibody conjugation technique"; rdfs:subClassOf , , _:2eca49, _:2eca59, _:2eca69, _:2ecab9 . _:2eca49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eca59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eca69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eca79 . _:2eca79 a owl:Class; owl:intersectionOf _:2eca89 . _:2eca89 rdf:first ; rdf:rest _:2ecaa9 . _:2ecaa9 rdf:first _:2eca99; rdf:rest rdf:nil . _:2eca99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ecac9 . _:2ecac9 a owl:Class; owl:intersectionOf _:2ecad9 . _:2ecad9 rdf:first ; rdf:rest _:2ecaf9 . _:2ecaf9 rdf:first _:2ecae9; rdf:rest rdf:nil . _:2ecae9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cancer model cell line"; owl:equivalentClass _:2ecb09; rdfs:subClassOf , _:2ecb49; "ERO - their definition (A cell line that is derived from a transformed cell that was part of a malignant tumor) would exclude cell lines that are artificially transformed to model some aspect of cancer. Need to decide what they intend to represent for their needs and then define this class accordingly. Also, in order to define this class using a model_of property, need to addrress the fact that cell lines are not in the domain of this property in ERO."; "an immortal cell line that is used in scientific experiments as a model for cancer"; . _:2ecb09 a owl:Class; owl:intersectionOf _:2ecb19 . _:2ecb19 rdf:first ; rdf:rest _:2ecb39 . _:2ecb39 rdf:first _:2ecb29; rdf:rest rdf:nil . _:2ecb29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecb49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "stem cell-derived cell line"; owl:equivalentClass _:2ecb59; rdfs:subClassOf , _:2ecb99; "A cell line that is derived from a stem cell."; "mouse embryonic stem cell line"; . _:2ecb59 a owl:Class; owl:intersectionOf _:2ecb69 . _:2ecb69 rdf:first ; rdf:rest _:2ecb89 . _:2ecb89 rdf:first _:2ecb79; rdf:rest rdf:nil . _:2ecb79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecb99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA construct library"; owl:equivalentClass _:2ecba9; rdfs:subClassOf , _:2ecc89, _:2eccd9; "A cDNA construct library."; "A nucleic acid library that contains a collection of distinct populations of microorganisms, each of which expresses a DNA construct carrying a piece of DNA from a source organism or cell line. In certain cases, this term can also refer to the collection of DNA constructs themselves, although large construct libraries are typically stored in microorganism hosts as described above."; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky" . _:2ecba9 a owl:Class; owl:intersectionOf _:2ecbb9 . _:2ecbb9 rdf:first ; rdf:rest _:2ecbd9 . _:2ecbd9 rdf:first _:2ecbc9; rdf:rest _:2ecc39 . _:2ecbc9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ecbe9 . _:2ecbe9 a owl:Class; owl:intersectionOf _:2ecbf9 . _:2ecbf9 rdf:first ; rdf:rest _:2ecc19 . _:2ecc19 rdf:first _:2ecc09; rdf:rest rdf:nil . _:2ecc09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecc39 rdf:first _:2ecc29; rdf:rest rdf:nil . _:2ecc29 a owl:Restriction; owl:onProperty ; owl:onClass _:2ecc49; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ecc49 a owl:Class; owl:intersectionOf _:2ecc59 . _:2ecc59 rdf:first ; rdf:rest _:2ecc79 . _:2ecc79 rdf:first _:2ecc69; rdf:rest rdf:nil . _:2ecc69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecc89 a owl:Restriction; owl:onProperty ; owl:onClass _:2ecc99; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ecc99 a owl:Class; owl:intersectionOf _:2ecca9 . _:2ecca9 rdf:first ; rdf:rest _:2eccc9 . _:2eccc9 rdf:first _:2eccb9; rdf:rest rdf:nil . _:2eccb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eccd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ecce9 . _:2ecce9 a owl:Class; owl:intersectionOf _:2eccf9 . _:2eccf9 rdf:first ; rdf:rest _:2ecd19 . _:2ecd19 rdf:first _:2ecd09; rdf:rest rdf:nil . _:2ecd09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "RNA interference construct library"; owl:equivalentClass _:2ecd29; rdfs:subClassOf , , _:2ece09, _:2ece59; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky"; "RNAi construct library"; "a DNA construct library that is a collection of constructs expressing transcripts, which are processed into small RNA molecules that target genes for post-transcriptional silencing through the RNAi pathway." . _:2ecd29 a owl:Class; owl:intersectionOf _:2ecd39 . _:2ecd39 rdf:first ; rdf:rest _:2ecd59 . _:2ecd59 rdf:first _:2ecd49; rdf:rest _:2ecdb9 . _:2ecd49 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ecd69 . _:2ecd69 a owl:Class; owl:intersectionOf _:2ecd79 . _:2ecd79 rdf:first ; rdf:rest _:2ecd99 . _:2ecd99 rdf:first _:2ecd89; rdf:rest rdf:nil . _:2ecd89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecdb9 rdf:first _:2ecda9; rdf:rest rdf:nil . _:2ecda9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ecdc9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ecdc9 a owl:Class; owl:intersectionOf _:2ecdd9 . _:2ecdd9 rdf:first ; rdf:rest _:2ecdf9 . _:2ecdf9 rdf:first _:2ecde9; rdf:rest rdf:nil . _:2ecde9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ece09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ece19 . _:2ece19 a owl:Class; owl:intersectionOf _:2ece29 . _:2ece29 rdf:first ; rdf:rest _:2ece49 . _:2ece49 rdf:first _:2ece39; rdf:rest rdf:nil . _:2ece39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ece59 a owl:Restriction; owl:onProperty ; owl:onClass _:2ece69; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ece69 a owl:Class; owl:intersectionOf _:2ece79 . _:2ece79 rdf:first ; rdf:rest _:2ece99 . _:2ece99 rdf:first _:2ece89; rdf:rest rdf:nil . _:2ece89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dsRNA construct library"; owl:equivalentClass _:2ecea9; rdfs:subClassOf , _:2ecf89, _:2ecfd9; "An RNA interference construct library that is a collection of dsRNA constructs used to generate dsRNA, which serve as substrates for the RNAi pathway to generate siRNA molecules"; "PERSON: Nicole Vasilevsky"; "double stranded RNA construct library"; "http://cshprotocols.cshlp.org/cgi/content/extract/2006/3/pdb.prot4512" . _:2ecea9 a owl:Class; owl:intersectionOf _:2eceb9 . _:2eceb9 rdf:first ; rdf:rest _:2eced9 . _:2eced9 rdf:first _:2ecec9; rdf:rest _:2ecf39 . _:2ecec9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ecee9 . _:2ecee9 a owl:Class; owl:intersectionOf _:2ecef9 . _:2ecef9 rdf:first ; rdf:rest _:2ecf19 . _:2ecf19 rdf:first _:2ecf09; rdf:rest rdf:nil . _:2ecf09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecf39 rdf:first _:2ecf29; rdf:rest rdf:nil . _:2ecf29 a owl:Restriction; owl:onProperty ; owl:onClass _:2ecf49; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ecf49 a owl:Class; owl:intersectionOf _:2ecf59 . _:2ecf59 rdf:first ; rdf:rest _:2ecf79 . _:2ecf79 rdf:first _:2ecf69; rdf:rest rdf:nil . _:2ecf69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecf89 a owl:Restriction; owl:onProperty ; owl:onClass _:2ecf99; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ecf99 a owl:Class; owl:intersectionOf _:2ecfa9 . _:2ecfa9 rdf:first ; rdf:rest _:2ecfc9 . _:2ecfc9 rdf:first _:2ecfb9; rdf:rest rdf:nil . _:2ecfb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ecfd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ecfe9 . _:2ecfe9 a owl:Class; owl:intersectionOf _:2ecff9 . _:2ecff9 rdf:first ; rdf:rest _:2ed019 . _:2ed019 rdf:first _:2ed009; rdf:rest rdf:nil . _:2ed009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA construct library"; owl:equivalentClass _:2ed029; rdfs:subClassOf , _:2ed109, _:2ed159; "An RNA interference construct library that is a collection of miRNA plasmids."; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky"; "micro RNA construct library" . _:2ed029 a owl:Class; owl:intersectionOf _:2ed039 . _:2ed039 rdf:first ; rdf:rest _:2ed059 . _:2ed059 rdf:first _:2ed049; rdf:rest _:2ed0b9 . _:2ed049 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed069 . _:2ed069 a owl:Class; owl:intersectionOf _:2ed079 . _:2ed079 rdf:first ; rdf:rest _:2ed099 . _:2ed099 rdf:first _:2ed089; rdf:rest rdf:nil . _:2ed089 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed0b9 rdf:first _:2ed0a9; rdf:rest rdf:nil . _:2ed0a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed0c9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed0c9 a owl:Class; owl:intersectionOf _:2ed0d9 . _:2ed0d9 rdf:first ; rdf:rest _:2ed0f9 . _:2ed0f9 rdf:first _:2ed0e9; rdf:rest rdf:nil . _:2ed0e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed109 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed119; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed119 a owl:Class; owl:intersectionOf _:2ed129 . _:2ed129 rdf:first ; rdf:rest _:2ed149 . _:2ed149 rdf:first _:2ed139; rdf:rest rdf:nil . _:2ed139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed159 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed169 . _:2ed169 a owl:Class; owl:intersectionOf _:2ed179 . _:2ed179 rdf:first ; rdf:rest _:2ed199 . _:2ed199 rdf:first _:2ed189; rdf:rest rdf:nil . _:2ed189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "shRNA construct library"; owl:equivalentClass _:2ed1a9; rdfs:subClassOf , _:2ed289, _:2ed2d9; "An RNA interference construct library that is a collection of shRNA constructs."; "PERSON: Nicole Vasilevsky"; "short hairpin RNA construct library", "small hairpin RNA construct library" . _:2ed1a9 a owl:Class; owl:intersectionOf _:2ed1b9 . _:2ed1b9 rdf:first ; rdf:rest _:2ed1d9 . _:2ed1d9 rdf:first _:2ed1c9; rdf:rest _:2ed239 . _:2ed1c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed1e9 . _:2ed1e9 a owl:Class; owl:intersectionOf _:2ed1f9 . _:2ed1f9 rdf:first ; rdf:rest _:2ed219 . _:2ed219 rdf:first _:2ed209; rdf:rest rdf:nil . _:2ed209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed239 rdf:first _:2ed229; rdf:rest rdf:nil . _:2ed229 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed249; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed249 a owl:Class; owl:intersectionOf _:2ed259 . _:2ed259 rdf:first ; rdf:rest _:2ed279 . _:2ed279 rdf:first _:2ed269; rdf:rest rdf:nil . _:2ed269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed289 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed299 . _:2ed299 a owl:Class; owl:intersectionOf _:2ed2a9 . _:2ed2a9 rdf:first ; rdf:rest _:2ed2c9 . _:2ed2c9 rdf:first _:2ed2b9; rdf:rest rdf:nil . _:2ed2b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed2d9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed2e9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed2e9 a owl:Class; owl:intersectionOf _:2ed2f9 . _:2ed2f9 rdf:first ; rdf:rest _:2ed319 . _:2ed319 rdf:first _:2ed309; rdf:rest rdf:nil . _:2ed309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cDNA construct library"; owl:equivalentClass _:2ed329; rdfs:subClassOf , _:2ed409, _:2ed459; "PERSON: Nicole Vasilevsky"; "a DNA construct library that is a collection of cDNA plasmids."; "http://en.wikipedia.org/wiki/CDNA_library" . _:2ed329 a owl:Class; owl:intersectionOf _:2ed339 . _:2ed339 rdf:first ; rdf:rest _:2ed359 . _:2ed359 rdf:first _:2ed349; rdf:rest _:2ed3b9 . _:2ed349 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed369 . _:2ed369 a owl:Class; owl:intersectionOf _:2ed379 . _:2ed379 rdf:first ; rdf:rest _:2ed399 . _:2ed399 rdf:first _:2ed389; rdf:rest rdf:nil . _:2ed389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed3b9 rdf:first _:2ed3a9; rdf:rest rdf:nil . _:2ed3a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed3c9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed3c9 a owl:Class; owl:intersectionOf _:2ed3d9 . _:2ed3d9 rdf:first ; rdf:rest _:2ed3f9 . _:2ed3f9 rdf:first _:2ed3e9; rdf:rest rdf:nil . _:2ed3e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed409 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed419; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed419 a owl:Class; owl:intersectionOf _:2ed429 . _:2ed429 rdf:first ; rdf:rest _:2ed449 . _:2ed449 rdf:first _:2ed439; rdf:rest rdf:nil . _:2ed439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed459 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed469 . _:2ed469 a owl:Class; owl:intersectionOf _:2ed479 . _:2ed479 rdf:first ; rdf:rest _:2ed499 . _:2ed499 rdf:first _:2ed489; rdf:rest rdf:nil . _:2ed489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA cDNA construct library"; owl:equivalentClass _:2ed4a9; rdfs:subClassOf , _:2ed589, _:2ed5d9; "A cDNA construct library that carries small cDNA inserts from a pool of size-selected cDNAs, representing putative endogenous miRNAs."; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky"; "micro RNA cDNA library" . _:2ed4a9 a owl:Class; owl:intersectionOf _:2ed4b9 . _:2ed4b9 rdf:first ; rdf:rest _:2ed4d9 . _:2ed4d9 rdf:first _:2ed4c9; rdf:rest _:2ed539 . _:2ed4c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed4e9 . _:2ed4e9 a owl:Class; owl:intersectionOf _:2ed4f9 . _:2ed4f9 rdf:first ; rdf:rest _:2ed519 . _:2ed519 rdf:first _:2ed509; rdf:rest rdf:nil . _:2ed509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed539 rdf:first _:2ed529; rdf:rest rdf:nil . _:2ed529 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed549; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed549 a owl:Class; owl:intersectionOf _:2ed559 . _:2ed559 rdf:first ; rdf:rest _:2ed579 . _:2ed579 rdf:first _:2ed569; rdf:rest rdf:nil . _:2ed569 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed589 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed599; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed599 a owl:Class; owl:intersectionOf _:2ed5a9 . _:2ed5a9 rdf:first ; rdf:rest _:2ed5c9 . _:2ed5c9 rdf:first _:2ed5b9; rdf:rest rdf:nil . _:2ed5b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed5d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed5e9 . _:2ed5e9 a owl:Class; owl:intersectionOf _:2ed5f9 . _:2ed5f9 rdf:first ; rdf:rest _:2ed619 . _:2ed619 rdf:first _:2ed609; rdf:rest rdf:nil . _:2ed609 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "expression library"; owl:equivalentClass _:2ed629; rdfs:subClassOf , _:2ed709, _:2ed759; "PERSON: Nicole Vasilevsky"; "a DNA construct library that contains expression vectors, which are used to express a specific protein."; "http://en.wikipedia.org/wiki/Expression_cloning" . _:2ed629 a owl:Class; owl:intersectionOf _:2ed639 . _:2ed639 rdf:first ; rdf:rest _:2ed659 . _:2ed659 rdf:first _:2ed649; rdf:rest _:2ed6b9 . _:2ed649 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed669 . _:2ed669 a owl:Class; owl:intersectionOf _:2ed679 . _:2ed679 rdf:first ; rdf:rest _:2ed699 . _:2ed699 rdf:first _:2ed689; rdf:rest rdf:nil . _:2ed689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed6b9 rdf:first _:2ed6a9; rdf:rest rdf:nil . _:2ed6a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed6c9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed6c9 a owl:Class; owl:intersectionOf _:2ed6d9 . _:2ed6d9 rdf:first ; rdf:rest _:2ed6f9 . _:2ed6f9 rdf:first _:2ed6e9; rdf:rest rdf:nil . _:2ed6e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed709 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed719 . _:2ed719 a owl:Class; owl:intersectionOf _:2ed729 . _:2ed729 rdf:first ; rdf:rest _:2ed749 . _:2ed749 rdf:first _:2ed739; rdf:rest rdf:nil . _:2ed739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed759 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed769; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed769 a owl:Class; owl:intersectionOf _:2ed779 . _:2ed779 rdf:first ; rdf:rest _:2ed799 . _:2ed799 rdf:first _:2ed789; rdf:rest rdf:nil . _:2ed789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "yeast two-hybrid library"; owl:equivalentClass _:2ed7a9; rdfs:subClassOf , _:2ed889, _:2ed8d9; "A library used to screen interacting proteins."; "An expression library that is a collection of yeast two hybrid constructs. "; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Two-hybrid_screening" . _:2ed7a9 a owl:Class; owl:intersectionOf _:2ed7b9 . _:2ed7b9 rdf:first ; rdf:rest _:2ed7d9 . _:2ed7d9 rdf:first _:2ed7c9; rdf:rest _:2ed839 . _:2ed7c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed7e9 . _:2ed7e9 a owl:Class; owl:intersectionOf _:2ed7f9 . _:2ed7f9 rdf:first ; rdf:rest _:2ed819 . _:2ed819 rdf:first _:2ed809; rdf:rest rdf:nil . _:2ed809 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed839 rdf:first _:2ed829; rdf:rest rdf:nil . _:2ed829 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed849; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed849 a owl:Class; owl:intersectionOf _:2ed859 . _:2ed859 rdf:first ; rdf:rest _:2ed879 . _:2ed879 rdf:first _:2ed869; rdf:rest rdf:nil . _:2ed869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed889 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed899; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ed899 a owl:Class; owl:intersectionOf _:2ed8a9 . _:2ed8a9 rdf:first ; rdf:rest _:2ed8c9 . _:2ed8c9 rdf:first _:2ed8b9; rdf:rest rdf:nil . _:2ed8b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ed8d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ed8e9 . _:2ed8e9 a owl:Class; owl:intersectionOf _:2ed8f9 . _:2ed8f9 rdf:first ; rdf:rest _:2ed919 . _:2ed919 rdf:first _:2ed909; rdf:rest rdf:nil . _:2ed909 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genomic library"; rdfs:subClassOf , _:2ed929 . _:2ed929 a owl:Restriction; owl:onProperty ; owl:onClass _:2ed939 . _:2ed939 a owl:Class; owl:intersectionOf _:2ed949 . _:2ed949 rdf:first ; rdf:rest _:2ed969 . _:2ed969 rdf:first _:2ed959 . _:2ed959 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ed979 . _:2ed979 a owl:Class; owl:intersectionOf _:2ed989 . _:2ed989 rdf:first ; rdf:rest _:2ed9a9 . _:2ed9a9 rdf:first _:2ed999; rdf:rest rdf:nil . _:2ed999 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ed9b9 . _:2ed9b9 a owl:Class; owl:intersectionOf _:2ed9c9 . _:2ed9c9 rdf:first ; rdf:rest _:2ed9e9 . _:2ed9e9 rdf:first _:2ed9d9; rdf:rest rdf:nil . _:2ed9d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ed969 rdf:rest rdf:nil . _:2ed929 owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . rdfs:subClassOf _:2ed9f9, _:2eda19; "A DNA construct library comprised of constructs that carry insert DNA fragments covering the entire genome of a source organism. "; "A cDNA library for the mouse genome."; "http://en.wikipedia.org/wiki/Genomic_library" . _:2ed9f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eda09 . _:2eda09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eda19 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eda29 . _:2eda29 a owl:Class; owl:intersectionOf _:2eda39 . _:2eda39 rdf:first ; rdf:rest _:2eda59 . _:2eda59 rdf:first _:2eda49; rdf:rest rdf:nil . _:2eda49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eda69 . _:2eda69 a owl:Class; owl:intersectionOf _:2eda79 . _:2eda79 rdf:first ; rdf:rest _:2eda99 . _:2eda99 rdf:first _:2eda89; rdf:rest rdf:nil . _:2eda89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edaa9 . _:2edaa9 a owl:Class; owl:intersectionOf _:2edab9 . _:2edab9 rdf:first ; rdf:rest _:2edad9 . _:2edad9 rdf:first _:2edac9; rdf:rest rdf:nil . _:2edac9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2edae9 a owl:Axiom; "axiom meant to capture the notion that the entire genome of some orgnaism is represented in the particular contents of a genomic library."; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2edaf9 . _:2edaf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edb09 . _:2edb09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genomic DNA construct"; owl:equivalentClass _:2edb19; rdfs:subClassOf , _:2edb99, _:2edbe9; "a DNA construct that contains a construct insert that encodes only some natural genomic sequence from some organism."; rdfs:comment "Typically refers to constructs that carry inserts encoding non-coding sequences (e.g. intronic regions, regulatory regions, inter-geneic sequences, etc) that are uniquely characteristic of genomic DNA (as opposed to cDNA) . . . such that a construct encoding a single exon from a gene would not qualify as a genomic construct, despite encoding only a genomic sequence region."; . _:2edb19 a owl:Class; owl:intersectionOf _:2edb29 . _:2edb29 rdf:first ; rdf:rest _:2edb49 . _:2edb49 rdf:first _:2edb39; rdf:rest rdf:nil . _:2edb39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edb59 . _:2edb59 a owl:Class; owl:intersectionOf _:2edb69 . _:2edb69 rdf:first ; rdf:rest _:2edb89 . _:2edb89 rdf:first _:2edb79; rdf:rest rdf:nil . _:2edb79 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2edb99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edba9 . _:2edba9 a owl:Class; owl:intersectionOf _:2edbb9 . _:2edbb9 rdf:first ; rdf:rest _:2edbd9 . _:2edbd9 rdf:first _:2edbc9; rdf:rest rdf:nil . _:2edbc9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2edbe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edbf9 . _:2edbf9 a owl:Class; owl:intersectionOf _:2edc09 . _:2edc09 rdf:first ; rdf:rest _:2edc29 . _:2edc29 rdf:first _:2edc19; rdf:rest rdf:nil . _:2edc19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edc39 . _:2edc39 a owl:Class; owl:intersectionOf _:2edc49 . _:2edc49 rdf:first ; rdf:rest _:2edc69 . _:2edc69 rdf:first _:2edc59; rdf:rest rdf:nil . _:2edc59 a owl:Class; owl:intersectionOf _:2edc89 . _:2edc89 rdf:first _:2edc79; rdf:rest _:2edca9 . _:2edc79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2edca9 rdf:first _:2edc99; rdf:rest rdf:nil . _:2edc99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "obsolete_genomic material"; rdfs:subClassOf ; """Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class. former eq class axiom : 'nucleic acid' and (bears_concretization_of some 'genomic sequence region')"""; "nucelic acid that represents a genomic sequence from some organism"; rdfs:comment """1. a genomic nucleic acid molecule must in its entirety represent genomic sequence - thus it does not include things like cDNA reverse transcribed from some mRNA transcript, where introns and other genomic features are missing. 2. genomic nucleic acid does not necessarily need to physically derive from the genome of an organism - only encode sequence from the genome of some reference organism (so things like PCR products can qualify) 3. a genomic nucleic acid molecule does not need to be part of a cell or organism (i.e.an experimentally isolated genomic DNA prep, or a PCR product, would qualify) 4. genomic nucleic acid can be single or double stranded - it is the sequence information content of the molecule that matters, and this can be carried by single or double stranded nucleic acid"""; """A note on the distinction between 'genomic' and 'genetic' material: 'genomic material' need only encode sequence representing the genome of some organism. 'genetic material' must additionally be part of a cell or organism where it can be stable replicated and inherited by progeny."""; "genomic nucleic acid" . a owl:Class; rdfs:label "BAC genomic library"; rdfs:subClassOf , _:2edcb9, _:2edd89; "A BAC library containing the mouse genome."; "A genomic library that contains discrete collections of host bacteria, each of which carries a DNA insert from a source organism cloned into a BAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of BAC constructs prior to their delivery into the host cells."; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Genomic_library" . _:2edcb9 a owl:Restriction; owl:onProperty ; owl:onClass _:2edcc9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2edcc9 a owl:Class; owl:intersectionOf _:2edcd9 . _:2edcd9 rdf:first ; rdf:rest _:2edcf9 . _:2edcf9 rdf:first _:2edce9; rdf:rest rdf:nil . _:2edce9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edd09 . _:2edd09 a owl:Class; owl:intersectionOf _:2edd19 . _:2edd19 rdf:first ; rdf:rest _:2edd39 . _:2edd39 rdf:first _:2edd29; rdf:rest rdf:nil . _:2edd29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edd49 . _:2edd49 a owl:Class; owl:intersectionOf _:2edd59 . _:2edd59 rdf:first ; rdf:rest _:2edd79 . _:2edd79 rdf:first _:2edd69; rdf:rest rdf:nil . _:2edd69 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2edd89 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2edd99 . _:2edd99 a owl:Class; owl:intersectionOf _:2edda9 . _:2edda9 rdf:first ; rdf:rest _:2eddc9 . _:2eddc9 rdf:first _:2eddb9; rdf:rest rdf:nil . _:2eddb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eddd9 . _:2eddd9 a owl:Class; owl:intersectionOf _:2edde9 . _:2edde9 rdf:first ; rdf:rest _:2ede09 . _:2ede09 rdf:first _:2eddf9; rdf:rest rdf:nil . _:2eddf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ede19 . _:2ede19 a owl:Class; owl:intersectionOf _:2ede29 . _:2ede29 rdf:first ; rdf:rest _:2ede49 . _:2ede49 rdf:first _:2ede39; rdf:rest rdf:nil . _:2ede39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "PAC genomic library"; rdfs:subClassOf , _:2ede59, _:2edf29; "A genomic library that contains discrete collections of host bacteria, each of which carries a DNA insert from a source organism cloned into a PAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of PAC constructs prior to their delivery into the host cells."; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Genomic_library" . _:2ede59 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ede69 . _:2ede69 a owl:Class; owl:intersectionOf _:2ede79 . _:2ede79 rdf:first ; rdf:rest _:2ede99 . _:2ede99 rdf:first _:2ede89; rdf:rest rdf:nil . _:2ede89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edea9 . _:2edea9 a owl:Class; owl:intersectionOf _:2edeb9 . _:2edeb9 rdf:first ; rdf:rest _:2eded9 . _:2eded9 rdf:first _:2edec9; rdf:rest rdf:nil . _:2edec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edee9 . _:2edee9 a owl:Class; owl:intersectionOf _:2edef9 . _:2edef9 rdf:first ; rdf:rest _:2edf19 . _:2edf19 rdf:first _:2edf09; rdf:rest rdf:nil . _:2edf09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2edf29 a owl:Restriction; owl:onProperty ; owl:onClass _:2edf39; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2edf39 a owl:Class; owl:intersectionOf _:2edf49 . _:2edf49 rdf:first ; rdf:rest _:2edf69 . _:2edf69 rdf:first _:2edf59; rdf:rest rdf:nil . _:2edf59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edf79 . _:2edf79 a owl:Class; owl:intersectionOf _:2edf89 . _:2edf89 rdf:first ; rdf:rest _:2edfa9 . _:2edfa9 rdf:first _:2edf99; rdf:rest rdf:nil . _:2edf99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2edfb9 . _:2edfb9 a owl:Class; owl:intersectionOf _:2edfc9 . _:2edfc9 rdf:first ; rdf:rest _:2edfe9 . _:2edfe9 rdf:first _:2edfd9; rdf:rest rdf:nil . _:2edfd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "YAC genomic library"; rdfs:subClassOf , _:2edff9, _:2ee0c9; "A genomic library that contains discrete collections of host yeast cells, each of which carries a DNA insert from a source organism cloned into a YAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of YAC constructs prior to their delivery into the host cells."; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Genomic_library" . _:2edff9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee009; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee009 a owl:Class; owl:intersectionOf _:2ee019 . _:2ee019 rdf:first ; rdf:rest _:2ee039 . _:2ee039 rdf:first _:2ee029; rdf:rest rdf:nil . _:2ee029 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee049 . _:2ee049 a owl:Class; owl:intersectionOf _:2ee059 . _:2ee059 rdf:first ; rdf:rest _:2ee079 . _:2ee079 rdf:first _:2ee069; rdf:rest rdf:nil . _:2ee069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee089 . _:2ee089 a owl:Class; owl:intersectionOf _:2ee099 . _:2ee099 rdf:first ; rdf:rest _:2ee0b9 . _:2ee0b9 rdf:first _:2ee0a9; rdf:rest rdf:nil . _:2ee0a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ee0c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee0d9 . _:2ee0d9 a owl:Class; owl:intersectionOf _:2ee0e9 . _:2ee0e9 rdf:first ; rdf:rest _:2ee109 . _:2ee109 rdf:first _:2ee0f9; rdf:rest rdf:nil . _:2ee0f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee119 . _:2ee119 a owl:Class; owl:intersectionOf _:2ee129 . _:2ee129 rdf:first ; rdf:rest _:2ee149 . _:2ee149 rdf:first _:2ee139; rdf:rest rdf:nil . _:2ee139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee159 . _:2ee159 a owl:Class; owl:intersectionOf _:2ee169 . _:2ee169 rdf:first ; rdf:rest _:2ee189 . _:2ee189 rdf:first _:2ee179; rdf:rest rdf:nil . _:2ee179 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "cosmid genomic library"; rdfs:subClassOf , _:2ee199, _:2ee269; "A genomic library that contains discrete collections of cosmid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism. "; "PERSON: Nicole Vasilevsky"; "http://homepages.strath.ac.uk/~dfs99109/BB211/GenomicLibrary.html" . _:2ee199 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee1a9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee1a9 a owl:Class; owl:intersectionOf _:2ee1b9 . _:2ee1b9 rdf:first ; rdf:rest _:2ee1d9 . _:2ee1d9 rdf:first _:2ee1c9; rdf:rest rdf:nil . _:2ee1c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee1e9 . _:2ee1e9 a owl:Class; owl:intersectionOf _:2ee1f9 . _:2ee1f9 rdf:first ; rdf:rest _:2ee219 . _:2ee219 rdf:first _:2ee209; rdf:rest rdf:nil . _:2ee209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee229 . _:2ee229 a owl:Class; owl:intersectionOf _:2ee239 . _:2ee239 rdf:first ; rdf:rest _:2ee259 . _:2ee259 rdf:first _:2ee249; rdf:rest rdf:nil . _:2ee249 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ee269 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee279 . _:2ee279 a owl:Class; owl:intersectionOf _:2ee289 . _:2ee289 rdf:first ; rdf:rest _:2ee2a9 . _:2ee2a9 rdf:first _:2ee299; rdf:rest rdf:nil . _:2ee299 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee2b9 . _:2ee2b9 a owl:Class; owl:intersectionOf _:2ee2c9 . _:2ee2c9 rdf:first ; rdf:rest _:2ee2e9 . _:2ee2e9 rdf:first _:2ee2d9; rdf:rest rdf:nil . _:2ee2d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee2f9 . _:2ee2f9 a owl:Class; owl:intersectionOf _:2ee309 . _:2ee309 rdf:first ; rdf:rest _:2ee329 . _:2ee329 rdf:first _:2ee319; rdf:rest rdf:nil . _:2ee319 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "fosmid genomic library"; rdfs:subClassOf , _:2ee339, _:2ee409; "A genomic library that contains discrete collections of fosmid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism. "; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Fosmid" . _:2ee339 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee349 . _:2ee349 a owl:Class; owl:intersectionOf _:2ee359 . _:2ee359 rdf:first ; rdf:rest _:2ee379 . _:2ee379 rdf:first _:2ee369; rdf:rest rdf:nil . _:2ee369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee389 . _:2ee389 a owl:Class; owl:intersectionOf _:2ee399 . _:2ee399 rdf:first ; rdf:rest _:2ee3b9 . _:2ee3b9 rdf:first _:2ee3a9; rdf:rest rdf:nil . _:2ee3a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee3c9 . _:2ee3c9 a owl:Class; owl:intersectionOf _:2ee3d9 . _:2ee3d9 rdf:first ; rdf:rest _:2ee3f9 . _:2ee3f9 rdf:first _:2ee3e9; rdf:rest rdf:nil . _:2ee3e9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ee409 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee419; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee419 a owl:Class; owl:intersectionOf _:2ee429 . _:2ee429 rdf:first ; rdf:rest _:2ee449 . _:2ee449 rdf:first _:2ee439; rdf:rest rdf:nil . _:2ee439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee459 . _:2ee459 a owl:Class; owl:intersectionOf _:2ee469 . _:2ee469 rdf:first ; rdf:rest _:2ee489 . _:2ee489 rdf:first _:2ee479; rdf:rest rdf:nil . _:2ee479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee499 . _:2ee499 a owl:Class; owl:intersectionOf _:2ee4a9 . _:2ee4a9 rdf:first ; rdf:rest _:2ee4c9 . _:2ee4c9 rdf:first _:2ee4b9; rdf:rest rdf:nil . _:2ee4b9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "phagemid genomic library"; rdfs:subClassOf , _:2ee4d9, _:2ee5a9; " A genomic library that contains discrete collections of phagemid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism. "; "PERSON: Nicole Vasilevsky"; "http://en.wikipedia.org/wiki/Phagemid" . _:2ee4d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee4e9 . _:2ee4e9 a owl:Class; owl:intersectionOf _:2ee4f9 . _:2ee4f9 rdf:first ; rdf:rest _:2ee519 . _:2ee519 rdf:first _:2ee509; rdf:rest rdf:nil . _:2ee509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee529 . _:2ee529 a owl:Class; owl:intersectionOf _:2ee539 . _:2ee539 rdf:first ; rdf:rest _:2ee559 . _:2ee559 rdf:first _:2ee549; rdf:rest rdf:nil . _:2ee549 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee569 . _:2ee569 a owl:Class; owl:intersectionOf _:2ee579 . _:2ee579 rdf:first ; rdf:rest _:2ee599 . _:2ee599 rdf:first _:2ee589; rdf:rest rdf:nil . _:2ee589 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2ee5a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee5b9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee5b9 a owl:Class; owl:intersectionOf _:2ee5c9 . _:2ee5c9 rdf:first ; rdf:rest _:2ee5e9 . _:2ee5e9 rdf:first _:2ee5d9; rdf:rest rdf:nil . _:2ee5d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee5f9 . _:2ee5f9 a owl:Class; owl:intersectionOf _:2ee609 . _:2ee609 rdf:first ; rdf:rest _:2ee629 . _:2ee629 rdf:first _:2ee619; rdf:rest rdf:nil . _:2ee619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee639 . _:2ee639 a owl:Class; owl:intersectionOf _:2ee649 . _:2ee649 rdf:first ; rdf:rest _:2ee669 . _:2ee669 rdf:first _:2ee659; rdf:rest rdf:nil . _:2ee659 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "obsolete_gene knockdown library"; rdfs:subClassOf ; "A nucleic acid library that consists of a collection of gene knockdown reagents, which are capable of reducing the expression of target genes in a biological system."; "A siRNA library."; "Gene repression library", "Gene silencing library"; "PERSON: Matthew Brush"; "PERSON: Matthew Brush"; """decided not needed. previous logical def: 'nucleic acid library' and ('has aggregate part' only ('uniform collection' and ('has aggregate part' some 'gene knockdown reagent'))) and ('has aggregate part' min 2 ('uniform collection' and ('has aggregate part' some 'gene knockdown reagent')))""" . a owl:Class; rdfs:label "RNA interference library"; owl:equivalentClass _:2ee679; rdfs:subClassOf , _:2ee759, _:2ee7a9; "A gene knockdown library that consists of a collection of RNAi oligonucleotides or RNAi plasmids."; "PERSON: Matthew Brush"; "PERSON: Matthew Brush"; "RNAi library" . _:2ee679 a owl:Class; owl:intersectionOf _:2ee689 . _:2ee689 rdf:first ; rdf:rest _:2ee6a9 . _:2ee6a9 rdf:first _:2ee699; rdf:rest _:2ee709 . _:2ee699 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee6b9 . _:2ee6b9 a owl:Class; owl:intersectionOf _:2ee6c9 . _:2ee6c9 rdf:first ; rdf:rest _:2ee6e9 . _:2ee6e9 rdf:first _:2ee6d9; rdf:rest rdf:nil . _:2ee6d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ee709 rdf:first _:2ee6f9; rdf:rest rdf:nil . _:2ee6f9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee719; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee719 a owl:Class; owl:intersectionOf _:2ee729 . _:2ee729 rdf:first ; rdf:rest _:2ee749 . _:2ee749 rdf:first _:2ee739; rdf:rest rdf:nil . _:2ee739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ee759 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee769; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee769 a owl:Class; owl:intersectionOf _:2ee779 . _:2ee779 rdf:first ; rdf:rest _:2ee799 . _:2ee799 rdf:first _:2ee789; rdf:rest rdf:nil . _:2ee789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ee7a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee7b9 . _:2ee7b9 a owl:Class; owl:intersectionOf _:2ee7c9 . _:2ee7c9 rdf:first ; rdf:rest _:2ee7e9 . _:2ee7e9 rdf:first _:2ee7d9; rdf:rest rdf:nil . _:2ee7d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "oligonucleotide library"; owl:equivalentClass _:2ee7f9; rdfs:subClassOf , _:2ee939, _:2ee9b9; "A nucleic acid library that is a collection of nucleic acid molecules, stored in pools containing a single species of nucleic acid."; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky"; "nucleic acid molecule library", "nucleic acid oligonucleotide library", "nucleic acid oligo library" . _:2ee7f9 a owl:Class; owl:intersectionOf _:2ee809 . _:2ee809 rdf:first ; rdf:rest _:2ee829 . _:2ee829 rdf:first _:2ee819; rdf:rest _:2ee8b9 . _:2ee819 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee839 . _:2ee839 a owl:Class; owl:intersectionOf _:2ee849 . _:2ee849 rdf:first ; rdf:rest _:2ee869 . _:2ee869 rdf:first _:2ee859; rdf:rest rdf:nil . _:2ee859 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee879 . _:2ee879 a owl:Class; owl:unionOf _:2ee889 . _:2ee889 rdf:first ; rdf:rest _:2ee899 . _:2ee899 rdf:first ; rdf:rest rdf:nil . _:2ee8b9 rdf:first _:2ee8a9; rdf:rest rdf:nil . _:2ee8a9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee8c9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee8c9 a owl:Class; owl:intersectionOf _:2ee8d9 . _:2ee8d9 rdf:first ; rdf:rest _:2ee8f9 . _:2ee8f9 rdf:first _:2ee8e9; rdf:rest rdf:nil . _:2ee8e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee909 . _:2ee909 a owl:Class; owl:unionOf _:2ee919 . _:2ee919 rdf:first ; rdf:rest _:2ee929 . _:2ee929 rdf:first ; rdf:rest rdf:nil . _:2ee939 a owl:Restriction; owl:onProperty ; owl:onClass _:2ee949; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ee949 a owl:Class; owl:intersectionOf _:2ee959 . _:2ee959 rdf:first ; rdf:rest _:2ee979 . _:2ee979 rdf:first _:2ee969; rdf:rest rdf:nil . _:2ee969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ee989 . _:2ee989 a owl:Class; owl:unionOf _:2ee999 . _:2ee999 rdf:first ; rdf:rest _:2ee9a9 . _:2ee9a9 rdf:first ; rdf:rest rdf:nil . _:2ee9b9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ee9c9 . _:2ee9c9 a owl:Class; owl:intersectionOf _:2ee9d9 . _:2ee9d9 rdf:first ; rdf:rest _:2ee9f9 . _:2ee9f9 rdf:first _:2ee9e9; rdf:rest rdf:nil . _:2ee9e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eea09 . _:2eea09 a owl:Class; owl:unionOf _:2eea19 . _:2eea19 rdf:first ; rdf:rest _:2eea29 . _:2eea29 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "RNA interference oligonucleotide library"; owl:equivalentClass _:2eea39; rdfs:subClassOf , , _:2eeb19, _:2eeb69; "A nucleic acid molecule library containing RNA oligonucleotides used to silence gene expression in cells through the RNAi pathway."; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky"; "RNAi oligo library" . _:2eea39 a owl:Class; owl:intersectionOf _:2eea49 . _:2eea49 rdf:first ; rdf:rest _:2eea69 . _:2eea69 rdf:first _:2eea59; rdf:rest _:2eeac9 . _:2eea59 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eea79 . _:2eea79 a owl:Class; owl:intersectionOf _:2eea89 . _:2eea89 rdf:first ; rdf:rest _:2eeaa9 . _:2eeaa9 rdf:first _:2eea99; rdf:rest rdf:nil . _:2eea99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eeac9 rdf:first _:2eeab9; rdf:rest rdf:nil . _:2eeab9 a owl:Restriction; owl:onProperty ; owl:onClass _:2eead9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eead9 a owl:Class; owl:intersectionOf _:2eeae9 . _:2eeae9 rdf:first ; rdf:rest _:2eeb09 . _:2eeb09 rdf:first _:2eeaf9; rdf:rest rdf:nil . _:2eeaf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eeb19 a owl:Restriction; owl:onProperty ; owl:onClass _:2eeb29; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eeb29 a owl:Class; owl:intersectionOf _:2eeb39 . _:2eeb39 rdf:first ; rdf:rest _:2eeb59 . _:2eeb59 rdf:first _:2eeb49; rdf:rest rdf:nil . _:2eeb49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eeb69 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eeb79 . _:2eeb79 a owl:Class; owl:intersectionOf _:2eeb89 . _:2eeb89 rdf:first ; rdf:rest _:2eeba9 . _:2eeba9 rdf:first _:2eeb99; rdf:rest rdf:nil . _:2eeb99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dsRNA oligonucleotide library"; owl:equivalentClass _:2eebb9; rdfs:subClassOf , _:2eec99, _:2eece9; "An RNAi oligonucleotide library that contains dsRNA oligonucleotides used to silence gene expression"; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky"; "double stranded oligonucleotide library", "dsRNA oligo library" . _:2eebb9 a owl:Class; owl:intersectionOf _:2eebc9 . _:2eebc9 rdf:first ; rdf:rest _:2eebe9 . _:2eebe9 rdf:first _:2eebd9; rdf:rest _:2eec49 . _:2eebd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eebf9 . _:2eebf9 a owl:Class; owl:intersectionOf _:2eec09 . _:2eec09 rdf:first ; rdf:rest _:2eec29 . _:2eec29 rdf:first _:2eec19; rdf:rest rdf:nil . _:2eec19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eec49 rdf:first _:2eec39; rdf:rest rdf:nil . _:2eec39 a owl:Restriction; owl:onProperty ; owl:onClass _:2eec59; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eec59 a owl:Class; owl:intersectionOf _:2eec69 . _:2eec69 rdf:first ; rdf:rest _:2eec89 . _:2eec89 rdf:first _:2eec79; rdf:rest rdf:nil . _:2eec79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eec99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eeca9 . _:2eeca9 a owl:Class; owl:intersectionOf _:2eecb9 . _:2eecb9 rdf:first ; rdf:rest _:2eecd9 . _:2eecd9 rdf:first _:2eecc9; rdf:rest rdf:nil . _:2eecc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eece9 a owl:Restriction; owl:onProperty ; owl:onClass _:2eecf9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eecf9 a owl:Class; owl:intersectionOf _:2eed09 . _:2eed09 rdf:first ; rdf:rest _:2eed29 . _:2eed29 rdf:first _:2eed19; rdf:rest rdf:nil . _:2eed19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "bioinorganic molecular entity"; rdfs:subClassOf , _:2eed39; "A molecular entity comprised of 2 or more elements combined in a fixed ratio and containing metal, carbon, and hydrogen atoms."; "ChEBI - is this a class in ChEBI. If not, can we submit as one?" . _:2eed39 a owl:Class; owl:complementOf _:2eed49 . _:2eed49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eed59 . _:2eed59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eed69 . _:2eed69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA oligonucleotide library"; owl:equivalentClass _:2eed79; rdfs:subClassOf , _:2eee59, _:2eeea9; "An RNAi oligonucleotide library that contains miRNA oligonucleotides used to silence gene expression."; "PERSON: Matthew Brush"; "PERSON: Nicole Vasilevsky"; "miRNA oligo library", "micro RNA oliognucleotide library"; rdfs:comment "RNAi library that is comrpised of microRNA (21-22 nucelotides). miRNAs are endogenous post-transcriptional regulators that bind to complementary sequences in the three prime untranslated regions (3' UTRs) of mRNA, usually resulting in gene silencing. Each miRNA may repress hundreds of mRNAs. miRNA libraries are not in expression vectors but are directly transfected into cells." . _:2eed79 a owl:Class; owl:intersectionOf _:2eed89 . _:2eed89 rdf:first ; rdf:rest _:2eeda9 . _:2eeda9 rdf:first _:2eed99; rdf:rest _:2eee09 . _:2eed99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eedb9 . _:2eedb9 a owl:Class; owl:intersectionOf _:2eedc9 . _:2eedc9 rdf:first ; rdf:rest _:2eede9 . _:2eede9 rdf:first _:2eedd9; rdf:rest rdf:nil . _:2eedd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eee09 rdf:first _:2eedf9; rdf:rest rdf:nil . _:2eedf9 a owl:Restriction; owl:onProperty ; owl:onClass _:2eee19; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eee19 a owl:Class; owl:intersectionOf _:2eee29 . _:2eee29 rdf:first ; rdf:rest _:2eee49 . _:2eee49 rdf:first _:2eee39; rdf:rest rdf:nil . _:2eee39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eee59 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eee69 . _:2eee69 a owl:Class; owl:intersectionOf _:2eee79 . _:2eee79 rdf:first ; rdf:rest _:2eee99 . _:2eee99 rdf:first _:2eee89; rdf:rest rdf:nil . _:2eee89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eeea9 a owl:Restriction; owl:onProperty ; owl:onClass _:2eeeb9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eeeb9 a owl:Class; owl:intersectionOf _:2eeec9 . _:2eeec9 rdf:first ; rdf:rest _:2eeee9 . _:2eeee9 rdf:first _:2eeed9; rdf:rest rdf:nil . _:2eeed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "siRNA oligonucleotide library"; owl:equivalentClass _:2eeef9; rdfs:subClassOf , _:2eefd9 . _:2eeef9 a owl:Class; owl:intersectionOf _:2eef09 . _:2eef09 rdf:first ; rdf:rest _:2eef29 . _:2eef29 rdf:first _:2eef19; rdf:rest _:2eef89 . _:2eef19 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eef39 . _:2eef39 a owl:Class; owl:intersectionOf _:2eef49 . _:2eef49 rdf:first ; rdf:rest _:2eef69 . _:2eef69 rdf:first _:2eef59; rdf:rest rdf:nil . _:2eef59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eef89 rdf:first _:2eef79; rdf:rest rdf:nil . _:2eef79 a owl:Restriction; owl:onProperty ; owl:onClass _:2eef99; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2eef99 a owl:Class; owl:intersectionOf _:2eefa9 . _:2eefa9 rdf:first ; rdf:rest _:2eefc9 . _:2eefc9 rdf:first _:2eefb9; rdf:rest rdf:nil . _:2eefb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2eefd9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2eefe9 . _:2eefe9 a owl:Class; owl:intersectionOf _:2eeff9 . _:2eeff9 rdf:first ; rdf:rest _:2ef019 . _:2ef019 rdf:first _:2ef009; rdf:rest rdf:nil . _:2ef009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf _:2ef029; "An RNAi oligonucleotide library that contains siRNA oligonucleotides used to silence gene expression."; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky"; "siRNA oligo library", "small interfering RNA oligonucleotide library"; rdfs:comment "RNAi library that is comprised of small (20-25 nucleotides) interfering RNA or silencing RNA that targets mRNA for degradation. siRNAs are synthetic double-stranded RNA. siRNA libraries are not in expression vectors. The siRNAs are directly transfected into cells." . _:2ef029 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef039; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef039 a owl:Class; owl:intersectionOf _:2ef049 . _:2ef049 rdf:first ; rdf:rest _:2ef069 . _:2ef069 rdf:first _:2ef059; rdf:rest rdf:nil . _:2ef059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "miRNA inhibitor siRNA library"; owl:equivalentClass _:2ef079; rdfs:subClassOf , _:2ef159, _:2ef1a9; "An siRNA oligonucleotide library that contains miRNA inhibitors, which are chemically synthesized siRNAs, which specifically inhibit endogenous miRNA function after transfection into cells."; "PERSON: Nicole Vasilevsky"; "http://www.qiagen.com/products/miscriptmirnainhibitors.aspx#Tabs=t0"; "micro RNA inhibitor siRNA library" . _:2ef079 a owl:Class; owl:intersectionOf _:2ef089 . _:2ef089 rdf:first ; rdf:rest _:2ef0a9 . _:2ef0a9 rdf:first _:2ef099; rdf:rest _:2ef109 . _:2ef099 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ef0b9 . _:2ef0b9 a owl:Class; owl:intersectionOf _:2ef0c9 . _:2ef0c9 rdf:first ; rdf:rest _:2ef0e9 . _:2ef0e9 rdf:first _:2ef0d9; rdf:rest rdf:nil . _:2ef0d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef109 rdf:first _:2ef0f9; rdf:rest rdf:nil . _:2ef0f9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef119; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef119 a owl:Class; owl:intersectionOf _:2ef129 . _:2ef129 rdf:first ; rdf:rest _:2ef149 . _:2ef149 rdf:first _:2ef139; rdf:rest rdf:nil . _:2ef139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef159 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef169; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef169 a owl:Class; owl:intersectionOf _:2ef179 . _:2ef179 rdf:first ; rdf:rest _:2ef199 . _:2ef199 rdf:first _:2ef189; rdf:rest rdf:nil . _:2ef189 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef1a9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ef1b9 . _:2ef1b9 a owl:Class; owl:intersectionOf _:2ef1c9 . _:2ef1c9 rdf:first ; rdf:rest _:2ef1e9 . _:2ef1e9 rdf:first _:2ef1d9; rdf:rest rdf:nil . _:2ef1d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "bioinorganic reagent"; owl:equivalentClass _:2ef1f9; rdfs:subClassOf , , _:2ef239, _:2ef249; "A chemical reagent comprised of 2 or more elements combined in a fixed ratio and containing metal, carbon, and hydrogen atoms."; "hemoglobin" . _:2ef1f9 a owl:Class; owl:intersectionOf _:2ef209 . _:2ef209 rdf:first ; rdf:rest _:2ef229 . _:2ef229 rdf:first _:2ef219; rdf:rest rdf:nil . _:2ef219 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "lambda phage library"; owl:equivalentClass _:2ef259; rdfs:subClassOf , _:2ef339, _:2ef349, _:2ef399; "An organism library containing trangenic lambda phage."; "PERSON: Nicole Vasilevsky"; "PERSON: Nicole Vasilevsky" . _:2ef259 a owl:Class; owl:intersectionOf _:2ef269 . _:2ef269 rdf:first ; rdf:rest _:2ef289 . _:2ef289 rdf:first _:2ef279; rdf:rest _:2ef2e9 . _:2ef279 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ef299 . _:2ef299 a owl:Class; owl:intersectionOf _:2ef2a9 . _:2ef2a9 rdf:first ; rdf:rest _:2ef2c9 . _:2ef2c9 rdf:first _:2ef2b9; rdf:rest rdf:nil . _:2ef2b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef2e9 rdf:first _:2ef2d9; rdf:rest rdf:nil . _:2ef2d9 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef2f9; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef2f9 a owl:Class; owl:intersectionOf _:2ef309 . _:2ef309 rdf:first ; rdf:rest _:2ef329 . _:2ef329 rdf:first _:2ef319; rdf:rest rdf:nil . _:2ef319 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef349 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef359; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef359 a owl:Class; owl:intersectionOf _:2ef369 . _:2ef369 rdf:first ; rdf:rest _:2ef389 . _:2ef389 rdf:first _:2ef379; rdf:rest rdf:nil . _:2ef379 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef399 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ef3a9 . _:2ef3a9 a owl:Class; owl:intersectionOf _:2ef3b9 . _:2ef3b9 rdf:first ; rdf:rest _:2ef3d9 . _:2ef3d9 rdf:first _:2ef3c9; rdf:rest rdf:nil . _:2ef3c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polypeptide library"; owl:equivalentClass _:2ef3e9; rdfs:subClassOf , _:2ef4c9, _:2ef4d9, _:2ef529; "PERSON: Melissa Haendel"; "Reagent library that is comprosed of peptides that have a systematic combination of amino acids. Usually, a peptide library is synthesized on solid phase, mostly on resin, which can be made as flat surface or beads."; "http://en.wikipedia.org/wiki/Peptide_library"; "peptide library" . _:2ef3e9 a owl:Class; owl:intersectionOf _:2ef3f9 . _:2ef3f9 rdf:first ; rdf:rest _:2ef419 . _:2ef419 rdf:first _:2ef409; rdf:rest _:2ef479 . _:2ef409 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ef429 . _:2ef429 a owl:Class; owl:intersectionOf _:2ef439 . _:2ef439 rdf:first ; rdf:rest _:2ef459 . _:2ef459 rdf:first _:2ef449; rdf:rest rdf:nil . _:2ef449 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef479 rdf:first _:2ef469; rdf:rest rdf:nil . _:2ef469 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef489; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef489 a owl:Class; owl:intersectionOf _:2ef499 . _:2ef499 rdf:first ; rdf:rest _:2ef4b9 . _:2ef4b9 rdf:first _:2ef4a9; rdf:rest rdf:nil . _:2ef4a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef4c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef4d9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2ef4e9 . _:2ef4e9 a owl:Class; owl:intersectionOf _:2ef4f9 . _:2ef4f9 rdf:first ; rdf:rest _:2ef519 . _:2ef519 rdf:first _:2ef509; rdf:rest rdf:nil . _:2ef509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef529 a owl:Restriction; owl:onProperty ; owl:onClass _:2ef539; owl:minQualifiedCardinality "2"^^xsd:nonNegativeInteger . _:2ef539 a owl:Class; owl:intersectionOf _:2ef549 . _:2ef549 rdf:first ; rdf:rest _:2ef569 . _:2ef569 rdf:first _:2ef559; rdf:rest rdf:nil . _:2ef559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "alanine scanning peptide library"; rdfs:subClassOf ; "A peptide library containing peptides in which each non-alanine residue is substituted one at a time with an alanine residue, allowing determination of each residue's contribution to the peptides functionality. Alanine scanning library is able to identify specific amino acid residues responsible for the peptide's function, stability, and conformation."; "PERSON: Matthew Brush"; "http://www.genscript.com/alanine_scanning.html" . a owl:Class; rdfs:label "combinatorial peptide library"; rdfs:subClassOf ; "A peptide library synthesized through combinatorial chemistry techniques."; "PERSON: Matthew Brush"; "http://www.genomicglossaries.com/content/libraries_synthesis.asp" . a owl:Class; rdfs:label "overlapping peptide peptide library"; rdfs:subClassOf ; "A peptide library in which peptide sequences are engineered to exhibit a specified degree of overlap with other peptides in the library. The library generation process is characterized by two parameters, fragment length and offset number, each library is generated by breaking the original protein or peptide into many equal-length overlapping fragment, each has 8 to 20 residues in size."; "PERSON: Matthew Brush"; "http://www.genscript.com/overlapping_library.html" . a owl:Class; rdfs:label "phage display peptide library"; rdfs:subClassOf ; "A peptide library that contains phage display, an expression system of peptides, at the surface of phage particles. The construction of a phage display library is accomplished by the incorporation of the nucleotide sequence encoding the peptide to be displayed into a phage genome as a fusion to a gene encoding a phage coat protein. The fusion of the protein with the phage coat protein ensures that the peptide to be displayed is presented at the surface of the mature phage, while the sequence encoding it is contained within the same phage particle, allowing a physical link between the phenotype and genotype of the expressed peptide."; "PERSON: Nicole Vasilevsky"; "http://www.phagedisplay.net/" . a owl:Class; rdfs:label "employee role"; rdfs:subClassOf ; "ERO:employee role" . a owl:Class; rdfs:label "achieved role"; rdfs:subClassOf , _:2ef579, _:2ef589; "intentional agent role"; "http://en.wikipedia.org/wiki/Role"; "a social role that inheres in an agent as a result of the bearer's self-motivated actions or intentions that reflect the bearer's skills, abilities, or efforts" . _:2ef579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ef599 . _:2ef599 a owl:Class; owl:intersectionOf _:2ef5b9 . _:2ef5b9 rdf:first _:2ef5a9; rdf:rest _:2ef5f9 . _:2ef5a9 a owl:Class; owl:unionOf _:2ef5c9 . _:2ef5c9 rdf:first ; rdf:rest _:2ef5d9 . _:2ef5d9 rdf:first ; rdf:rest rdf:nil . _:2ef5f9 rdf:first _:2ef5e9; rdf:rest rdf:nil . _:2ef5e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "student role"; rdfs:subClassOf ; "ERO:student role" . a owl:Class; rdfs:label "transfection agent"; owl:equivalentClass _:2ef609; rdfs:subClassOf , _:2ef649; "transfection carrier reagent", "transfection carrier agent"; "A reagent that is used to introduced foreign material (typically DNA) into a cell."; rdfs:comment "Transfection agents typically encapsulate, coat, or otherwise interact with the material to be transfected in order to ferry it into its target cell. But not all transfection methods require a transfeciton agent, for example electroporation."; "Lipofectamine, Fugene, calcium phosphate"; . _:2ef609 a owl:Class; owl:intersectionOf _:2ef619 . _:2ef619 rdf:first ; rdf:rest _:2ef639 . _:2ef639 rdf:first _:2ef629; rdf:rest rdf:nil . _:2ef629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef649 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_material transfer function"; rdfs:subClassOf ; "OBI:transfer function"; "replaced with OBI:transfer function"; "a function to to deliver some 'material to be combined' to a new location within or attached to some 'target of material combination'" . a owl:Class; rdfs:label "metal atomic molecular entity"; rdfs:subClassOf , , _:2ef659 . _:2ef659 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "nonmetal atomic molecular entity"; rdfs:subClassOf , , _:2ef669 . _:2ef669 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "metalloid atomic molecular entity"; rdfs:subClassOf , , _:2ef679 . _:2ef679 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "elemental molecule reagent"; owl:equivalentClass _:2ef689; rdfs:subClassOf , , _:2ef6c9; "an elemental molecule that bears a reagent role"; "molecular oxygen (O2), molecular nitrogen (N2), graphite (C4), or dizinc (Zn2) applied as reagents" . _:2ef689 a owl:Class; owl:intersectionOf _:2ef699 . _:2ef699 rdf:first ; rdf:rest _:2ef6b9 . _:2ef6b9 rdf:first _:2ef6a9; rdf:rest rdf:nil . _:2ef6a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef6c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "phosphorous-32 molecular label"; owl:equivalentClass _:2ef6d9; rdfs:subClassOf , , _:2ef719, _:2ef729; "P32 label", "P32-derived molecular label", "P32-containing molecular label"; " dATP[P32]), a P32-labeled oligonucleotide"; "a molecular entity containing phosphorous-32, that is used to label some target molecule of interest to allow for its detection in some assay"; . _:2ef6d9 a owl:Class; owl:intersectionOf _:2ef6e9 . _:2ef6e9 rdf:first ; rdf:rest _:2ef709 . _:2ef709 rdf:first _:2ef6f9; rdf:rest rdf:nil . _:2ef6f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef729 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "radioactive molecular reagent"; owl:equivalentClass _:2ef739, _:2ef799; rdfs:subClassOf , _:2ef839, _:2ef849, _:2ef899; "radioisotope reagent", "radiochemical", "radioactive isotope reagent", "radionuclide reagent"; "a molecular entity that is engineered to incorporate a radioactive isotope"; "ATP Alpha[P32], disodium phosphate[P32], Methionine [S35], Glutathione [S35]"; . _:2ef739 a owl:Class; owl:intersectionOf _:2ef749 . _:2ef749 rdf:first ; rdf:rest _:2ef769 . _:2ef769 rdf:first _:2ef759; rdf:rest _:2ef789 . _:2ef759 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef789 rdf:first _:2ef779; rdf:rest rdf:nil . _:2ef779 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef799 a owl:Class; owl:intersectionOf _:2ef7a9 . _:2ef7a9 rdf:first ; rdf:rest _:2ef7c9 . _:2ef7c9 rdf:first _:2ef7b9; rdf:rest _:2ef7e9 . _:2ef7b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef7e9 rdf:first _:2ef7d9; rdf:rest rdf:nil . _:2ef7d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ef7f9 . _:2ef7f9 a owl:Class; owl:intersectionOf _:2ef809 . _:2ef809 rdf:first ; rdf:rest _:2ef829 . _:2ef829 rdf:first _:2ef819; rdf:rest rdf:nil . _:2ef819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ef859 . _:2ef859 a owl:Class; owl:intersectionOf _:2ef869 . _:2ef869 rdf:first ; rdf:rest _:2ef889 . _:2ef889 rdf:first _:2ef879; rdf:rest rdf:nil . _:2ef879 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "iodine-125"; rdfs:subClassOf , _:2ef8a9 . _:2ef8a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "iodine-131"; rdfs:subClassOf , _:2ef8b9 . _:2ef8b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "L-methionine[S35]"; rdfs:subClassOf , , , _:2ef8c9, _:2ef8d9, _:2ef8e9; "a methionine amino acid engineered to contain the sulfur-35 radioisotope"; . _:2ef8c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef8d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef8e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biotin reagent"; rdfs:subClassOf , , , _:2ef8f9; "An organic small molecule reagent that has formula C10H16N2O3S."; . _:2ef8f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "tunicamycin reagent"; rdfs:subClassOf , , _:2ef909; "an organic small molecule reagent that derives from Streptomyces lysosuperificus, and which blocks the reaction of UDP-GlcNAc and Dol-P in the first step of glycoprotein synthesis, thus inhibiting the synthesis of all N-linked glycoproteins"; . _:2ef909 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "digoxygenin reagent"; rdfs:subClassOf , , , _:2ef919; "A 12beta-hydroxy steroid that has formula C23H34O5, and is applied as a reagent"; . _:2ef919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleobase-containing small molecule"; owl:equivalentClass _:2ef929; rdfs:subClassOf , _:2ef969, _:2ef979; "nucleosides such as adenosine or guanosine, or nucleoside phosphates such as ATP or GTP"; "nucleosidic small molecule"; "an organic small molecule that contains a nucleobase conjugated to a ribose-based sugar moiety to form a nucleoside-like structure. Addition of a phosphate to such structures generates nucleotide subunits of nucleic acids." . _:2ef929 a owl:Class; owl:intersectionOf _:2ef939 . _:2ef939 rdf:first ; rdf:rest _:2ef959 . _:2ef959 rdf:first _:2ef949; rdf:rest rdf:nil . _:2ef949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2ef979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleobase analog"; owl:equivalentClass _:2ef989; rdfs:subClassOf , , _:2efa29, _:2efa39; "an organic small molecule reagent that is engineered to exhibit structurally similarity to some natural nucleobase, such that it maintains some similar chemical properties and activity, while its structural differences allow probing or manipulation of the biochemical environment of the analog"; "unnatural nucleobase"; . _:2ef989 a owl:Class; owl:intersectionOf _:2ef999 . _:2ef999 rdf:first ; rdf:rest _:2ef9b9 . _:2ef9b9 rdf:first _:2ef9a9; rdf:rest _:2efa19 . _:2ef9a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2ef9c9 . _:2ef9c9 a owl:Class; owl:intersectionOf _:2ef9d9 . _:2ef9d9 rdf:first ; rdf:rest _:2ef9f9 . _:2ef9f9 rdf:first _:2ef9e9; rdf:rest rdf:nil . _:2ef9e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efa19 rdf:first _:2efa09; rdf:rest rdf:nil . _:2efa09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efa29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efa39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efa49 . _:2efa49 a owl:Class; owl:intersectionOf _:2efa59 . _:2efa59 rdf:first ; rdf:rest _:2efa79 . _:2efa79 rdf:first _:2efa69; rdf:rest rdf:nil . _:2efa69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleobasic reagent"; owl:equivalentClass _:2efa89; rdfs:subClassOf , _:2efb49; "an organic small molecule reagent that exhibits a core nucleobase-like structure. Can be an actual nucleobase, nucleoside, or nucleotide, or an analog engineered to resemble such molecules."; "nucleobase-related reagent", "nucleobase-containing reagent"; ; . _:2efa89 a owl:Class; owl:intersectionOf _:2efaa9 . _:2efaa9 rdf:first _:2efa99; rdf:rest _:2efb39 . _:2efa99 a owl:Class; owl:unionOf _:2efab9 . _:2efab9 rdf:first ; rdf:rest _:2efad9 . _:2efad9 rdf:first _:2efac9; rdf:rest rdf:nil . _:2efac9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efae9 . _:2efae9 a owl:Class; owl:intersectionOf _:2efaf9 . _:2efaf9 rdf:first ; rdf:rest _:2efb19 . _:2efb19 rdf:first _:2efb09; rdf:rest rdf:nil . _:2efb09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efb39 rdf:first _:2efb29; rdf:rest rdf:nil . _:2efb29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efb49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "reagent mixture"; owl:equivalentClass _:2efb59; rdfs:subClassOf , , _:2efb99; "reagent mix"; "a reagent that is a mixture of molecular entities of different types, either dry or in solution. Can refer to a collection of separate, molecular or material entities, a compound substance comprised of different types of molecules, or a chemical solution."; "a dNTP mix, a Tris buffer solution, a protein extract."; "reagent mixture or solution"; . _:2efb59 a owl:Class; owl:intersectionOf _:2efb69 . _:2efb69 rdf:first ; rdf:rest _:2efb89 . _:2efb89 rdf:first _:2efb79; rdf:rest rdf:nil . _:2efb79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efb99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "deoxyribonucleotide mix"; owl:equivalentClass _:2efba9; rdfs:subClassOf , _:2efc09, _:2efc19, _:2efc29; "a reagent mixture that contains a mix of dNTP molecules (typically dATP, dCTP, dGTP, and dTTP to be used in PCR reactions)"; "note that the axiom 'has principle part' only protein does not mean that this reagent cannot come as part of a solution containing other solute and solvent molecules . . . but the dNTPs are considered the key components of interest in the reagent"; . _:2efba9 a owl:Class; owl:intersectionOf _:2efbb9 . _:2efbb9 rdf:first ; rdf:rest _:2efbd9 . _:2efbd9 rdf:first _:2efbc9; rdf:rest _:2efbf9 . _:2efbc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efbf9 rdf:first _:2efbe9; rdf:rest rdf:nil . _:2efbe9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2efc09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efc19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efc29 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "ATP reagent"; rdfs:subClassOf , , _:2efc39; . _:2efc39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "CTP reagent"; rdfs:subClassOf , , _:2efc49; . _:2efc49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "GTP reagent"; rdfs:subClassOf , , _:2efc59; . _:2efc59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "TTP reagent"; rdfs:subClassOf , , _:2efc69; . _:2efc69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dATP reagent"; rdfs:subClassOf , , _:2efc79; . _:2efc79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dCTP reagent"; rdfs:subClassOf , , _:2efc89; . _:2efc89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dGTP reagent"; rdfs:subClassOf , , _:2efc99; . _:2efc99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "dTTP reagent"; rdfs:subClassOf , , _:2efca9; . _:2efca9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "LNA residue"; rdfs:subClassOf , _:2efcb9, _:2efcc9; "locked nucleic acid residue" . _:2efcb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efcc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "prokaryotic expression construct"; owl:equivalentClass _:2efcd9; rdfs:subClassOf , _:2efd99, _:2efe39; "An expression construct that contains promoter elements to drive expression of downstream genes in prokaryotic cells or prokaryote-derived in vitro expression systems."; . _:2efcd9 a owl:Class; owl:intersectionOf _:2efce9 . _:2efce9 rdf:first ; rdf:rest _:2efd09 . _:2efd09 rdf:first _:2efcf9; rdf:rest rdf:nil . _:2efcf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efd19 . _:2efd19 a owl:Class; owl:intersectionOf _:2efd29 . _:2efd29 rdf:first ; rdf:rest _:2efd49 . _:2efd49 rdf:first _:2efd39; rdf:rest rdf:nil . _:2efd39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efd59 . _:2efd59 a owl:Class; owl:unionOf _:2efd69 . _:2efd69 rdf:first ; rdf:rest _:2efd89 . _:2efd89 rdf:first _:2efd79; rdf:rest rdf:nil . _:2efd79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efd99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efda9 . _:2efda9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efdb9 . _:2efdb9 a owl:Class; owl:intersectionOf _:2efdc9 . _:2efdc9 rdf:first ; rdf:rest _:2efde9 . _:2efde9 rdf:first _:2efdd9; rdf:rest rdf:nil . _:2efdd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efdf9 . _:2efdf9 a owl:Class; owl:intersectionOf _:2efe09 . _:2efe09 rdf:first ; rdf:rest _:2efe29 . _:2efe29 rdf:first _:2efe19; rdf:rest rdf:nil . _:2efe19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efe39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efe49 . _:2efe49 a owl:Class; owl:intersectionOf _:2efe59 . _:2efe59 rdf:first ; rdf:rest _:2efe79 . _:2efe79 rdf:first _:2efe69; rdf:rest rdf:nil . _:2efe69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efe89 . _:2efe89 a owl:Class; owl:unionOf _:2efe99 . _:2efe99 rdf:first ; rdf:rest _:2efeb9 . _:2efeb9 rdf:first _:2efea9; rdf:rest rdf:nil . _:2efea9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2efec9 a owl:Axiom; ""; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2efed9 . _:2efed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efee9 . _:2efee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2efef9 . _:2efef9 a owl:Class; owl:intersectionOf _:2eff09 . _:2eff09 rdf:first ; rdf:rest _:2eff29 . _:2eff29 rdf:first _:2eff19; rdf:rest rdf:nil . _:2eff19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2eff39 . _:2eff39 a owl:Class; owl:intersectionOf _:2eff49 . _:2eff49 rdf:first ; rdf:rest _:2eff69 . _:2eff69 rdf:first _:2eff59; rdf:rest rdf:nil . _:2eff59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete__miRNA plasmid"; rdfs:subClassOf ; "An RNA interference plasmid that expresses a short sequence of RNA that includes elements required for processing by endogenous microRNA processing machinery into active microRNA molecules."; "Small hairpin RNA plasmid"; rdfs:comment "The gene specific targeting sequences in these small RNAs may or may not represent a naturally occurring miRNA, but they will contain flanking RNA regions that allow processing by endogenous miRNA pathway." . a owl:Class; rdfs:label "oligonucleotide probe"; owl:equivalentClass _:2eff79; rdfs:subClassOf , , , _:2effb9; "a nucleic acid reagent that is a single-stranded molecule applied experimentally to probe the biomolecular environment of some specimen. Typically used to detect, isolate, or affect the activity of nucleic acid molecules bearing complementary sequence among a mixture of other nucleic acid molecules"; "nucleic acid-based molecular labels and microarray probes, as well as oligos used to activate or repress the activity of some target, are all considered probes."; rdfs:comment "Note here that the term 'probe' here is interpreted generally to cover targeted molecular effectors. Application in a technique serves to target some molecular entity for a range of purposes, including detection of some target (e.g. molecular labels as probes), isolation of some target (e.g. microarray probes), or altering some biochemical property of some target (e.g. probes used for activation or inhibition of some activity, blocking progress of a polymerase, etc"; "oligo probe"; . _:2eff79 a owl:Class; owl:intersectionOf _:2eff89 . _:2eff89 rdf:first ; rdf:rest _:2effa9 . _:2effa9 rdf:first _:2eff99; rdf:rest rdf:nil . _:2eff99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2effb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular captor role"; rdfs:subClassOf ; "bearers of this role would include antibodies adsorbed on some capture resin to immunoprecipitate some target antigen, or microcystin immobilized on agarose beads to isolate protein phosphatases form a cell lysate"; "a molecular probe role inhereing in a molecular entity used to capture specified target molecules from a complex mixture as part of some isolation technique" . a owl:Class; rdfs:label "molecular probe"; owl:equivalentClass _:2effc9; rdfs:subClassOf , _:2f0009; "a molecular reagent applied in a scientific technique in order to target and interact with some molecular target of interest, typically with the goal of labeling the target for detection, purifying it, or altering its structure or behavior."; "molecular agent", "molecular effector"; rdfs:comment """This class is broadly conceived to cover: (1)'targeted' molecular labels (ie targeted trackers and targeted reporters) used to facilitate detection of some molecular target of interest (2) bioactive/pharmacological agents such as drugs, inhibitors, etc that are used to alter the biological activity of their targets in some investigation (3) molecular entities used as 'captors' to purify target molecules from a complex mixture, such as antibodies used in immunoprecipitations, or chemicals affixed to resins to isolate some interaction target"""; . _:2effc9 a owl:Class; owl:intersectionOf _:2effd9 . _:2effd9 rdf:first ; rdf:rest _:2efff9 . _:2efff9 rdf:first _:2effe9; rdf:rest rdf:nil . _:2effe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "tumorigenesis"; rdfs:subClassOf ; "for now, we consider tumorigenesis to be temporally distinct and non-overlapping withcell transformation, such that cell transformation precedes tumorigenesis. will revisit this interpretation later, and also whether terms such as oncogenesis and carcinogenesis are synonyms, or if these may represent the broader process that includes cell transformation as well as the proliferation of the transformed cell(s) into a tumor."; "OGMS or some other ontology class representing the pathological process of tumor formation from a transfomred cell. Need to determine if both benign and malignant tumorigenesis qualify as 'pathological' according to OGMS, and if tumorigenesis has as a processual part the transfromation of a cell, or if it only includes the proliferation of a transformed cell into a cancerous mass"; "a pathological derivation whereby one or more transformed cells proliferate to form a tumor - an abnormal mass of tissue that results from excessive cell division that is uncontrolled and progressive." . a owl:Class; rdfs:label "genetic material"; rdfs:subClassOf , _:2f0019, _:2f0029, _:2f0039 . _:2f0019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0029 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . "genetic nucleic acid", "genomic material", "genomic nucleic acid"; """1. Genetic material here is considered as a DNA or RNA molecule that is found in a cell or virus, and capable of being replicated and inherited by progeny cells or virus. As such, this nucleic acid is either chromosomal DNA, or some replicative epi-chromosomal plasmid or transposon. 2. Genetic material need not be inherited from an immediate ancestor cell or organism (e.g. a replicative plasmid or transposon acquired through some experimental modification), but must be capable of being inherited by progeny cells or organism. 3. Genetic material necessarily bears the concretization of some genomic sequence region. However, note that this relation is not reciprocal, in that a genomic sequence region is not necessarily encoded by genetic material (ie. it can also be encoded by nucleic acids that are not heritable parts of a cell or virus, such as PCR products or synthetic oligos, where the sequence encoded represents that from the genome of some organsim)"""; "adapted from 'genetic material' class definition in OBI ExpDesign.owl "; "OBI - The concept of 'genetic material' was discussed in 2011 among OBI members, but a final definition or implementation was nver reached. There is a definition in OBO ExpDesign sandbox version, which was used to inform our definition and usage here. Further discussions with OBI will be required, however."; "A nucleic acid macromolecule that is part of a cell or virion and can be replicated within it (and thus considered part of its material genome). 'Genetic material' here is considered to be any nucleic acid that is capable of being replicated and inherited by progeny cells or virus." . a owl:Class; rdfs:label "target of physical modification role"; rdfs:subClassOf , _:2f0049; "a role realized by a planned process in which the bearer is physically modified by some agent, through the addition or removal of material, or the alteration of its internal structure"; "target of modification role", "material to be modified role" . _:2f0049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0059 . _:2f0059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "target genetic modification role"; rdfs:subClassOf , _:2f0069; "a role that inheres in an organism, cell, or cell line that is realized through some genetic modification technique whereby the sequence of the bearers exisitng genetic material is altered, or exogneous DNA is introduced into the bearer in such a way that it can be stably replicated and thus heritable by progeny." . _:2f0069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0079 . _:2f0079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "structural rearrangement objective"; rdfs:subClassOf ; "a material processing objective to structural rearrange the existing components of some material entity, such that no new material becomes physically associated, and no material is removed (ie no net gain or loss of matter)." . a owl:Class; rdfs:label "native bovine serum albumin reagent"; owl:equivalentClass _:2f0089; rdfs:subClassOf , , , _:2f00d9; owl:disjointWith ; "bovine serum albumin that has been purified from some natural source (ie not bioengineered)"; "naturally-produced bovine serum albumin", "naturally-produced BSA"; . _:2f0089 a owl:Class; owl:intersectionOf _:2f0099 . _:2f0099 rdf:first ; rdf:rest _:2f00b9 . _:2f00b9 rdf:first _:2f00a9; rdf:rest rdf:nil . _:2f00a9 a owl:Class; owl:complementOf _:2f00c9 . _:2f00c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f00d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant bovine serum albumin"; owl:equivalentClass _:2f00e9; rdfs:subClassOf , , _:2f0129; "recombinant BSA"; "bovine serum albumin that has been produced using some recombinant plasmid in a bioengineering process "; . _:2f00e9 a owl:Class; owl:intersectionOf _:2f00f9 . _:2f00f9 rdf:first ; rdf:rest _:2f0119 . _:2f0119 rdf:first _:2f0109; rdf:rest rdf:nil . _:2f0109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "bioengineered protein production"; owl:equivalentClass _:2f0139; rdfs:subClassOf , _:2f01e9, _:2f01f9; "a material processing technique whereby some protein synthesis biological process is intentionally and manipulated by an agent in such a way as to determine or impact the sequence of the specified protein output from this process. The sequence of the desired output protein is in some way designed or engineered by an intentional agent. "; """A recombinant protein production technique is an example where the sequence of the bioengineered protein is directly and precisely and completely specified through the engineering of a recombinant DNA construct that serves as the genetic template for transcription and translation. An antibody production technique is an example where the exact sequence of specified output antibodies is not fully specified, but is determined by the administration of some immunogen that triggers the immune system to produce antibodies that will bear a sequence in their paratope that will recognize the specified immunogen. A non-example is the stimulation of a pancreatic beta cell line with glucose in order to stimulate the secretion of insulin. Here, the insulin produced is not considered 'bioengineered', because despite being output from some planned process, its sequence was not designed or engineered in any way by an intentional agent.""" . _:2f0139 a owl:Class; owl:intersectionOf _:2f0149 . _:2f0149 rdf:first ; rdf:rest _:2f0169 . _:2f0169 rdf:first _:2f0159; rdf:rest rdf:nil . _:2f0159 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0179 . _:2f0179 a owl:Class; owl:intersectionOf _:2f0199 . _:2f0199 rdf:first _:2f0189; rdf:rest _:2f01d9 . _:2f0189 a owl:Class; owl:unionOf _:2f01a9 . _:2f01a9 rdf:first ; rdf:rest _:2f01b9 . _:2f01b9 rdf:first ; rdf:rest rdf:nil . _:2f01d9 rdf:first _:2f01c9; rdf:rest rdf:nil . _:2f01c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f01e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f01f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0209 . _:2f0209 a owl:Class; owl:intersectionOf _:2f0229 . _:2f0229 rdf:first _:2f0219; rdf:rest _:2f0269 . _:2f0219 a owl:Class; owl:unionOf _:2f0239 . _:2f0239 rdf:first ; rdf:rest _:2f0249 . _:2f0249 rdf:first ; rdf:rest rdf:nil . _:2f0269 rdf:first _:2f0259; rdf:rest rdf:nil . _:2f0259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "recombinant protein production"; rdfs:subClassOf , , _:2f0279 . _:2f0279 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0289 . _:2f0289 a owl:Class; owl:intersectionOf _:2f0299 . _:2f0299 rdf:first ; rdf:rest _:2f02b9 . _:2f02b9 rdf:first _:2f02a9; rdf:rest rdf:nil . _:2f02a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f02c9 . _:2f02c9 a owl:Class; owl:intersectionOf _:2f02d9 . _:2f02d9 rdf:first ; rdf:rest _:2f02f9 . _:2f02f9 rdf:first _:2f02e9; rdf:rest rdf:nil . _:2f02e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_conferred quality"; rdfs:subClassOf ; "decided not needed for now - formerpy the parent of 'engineered' and 'naturally produced', but not clear that this was correct"; "OBI - recall earlier OBI discussions about the notion of conferred qualities."; "a quality that inheres in its bearer based on the processes through which it was created or modified"; . a owl:Class; rdfs:label "molecular analog"; owl:equivalentClass _:2f0309; rdfs:subClassOf , _:2f03a9, _:2f03f9; """IAO/OBI/PATO? (the towards relation is defined as having a relational quality or a disposition as a domain, but I use it here to have a role as a domain. Is this OK?) . . . note that in BFO2 funciton is a child of disposition, so if towards remains a valid relation, this may be OK. Also, ChEBI should have the analog role, and possibly an analog class?"""; "a molecular reagent that is a synthetic molecule designed to exhibit structural similarity to some other (typically naturally occurring) molecule, which the analog mimics in some scientific technique. The specified structural similarity is such that the analog can mimic some attributes or activity of the analogous natural material entity, while also exhibiting specified structural differences that confer some novel activity which allows it to probe or alter the environment of the bearer"; . _:2f0309 a owl:Class; owl:intersectionOf _:2f0319 . _:2f0319 rdf:first ; rdf:rest _:2f0339 . _:2f0339 rdf:first _:2f0329; rdf:rest _:2f0399 . _:2f0329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0349 . _:2f0349 a owl:Class; owl:intersectionOf _:2f0359 . _:2f0359 rdf:first ; rdf:rest _:2f0379 . _:2f0379 rdf:first _:2f0369; rdf:rest rdf:nil . _:2f0369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0399 rdf:first _:2f0389; rdf:rest rdf:nil . _:2f0389 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f03a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f03b9 . _:2f03b9 a owl:Class; owl:intersectionOf _:2f03c9 . _:2f03c9 rdf:first ; rdf:rest _:2f03e9 . _:2f03e9 rdf:first _:2f03d9; rdf:rest rdf:nil . _:2f03d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f03f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "PNA residue"; rdfs:subClassOf , _:2f0409, _:2f0419 . _:2f0409 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0419 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "PNA nucleotide"; rdfs:subClassOf . a owl:Class; rdfs:label "cytokine reagent"; owl:equivalentClass _:2f0429; rdfs:subClassOf , , _:2f0469; "An example protein reagent class defined by bearing a molecular function (cytokine activity)."; "a protein reagent that is a small cell-signaling molecule of a type secreted by numerous cell types, and used as signaling molecules in intercellular communication. Cytokines can be classified as proteins, peptides, or glycoproteins; the term \"cytokine\" encompasses a large and diverse family of regulators produced throughout the body by cells of diverse embryological origin"; . _:2f0429 a owl:Class; owl:intersectionOf _:2f0439 . _:2f0439 rdf:first ; rdf:rest _:2f0459 . _:2f0459 rdf:first _:2f0449; rdf:rest rdf:nil . _:2f0449 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0469 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_glucose"; rdfs:subClassOf ; "monosaccharide sugar that is an important energy source in living organisms and is a component of many carbohydrates"; "ChEBI:glucose"; . a owl:Class; rdfs:label "obsolete_dextran"; rdfs:subClassOf ; "http://en.wikipedia.org/wiki/Dextran"; "ChEBI:dextran"; "a polysachharide that is a complex, branched glucan made of many glucose molecules, composed of chains of varying lengths (from 3 to 2000 kilodaltons)."; . a owl:Class; rdfs:label "dextran reagent"; owl:equivalentClass _:2f0479; rdfs:subClassOf , , _:2f04b9; "a polysaccharide reagent that is a complex, branched glucan made of many glucose molecules, composed of chains of varying lengths (from 3 to 2000 kilodaltons)."; . _:2f0479 a owl:Class; owl:intersectionOf _:2f0489 . _:2f0489 rdf:first ; rdf:rest _:2f04a9 . _:2f04a9 rdf:first _:2f0499; rdf:rest rdf:nil . _:2f0499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f04b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "glucose reagent"; owl:equivalentClass _:2f04c9; rdfs:subClassOf , , _:2f0509; "a glucose molecule that is applied as a reagent in a scientific technique (e.g. as a component of a buffer or culture medium)"; . _:2f04c9 a owl:Class; owl:intersectionOf _:2f04d9 . _:2f04d9 rdf:first ; rdf:rest _:2f04f9 . _:2f04f9 rdf:first _:2f04e9; rdf:rest rdf:nil . _:2f04e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_zebularine"; rdfs:subClassOf ; "a cytidine analog that acts as a DNA methylation inhibitor by forming a covalent complex with DNA methyltransferases (DNMTs) By stabilizing the binding of DNMTs to DNA, zebularine hinders methylation and decreases dissociation, trapping DNMT and preventing its turnover"; "ChEBI:zebularine"; "http://www.caymanchem.com/app/template/Product.vm/catalog/10975"; . a owl:Class; rdfs:label "obsolete_cytidine"; rdfs:subClassOf ; "ChEBI:cytidine"; . a owl:Class; rdfs:label "obsolete_5-azacytidine"; rdfs:subClassOf ; "ChEBI:5-azacytidine"; . a owl:Class; rdfs:label "DNA methyltransferase activity"; rdfs:subClassOf ; "GO:DNA methyltransferase activity" . a owl:Class; rdfs:label "modified canonical amino acid"; owl:equivalentClass _:2f0519; rdfs:subClassOf , _:2f0559 . _:2f0519 a owl:Class; owl:intersectionOf _:2f0529 . _:2f0529 rdf:first ; rdf:rest _:2f0549 . _:2f0549 rdf:first _:2f0539; rdf:rest rdf:nil . _:2f0539 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "modified amino acid reagent"; owl:equivalentClass _:2f0569; rdfs:subClassOf , , _:2f05a9; "O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine, O-phospho-L-carnitine, N-acetly-D-ornithine, biotin-conjugated citrullene"; "an amino acid reagent representing a modified version of some amino acid (i.e. is functionally derived from some other amino acid)"; "This class includes all amino acid reagents, natural or unnatural, that are functional derivatives of some as of yet undefiend set of foundational, 'unmodified' amino acids (which includes at minimum the set of canonical amino acids). We acknowledge this definition is vague and imprecise, and are working with ChEBI and others to address this. However, we implement this class now with the expectation that users will apply common sense to determine if a given amino acid is modified or not. As a point of reference, see the Sigma catalog entries for 'amino acids' (http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16181993) vs 'modified amino acids' (http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16360557) " . _:2f0569 a owl:Class; owl:intersectionOf _:2f0579 . _:2f0579 rdf:first ; rdf:rest _:2f0599 . _:2f0599 rdf:first _:2f0589; rdf:rest rdf:nil . _:2f0589 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f05a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "modified non-canonical amino acid reagent"; owl:equivalentClass _:2f05b9; rdfs:subClassOf , _:2f0619, _:2f0629; "O-phospho-L-carnitine, N-acetly-D-ornithine, biotin-conjugated citrullene"; "an amino acid reagent representing a modified version of some non-canonical amino acid" . _:2f05b9 a owl:Class; owl:intersectionOf _:2f05c9 . _:2f05c9 rdf:first ; rdf:rest _:2f05e9 . _:2f05e9 rdf:first _:2f05d9; rdf:rest _:2f0609 . _:2f05d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0609 rdf:first _:2f05f9; rdf:rest rdf:nil . _:2f05f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0629 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "microarray oligonucleotide probe"; owl:equivalentClass _:2f0639; rdfs:subClassOf , _:2f0699, _:2f06a9, _:2f06b9; "microarray probe"; "an oligonucleotide that is immobilized on the surface of a microarray support substrate, to sequester and allow for the quantification of complementary target oligonucleotides from some nucleic acid sample under investigation" . _:2f0639 a owl:Class; owl:intersectionOf _:2f0649 . _:2f0649 rdf:first ; rdf:rest _:2f0669 . _:2f0669 rdf:first _:2f0659; rdf:rest _:2f0689 . _:2f0659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0689 rdf:first _:2f0679; rdf:rest rdf:nil . _:2f0679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0699 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f06a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f06b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular inhibitor"; owl:equivalentClass _:2f06c9; rdfs:subClassOf , _:2f0709 . _:2f06c9 a owl:Class; owl:intersectionOf _:2f06d9 . _:2f06d9 rdf:first ; rdf:rest _:2f06f9 . _:2f06f9 rdf:first _:2f06e9; rdf:rest rdf:nil . _:2f06e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0709 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "molecular activator"; owl:equivalentClass _:2f0719; rdfs:subClassOf , _:2f0759 . _:2f0719 a owl:Class; owl:intersectionOf _:2f0729 . _:2f0729 rdf:first ; rdf:rest _:2f0749 . _:2f0749 rdf:first _:2f0739; rdf:rest rdf:nil . _:2f0739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0759 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "data processing technique"; owl:equivalentClass _:2f0769; rdfs:subClassOf , , _:2f07a9; "a technique which produces output data from input data"; . _:2f0769 a owl:Class; owl:intersectionOf _:2f0779 . _:2f0779 rdf:first ; rdf:rest _:2f0799 . _:2f0799 rdf:first _:2f0789; rdf:rest rdf:nil . _:2f0789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f07a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "unmodified non-canonical amino acid"; rdfs:subClassOf , , _:2f07b9 . _:2f07b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "modified canonical amino acid reagent"; owl:equivalentClass _:2f07c9; rdfs:subClassOf , , _:2f0809; "an amino acid reagent representing a modified version of some canonical amino acid"; "O-phospho-L-serine, N-acetly-D-Alanine, N-benzoyl-L-alanine, biotin-conjugated lysine" . _:2f07c9 a owl:Class; owl:intersectionOf _:2f07d9 . _:2f07d9 rdf:first ; rdf:rest _:2f07f9 . _:2f07f9 rdf:first _:2f07e9; rdf:rest rdf:nil . _:2f07e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0809 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "protein reagent"; owl:equivalentClass _:2f0819; rdfs:subClassOf , _:2f0889; "a polypeptide reagent that is a protein produced de novo by ribosome-mediated translation, or a protein complex assembled from such proteins, and applied as a reagent in an experimental technique"; . _:2f0819 a owl:Class; owl:intersectionOf _:2f0839 . _:2f0839 rdf:first _:2f0829; rdf:rest _:2f0879 . _:2f0829 a owl:Class; owl:unionOf _:2f0849 . _:2f0849 rdf:first ; rdf:rest _:2f0859 . _:2f0859 rdf:first ; rdf:rest rdf:nil . _:2f0879 rdf:first _:2f0869; rdf:rest rdf:nil . _:2f0869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0889 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "person"; rdfs:subClassOf , , _:2f0899; "foaf:person"; . _:2f0899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f08a9 a owl:Axiom; "exploratory axiom - likely to change"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2f08b9 . _:2f08b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "group"; rdfs:subClassOf , _:2f08c9; "foaf:group" . _:2f08c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "laboratory"; rdfs:subClassOf ; "VIVO:Laboratory"; "An organizational unit (as opposed to the physical facility) that performs research, provides services, or processes materials" . a owl:Class; rdfs:label "uniform collection"; rdfs:subClassOf ; "an object aggregate that is a collection of material entities that are of the same type and exhibit similar or identical structure "; "a collection of chemicals sharing the same/similar molecular structure, a collection of protein macromolecules, a collection of cells of the same type, a collection of microorganisms of the same species" . a owl:Class; rdfs:label "green fluorescent protein"; rdfs:subClassOf ; "GFP"; . a owl:Class; rdfs:label "product role"; rdfs:subClassOf , _:2f08d9, _:2f08f9; "a role inhereing in the material entity that is indicated in some objective specification as the specified output of some material processing."; rdfs:comment "Note that not all outputs of a material processing are considered products - only those conferred special status as the desired/specified outputs according to the objective specification."; "specified material output role", "material product role", "specified product role" . _:2f08d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f08e9 . _:2f08e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f08f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "purified protein reagent"; owl:equivalentClass _:2f0909; rdfs:subClassOf , , _:2f0969, _:2f0979; "Purified insulin protein."; "A protein reagent that is output of some purification process, which aims to produce a solution containing a single species of protein."; "as protein reagents in ReO are molecular entities, a purified protein reagent is defined based on its context (ie being part of a pure collection containing only one type of protein, which results from a purification process)" . _:2f0909 a owl:Class; owl:intersectionOf _:2f0919 . _:2f0919 rdf:first ; rdf:rest _:2f0939 . _:2f0939 rdf:first _:2f0929; rdf:rest _:2f0959 . _:2f0929 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0959 rdf:first _:2f0949; rdf:rest rdf:nil . _:2f0949 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "protein mixture"; owl:equivalentClass _:2f0989; rdfs:subClassOf , _:2f09e9, _:2f09f9, _:2f0a09; "A reagent mixture that has protein molecules as its principal part, members of which are of more than one species of protein"; "note that the axiom 'has principle part' only protein does not mean that this reagent cannot come as part of a solution containing other solute and solvent molecules . . . but the proteins are considered the key components of interest in the reagent"; . _:2f0989 a owl:Class; owl:intersectionOf _:2f0999 . _:2f0999 rdf:first ; rdf:rest _:2f09b9 . _:2f09b9 rdf:first _:2f09a9; rdf:rest _:2f09d9 . _:2f09a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f09d9 rdf:first _:2f09c9; rdf:rest rdf:nil . _:2f09c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2f09e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f09f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0a09 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "biomaterial"; rdfs:subClassOf ; rdfs:comment "Biomaterials are any material output from some biological process occurring in a biological system, regardless of whether this occurs as part of a planned process (ie regardless of whether they are biologically created or bioengineered)"; "a material entity or organismal origin, ie is part of, derives from, or is produced by an organism, or is part of, derives from, or is produced by some material that derives from an organism (such as a cell line)"; "biological material"; """Examples of biomaterials: - organisms and their parts - biological specimens such as blood samples or tissue samples - cultured anatomical entities such as a cell line - a DNA oligonucleotide endogenously produced in some cell - a protein endogenously, whether produced by some organsim from its own genomic DNA, or produced in a bacterial cell from some recombinant plasmid - an antibody, whether produced by an organism as a result of natural or experimental exposure to some immunogen Examples that are NOT biomaterials: - a chemically synthesized DNA oligonucleotide, or DNA analogs such as morpholinos - a polypeptide chemically synthesized de novo"""; . a owl:Class; rdfs:label "biological antibody target"; owl:equivalentClass _:2f0a19; rdfs:subClassOf , _:2f0ab9, _:2f0ac9, _:2f0b19; "a material that is 'biological (ie biologically-occurring - of a type produced or derived from an organism), which represents an intended target of some antibody reagent in some scientific technique (in virtue of it being or having as part an antigen recognized by the antibody)" . _:2f0a19 a owl:Class; owl:intersectionOf _:2f0a29 . _:2f0a29 rdf:first ; rdf:rest _:2f0a49 . _:2f0a49 rdf:first _:2f0a39; rdf:rest _:2f0a69 . _:2f0a39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0a69 rdf:first _:2f0a59; rdf:rest rdf:nil . _:2f0a59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0a79 . _:2f0a79 a owl:Class; owl:intersectionOf _:2f0a89 . _:2f0a89 rdf:first ; rdf:rest _:2f0aa9 . _:2f0aa9 rdf:first _:2f0a99; rdf:rest rdf:nil . _:2f0a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0ab9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0ac9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0ad9 . _:2f0ad9 a owl:Class; owl:intersectionOf _:2f0ae9 . _:2f0ae9 rdf:first ; rdf:rest _:2f0b09 . _:2f0b09 rdf:first _:2f0af9; rdf:rest rdf:nil . _:2f0af9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0b19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_biologically-based material"; rdfs:subClassOf ; "Originally created to be parent for the 'biological antibody target' class - which needed to be defined as any mateiral that is biologically occurring or bioengineered - but decided to jsut apply these axioms to the biological antibody target class" . a owl:Class; rdfs:label "material to be removed role"; rdfs:subClassOf , _:2f0b29 . _:2f0b29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0b39 . _:2f0b39 a owl:Class; owl:intersectionOf _:2f0b49 . _:2f0b49 rdf:first ; rdf:rest _:2f0b69 . _:2f0b69 rdf:first _:2f0b59; rdf:rest rdf:nil . _:2f0b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material to be extracted role"; rdfs:subClassOf . a owl:Class; rdfs:label "obsolete_adjuvant role"; rdfs:subClassOf ; "replaced by OBI class"; "OBI:adjuvant role" . a owl:Class; rdfs:label "linear epitope"; owl:equivalentClass _:2f0b79; rdfs:subClassOf , , _:2f0bb9; "continuous epitope" . _:2f0b79 a owl:Class; owl:intersectionOf _:2f0b89 . _:2f0b89 rdf:first ; rdf:rest _:2f0ba9 . _:2f0ba9 rdf:first _:2f0b99; rdf:rest rdf:nil . _:2f0b99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0bb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "conformational epitope"; owl:equivalentClass _:2f0bc9; rdfs:subClassOf , , _:2f0c09; "Sequence elements from some protein that are spatially separated along the linear sequence of a polypeptide, but exist in close proximity as a result of the three-dimentional folding conformation of the molecule to form a chemical arragnement that is recognized by some antibody"; "discontinuous epitope", "distributed epitope"; "an epitope that is part of a single molecular entity, but not directly contiguous along its connected surface or linear span. The separated chemical groups that comprise a discontinuous epitope will typically exist proximally in a defined spatial region in virtue of the three-dimensional conformation of the molecular entity" . _:2f0bc9 a owl:Class; owl:intersectionOf _:2f0bd9 . _:2f0bd9 rdf:first ; rdf:rest _:2f0bf9 . _:2f0bf9 rdf:first _:2f0be9; rdf:rest rdf:nil . _:2f0be9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0c09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "discontiguous chemical group"; rdfs:subClassOf ; "a collection of chemical groups that are part of a single molecular entity, but not directly contiguous along its connected surface or linear span. the separated chemical groups that comprise such a discontiguous group will typically exist proximally in a defined spatial region, in virtue of the three-dimensional conformation of the molecular entity. For example, a 'discontinuous epitope' is comprised of sequence elements from some protein that are spatially separated along the linear sequence of a polypeptide, but exist in close proximity as a result of the three-dimentional folding conformation of the molecule."; "discontinuous chemical group"; rdfs:comment "not directly physically connected and self-containied, but rather linked through molecular interactions within the same molecule, but separated by moelcular sequence or groups."; . a owl:Class; rdfs:label "paratope"; rdfs:subClassOf , _:2f0c19; "a discontinuous chemical group that represents the part of an antibody which recognises an epitope on an antigen. A paratope consists of the small regions (of 15–22 amino acids) on the antibody's Fv region that contains parts of the antibody's heavy and light chains." . _:2f0c19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "stabilization reagent role"; rdfs:subClassOf ; "a reagent role inhering in a molecular entity in solution that facilitates the maintenance of conformation and/or stability of other molecular entities in the solution."; "BSA plays a stabilization reagent role in many solutions, including antibody reagent solutions" . a owl:Class; rdfs:label "preservative reagent role"; rdfs:subClassOf ; "sodium azide plays a perservative role in many antibody reagent solutions"; "a reagent role inhering in a material entity that serves to preserve the integrity, stability, conformation, or activity of some other material with which it interacts" . a owl:Class; rdfs:label "developer role"; rdfs:subClassOf ; "an achieved role inhereing in a person or organization that has intellectual input into the design, development, engineering, or testing of some manufactured material" . a owl:Class; rdfs:label "green fluorescent protein reagent"; owl:equivalentClass _:2f0c29; rdfs:subClassOf , , , _:2f0c69, _:2f0c79, _:2f0c89, _:2f0c99; "Assumption here is that all GFP reagents are recombinantly produced, and not isolated from natural biological sources."; . _:2f0c29 a owl:Class; owl:intersectionOf _:2f0c39 . _:2f0c39 rdf:first ; rdf:rest _:2f0c59 . _:2f0c59 rdf:first _:2f0c49; rdf:rest rdf:nil . _:2f0c49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0c79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0c89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0c99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0ca9 a owl:Axiom; "in context of biomedical research, GFP reagents are always bioengineered from some plasmid"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2f0cb9 . _:2f0cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_experimental antibody target 0"; rdfs:subClassOf ; """antigenic material that is the specified/intended target of an antibody reagent during an experimental technique. (This requires its having been demonstrated to be recognized/bound by some antibody reagent - in virtue of it being or having as part some antigen)."""; "material antibody target"; rdfs:comment """This class allows us to talk about the material entity which an antibody is used to target in an experiment, even in cases where the actual antigen is not known (e.g. antibodies known to recognize a certain cell or organelle type, for example, but where the actual molecular antigen associated with these targets is not known). As the part_of relation is reflexive, it is acceptible for antigens themselves to be experimental antibody targets (ie they are still part_of some experimental antigen, in that they are part_of themselves)""" . a owl:Class; rdfs:label "obsolete_biological antibody target 2"; rdfs:subClassOf ; "a material entity that is biologically-occurring (ie of a type produced or derived from an organism), and is the intended experimental target of some antibody reagent in virtue of its containing as part some molecular antigen" . a owl:Class; rdfs:label "DNA sequence region"; owl:equivalentClass _:2f0cc9; rdfs:subClassOf , _:2f0d39 . _:2f0cc9 a owl:Class; owl:intersectionOf _:2f0cd9 . _:2f0cd9 rdf:first ; rdf:rest _:2f0cf9 . _:2f0cf9 rdf:first _:2f0ce9; rdf:rest rdf:nil . _:2f0ce9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2f0d09 . _:2f0d09 a owl:Class; owl:unionOf _:2f0d19 . _:2f0d19 rdf:first ; rdf:rest _:2f0d29 . _:2f0d29 rdf:first ; rdf:rest rdf:nil . _:2f0d39 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2f0d49 . _:2f0d49 a owl:Class; owl:unionOf _:2f0d59 . _:2f0d59 rdf:first ; rdf:rest _:2f0d69 . _:2f0d69 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "RNA sequence region"; owl:equivalentClass _:2f0d79; rdfs:subClassOf , _:2f0de9 . _:2f0d79 a owl:Class; owl:intersectionOf _:2f0d89 . _:2f0d89 rdf:first ; rdf:rest _:2f0da9 . _:2f0da9 rdf:first _:2f0d99; rdf:rest rdf:nil . _:2f0d99 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2f0db9 . _:2f0db9 a owl:Class; owl:unionOf _:2f0dc9 . _:2f0dc9 rdf:first ; rdf:rest _:2f0dd9 . _:2f0dd9 rdf:first ; rdf:rest rdf:nil . _:2f0de9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2f0df9 . _:2f0df9 a owl:Class; owl:unionOf _:2f0e09 . _:2f0e09 rdf:first ; rdf:rest _:2f0e19 . _:2f0e19 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "biomolecular entity"; owl:equivalentClass _:2f0e29; rdfs:subClassOf , _:2f0e69; "biological molecule"; "an organic molecular entity that is biologically-occurring (ie of a type produced or derived from an organism)" . _:2f0e29 a owl:Class; owl:intersectionOf _:2f0e39 . _:2f0e39 rdf:first ; rdf:rest _:2f0e59 . _:2f0e59 rdf:first _:2f0e49; rdf:rest rdf:nil . _:2f0e49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0e69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biomolecule antibody target"; owl:equivalentClass _:2f0e79; rdfs:subClassOf , , _:2f0ef9, _:2f0f09, _:2f0f19; "a molecular entity that is biologically-occurring (ie of a type produced or derived from an organism), and is the intended experimental target of some antibody reagent in virtue of its containing as part some molecular antigen" . _:2f0e79 a owl:Class; owl:intersectionOf _:2f0e99 . _:2f0e99 rdf:first _:2f0e89; rdf:rest _:2f0ed9 . _:2f0e89 a owl:Class; owl:unionOf _:2f0ea9 . _:2f0ea9 rdf:first ; rdf:rest _:2f0eb9 . _:2f0eb9 rdf:first ; rdf:rest rdf:nil . _:2f0ed9 rdf:first _:2f0ec9; rdf:rest rdf:nil . _:2f0ec9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0ee9 . _:2f0ee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0ef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0f19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0f29 . _:2f0f29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "carbohydrate antibody target"; owl:equivalentClass _:2f0f39; rdfs:subClassOf , _:2f0fb9 . _:2f0f39 a owl:Class; owl:intersectionOf _:2f0f59 . _:2f0f59 rdf:first _:2f0f49; rdf:rest _:2f0f99 . _:2f0f49 a owl:Class; owl:unionOf _:2f0f69 . _:2f0f69 rdf:first ; rdf:rest _:2f0f79 . _:2f0f79 rdf:first ; rdf:rest rdf:nil . _:2f0f99 rdf:first _:2f0f89; rdf:rest rdf:nil . _:2f0f89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0fa9 . _:2f0fa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0fb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . rdfs:subClassOf _:2f0fc9, _:2f0fe9; "a carbohydrate (or carbohydrate group attached to some other molecular entity such as a protein) which represents an intended target of some antibody reagent in some scientific technique." . _:2f0fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f0fd9 . _:2f0fd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f0fe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "carbohydrate group"; owl:equivalentClass _:2f0ff9; rdfs:subClassOf , _:2f1039, _:2f1049; "an organic chemical group that consists of some carbohydrate moiety derived from a carbohydrate molecular entity" . _:2f0ff9 a owl:Class; owl:intersectionOf _:2f1009 . _:2f1009 rdf:first ; rdf:rest _:2f1029 . _:2f1029 rdf:first _:2f1019; rdf:rest rdf:nil . _:2f1019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "carbohydrate protein modification"; rdfs:subClassOf , _:2f1059 . _:2f1059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "lipid antibody target"; owl:equivalentClass _:2f1069; rdfs:subClassOf , _:2f10e9, _:2f10f9, _:2f1119 . _:2f1069 a owl:Class; owl:intersectionOf _:2f1089 . _:2f1089 rdf:first _:2f1079; rdf:rest _:2f10c9 . _:2f1079 a owl:Class; owl:unionOf _:2f1099 . _:2f1099 rdf:first ; rdf:rest _:2f10a9 . _:2f10a9 rdf:first ; rdf:rest rdf:nil . _:2f10c9 rdf:first _:2f10b9; rdf:rest rdf:nil . _:2f10b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f10d9 . _:2f10d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f10e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f10f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1109 . _:2f1109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1119 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "lipid group"; owl:equivalentClass _:2f1129; rdfs:subClassOf , _:2f1169, _:2f1179; "an organic chemical group that consists of some lipid moiety derived from a lipid molecular entity. here we consider only lipids of biological origin." . _:2f1129 a owl:Class; owl:intersectionOf _:2f1139 . _:2f1139 rdf:first ; rdf:rest _:2f1159 . _:2f1159 rdf:first _:2f1149; rdf:rest rdf:nil . _:2f1149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1169 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleic acid antibody target"; owl:equivalentClass _:2f1189; rdfs:subClassOf , , _:2f11d9, _:2f11f9, _:2f1209 . _:2f1189 a owl:Class; owl:intersectionOf _:2f1199 . _:2f1199 rdf:first ; rdf:rest _:2f11b9 . _:2f11b9 rdf:first _:2f11a9; rdf:rest rdf:nil . _:2f11a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f11c9 . _:2f11c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f11d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f11e9 . _:2f11e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f11f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1209 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "biomolecule group"; owl:equivalentClass _:2f1219; rdfs:subClassOf , _:2f1259, _:2f1269; "an organic chemical group that consists of some chemical moiety derived from a biomolecular entity" . _:2f1219 a owl:Class; owl:intersectionOf _:2f1229 . _:2f1229 rdf:first ; rdf:rest _:2f1249 . _:2f1249 rdf:first _:2f1239; rdf:rest rdf:nil . _:2f1239 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1269 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "polypeptide antibody target"; owl:equivalentClass _:2f1279; rdfs:subClassOf , , _:2f12f9, _:2f1309, _:2f1319 . _:2f1279 a owl:Class; owl:intersectionOf _:2f1299 . _:2f1299 rdf:first _:2f1289; rdf:rest _:2f12d9 . _:2f1289 a owl:Class; owl:unionOf _:2f12a9 . _:2f12a9 rdf:first ; rdf:rest _:2f12b9 . _:2f12b9 rdf:first ; rdf:rest rdf:nil . _:2f12d9 rdf:first _:2f12c9; rdf:rest rdf:nil . _:2f12c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f12e9 . _:2f12e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f12f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1309 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1319 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1329 . _:2f1329 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell antibody target"; owl:equivalentClass _:2f1339; rdfs:subClassOf , , _:2f13b9, _:2f13c9; . _:2f1339 a owl:Class; owl:intersectionOf _:2f1349 . _:2f1349 rdf:first ; rdf:rest _:2f1369 . _:2f1369 rdf:first _:2f1359; rdf:rest rdf:nil . _:2f1359 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1379 . _:2f1379 a owl:Class; owl:intersectionOf _:2f1389 . _:2f1389 rdf:first ; rdf:rest _:2f13a9 . _:2f13a9 rdf:first _:2f1399; rdf:rest rdf:nil . _:2f1399 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f13b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f13c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f13d9 . _:2f13d9 a owl:Class; owl:intersectionOf _:2f13e9 . _:2f13e9 rdf:first ; rdf:rest _:2f1409 . _:2f1409 rdf:first _:2f13f9; rdf:rest rdf:nil . _:2f13f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cell component antibody target"; owl:equivalentClass _:2f1419; rdfs:subClassOf , , _:2f1499, _:2f14a9 . _:2f1419 a owl:Class; owl:intersectionOf _:2f1429 . _:2f1429 rdf:first ; rdf:rest _:2f1449 . _:2f1449 rdf:first _:2f1439; rdf:rest rdf:nil . _:2f1439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1459 . _:2f1459 a owl:Class; owl:intersectionOf _:2f1469 . _:2f1469 rdf:first ; rdf:rest _:2f1489 . _:2f1489 rdf:first _:2f1479; rdf:rest rdf:nil . _:2f1479 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1499 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f14a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f14b9 . _:2f14b9 a owl:Class; owl:intersectionOf _:2f14c9 . _:2f14c9 rdf:first ; rdf:rest _:2f14e9 . _:2f14e9 rdf:first _:2f14d9; rdf:rest rdf:nil . _:2f14d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "whole organism antibody target"; owl:equivalentClass _:2f14f9; rdfs:subClassOf , , _:2f1579, _:2f15c9 . _:2f14f9 a owl:Class; owl:intersectionOf _:2f1509 . _:2f1509 rdf:first ; rdf:rest _:2f1529 . _:2f1529 rdf:first _:2f1519; rdf:rest rdf:nil . _:2f1519 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1539 . _:2f1539 a owl:Class; owl:intersectionOf _:2f1549 . _:2f1549 rdf:first ; rdf:rest _:2f1569 . _:2f1569 rdf:first _:2f1559; rdf:rest rdf:nil . _:2f1559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1579 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1589 . _:2f1589 a owl:Class; owl:intersectionOf _:2f1599 . _:2f1599 rdf:first ; rdf:rest _:2f15b9 . _:2f15b9 rdf:first _:2f15a9; rdf:rest rdf:nil . _:2f15a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f15c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "chemical antibody target"; owl:equivalentClass _:2f15d9; rdfs:subClassOf , , _:2f16e9, _:2f1739; "graphite is a chemical that antibodies have been generated against" . _:2f15d9 a owl:Class; owl:intersectionOf _:2f15f9 . _:2f15f9 rdf:first _:2f15e9; rdf:rest _:2f1699 . _:2f15e9 a owl:Class; owl:unionOf _:2f1609 . _:2f1609 rdf:first ; rdf:rest _:2f1629 . _:2f1629 rdf:first _:2f1619; rdf:rest rdf:nil . _:2f1619 a owl:Class; owl:intersectionOf _:2f1639 . _:2f1639 rdf:first ; rdf:rest _:2f1659 . _:2f1659 rdf:first _:2f1649; rdf:rest rdf:nil . _:2f1649 a owl:Class; owl:complementOf _:2f1669 . _:2f1669 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1679 . _:2f1679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1699 rdf:first _:2f1689; rdf:rest rdf:nil . _:2f1689 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f16a9 . _:2f16a9 a owl:Class; owl:intersectionOf _:2f16b9 . _:2f16b9 rdf:first ; rdf:rest _:2f16d9 . _:2f16d9 rdf:first _:2f16c9; rdf:rest rdf:nil . _:2f16c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f16e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f16f9 . _:2f16f9 a owl:Class; owl:intersectionOf _:2f1709 . _:2f1709 rdf:first ; rdf:rest _:2f1729 . _:2f1729 rdf:first _:2f1719; rdf:rest rdf:nil . _:2f1719 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1739 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "bio-organic small molecule"; owl:equivalentClass _:2f1749; rdfs:subClassOf , , _:2f1789; . _:2f1749 a owl:Class; owl:intersectionOf _:2f1759 . _:2f1759 rdf:first ; rdf:rest _:2f1779 . _:2f1779 rdf:first _:2f1769; rdf:rest rdf:nil . _:2f1769 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "huntingtin protein"; rdfs:subClassOf ; "PRO class"; . a owl:Class; rdfs:label "microarray quadrant"; rdfs:subClassOf , _:2f1799, _:2f17a9, _:2f17b9; "microarray matrix cell", "microarray cell"; "A microarray quadrant is part of a microarray support substrate that consists of a demarcated portion of the solid substrate, onto which some uniform collection of molecular entities is spotted. It is the sum total of all of these contiguous quadrants and their spotted collections of molecules that represents a single microarray reagent. "; "A microarray quadrant is part of a microarray support substrate that consists of a demarcated portion of the solid substrate, onto which some uniform collection of molecular entities is spotted." . _:2f1799 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f17a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f17b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "microarray spot"; rdfs:subClassOf , _:2f17c9 . _:2f17c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "microarray support substrate"; rdfs:subClassOf , _:2f17d9, _:2f17e9, _:2f17f9; "a solid surface which provide structure and support for individual spots/samples of a microarray. In the case of molecular microarrays, support substrates are typically referred to as 'chips', and comprised of glass, silicon or plastic. Tissue microarray support substrates are typically comprised of paraffin into which tissue specimens are embedded." . _:2f17d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f17e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f17f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleoside reagent"; owl:equivalentClass _:2f1809; rdfs:subClassOf , , , _:2f1849; "a nucleoside molecule that bears a reagent role" . _:2f1809 a owl:Class; owl:intersectionOf _:2f1819 . _:2f1819 rdf:first ; rdf:rest _:2f1839 . _:2f1839 rdf:first _:2f1829; rdf:rest rdf:nil . _:2f1829 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1849 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "nucleobase reagent"; owl:equivalentClass _:2f1859; rdfs:subClassOf , , , _:2f1899; "a nucleobase molecule that has a reagent role" . _:2f1859 a owl:Class; owl:intersectionOf _:2f1869 . _:2f1869 rdf:first ; rdf:rest _:2f1889 . _:2f1889 rdf:first _:2f1879; rdf:rest rdf:nil . _:2f1879 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1899 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_molecular captor"; rdfs:subClassOf ; """decided not deirable/needed for now, but may implement in the future logical definition: 'molecular probe' and ('has role' some 'molecular captor role')""" . a owl:Class; rdfs:label "targeted molecular label"; owl:equivalentClass _:2f18a9; rdfs:subClassOf , , _:2f1919; rdfs:comment "an organizational class to group targeted tracker and targeted reporter under the 'molecular probe' class"; . _:2f18a9 a owl:Class; owl:intersectionOf _:2f18b9 . _:2f18b9 rdf:first ; rdf:rest _:2f18d9 . _:2f18d9 rdf:first _:2f18c9; rdf:rest rdf:nil . _:2f18c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f18e9 . _:2f18e9 a owl:Class; owl:unionOf _:2f18f9 . _:2f18f9 rdf:first ; rdf:rest _:2f1909 . _:2f1909 rdf:first ; rdf:rest rdf:nil . _:2f1919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1929 . _:2f1929 a owl:Class; owl:unionOf _:2f1939 . _:2f1939 rdf:first ; rdf:rest _:2f1949 . _:2f1949 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "long oligonucleotide DNA microarray"; rdfs:subClassOf ; "http://www.ncbi.nlm.nih.gov/pubmed/15876355"; "a DNA microarray that is comprised of numerous collections of long DNA oligonucleotides (typically 50-80 nculeotides in length), which are spotted in a two-dimensional array onto a solid support matrix. The arrayed long oligo 'probes' are used to determine the identity or quantity of 'target' nucleic acid molecules (or nucleic acid-associated molecules) in some biological specimen of interest, based on quantification of hybridization between specimen nucleic acid targets and immobilized microarray oligos." . a owl:Class; rdfs:label "short oligonucleotide DNA microarray"; rdfs:subClassOf ; "a DNA microarray that is comprised of numerous collections of short DNA oligonucleotides (typically 25-30 nculeotides in length), which are spotted in a two-dimensional array onto a solid support matrix. The arrayed short oligo 'probes' are used to determine the identity or quantity of 'target' nucleic acid molecules (or nucleic acid-associated molecules) in some biological specimen of interest, based on quantification of hybridization between specimen nucleic acid targets and immobilized microarray oligos."; "http://www.ncbi.nlm.nih.gov/pubmed/15876355" . a owl:Class; rdfs:label "cDNA microarray"; rdfs:subClassOf , _:2f1959; "a DNA microarray that is comprised of numerous collections of like cDNA molecules, which are spotted in a two-dimensional array onto a solid support matrix, typically made of glass or silicon. The arrayed cDNA 'probes' are used to determine the identity or quantity of 'target' nucleic acid molecules (or nucleic acid-associated molecules) in some biological specimen of interest, based on quantification of hybridization between specimen nucleic acid targets and immobilized microarray cDNA molecules."; "http://www.ncbi.nlm.nih.gov/pubmed/15876355" . _:2f1959 a owl:Class; owl:intersectionOf _:2f1969 . _:2f1969 rdf:first ; rdf:rest _:2f1989 . _:2f1989 rdf:first _:2f1979; rdf:rest rdf:nil . _:2f1979 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1999 . _:2f1999 a owl:Class; owl:intersectionOf _:2f19a9 . _:2f19a9 rdf:first ; rdf:rest _:2f19c9 . _:2f19c9 rdf:first _:2f19b9; rdf:rest rdf:nil . _:2f19b9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom _:2f19d9 . _:2f19d9 a owl:Class; owl:intersectionOf _:2f19e9 . _:2f19e9 rdf:first ; rdf:rest _:2f1a09 . _:2f1a09 rdf:first _:2f19f9; rdf:rest rdf:nil . _:2f19f9 a owl:Class; owl:intersectionOf _:2f1a29 . _:2f1a29 rdf:first _:2f1a19; rdf:rest _:2f1a49 . _:2f1a19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1a49 rdf:first _:2f1a39; rdf:rest rdf:nil . _:2f1a39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "experimentally transformed cell line cell"; owl:equivalentClass _:2f1a59; rdfs:subClassOf , , _:2f1a99, _:2f1aa9; "a cell line cell that has been experimentally transformed through genetic modifications to exhibit properties of cancer (including the ability to grow in the absence of survival factors, the ability to divide without being specifically instructed to do so from outside the cell, the absence of contact inhibition when grown in culture, and the ability to form tumors in animal models)"; rdfs:comment "'cell immortalization' is different from 'cell transformation' in that the former requires only that a cell is able to replicate indefinitely in culture, while the latter further requires that the cell undergoes a set of genetic modifications that confers the properties of cancer - including the ability to grow in the absence of survival factors and the ability to divide without being specifically instructed to do so from outside the cell. In experimental settings, these qualities allow transformed cells to form tumors in animal models, and to escape contact inhibition in culture and thus grow on top of each other." . _:2f1a59 a owl:Class; owl:intersectionOf _:2f1a69 . _:2f1a69 rdf:first ; rdf:rest _:2f1a89 . _:2f1a89 rdf:first _:2f1a79; rdf:rest rdf:nil . _:2f1a79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1aa9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "experimentally immortalized cell line cell"; owl:equivalentClass _:2f1ab9; rdfs:subClassOf , , _:2f1af9, _:2f1b09; "a cell line cell that has been experimentally immortalized through genetic modifications such that a culture of such cells has the capacity to replicate indefinitely in culture"; rdfs:comment "'cell immortalization' is different from 'cell transformation' in that the former requires only that a cell is able to replicate indefinitely in culture, while the latter further requires that the cell undergoes a set of genetic modifications that confers the properties of cancer - including the ability to grow in the absence of survival factors and the ability to divide without being specifically instructed to do so from outside the cell. In experimental settings, these qualities allow transformed cells to form tumors in animal models, and to escape contact inhibition in culture and thus grow on top of each other." . _:2f1ab9 a owl:Class; owl:intersectionOf _:2f1ac9 . _:2f1ac9 rdf:first ; rdf:rest _:2f1ae9 . _:2f1ae9 rdf:first _:2f1ad9; rdf:rest rdf:nil . _:2f1ad9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1af9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "experimentally transformed cell line"; owl:equivalentClass _:2f1b19; rdfs:subClassOf , _:2f1b59, _:2f1b69; "an immortal cell line that is genetically modified to exhibit the properties of cancer, including the ability to grow in the absence of survival factors and without being specifically instructed to do so from outside the cell, the absence of contact inhibited growth, and the ability to form tumors in animal models"; . _:2f1b19 a owl:Class; owl:intersectionOf _:2f1b29 . _:2f1b29 rdf:first ; rdf:rest _:2f1b49 . _:2f1b49 rdf:first _:2f1b39; rdf:rest rdf:nil . _:2f1b39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1b59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1b69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transient expression technique"; rdfs:subClassOf , _:2f1b79, _:2f1bf9; "transient DNA transfection or viral transduction of a cell line"; "exogenous expression technique"; "a material processing technique whereby nucleic acids are delivered as part of some DNA construct into an expression system, typically a cell or organism,with the objective of transient expression of the construct insert (ie the goal is not for stable integration into the host genome or replication outside the genome in a heritable manner)"; . _:2f1b79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1b89 . _:2f1b89 a owl:Class; owl:intersectionOf _:2f1ba9 . _:2f1ba9 rdf:first _:2f1b99; rdf:rest _:2f1be9 . _:2f1b99 a owl:Class; owl:unionOf _:2f1bb9 . _:2f1bb9 rdf:first ; rdf:rest _:2f1bc9 . _:2f1bc9 rdf:first ; rdf:rest rdf:nil . _:2f1be9 rdf:first _:2f1bd9; rdf:rest rdf:nil . _:2f1bd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1bf9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1c09 . _:2f1c09 a owl:Class; owl:intersectionOf _:2f1c19 . _:2f1c19 rdf:first ; rdf:rest _:2f1c39 . _:2f1c39 rdf:first _:2f1c29; rdf:rest rdf:nil . _:2f1c29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "selected multicellular organism culture"; owl:equivalentClass _:2f1c49; rdfs:subClassOf , , _:2f1cb9; "a multicellular organism cell culture that is the output of some selective cell subculturing or establishing selected cell culture technique, whereby a specified subset of cells from an input cell culture or biological specimen is selected based on their exhibiting some desired feature, and propagated as a new cell culture."; . _:2f1c49 a owl:Class; owl:intersectionOf _:2f1c59 . _:2f1c59 rdf:first ; rdf:rest _:2f1c79 . _:2f1c79 rdf:first _:2f1c69; rdf:rest rdf:nil . _:2f1c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1c89 . _:2f1c89 a owl:Class; owl:unionOf _:2f1c99 . _:2f1c99 rdf:first ; rdf:rest _:2f1ca9 . _:2f1ca9 rdf:first ; rdf:rest rdf:nil . _:2f1cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1cc9 . _:2f1cc9 a owl:Class; owl:unionOf _:2f1cd9 . _:2f1cd9 rdf:first ; rdf:rest _:2f1ce9 . _:2f1ce9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "transgenic virus production"; owl:equivalentClass _:2f1cf9; rdfs:subClassOf , _:2f1db9, _:2f1e49, _:2f1e59, _:2f1e69, _:2f1ef9; "a material processing technique with the goal of producing a transgenic virus, typically through the transfection of plasmids encoding a gene of interest along with viral coat protein, replication, and packaging genes that encode the machinery necessary to package the gene of interest into viral capsids secreted from the transfected cells." . _:2f1cf9 a owl:Class; owl:intersectionOf _:2f1d09 . _:2f1d09 rdf:first ; rdf:rest _:2f1d29 . _:2f1d29 rdf:first _:2f1d19; rdf:rest rdf:nil . _:2f1d19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1d39 . _:2f1d39 a owl:Class; owl:intersectionOf _:2f1d49 . _:2f1d49 rdf:first ; rdf:rest _:2f1d69 . _:2f1d69 rdf:first _:2f1d59; rdf:rest rdf:nil . _:2f1d59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1d79 . _:2f1d79 a owl:Class; owl:intersectionOf _:2f1d89 . _:2f1d89 rdf:first ; rdf:rest _:2f1da9 . _:2f1da9 rdf:first _:2f1d99; rdf:rest rdf:nil . _:2f1d99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1dc9 . _:2f1dc9 a owl:Class; owl:intersectionOf _:2f1dd9 . _:2f1dd9 rdf:first ; rdf:rest _:2f1df9 . _:2f1df9 rdf:first _:2f1de9; rdf:rest rdf:nil . _:2f1de9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1e09 . _:2f1e09 a owl:Class; owl:intersectionOf _:2f1e19 . _:2f1e19 rdf:first ; rdf:rest _:2f1e39 . _:2f1e39 rdf:first _:2f1e29; rdf:rest rdf:nil . _:2f1e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1e49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1e59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1e69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1e79 . _:2f1e79 a owl:Class; owl:intersectionOf _:2f1e89 . _:2f1e89 rdf:first ; rdf:rest _:2f1ea9 . _:2f1ea9 rdf:first _:2f1e99; rdf:rest rdf:nil . _:2f1e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f1eb9 . _:2f1eb9 a owl:Class; owl:intersectionOf _:2f1ec9 . _:2f1ec9 rdf:first ; rdf:rest _:2f1ee9 . _:2f1ee9 rdf:first _:2f1ed9; rdf:rest rdf:nil . _:2f1ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1ef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_stable DNA transfection"; rdfs:subClassOf ; """decided this is not really a technique - there are no stable and transient transfecitons. whether a stable or transient genetic modificaiton is made depends on what happens after the trasnfection (ie selection for stable modified clones) previous superclass axiom: has_specified_input some (cell and (('has role' some 'target of stable genetic modification role') and (has_proper_part some ('genetic material' and ('has role' some 'target of physical modification role')))))""" . a owl:Class; rdfs:label "obsolete_transient DNA transfection"; rdfs:subClassOf ; """decided this is not really a technique - there are no stable and transient transfecitons. whether a stable or transient genetic modificaiton is made depends on what happens after the trasnfection (ie selection for stable modified clones) previous superclass axioms: has_specified_input some ('nucleic acid' and ('has role' some 'material to be added role')) has_specified_input some (cell and ('has role' some 'target of transient genetic modification role')) has_specified_output some cell""" . a owl:Class; rdfs:label "obsolete_target of transient genetic modification role"; rdfs:subClassOf ; """8-24-12 modeling changes - elim this notion and replaced with notion of transient expression former superclass axiom: 'is realized by' some ('material processing' and (achieves_objective_specification some 'transient genetic modification objective'))""" . a owl:Class; rdfs:label "maintenance function"; rdfs:subClassOf ; "a function realized in the maintaining of some material of interest in a stable or unaltered state, for future application in some planned process"; "maintain function" . a owl:Class; rdfs:label "obsolete_transient genetic modification objective"; rdfs:subClassOf ; "a material transformation objective to generate a genetically modified organism, cell, or cell line that transiently carries some novel genetic material that is not heritable (ie not capable of being replicated and propagated to progeny)."; "8-24-12 modeling changes - elim this notion and replaced with notion of transient expression " . a owl:Class; rdfs:label "heritable"; rdfs:subClassOf ; "a physical object quality that inheres in some nucleic acid in virtue of its disposition to be replicated in its cellular host and inherited by progeny cells (such that the sequence content it encodes is stably propagated in the genetic material of subsequence generations of cells)" . a owl:Class; rdfs:label "material polypeptide span"; owl:equivalentClass _:2f1f09; rdfs:subClassOf , , _:2f1f69, _:2f1f79, _:2f1f89, _:2f1f99; "polypeptide submolecule", "material polypeptide region"; "a span of one or more linearly adjacent amino acid residues (ie a continuous stretch or primary sequence) that comprise part of a polypeptide macromolecule" . _:2f1f09 a owl:Class; owl:intersectionOf _:2f1f19 . _:2f1f19 rdf:first ; rdf:rest _:2f1f39 . _:2f1f39 rdf:first _:2f1f29; rdf:rest _:2f1f59 . _:2f1f29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1f59 rdf:first _:2f1f49; rdf:rest rdf:nil . _:2f1f49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1f69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1f79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1f89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1f99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material nucleic acid span"; owl:equivalentClass _:2f1fa9; rdfs:subClassOf , , _:2f2009, _:2f2019, _:2f2029, _:2f2039; "material nucleic acid region", "nucleic acid submolecule"; "a span of one or more linearly adjacent nucleotide residues (ie a continuous stretch or primary sequence) that comprise part of a nucleic acid macromolecule" . _:2f1fa9 a owl:Class; owl:intersectionOf _:2f1fb9 . _:2f1fb9 rdf:first ; rdf:rest _:2f1fd9 . _:2f1fd9 rdf:first _:2f1fc9; rdf:rest _:2f1ff9 . _:2f1fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f1ff9 rdf:first _:2f1fe9; rdf:rest rdf:nil . _:2f1fe9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2009 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2019 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2029 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2039 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material DNA span"; rdfs:subClassOf , _:2f2049, _:2f2059; "a span of one or more linearly adjacent DNA nucleotide residues (ie a continuous stretch or primary sequence) that comprise part of a DNA macromolecule"; "material DNA region", "DNA submolecule" . _:2f2049 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2059 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "material RNA span"; rdfs:subClassOf , _:2f2069, _:2f2079; "a span of one or more linearly adjacent RNA nucleotide residues (ie a continuous stretch or primary sequence) that comprise part of a RNA macromolecule"; "RNA submolecule", "material RNA region" . _:2f2069 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2079 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "natural genome"; rdfs:subClassOf , _:2f2089; "a sequence collection representing the naturally-occuring genome of a cell or virion, that not been experimentally modified to contain specified mutations, insertions, deletions, epi-chromosomal elements, etc"; "Note also that there is no requirement that a 'natural genome' is physically encoded in the 'material genome' or 'genetic material' of some particular cell or virion (i.e. it can be encoded in DNA preps isolated from some cell and stored in vitro, or a genomic library, or even in chemically synthesized DNA oligos). For a similar reason, there is no requirement that this is encoded in some (bearer_of some 'natural')." . _:2f2089 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "genomic sequence region"; owl:equivalentClass _:2f2099; rdfs:subClassOf , , _:2f20d9; "a genomic sequence feature with an extent fo one or more, that represents part of the genome of some cell or virion"; """1. Note that a genomic sequence region has an extent of at least one base - distinguishing it from genomic sequence features which can have extent sof zero (to account for things like deletions and junctions) 2. Note also that there is no requirement that a 'genomic sequence region' is physically encoded in the 'genetic material' of some particular cell or virion, because we want to include sequence encoded in things like recombinant plasmid reagents and synthetic oligos that have sequence from the genome of some organism, but are not part of a cell or virion."""; . _:2f2099 a owl:Class; owl:intersectionOf _:2f20a9 . _:2f20a9 rdf:first ; rdf:rest _:2f20c9 . _:2f20c9 rdf:first _:2f20b9; rdf:rest rdf:nil . _:2f20b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f20d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_modified genetic material"; rdfs:subClassOf ; "genetic material that is a 'nucleic acid' or 'nucleic acid span' that is experimentally introduced into a host cell or organism. As 'genetic material', it is necessarily a proper_part_of some cell, and heritable by progeny, such that the sequence content it encodes is stably propagated in subsequent generations of cells."; """Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class. former axioms : 'nucleic acid' or 'material nucleic acid region' bears_concretization_of some 'genomic sequence region' has_disposition some heritable proper_part_of some (cell or virion)"""; rdfs:comment "This class essentially represents any nucleic acid molecule or nucleic acid span that is experimentally introduced as genetic material into a cell or organism. Such nucleic acid in practice are typically 'trans-genomic'' - ie thier sequence content is not represented in a reference genome of the host cell's source organism. However, exogenously supplied nucleic acid bearing duplicated genomic sequence (ie a foreign nucleic acid that encodes additional copies of a sequence that IS part of a reference genome for the host cell's source organism) also qualifies as 'modified genetic material'"; """Exogenous epichromosomal examples are independent nucleic acid molecules, and include plasmids capable of stable replication introduced into a bacterai strain, or replicative transposons introduced into some cell line. Integral chromosomal examples are 'nucleic acid spans', and include inserted spans or mutated residues that change the natural sequence of the host's genetic material. """; """1. Note that we consider here only genetic material that results from an experimental procedure (ie this class does not cover naturally occuring cases of genetic material transfered between organisms) 2. A note on the distinction between 'genetic material' and 'modified genetic material' - the latter is not a child of the former because 'genetic material' is always an independently-existing molecular entity. By contrast, 'modified genetic material' can refer to such an independent molecular entity, but also to parts of such entities (ie 'nucleic acid spans') that represent modifeid sequence (e.g. nucleic acid spans inserted into the chromosomal genome of a cell). Such molecular parts are modeled as 'chemical groups' (according to the ChEBI framework we adopt for ReO).""" . a owl:Class; rdfs:label "obsolete_transgenomic genetic material"; rdfs:subClassOf ; "Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class."; """DNA representing a mouse gene that is stably integrated into the genomic DNA of a human cell line, or overexpressed from a stably replicating plasmid loxP sites derived from the bacteriophage genome, that are inserted to surround a gene to be excised in a knockout mouse. """; rdfs:comment "this class is distinguished from 'extra-genomic sequence' in that it is specific to cases where some stably incorporated exogenous nucleic acid carries sequence information that is NOT found in the genome of the class of organism of whcih the host is a member, but rather bears sequence from the genome of some other organism. Exogneously added genetic material that duplicates sequence in the host cell's own genome does not qualify."; "modified genetic material that bears sequence from the natural genome of some organism other than that of the host cell in which the material is introduced." . a owl:Class; rdfs:label "material information macromolecule span"; owl:equivalentClass _:2f20e9; rdfs:subClassOf , _:2f2129, _:2f2139; "material information macromolecule region", "information submolecule"; "a span of one or more linearly adjacent nucleotide residues (ie a continuous stretch or primary sequence) that comprise part of an information macromolecule" . _:2f20e9 a owl:Class; owl:intersectionOf _:2f20f9 . _:2f20f9 rdf:first ; rdf:rest _:2f2119 . _:2f2119 rdf:first _:2f2109; rdf:rest rdf:nil . _:2f2109 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2129 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2139 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "obsolete_natural genomic material"; rdfs:subClassOf ; """Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class. former axiom: bears_concretization_of some 'natural genomic sequence region'""" . a owl:Class; rdfs:label "natural genomic sequence feature"; rdfs:subClassOf , _:2f2149; "a genomic sequence feature that represents part of a naturally occuring genome of some organism (ie not an experimentally modified genome)"; "Note also that there is no requirement that a 'natural genomic sequence region' is physically encoded in the 'genetic material' of some particular cell or virion , becasue we want to include sequence encoded in things like plasmids and synthetic oligos that represent sequence from the natural or reference genome of some organism. " . _:2f2149 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "cDNA sequence region"; rdfs:subClassOf , _:2f2159; rdfs:comment "a DNA sequence that represents exon sequences of a gene, joined in the order they appear in the full gene sequence. This sequence is typically represented in a cDNA molecule, which is synthesized by reverse transcriptase using RNA as a template, and reflects the seqeunce of some mRNA transcribable from the gene. Thus, cDNA sequence is constrained to represent the complement of some mRNA sequence that can be transcribed from a particular gene." . _:2f2159 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "0"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "obsolete_exogenous genomic sequenceee"; rdfs:subClassOf ; rdfs:comment "epi-chromosomal genomic sequence"; "Note this is not disjoint from transgenic sequence"; """a genomic sequence region that is encoded by genetic material that is experimentally introduced into a cell or organism, and remains epi-chromosomal (ie. is not integrated into the or mitochondrial or nuclear chromosmal genome). As experimentally introduced 'genetic material', the bearer of such exogneous genomic sequence is necessarily: (1) a proper_part_of some host cell or organism, and (2) heritable by the progeny of this host, such that the sequence content it encodes is stably propagated in subsequent generations of cells"""; "Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class." . a owl:Class; rdfs:label "obsolete_transgenic sequence"; rdfs:subClassOf ; "transgenomic sequence"; "Note this is not disjoint from exogenous genomic sequence"; "a genomic sequence region that is (1) encoded by genetic material that is experimentally introduced into a cell or organism, and (2) represents some natural genomic sequence from an organism other than the organism or cell in which the nucleic acid bearer of this sequence was experimentally delivered."; "Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class."; rdfs:comment "transgenomic sequence can be encoded in nucleic acid that becomes stably integrated into the core nuclear/chromosomal genome of a host cell, or reside in an epi-chromosomal element such as a replicative plasmid or transposon." . a owl:Class; rdfs:label "obsolete_experimental genomic sequence region"; rdfs:subClassOf ; "Revamped modeling of genome, genomic sequence region, genetic material, and genomic sequence alterations so as not to require this class." . a owl:Class; rdfs:label "material genome"; rdfs:subClassOf , _:2f2169, _:2f2179, _:2f21b9; rdfs:comment "A genome is the collection of all nucleic acids in a cell or virus, representing all of an organism's hereditary information. It is typically DNa, but many viruses have RNA genomoes. The genome includes both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), as well as non-chromosomal elements such as replicative viruses, plasmids, and transposable elements."; "a material entity that represents all genetic material in a cell or virion. The material genome is typically molecular aggregate of all the chromosomal DNA and epi-chromosomal DNA that represents all sequences that are heritable by progeny of a cell or virion."; "Note that a material genome is necessarily part of some cell or virion, so a genomic library is not considered a material genome. Rather, we could say that this genomic library bears the concretization of some genome (as the genome sequence entity allows for such cases)." . _:2f2169 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2179 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2189 . _:2f2189 a owl:Class; owl:unionOf _:2f2199 . _:2f2199 rdf:first ; rdf:rest _:2f21a9 . _:2f21a9 rdf:first ; rdf:rest rdf:nil . _:2f21b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "epi-chromosomal genomic sequence alteration"; owl:equivalentClass _:2f21c9; rdfs:subClassOf , _:2f2259; owl:disjointWith ; "a genomic sequence alteration that is encoded by some epi-chromosomal element such as a replicative plasmid or transposon, that becomes a heritable part of the material genome of some cell and thereby alters the total sequence of its genome."; "epi-chromosomal genomic sequence addition", "exogenous genomic sequence alteration"; rdfs:comment "An epi-chromosomal genomic sequence alteration is encoded in some extra-chromosomal genetic material that is added to the genome of some cell or virus. It is considered here to be a type of sequence alteration in that it alters the total sequence content of the genome of some cell or virion (while the original 'chromosomal' genome of the cell remains unaltered)"; "sequence information carreid by a exogneous transposon element introduced into the genomic DNA of some host cell, sequence information carried by a replication competent plasmid transformed into a E coli bacterial strain" . _:2f21c9 a owl:Class; owl:intersectionOf _:2f21d9 . _:2f21d9 rdf:first ; rdf:rest _:2f21f9 . _:2f21f9 rdf:first _:2f21e9; rdf:rest rdf:nil . _:2f21e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2209 . _:2f2209 a owl:Class; owl:intersectionOf _:2f2219 . _:2f2219 rdf:first ; rdf:rest _:2f2239 . _:2f2239 rdf:first _:2f2229; rdf:rest rdf:nil . _:2f2229 a owl:Class; owl:complementOf _:2f2249 . _:2f2249 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2259 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2269 . _:2f2269 a owl:Class; owl:intersectionOf _:2f2279 . _:2f2279 rdf:first ; rdf:rest _:2f2299 . _:2f2299 rdf:first _:2f2289; rdf:rest rdf:nil . _:2f2289 a owl:Class; owl:complementOf _:2f22a9 . _:2f22a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transgenic sequence alteration"; rdfs:subClassOf ; "sequence of a mouse gene that is stable overexpressed in a human cell line. loxP sequence derived from bacteriophage that are inserted to surround a gene to be excised in a knockout mouse. "; "a genomic sequence alteration that introduces sequence that is represented in a reference genome of some organism OTHER than the organism or cell in which the nucleic acid bearer of this sequence is located" . a owl:Class; rdfs:label "genetic modification objective"; rdfs:subClassOf . a owl:Class; rdfs:label "gene mutation objective"; rdfs:subClassOf ; "a genetic modification objective to introduce a sequence alteration into a specified gene of interest, typically in order to alter the activity of the target gene" . a owl:Class; rdfs:label "chromosomal sequence alteration"; owl:equivalentClass _:2f22b9; rdfs:subClassOf , _:2f2339; "a genomic sequence alteration that is encoded in the chromosomal DNA of some cell" . _:2f22b9 a owl:Class; owl:intersectionOf _:2f22c9 . _:2f22c9 rdf:first ; rdf:rest _:2f22e9 . _:2f22e9 rdf:first _:2f22d9; rdf:rest rdf:nil . _:2f22d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f22f9 . _:2f22f9 a owl:Class; owl:intersectionOf _:2f2309 . _:2f2309 rdf:first ; rdf:rest _:2f2329 . _:2f2329 rdf:first _:2f2319; rdf:rest rdf:nil . _:2f2319 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2339 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2349 . _:2f2349 a owl:Class; owl:intersectionOf _:2f2359 . _:2f2359 rdf:first ; rdf:rest _:2f2379 . _:2f2379 rdf:first _:2f2369; rdf:rest rdf:nil . _:2f2369 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "DNA construct engineering"; owl:equivalentClass _:2f2389; rdfs:subClassOf , _:2f23e9, _:2f23f9, _:2f2409; rdfs:comment "a material processing technique with the objective to engineer and produce a DNA construct capable of carrying nucleic acids sequences for delivery to and propagation in cells", "DNA construct production"; "Note that this technique includes the creation of empty' DNA constructs (backbones) that carry no 'construct insert' - either de novo or through modification of pre-exisiting constructs. This generally includes construction of elements to support insertion, propagation, and expression of cloned inserts that may ultimately be carried by the construct (e.g. antibiotic resistance genes, selectble markers, promoters, multiple cloning sites)" . _:2f2389 a owl:Class; owl:intersectionOf _:2f2399 . _:2f2399 rdf:first ; rdf:rest _:2f23b9 . _:2f23b9 rdf:first _:2f23a9; rdf:rest _:2f23d9 . _:2f23a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f23d9 rdf:first _:2f23c9; rdf:rest rdf:nil . _:2f23c9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . _:2f23e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f23f9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2409 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "nucleic acid analog sequence region"; rdfs:subClassOf . a owl:Class; rdfs:label "mutagen role"; rdfs:subClassOf ; "http://en.wikipedia.org/wiki/Mutagen"; "a role inhering in a physical or chemical agent that can alter the genetic material of a call or organism and thus increases the frequency of mutations above the natural background level."; "can inhere in chemical entities such as ethidium bromite or benzene, or in 'physical' entities such as UV or ionizing radiation, or radioactive decay" . a owl:Class; rdfs:label "mutagen"; owl:equivalentClass _:2f2419; rdfs:subClassOf , _:2f2459; "a physical or chemical agent that can alter the genetic material of a call or organism and thus increases the frequency of mutations above the natural background level."; "chemical entities such as ethidium bromite or benzene, or in 'physical' entities such as UV or ionizing radiation, or radioactive decay" . _:2f2419 a owl:Class; owl:intersectionOf _:2f2429 . _:2f2429 rdf:first ; rdf:rest _:2f2449 . _:2f2449 rdf:first _:2f2439; rdf:rest rdf:nil . _:2f2439 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2459 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "transgenic organism production"; owl:equivalentClass _:2f2469; rdfs:subClassOf , _:2f2529; """a material processing technique with the goal of producing an organism that stably carries some transgenic genetic material (ie encoding sequence from the genome of some other organism). This can be achieved through: (1) de novo creation of a transgenic organism - using embryonic stem cells into which genomic sequence alterations have been made through addition of exogneous genes from other organisms. In the case of genetically modified virus, this is achieved through the transfection of plasmids encoding a transgene of interest along with viral coat protein, replication, and packaging genes that encode the machinery necessary to assemble a viral capsid containing the transgene and secrete it from the transfected cells; or (2) by modification of an existing organism through the stable introduction of an exogneous trasngene into one or more cells from the organism. """ . _:2f2469 a owl:Class; owl:intersectionOf _:2f2479 . _:2f2479 rdf:first ; rdf:rest _:2f2499 . _:2f2499 rdf:first _:2f2489; rdf:rest rdf:nil . _:2f2489 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f24a9 . _:2f24a9 a owl:Class; owl:intersectionOf _:2f24b9 . _:2f24b9 rdf:first ; rdf:rest _:2f24d9 . _:2f24d9 rdf:first _:2f24c9; rdf:rest rdf:nil . _:2f24c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f24e9 . _:2f24e9 a owl:Class; owl:intersectionOf _:2f24f9 . _:2f24f9 rdf:first ; rdf:rest _:2f2519 . _:2f2519 rdf:first _:2f2509; rdf:rest rdf:nil . _:2f2509 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2529 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2539 . _:2f2539 a owl:Class; owl:intersectionOf _:2f2549 . _:2f2549 rdf:first ; rdf:rest _:2f2569 . _:2f2569 rdf:first _:2f2559; rdf:rest rdf:nil . _:2f2559 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2579 . _:2f2579 a owl:Class; owl:intersectionOf _:2f2589 . _:2f2589 rdf:first ; rdf:rest _:2f25a9 . _:2f25a9 rdf:first _:2f2599; rdf:rest rdf:nil . _:2f2599 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetically modified organism production"; owl:equivalentClass _:2f25b9; rdfs:subClassOf , _:2f2679; """a material processing technique with the goal of producing an organism that stably carries some genetic mutation or exogenous genetic material. This can be achieved through: (1) de novo creation of an organism - using embryonic stem cells into which genomic sequence alterations have been made through mutation or addition of exogneous genes. In the case of genetically modified virus, this is typically achieved through the transfection of plasmids encoding a gene of interest along with viral coat protein, replication, and packaging genes that encode the machinery necessary to assemble a viral capsid containing the gene of interest and secrete it from the transfected cells; or (2) by modification of an existing organism through the mutation of existing genetic material, or stable introduction of exogneous genetic material into one or more cells from the organism. """ . _:2f25b9 a owl:Class; owl:intersectionOf _:2f25c9 . _:2f25c9 rdf:first ; rdf:rest _:2f25e9 . _:2f25e9 rdf:first _:2f25d9; rdf:rest rdf:nil . _:2f25d9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f25f9 . _:2f25f9 a owl:Class; owl:intersectionOf _:2f2609 . _:2f2609 rdf:first ; rdf:rest _:2f2629 . _:2f2629 rdf:first _:2f2619; rdf:rest rdf:nil . _:2f2619 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2639 . _:2f2639 a owl:Class; owl:intersectionOf _:2f2649 . _:2f2649 rdf:first ; rdf:rest _:2f2669 . _:2f2669 rdf:first _:2f2659; rdf:rest rdf:nil . _:2f2659 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2679 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2689 . _:2f2689 a owl:Class; owl:intersectionOf _:2f2699 . _:2f2699 rdf:first ; rdf:rest _:2f26b9 . _:2f26b9 rdf:first _:2f26a9; rdf:rest rdf:nil . _:2f26a9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f26c9 . _:2f26c9 a owl:Class; owl:intersectionOf _:2f26d9 . _:2f26d9 rdf:first ; rdf:rest _:2f26f9 . _:2f26f9 rdf:first _:2f26e9; rdf:rest rdf:nil . _:2f26e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "establishing clonal cell culture"; owl:equivalentClass _:2f2709; rdfs:subClassOf , _:2f2749, _:2f2759 . _:2f2709 a owl:Class; owl:intersectionOf _:2f2719 . _:2f2719 rdf:first ; rdf:rest _:2f2739 . _:2f2739 rdf:first _:2f2729; rdf:rest rdf:nil . _:2f2729 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . _:2f2749 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2759 a owl:Restriction; owl:onProperty ; owl:onClass ; owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger . a owl:Class; rdfs:label "establishing selected cell culture"; owl:equivalentClass _:2f2769; rdfs:subClassOf , _:2f27e9, _:2f2839; rdfs:comment """As an 'establishing' cell culture technique, this does not include cases where some inital culture is first establilshed, and then a subpopulation of these cultured cells is slected and propagated. This would classify as a 'selective cell subculturing' technique. This also does not include cases where some portion of tissue or mixed population of cells is plated and those that adhere and grow are propagated, as the initial input here is not some uniform population of cells of a similar type. This process would simply qualify as establishing cell culture."""; "an establishing cell culture process whereby a culture is established from some selected population of cells. In this process, some initial, uniform populaiton of like cells of a certain type are isolated from a biological specimen, and then a selection process is applied on this population input cells to isolate only some subpopulation exhibitiing specified attributes (e.g. T-cells expression of certain cell surface marker)." . _:2f2769 a owl:Class; owl:intersectionOf _:2f2779 . _:2f2779 rdf:first ; rdf:rest _:2f2799 . _:2f2799 rdf:first _:2f2789; rdf:rest rdf:nil . _:2f2789 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f27a9 . _:2f27a9 a owl:Class; owl:intersectionOf _:2f27b9 . _:2f27b9 rdf:first ; rdf:rest _:2f27d9 . _:2f27d9 rdf:first _:2f27c9; rdf:rest rdf:nil . _:2f27c9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f27e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f27f9 . _:2f27f9 a owl:Class; owl:intersectionOf _:2f2809 . _:2f2809 rdf:first ; rdf:rest _:2f2829 . _:2f2829 rdf:first _:2f2819; rdf:rest rdf:nil . _:2f2819 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2839 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "covalent molecular label"; owl:equivalentClass _:2f2849; rdfs:subClassOf , _:2f28b9; . _:2f2849 a owl:Class; owl:intersectionOf _:2f2859 . _:2f2859 rdf:first ; rdf:rest _:2f2879 . _:2f2879 rdf:first _:2f2869; rdf:rest rdf:nil . _:2f2869 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2889 . _:2f2889 a owl:Class; owl:unionOf _:2f2899 . _:2f2899 rdf:first ; rdf:rest _:2f28a9 . _:2f28a9 rdf:first ; rdf:rest rdf:nil . _:2f28b9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f28c9 . _:2f28c9 a owl:Class; owl:unionOf _:2f28d9 . _:2f28d9 rdf:first ; rdf:rest _:2f28e9 . _:2f28e9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "artificial organic small molecule"; owl:equivalentClass _:2f28f9; rdfs:subClassOf , _:2f2939; "an organic small molecule that is not 'natural', in that it exhibits a structure that is not found in nature. Such molecules are produced through some directed chemical synthesis or engineering technique."; "exploratory defined class - may not be practical to require knowledge of the 'natural-ness' of a given chemical"; . _:2f28f9 a owl:Class; owl:intersectionOf _:2f2909 . _:2f2909 rdf:first ; rdf:rest _:2f2929 . _:2f2929 rdf:first _:2f2919; rdf:rest rdf:nil . _:2f2919 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2939 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "genetic modification technique"; owl:equivalentClass _:2f2949; rdfs:subClassOf , _:2f2a09, _:2f2a99, _:2f2b69, _:2f2b79; "MHB:created editor preferred term 'genetic modification technique' in oplace of the OBI label 'genetic transformation' for two reasons: (1) used 'modification' to avoid confusion with 'cell transformation' (a process through which genetic modifications confer properties of cancer upon a cell); (2) appended with 'technique' to clarify that this is a planned process and not a naturally occuring genetic transformation/modification event."; "http://en.wikipedia.org/wiki/Genetic_engineering#Definition"; rdfs:comment "Note that here we do NOT include cases such as transient transfections where the added genetic material may not be capable of stable replication and propagation to progenitors. While such process allow for expression of exogenous genes in a target cell or organism, there is no stable, heritable changes to what we consider to be the 'genetic material' of the target."; "transient or stable transfection of DNA into a cell or organism. exposure of cells to mutagenizing radiation to introduce random mutations into the genome."; """OBI (re: clarification of OBI class label 'genetic transformation': a technique involving the alteration of existing genetic material of a target cell or organism, or the introduction of exogenous DNA to be expressed in a cell or organism). 1. The OBI definition is vague here. they reference 'genetic material' in their textual definition, but this term is not defined in OBI proper. It is tentatively defined in OBI exp design, however, to include only stably inherited genetic content of a cell or organism. However, transfection is a child of genetic transformation in OBI, and not all transfections (arguable, none of them) result in stable, heritable alterations to genetic material. If this is the case, we should not import here, as meaning is different than what we intend with 'genetic modification technique'. Consider making two classes in ReO: 'genetic modification technique' being more inclusive, and including things like stable transfections (since these are material delivery and thus modifications), and then the subtype 'stable/heritable/integral genetic modification technique' or 'genetic material modification technique' to be equivalent to my current meaning here - where genetic material is truly modified. 2. Note that using our design pattern here, we are able to create defined classes for all asserted children of the OBI:genetic transformation class (e.g. induced mutation, gene knock in, etc) 3. Note that we at one time importedOBI:genetic trasnformation here, but not clear that their meaning is same as ours. For example, ReO uses this class to describe only modifications that result in heritable, stable changes to the genetic material of a cell or organism. So we do NOT include cases such as transfections, where the added genetic material may not be capable of stable replication and propagation to progenitors. While such process allow for expression of exogenous genes in a target cell or organism, there is no stable, heritable changes to what we consider to be the 'genetic material' of the target. """; "a technique whereby the sequence of exisitng genetic material of a target cell or organism is altered, or exogneous DNA is introduced into a cell or orgnaism in such a way that it can be stably replicated and thus heritable by progeny." . _:2f2949 a owl:Class; owl:intersectionOf _:2f2959 . _:2f2959 rdf:first ; rdf:rest _:2f2979 . _:2f2979 rdf:first _:2f2969; rdf:rest rdf:nil . _:2f2969 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2989 . _:2f2989 a owl:Class; owl:intersectionOf _:2f29a9 . _:2f29a9 rdf:first _:2f2999; rdf:rest _:2f29f9 . _:2f2999 a owl:Class; owl:unionOf _:2f29b9 . _:2f29b9 rdf:first ; rdf:rest _:2f29c9 . _:2f29c9 rdf:first ; rdf:rest _:2f29d9 . _:2f29d9 rdf:first ; rdf:rest rdf:nil . _:2f29f9 rdf:first _:2f29e9; rdf:rest rdf:nil . _:2f29e9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2a09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2a19 . _:2f2a19 a owl:Class; owl:intersectionOf _:2f2a39 . _:2f2a39 rdf:first _:2f2a29; rdf:rest _:2f2a89 . _:2f2a29 a owl:Class; owl:unionOf _:2f2a49 . _:2f2a49 rdf:first ; rdf:rest _:2f2a59 . _:2f2a59 rdf:first ; rdf:rest _:2f2a69 . _:2f2a69 rdf:first ; rdf:rest rdf:nil . _:2f2a89 rdf:first _:2f2a79; rdf:rest rdf:nil . _:2f2a79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2a99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2aa9 . _:2f2aa9 a owl:Class; owl:intersectionOf _:2f2ac9 . _:2f2ac9 rdf:first _:2f2ab9; rdf:rest _:2f2b19 . _:2f2ab9 a owl:Class; owl:unionOf _:2f2ad9 . _:2f2ad9 rdf:first ; rdf:rest _:2f2ae9 . _:2f2ae9 rdf:first ; rdf:rest _:2f2af9 . _:2f2af9 rdf:first ; rdf:rest rdf:nil . _:2f2b19 rdf:first _:2f2b09; rdf:rest rdf:nil . _:2f2b09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2b29 . _:2f2b29 a owl:Class; owl:intersectionOf _:2f2b39 . _:2f2b39 rdf:first ; rdf:rest _:2f2b59 . _:2f2b59 rdf:first _:2f2b49; rdf:rest rdf:nil . _:2f2b49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2b69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2b79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2b89 . _:2f2b89 a owl:Class; owl:intersectionOf _:2f2ba9 . _:2f2ba9 rdf:first _:2f2b99; rdf:rest _:2f2be9 . _:2f2b99 a owl:Class; owl:unionOf _:2f2bb9 . _:2f2bb9 rdf:first ; rdf:rest _:2f2bc9 . _:2f2bc9 rdf:first ; rdf:rest rdf:nil . _:2f2be9 rdf:first _:2f2bd9; rdf:rest rdf:nil . _:2f2bd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "plasmid construct"; owl:equivalentClass _:2f2bf9; rdfs:subClassOf , , _:2f2c39; "A plasmid engineered in vitro to be capable of delivering, replicating, and often expressing exogenous DNA sequences in some host cell. These sequences, called 'construct inserts' or 'cloned inserts', are are maintained in some host cell through the action of various functional elements in the construct that facilitate plasmid amplification, selection, and antibiotic resistance."; "engineered plasmid"; . _:2f2bf9 a owl:Class; owl:intersectionOf _:2f2c09 . _:2f2c09 rdf:first ; rdf:rest _:2f2c29 . _:2f2c29 rdf:first _:2f2c19; rdf:rest rdf:nil . _:2f2c19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2c39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "artificial organic small molecule reagent"; owl:equivalentClass _:2f2c49; rdfs:subClassOf , , _:2f2c89; "exploratory defined class - may not be practical to require knowledge of the 'natural-ness' of a given chemical"; "a chemical reagent that is an organic small molecule that is not 'natural', in that it exhibits a structure that is not found in nature. Such molecules are produced through some directed chemical synthesis or engineering technique."; . _:2f2c49 a owl:Class; owl:intersectionOf _:2f2c59 . _:2f2c59 rdf:first ; rdf:rest _:2f2c79 . _:2f2c79 rdf:first _:2f2c69; rdf:rest rdf:nil . _:2f2c69 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2c89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "natural organic small molecule"; owl:equivalentClass _:2f2c99; rdfs:subClassOf , _:2f2cd9; "an organic small molecule that is 'natural', in that it exhibits a structure that is found in nature. Such molecules can be produced naturally or through some directed chemical synthesis or engineering technique."; "exploratory defined class - may not be practical to require knowledge of the 'natural-ness' of a given chemical"; . _:2f2c99 a owl:Class; owl:intersectionOf _:2f2ca9 . _:2f2ca9 rdf:first ; rdf:rest _:2f2cc9 . _:2f2cc9 rdf:first _:2f2cb9; rdf:rest rdf:nil . _:2f2cb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2cd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "natural organic small molecule reagent"; owl:equivalentClass _:2f2ce9; rdfs:subClassOf , , _:2f2d29; "exploratory defined class - may not be practical to require knowledge of the 'natural-ness' of a given chemical"; "a chemical reagent that is an organic small molecule that is 'natural', in that it exhibits a structure that is found in nature. Such molecules can be isolated from natural sources, or produced through some directed chemical synthesis or engineering technique."; . _:2f2ce9 a owl:Class; owl:intersectionOf _:2f2cf9 . _:2f2cf9 rdf:first ; rdf:rest _:2f2d19 . _:2f2d19 rdf:first _:2f2d09; rdf:rest rdf:nil . _:2f2d09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2d29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "blocking reagent role"; rdfs:subClassOf ; "a reagent role inhering in a molecular entity that serves to sterically block the binding of some other reagent, typically a molecular label, by non-specifically interacting with some target molecules or surface." . a owl:Class; rdfs:label "in vitro environment"; rdfs:subClassOf ; "an artificial environment in which conditions are controlled or specified to allow for performance of some technique or investigation. This term typically refers to laboratory environments under which experimetnal procedures are carried out."; . a owl:Class; rdfs:label "APotentiallyUsefulObsoleteClass"; rdfs:subClassOf . a owl:Class; rdfs:label "reporter gene"; rdfs:subClassOf , _:2f2d39, _:2f2d59; "a gene that is engineered to conatin a regulatory sequences that are responsive to a specified transcriptional activator, and a coding sequence capable of producing some detectable indicator that is measured as a readout of the abundance of the transcriptional activator, or the activity of the promoter" . _:2f2d39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2d49 . _:2f2d49 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2d59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "selectable marker gene"; owl:equivalentClass _:2f2d69; rdfs:subClassOf , _:2f2db9; """The LacZ gene produces the beta-galatosidase enzyme that catalyzes the conversion of X-gal substrte into a colorimetric indicator. The LEU2 gene is often used in LEU2-deficient yeast strains as a selectble marker, where its presence in a successful transformant allows growth on a leucine-free substrate."""; "a gene is encoded in soem genetic element that encodes some product whose presence or abundance is detected, directly or indirectly, in order to determine is some specified experimental modification has occurred successfully" . _:2f2d69 a owl:Class; owl:intersectionOf _:2f2d79 . _:2f2d79 rdf:first ; rdf:rest _:2f2d99 . _:2f2d99 rdf:first _:2f2d89; rdf:rest rdf:nil . _:2f2d89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2da9 . _:2f2da9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2db9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2dc9 . _:2f2dc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "selectable marker role"; rdfs:subClassOf ; rdfs:comment "Most common usage is in reference to genes whose product is detectable or confers some assayable feature such as resistance to an antibiotic or growth on nutrient depleted substrate. This allows for determination of the success of a subcloning, bacterial transformation, or cell transfection."; "an ascribed role inhereing in a material entity whose presence or abundance is detected, directly or indirectly, in order to determine is some specified experimental modification has occurred successfuly"; "Here we allow for this role to inhere in both the gene and the gene product that allows for selection. For example, in the case of the LacZ gene which produces beta-galatosidase that catalyzes the conversion of X-gal substrte into a colorimetric indicator, both the LacZ gene and the beta-galatosidase enzyme could be said to bear a selctable marker role." . a owl:Class; rdfs:label "gene knock out"; rdfs:subClassOf . a owl:Class; rdfs:label "gene knock in"; rdfs:subClassOf . a owl:Class; rdfs:label "genomic sequence feature"; owl:equivalentClass _:2f2dd9; rdfs:subClassOf , _:2f2e19; "a sequence feature that represents an extent of nucleic acid sequence (zero or greater) from the genome of some cell or virion"; """1. Note that a 'genomic sequence feature' ism different from a 'genomic sequence region' in that its extent can be zero, and thus covers cases such as 'junctions' and 'deletions'. 2. Note also that there is no requirement that a 'genomic sequence feature' is physically encoded in the 'genetic material' of some particular cell or virion, because we want to include sequence encoded in things like recombinant plasmid reagents and synthetic oligos that encode sequence from the genome of some organism, but are not part of a cell or virion.""" . _:2f2dd9 a owl:Class; owl:intersectionOf _:2f2de9 . _:2f2de9 rdf:first ; rdf:rest _:2f2e09 . _:2f2e09 rdf:first _:2f2df9; rdf:rest rdf:nil . _:2f2df9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2e19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "establishing biomaterial culture"; rdfs:subClassOf , _:2f2e29, _:2f2e39, _:2f2ed9; "a process which results in creating an in vitro environment in which some virus or cell-based biomaterial (cells, tissue, organisms) is sustained "; "Establishing a biomateiral culture could be said to achieve a manufacturing objective, as the culture itself is a new entity manufactured from the assembly of input biomaterial. This technique also qualifies as an 'experimental modification' in the sense that the cultured mateiral represent physically modified versions of the input (ie it has been cultured to incorporate nutrients and often express novel gene patterns required for their survival in vitro). This view is taken to support the convention of viewing cultured cells as 'experimentally modified', as established in the Cell Ontology." . _:2f2e29 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2e39 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2e49 . _:2f2e49 a owl:Class; owl:intersectionOf _:2f2e69 . _:2f2e69 rdf:first _:2f2e59; rdf:rest _:2f2ec9 . _:2f2e59 a owl:Class; owl:unionOf _:2f2e79 . _:2f2e79 rdf:first ; rdf:rest _:2f2e89 . _:2f2e89 rdf:first ; rdf:rest _:2f2ea9 . _:2f2ea9 rdf:first _:2f2e99; rdf:rest rdf:nil . _:2f2e99 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2ec9 rdf:first _:2f2eb9; rdf:rest rdf:nil . _:2f2eb9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2ed9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "region"; rdfs:subClassOf ; "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids."; "sequence"; "A generically dependent continuant that is encoded in a information macromolecule with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids."; "sequence region"; "Note that a guiding principle for h9ow the sequence feature hierarchy is modeled and the axioms created wrt sequence feature vs region) are guided by the fact that we conceive of deletions (sequence alterations) as parts of a genome, and since deletions are sequence features and not regions (because they have an extent of zero), we must model things in accordance (e.g. genomic sequence feature is a seq feature, and not a region>nucleic acid seq region, and sequence collections have proepr parts some/only sequence features, not regions)"; . a owl:Class; rdfs:label "aneuploid"; rdfs:subClassOf ; "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number."; "http://en.wikipedia.org/wiki/Aneuploid"; , . a owl:Class; rdfs:label "hyperploid"; rdfs:subClassOf ; "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present."; "http://en.wikipedia.org/wiki/Hyperploid"; , . a owl:Class; rdfs:label "hypoploid"; rdfs:subClassOf ; "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing."; "http://en.wikipedia.org/wiki/Hypoploid"; , . a owl:Class; rdfs:label "compound_chromosome_arm"; rdfs:subClassOf ; rdfs:comment "FLAG - this term is should probably be a part of rather than an is_a."; "compound chromosome arm"; , . a owl:Class; rdfs:label "deficient_intrachromosomal_transposition"; rdfs:subClassOf ; "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining."; "deficient intrachromosomal transposition"; , . a owl:Class; rdfs:label "deficient_interchromosomal_transposition"; rdfs:subClassOf ; "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining."; "deficient interchromosomal transposition"; , . a owl:Class; rdfs:label "free_chromosome_arm"; rdfs:subClassOf ; "A chromosome structure variation whereby an arm exists as an individual chromosome element."; "free chromosome arm"; , . a owl:Class; rdfs:label "sequence_feature"; rdfs:subClassOf ; "An extent of biological sequence."; "located sequence feature", "located_sequence_feature", "sequence feature"; "Note that a guiding principle for how this hierarchy is modeled and the axioms we create (wrt use of 'sequence feature' vs 'sequence region') are guided by the fact that we conceive of deletions (sequence alterations) as parts of a genome, and since deletions are sequence features and not regions (because they have an extent of zero), we must model things in accordance (e.g. genomic sequence feature is a seq feature, and not a region>nucleic acid seq region, and sequence collections have proepr parts some/only sequence features, not regions)"; "sequence feature"; rdfs:comment "sequence features can have an extend of zero - in the case of SO:junctions. 'Sequence regions' (aka 'genetic sequence regions' in ReO) have an extent greater than zero."; . a owl:Class; rdfs:label "exon"; rdfs:subClassOf , _:2f2ee9; "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing."; rdfs:comment "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."; "http://en.wikipedia.org/wiki/Exon"; "exon sequence region"; "exon", "exon sequence"; . _:2f2ee9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "deletion"; rdfs:subClassOf ; "The point at which one or more contiguous nucleotides were excised."; "deleted_sequence", "nucleotide deletion", "nucleotide_deletion"; "http://en.wikipedia.org/wiki/Nucleotide_deletion"; , . a owl:Class; rdfs:label "promoter"; rdfs:subClassOf ; "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery."; rdfs:comment "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription."; "http://en.wikipedia.org/wiki/Promoter"; "promoter sequence", "promoter"; "promoter sequence region"; , . a owl:Class; rdfs:label "non_transcribed_region"; rdfs:subClassOf ; "A region of the gene which is not transcribed."; "non transcribed region", "non-transcribed sequence", "nontranscribed region", "nontranscribed sequence"; . a owl:Class; rdfs:label "primary_transcript"; rdfs:subClassOf ; "A transcript that in its initial state requires modification to be functional."; "http://en.wikipedia.org/wiki/Primary_transcript"; "precursor RNA", "primary transcript", "primary transcript sequence"; "primary transcript sequence region"; . a owl:Class; rdfs:label "intron"; rdfs:subClassOf , _:2f2ef9; "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it."; rdfs:comment "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."; "http://en.wikipedia.org/wiki/Intron"; "intron sequence region"; "intron sequence", "intron"; . _:2f2ef9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "translocation"; rdfs:subClassOf ; "A region of nucleotide sequence that has translocated to a new position."; "transchr", "translocated sequence"; , . a owl:Class; rdfs:label "simple_sequence_length_variation"; rdfs:subClassOf ; "SSLP", "simple sequence length polymorphism", "simple sequence length variation"; , . a owl:Class; rdfs:label "mature_transcript"; rdfs:subClassOf ; rdfs:comment "A processed transcript cannot contain introns."; "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified."; "http://en.wikipedia.org/wiki/Mature_transcript"; "mature transcript", "mature transcript sequence"; "mature transcript sequence region"; . a owl:Class; rdfs:label "chromosome_variation"; rdfs:subClassOf ; "chromosome variation"; , . a owl:Class; rdfs:label "sequence_length_variation"; rdfs:subClassOf ; "sequence length variation"; , . a owl:Class; rdfs:label "inverted_ring_chromosome"; rdfs:subClassOf ; "inverted ring chromosome"; , . a owl:Class; rdfs:label "chromosomal_transposition"; rdfs:subClassOf ; "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type."; "chromosomal transposition", "transposition"; , . a owl:Class; rdfs:label "interchromosomal_duplication"; rdfs:subClassOf ; "A chromosome duplication involving an insertion from another chromosome."; "interchromosomal duplication"; , . a owl:Class; rdfs:label "inversion_derived_bipartite_deficiency"; rdfs:subClassOf ; "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion."; "inversion derived bipartite deficiency"; , . a owl:Class; rdfs:label "inversion_derived_deficiency_plus_duplication"; rdfs:subClassOf ; "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion."; "inversion derived deficiency plus duplication"; , . a owl:Class; rdfs:label "inversion_derived_deficiency_plus_aneuploid"; rdfs:subClassOf ; "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion."; "inversion derived deficiency plus aneuploid"; , . a owl:Class; rdfs:label "inversion_derived_bipartite_duplication"; rdfs:subClassOf ; "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion."; "inversion derived bipartite duplication"; , . a owl:Class; rdfs:label "inversion_derived_duplication_plus_aneuploid"; rdfs:subClassOf ; "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion."; "inversion derived duplication plus aneuploid"; , . a owl:Class; rdfs:label "aneuploid_chromosome"; rdfs:subClassOf ; "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking."; rdfs:comment "Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila."; "aneuploid chromosome"; , . a owl:Class; rdfs:label "polyA_signal_sequence"; rdfs:subClassOf ; "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA."; "poly(A) signal", "polyA signal sequence", "polyadenylation termination signal"; "polyA signal sequence region"; . a owl:Class; rdfs:label "inversion_derived_aneuploid_chromosome"; rdfs:subClassOf ; "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion."; "inversion derived aneuploid chromosome"; , . a owl:Class; rdfs:label "insertion"; rdfs:subClassOf ; "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence."; "insertion", "nucleotide insertion", "nucleotide_insertion"; , . a owl:Class; rdfs:label "transcript"; rdfs:subClassOf ; "An RNA synthesized on a DNA or RNA template by an RNA polymerase."; "http://en.wikipedia.org/wiki/RNA"; "My interpretation of tis class is that it represents a DNA sequence in the genome of some organism that is comprised of the assembled represenation of all sequence regions within a gene that are transcribed and represented in a given transcript. I do not take this to represent a sequence encoded in an mRNA transcript. This interpretation is based on the axiom in SO that a transcript is part of (member_of) some gene, and a gene is defined as 'a region (or regions) that includes all of the sequence elements necessary to encode a functional transcript.'"; "transcribed sequence"; "transcribed sequence region"; "a genomic sequence region representing the collective and continuous sequence of all portions of a gene that are transcribed and encoded in an mRNA transcript"; . a owl:Class; rdfs:label "translocation_element"; rdfs:subClassOf ; "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations."; "translocation element"; , . a owl:Class; rdfs:label "SNP"; rdfs:subClassOf ; "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater."; "single nucleotide polymorphism"; , . a owl:Class; rdfs:label "gene"; rdfs:subClassOf , _:2f2f09, _:2f2f59; "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions."; rdfs:comment "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance."; "http://en.wikipedia.org/wiki/Gene"; "A genetic locus (or loci) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions."; "PERSON: Matthew Brush"; . _:2f2f09 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2f19 . _:2f2f19 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2f29 . _:2f2f29 a owl:Class; owl:unionOf _:2f2f39 . _:2f2f39 rdf:first ; rdf:rest _:2f2f49 . _:2f2f49 rdf:first ; rdf:rest rdf:nil . _:2f2f59 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2f69 a owl:Axiom; ""; "exploratory axiom to test design pattern linking a gene to its expressed physical products. Note if I use 'only' instead of 'some' in this axiom it can prevent transgenic modification technique from classifying as a type of genetic modification technique"; owl:annotatedSource ; owl:annotatedProperty rdfs:subClassOf; owl:annotatedTarget _:2f2f79 . _:2f2f79 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2f89 . _:2f2f89 a owl:Restriction; owl:onProperty ; owl:someValuesFrom _:2f2f99 . _:2f2f99 a owl:Class; owl:unionOf _:2f2fa9 . _:2f2fa9 rdf:first ; rdf:rest _:2f2fb9 . _:2f2fb9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "kinetoplast"; rdfs:subClassOf ; "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species."; "http://en.wikipedia.org/wiki/Kinetoplast"; "kinetoplast_chromosome"; , . a owl:Class; rdfs:label "cloned_region"; rdfs:subClassOf ; rdfs:comment "Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions."; "cloned region", "cloned segment"; "cloned sequence region"; . a owl:Class; rdfs:label "assortment_derived_duplication"; rdfs:subClassOf ; "A multi-chromosome duplication aberration generated by reassortment of other aberration components."; "assortment derived duplication"; , . a owl:Class; rdfs:label "assortment_derived_deficiency_plus_duplication"; rdfs:subClassOf ; "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication."; "assortment derived deficiency plus duplication"; , . a owl:Class; rdfs:label "assortment_derived_deficiency"; rdfs:subClassOf ; "A multi-chromosome deficiency aberration generated by reassortment of other aberration components."; "assortment-derived deficiency"; , . a owl:Class; rdfs:label "assortment_derived_aneuploid"; rdfs:subClassOf ; "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication."; "assortment derived aneuploid"; , . a owl:Class; rdfs:label "gene_member_region"; rdfs:subClassOf , _:2f2fc9; rdfs:comment "A manufactured term used to allow the parts of a gene to have an is_a path to the root."; "A region of a gene."; "gene member region"; "gene member sequence region"; "SO: Clarify the following interpretation - gene member regions are SO:members_of some gene (where member of is akin to aggregate part of) . . . such that this includes discontinuous collecitons of regions along a gene (e.g. mature transcript region). By contrast, gene component region is part_of some gene, and seems to refer to continuous regions."; . _:2f2fc9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "gene_component_region"; rdfs:subClassOf ; "gene component region"; "SO: Clarify the following interpretation - gene member regions are SO:members_of some gene (where member of is akin to aggregate part of) . . . such that this includes discontinuous collecitons of regions along a gene (e.g. mature transcript region). By contrast, gene component region is part_of some gene, and seems to refer to continuous regions."; . a owl:Class; rdfs:label "gene_fragment"; rdfs:subClassOf ; rdfs:comment "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."; "gene fragment"; . a owl:Class; rdfs:label "MNP"; rdfs:subClassOf ; "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT."; "multiple nucleotide polymorphism"; , . a owl:Class; rdfs:label "copy_number_variation"; rdfs:subClassOf ; "A variation that increases or decreases the copy number of a given region."; "CNP", "CNV", "copy number polymorphism", "copy number variation"; "http://en.wikipedia.org/wiki/Copy_number_variation"; , . a owl:Class; rdfs:label "allele"; rdfs:subClassOf ; "An allele is one of a set of coexisting sequence variants of a gene."; "allelomorph"; "http://en.wikipedia.org/wiki/Allele"; , . a owl:Class; rdfs:label "haplotype"; rdfs:subClassOf ; "A haplotype is one of a set of coexisting sequence variants of a haplotype block."; "http://en.wikipedia.org/wiki/Haplotype"; , . a owl:Class; rdfs:label "polymorphic_sequence_variant"; rdfs:subClassOf ; "A sequence variant that is segregating in one or more natural populations of a species."; "polymorphic sequence variant"; , . a owl:Class; rdfs:label "genome"; rdfs:subClassOf , _:2f2fd9, _:2f2fe9; "A genome is the sum of genetic material within a cell or virion."; "http://en.wikipedia.org/wiki/Genome"; """Note also that there is no requirement that a 'genome' is physically encoded in the 'material genome' or 'genetic material' of some particular cell or virion (i.e. it can be encoded in DNA preps isolated from some cell and stored in vitro, or a genomic library, or even in chemically synthesized DNA oligos). Therefore, we COULD apply the axiom encoded_in_material_bearer only ('nucleic acid' or (object_aggregate and (has_aggregate_part only 'nucleic acid'))), rather than encoded_in_material_bearer only 'genetic material' (as 'genetic material' is defined as necessarily part of some particular cell or virion) . . .but note below that this may have casued issues upon classification (ie material genome classifying as a nucleic acid)"""; "the sum of all genomic sequence regions within a cell or virion, representing all heritable sequence that can be propagated to progeny. "; rdfs:comment "A genome is the entirety of sequence representing an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome sequence includes both the genes and the non-coding sequences, and it includes sequence of both nuclear chromosomes (ie nuclear and micronucleus chromosomes) and cytoplasmic chromosomes stored in various organelles (e.g. mitochondrial or chloroplast chromosomes), as well as sequence encoded in nonchromosomal elements such as replicative viruses, plasmids, and transposable elements."; . _:2f2fd9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f2fe9 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "genotype"; rdfs:subClassOf ; "A genotype is a variant genome, complete or incomplete."; "http://en.wikipedia.org/wiki/Genotype"; , . a owl:Class; rdfs:label "diplotype"; rdfs:subClassOf ; "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known."; , . a owl:Class; rdfs:label "sequence_alteration"; rdfs:subClassOf ; "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence."; rdfs:comment "Merged with partially characterized change in nucleotide sequence."; "partially characterised change in DNA sequence", "partially_characterised_change_in_DNA_sequence", "sequence alteration"; "Note that in ReO we consider epi-chromosomal genomic sequence alteration (aka exogenous genomic sequence) to represent a type of sequence alteration, in the sense that it alters the total sequence content of a genome (which serves the role as the referenced 'another sequence'). Epi-chromosomal genomic sequence is nucleic acid sequence that is encoded by some epi-chromosomal element such as a replicative plasmid or transposon, that becomes part of the genome of some cell."; . a owl:Class; rdfs:label "transgenic_insertion"; rdfs:subClassOf ; "An insertion that derives from another organism, via the use of recombinant DNA technology."; "transgenic insertion"; , . a owl:Class; rdfs:label "TSS_region"; rdfs:subClassOf ; "TSS region"; "The region of a gene from the 5' most TSS to the 3' TSS."; . a owl:Class; rdfs:label "polyploid"; rdfs:subClassOf ; "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number."; "http://en.wikipedia.org/wiki/Polyploid"; , . a owl:Class; rdfs:label "autopolyploid"; rdfs:subClassOf ; "A polyploid where the multiple chromosome set was derived from the same organism."; "http://en.wikipedia.org/wiki/Autopolyploid"; , . a owl:Class; rdfs:label "allopolyploid"; rdfs:subClassOf ; "A polyploid where the multiple chromosome set was derived from a different organism."; "http://en.wikipedia.org/wiki/Allopolyploid"; , . a owl:Class; rdfs:label "sequence_collection"; rdfs:subClassOf , _:2f2ff9, _:2f3009; "A collection of discontinuous sequences."; "sequence collection"; "sequence collection"; . _:2f2ff9 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . _:2f3009 a owl:Restriction; owl:onProperty ; owl:allValuesFrom . a owl:Class; rdfs:label "biomaterial_region"; rdfs:subClassOf ; "A region which is intended for use in an experiment."; "biomaterial region"; "obsolete_biomaterial_region"; "decided was not needed, and made comlicated to classify other types of genetic seq regions"; . a owl:Class; rdfs:label "biological_region"; rdfs:subClassOf ; "A region defined by its disposition to be involved in a biological process."; "biological region"; "decided was not needed, and made comlicated to classify other types of genetic seq regions"; "obsolete_biological_region"; . a owl:Class; rdfs:label "contig_collection"; rdfs:subClassOf ; "A collection of contigs."; rdfs:comment "See tracker ID: 2138359."; "contig collection"; , . a owl:Class; rdfs:label "SNV"; rdfs:subClassOf ; "SNVs are single base pair positions in genomic DNA at which different sequence alternatives exist."; "single nucleotide variant"; , . a owl:Class; rdfs:label "peptide_collection"; rdfs:subClassOf ; "A collection of peptide sequences."; rdfs:comment "Term requested via tracker ID: 2910829."; "peptide collection", "peptide set"; "peptide collection"; , . a owl:Class; rdfs:label "assortment_derived_variation"; rdfs:subClassOf ; "A chromosome variation derived from an event during meiosis."; "assortment derived variation"; , . a owl:Class; rdfs:label "reference_genome"; rdfs:subClassOf ; "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly."; "reference genome"; , . a owl:Class; rdfs:label "variant_genome"; rdfs:subClassOf ; "A collection of sequences (often chromosomes) of an individual."; "variant genome"; "variant genome"; , . a owl:Class; rdfs:label "variant_collection"; rdfs:subClassOf ; "A collection of one or more sequences of an individual."; "variant collection"; "variant collection"; , . a owl:Class; rdfs:label "chromosomally_aberrant_genome"; rdfs:subClassOf ; "chromosomally aberrant genome"; , . a owl:Class; rdfs:label "pseudogenic_gene_segment"; rdfs:subClassOf ; "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product."; . a owl:Class; rdfs:label "copy_number_gain"; rdfs:subClassOf ; "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence."; "copy number gain", "gain"; , . a owl:Class; rdfs:label "copy_number_loss"; rdfs:subClassOf ; "A sequence alteration whereby the copy number of a given region is less than the reference sequence."; "copy number loss", "loss"; , . a owl:Class; rdfs:label "UPD"; rdfs:subClassOf ; "UPD", "uniparental disomy"; "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent."; "http:http\\://en.wikipedia.org/wiki/Uniparental_disomy"; , . a owl:Class; rdfs:label "maternal_uniparental_disomy"; rdfs:subClassOf ; "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father."; "maternal uniparental disomy"; , . a owl:Class; rdfs:label "paternal_uniparental_disomy"; rdfs:subClassOf ; "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother."; "paternal uniparental disomy"; , . a owl:Class; rdfs:label "complex_structural_alteration"; rdfs:subClassOf ; "A structural sequence alteration where there are multiple equally plausible explanations for the change."; "complex"; , . a owl:Class; rdfs:label "structural_alteration"; rdfs:subClassOf ; , . a owl:Class; rdfs:label "regulatory_region"; rdfs:subClassOf ; "A region of sequence that is involved in the control of a biological process."; "http://en.wikipedia.org/wiki/Regulatory_region"; "regulatory region"; "regulatory region"; . a owl:Class; rdfs:label "substitution"; rdfs:subClassOf ; "Any change in genomic DNA caused by a single event."; , . a owl:Class; rdfs:label "complex_substitution"; rdfs:subClassOf ; "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\\"complex\\\" should be used. Usually there are multiple equally plausible explanations for the change."; "complex substitution"; , . a owl:Class; rdfs:label "point_mutation"; rdfs:subClassOf ; "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence."; "http://en.wikipedia.org/wiki/Point_mutation"; "point mutation"; , . a owl:Class; rdfs:label "transition"; rdfs:subClassOf ; "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide."; , . a owl:Class; rdfs:label "pyrimidine_transition"; rdfs:subClassOf ; "A substitution of a pyrimidine, C or T, for another pyrimidine."; "pyrimidine transition"; , . a owl:Class; rdfs:label "C_to_T_transition"; rdfs:subClassOf ; "A transition of a cytidine to a thymine."; "C to T transition"; , . a owl:Class; rdfs:label "C_to_T_transition_at_pCpG_site"; rdfs:subClassOf ; "C to T transition at pCpG site"; "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine."; , . a owl:Class; rdfs:label "T_to_C_transition"; rdfs:subClassOf ; "T to C transition"; , . a owl:Class; rdfs:label "purine_transition"; rdfs:subClassOf ; "A substitution of a purine, A or G, for another purine."; "purine transition"; , . a owl:Class; rdfs:label "A_to_G_transition"; rdfs:subClassOf ; "A to G transition"; "A transition of an adenine to a guanine."; , . a owl:Class; rdfs:label "G_to_A_transition"; rdfs:subClassOf ; "A transition of a guanine to an adenine."; "G to A transition"; , . a owl:Class; rdfs:label "transversion"; rdfs:subClassOf ; "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa."; "http://en.wikipedia.org/wiki/Transversion"; , . a owl:Class; rdfs:label "pyrimidine_to_purine_transversion"; rdfs:subClassOf ; "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G."; "pyrimidine to purine transversion"; , . a owl:Class; rdfs:label "C_to_A_transversion"; rdfs:subClassOf ; "A transversion from cytidine to adenine."; "C to A transversion"; , . a owl:Class; rdfs:label "C_to_G_transversion"; rdfs:subClassOf ; "C to G transversion"; , . a owl:Class; rdfs:label "T_to_A_transversion"; rdfs:subClassOf ; "A transversion from T to A."; "T to A transversion"; , . a owl:Class; rdfs:label "T_to_G_transversion"; rdfs:subClassOf ; "A transversion from T to G."; "T to G transversion"; , . a owl:Class; rdfs:label "purine_to_pyrimidine_transversion"; rdfs:subClassOf ; "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T."; "purine to pyrimidine transversion"; , . a owl:Class; rdfs:label "A_to_C_transversion"; rdfs:subClassOf ; "A to C transversion"; "A transversion from adenine to cytidine."; , . a owl:Class; rdfs:label "A_to_T_transversion"; rdfs:subClassOf ; "A to T transversion"; "A transversion from adenine to thymine."; , . a owl:Class; rdfs:label "G_to_C_transversion"; rdfs:subClassOf ; "A transversion from guanine to cytidine."; "G to C transversion"; , . a owl:Class; rdfs:label "G_to_T_transversion"; rdfs:subClassOf ; "A transversion from guanine to thymine."; "G to T transversion"; , . a owl:Class; rdfs:label "intrachromosomal_mutation"; rdfs:subClassOf ; "A chromosomal structure variation within a single chromosome."; "intrachromosomal mutation"; , . a owl:Class; rdfs:label "chromosomal_deletion"; rdfs:subClassOf ; "(Drosophila)Df", "(bacteria)&Dgr;", "(fungi)D", "chromosomal deletion", "deficiency"; "An incomplete chromosome."; "http://en.wikipedia.org/wiki/Chromosomal_deletion"; , . a owl:Class; rdfs:label "chromosomal_inversion"; rdfs:subClassOf ; "(Drosophila)In", "(bacteria)IN", "(fungi)In", "chromosomal inversion"; "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type."; "http://en.wikipedia.org/wiki/Chromosomal_inversion"; , . a owl:Class; rdfs:label "interchromosomal_mutation"; rdfs:subClassOf ; "A chromosomal structure variation whereby more than one chromosome is involved."; "interchromosomal mutation"; , . a owl:Class; rdfs:label "indel"; rdfs:subClassOf ; "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases."; rdfs:comment "Indels can have a different number of bases than the corresponding reference sequence."; "http://en.wikipedia.org/wiki/Indel"; , . a owl:Class; rdfs:label "duplication"; rdfs:subClassOf ; "One or more nucleotides are added between two adjacent nucleotides in the sequence; the inserted sequence derives from, or is identical in sequence to, nucleotides adjacent to insertion point."; "nucleotide duplication", "nucleotide_duplication"; , . a owl:Class; rdfs:label "inversion"; rdfs:subClassOf ; "A continuous nucleotide sequence is inverted in the same position."; "inversion"; , . a owl:Class; rdfs:label "chromosomal_duplication"; rdfs:subClassOf ; "(Drosophila)Dp", "(fungi)Dp", "chromosomal duplication"; "An extra chromosome."; "http://en.wikipedia.org/wiki/Chromosomal_duplication"; , . a owl:Class; rdfs:label "intrachromosomal_duplication"; rdfs:subClassOf ; "A duplication that occurred within a chromosome."; "intrachromosomal duplication"; , . a owl:Class; rdfs:label "direct_tandem_duplication"; rdfs:subClassOf ; "A tandem duplication where the individual regions are in the same orientation."; "direct tandem duplication"; , . a owl:Class; rdfs:label "inverted_tandem_duplication"; rdfs:subClassOf ; "A tandem duplication where the individual regions are not in the same orientation."; "inverted tandem duplication", "mirror duplication"; , . a owl:Class; rdfs:label "intrachromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)Tp", "intrachromosomal transposition"; "A chromosome structure variation whereby a transposition occurred within a chromosome."; , . a owl:Class; rdfs:label "compound_chromosome"; rdfs:subClassOf ; "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms."; "compound chromosome"; , . a owl:Class; rdfs:label "Robertsonian_fusion"; rdfs:subClassOf ; "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere."; "Robertsonian fusion", "centric-fusion translocations", "whole-arm translocations"; "http://en.wikipedia.org/wiki/Robertsonian_fusion"; , . a owl:Class; rdfs:label "chromosomal_translocation"; rdfs:subClassOf ; "(Drosophila)T", "(fungi)T", "chromosomal translocation"; "An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations."; "http://en.wikipedia.org/wiki/Chromosomal_translocation"; , . a owl:Class; rdfs:label "ring_chromosome"; rdfs:subClassOf ; "(Drosophila)R", "(fungi)C", "ring chromosome"; "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome."; "http://en.wikipedia.org/wiki/Ring_chromosome"; , . a owl:Class; rdfs:label "pericentric_inversion"; rdfs:subClassOf ; "A chromosomal inversion that includes the centromere."; "pericentric inversion"; , . a owl:Class; rdfs:label "paracentric_inversion"; rdfs:subClassOf ; "A chromosomal inversion that does not include the centromere."; "paracentric inversion"; , . a owl:Class; rdfs:label "reciprocal_chromosomal_translocation"; rdfs:subClassOf ; "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged."; "reciprocal chromosomal translocation"; , . a owl:Class; rdfs:label "autosynaptic_chromosome"; rdfs:subClassOf ; "(Drosophila)A", "autosynaptic chromosome"; "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome."; , . a owl:Class; rdfs:label "homo_compound_chromosome"; rdfs:subClassOf ; "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved."; "homo compound chromosome", "homo-compound chromosome"; , . a owl:Class; rdfs:label "hetero_compound_chromosome"; rdfs:subClassOf ; "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them."; "hetero compound chromosome", "hetero-compound chromosome"; , . a owl:Class; rdfs:label "chromosome_fission"; rdfs:subClassOf ; "A chromosome that occurred by the division of a larger chromosome."; "chromosome fission"; , . a owl:Class; rdfs:label "dexstrosynaptic_chromosome"; rdfs:subClassOf ; "An autosynaptic chromosome carrying the two right (D = dextro) telomeres."; "dexstrosynaptic chromosome"; , . a owl:Class; rdfs:label "laevosynaptic_chromosome"; rdfs:subClassOf ; "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres."; "laevosynaptic chromosome"; , . a owl:Class; rdfs:label "free_duplication"; rdfs:subClassOf ; "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element."; "free duplication"; , . a owl:Class; rdfs:label "free_ring_duplication"; rdfs:subClassOf ; "(Drosophila)R", "free ring duplication"; "A ring chromosome which is a copy of another chromosome."; , . a owl:Class; rdfs:label "complex_chromosomal_mutation"; rdfs:subClassOf ; "A chromosome structure variant with 4 or more breakpoints."; "complex chromosomal mutation"; , . a owl:Class; rdfs:label "deficient_translocation"; rdfs:subClassOf ; "(Drosophila)Df", "(Drosophila)DfT", "deficient translocation"; "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining."; , . a owl:Class; rdfs:label "inversion_cum_translocation"; rdfs:subClassOf ; "(Drosophila)InT", "(Drosophila)T", "inversion cum translocation"; "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break."; , . a owl:Class; rdfs:label "bipartite_duplication"; rdfs:subClassOf ; "(Drosophila)bDp", "bipartite duplication"; "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break."; , . a owl:Class; rdfs:label "cyclic_translocation"; rdfs:subClassOf ; "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third."; "cyclic translocation"; , . a owl:Class; rdfs:label "bipartite_inversion"; rdfs:subClassOf ; "(Drosophila)bIn", "bipartite inversion"; "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)."; , . a owl:Class; rdfs:label "uninverted_insertional_duplication"; rdfs:subClassOf ; "(Drosophila)eDp", "uninverted insertional duplication"; "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments."; , . a owl:Class; rdfs:label "inverted_insertional_duplication"; rdfs:subClassOf ; "(Drosophila)iDp", "inverted insertional duplication"; "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments."; , . a owl:Class; rdfs:label "insertional_duplication"; rdfs:subClassOf ; "(Drosophila)Dpp", "insertional duplication"; "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)."; , . a owl:Class; rdfs:label "interchromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)Tp", "interchromosomal transposition"; "A chromosome structure variation whereby a transposition occurred between chromosomes."; , . a owl:Class; rdfs:label "inverted_interchromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)iTp", "inverted interchromosomal transposition"; "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment."; , . a owl:Class; rdfs:label "uninverted_interchromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)eTp", "uninverted interchromosomal transposition"; "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments."; , . a owl:Class; rdfs:label "inverted_intrachromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)iTp", "inverted intrachromosomal transposition"; "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments."; , . a owl:Class; rdfs:label "uninverted_intrachromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)eTp", "uninverted intrachromosomal transposition"; "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments."; , . a owl:Class; rdfs:label "unoriented_insertional_duplication"; rdfs:subClassOf ; "(Drosophila)uDp", "unoriented insertional duplication"; "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded."; rdfs:comment "Flag - unknown in the definition."; , . a owl:Class; rdfs:label "unoriented_interchromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)uTp", "unorientated interchromosomal transposition"; "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded."; rdfs:comment "FLAG - term describes an unknown."; , . a owl:Class; rdfs:label "unoriented_intrachromosomal_transposition"; rdfs:subClassOf ; "(Drosophila)uTp", "unorientated intrachromosomal transposition"; "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded."; rdfs:comment "FLAG - definition describes an unknown."; , . a owl:Class; rdfs:label "uncharacterised_chromosomal_mutation"; rdfs:subClassOf ; "uncharacterised chromosomal mutation"; , . a owl:Class; rdfs:label "deficient_inversion"; rdfs:subClassOf ; "(Drosophila)Df", "(Drosophila)DfIn", "deficient inversion"; "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted."; , . a owl:Class; rdfs:label "tandem_duplication"; rdfs:subClassOf ; "A duplication consisting of 2 identical adjacent regions."; "erverted", "tandem duplication"; , . a owl:Class; rdfs:label "partially_characterised_chromosomal_mutation"; rdfs:subClassOf ; "partially characterised chromosomal mutation"; , . a owl:Class; rdfs:label "chromosome_number_variation"; rdfs:subClassOf ; "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number."; "chromosome number variation"; , . a owl:Class; rdfs:label "chromosome_structure_variation"; rdfs:subClassOf ; "chromosome structure variation"; , . a owl:Class; rdfs:label "gene_segment"; rdfs:subClassOf ; "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination."; rdfs:comment "Requested by tracker 2021594, July 2008, by Alex."; "gene segment"; . a owl:Class; rdfs:label "uterine cervix"; rdfs:subClassOf ; "Lower, narrow portion of the uterus where it joins with the top end of the vagina."; "canalis cervicis uteri", "cervical canal", "cervical canal of uterus", "cervix", "cervix of uterus", "cervix uteri", "neck of uterus", "uterine cervix"; , . a owl:Class; rdfs:label "fully formed stage"; rdfs:subClassOf ; "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both juvenile stage, and adult stage. "; "fully formed animal stage", "juvenile-adult stage"; , . a owl:Class; rdfs:label "embryo stage part"; rdfs:subClassOf ; "A stage that is part of the embryo stage."; "embryonic stage part"; , . a owl:Class; rdfs:label "embryo stage"; rdfs:subClassOf ; "A life cycle stage that starts with fertilization and ends with the fully formed embryo."; "embryonic stage"; , . a owl:Class; rdfs:label "larval stage"; rdfs:subClassOf ; rdfs:comment "It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form[WP]. Uberon includes clade-specific subclasses."; "a distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle."; "larva stage"; , . a owl:Class; rdfs:label "pupal stage"; rdfs:subClassOf ; "A life stage of some insects undergoing transformation. The pupal stage is found only in holometabolous insects, those that undergo a complete metamorphosis, going through four life stages; embryo, larva, pupa and imago."; "pupa stage"; , . a owl:Class; rdfs:label "death stage"; rdfs:subClassOf ; rdfs:comment "AO notes - ncit:Death is an outcome"; "End of the life of an organism."; "death"; , . a owl:Class; rdfs:label "post-embryonic stage"; rdfs:subClassOf ; "postembryonic stage"; "stage succeeding embryo, including mature structure"; , . a owl:Class; rdfs:label "life cycle"; rdfs:subClassOf ; "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism."; "life", "lifespan"; , . a owl:Class; rdfs:label "life cycle stage"; rdfs:subClassOf ; "A spatiotemporal region encompassing some part of the life cycle of an organism."; "developmental stage"; , . a owl:Class; rdfs:label "zygote stage"; rdfs:subClassOf ; "1-cell stage", "fertilized egg stage", "one cell stage"; "A stage at which the organism is a single cell produced by means of sexual reproduction."; , . a owl:Class; rdfs:label "cleavage stage"; rdfs:subClassOf ; "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula."; , . a owl:Class; rdfs:label "blastula stage"; rdfs:subClassOf ; "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence."; , . a owl:Class; rdfs:label "gastrula stage"; rdfs:subClassOf ; "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm."; , . a owl:Class; rdfs:label "neurula stage"; rdfs:subClassOf ; "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system."; , . a owl:Class; rdfs:label "organogenesis stage"; rdfs:subClassOf ; "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism."; , . a owl:Class; rdfs:label "juvenile stage"; rdfs:subClassOf ; "The stage of being a sexually immature adult animal."; , . a owl:Class; rdfs:label "post-juvenile adult stage"; rdfs:subClassOf ; "The stage of being a sexually mature adult animal."; , . a owl:Class; rdfs:label "adrenal gland"; rdfs:subClassOf ; "Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]."; rdfs:comment "Taxon notes: The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole"; , . a owl:Class; rdfs:label "mesoderm-derived structure"; rdfs:subClassOf ; "An anatomical structure that develops (entirely or partially) from the mesoderm."; rdfs:comment "Grouping term for query purposes"; , . a owl:Class; rdfs:label "pharyngula stage"; rdfs:subClassOf ; "A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities."; rdfs:comment "TODO: check with evo-devo biologists"; "phylotypic stage"; , . a owl:Class; rdfs:label "amphibian larval stage"; rdfs:subClassOf ; "Amphibian larvae, sometimes called pollywogs or tadpoles, hatch from eggs and begin to grow limbs and other adult physical features at various times, depending on the species, before they metamorphose into the adult form."; , . a owl:Class; rdfs:label "nematode larval stage"; rdfs:subClassOf ; "Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew."; , . a owl:Class; rdfs:label "instar larval stage"; rdfs:subClassOf ; "This begins with the newly hatched first-instar larva, through its maturation to the end of the last larval stage. An example of this process is found in Drosophila melanogaster."; , . a owl:Class; rdfs:label "reproductive structure"; rdfs:subClassOf ; "An anatomical structure that is part of the reproductive system."; "reproductive system structure"; , . a owl:Class; rdfs:label "late embryonic stage"; rdfs:subClassOf ; "embryo late (growth) stage"; , . a owl:Class; rdfs:label "neonate stage"; rdfs:subClassOf ; "Of or pertaining to the period of time immediately following birth, or to the newborn."; "neonatal stage"; , . a owl:Class; rdfs:label "late adult stage"; rdfs:subClassOf ; , . a owl:Class; rdfs:label "2 cell stage"; rdfs:subClassOf ; "two-cell stage"; , . a owl:Class; rdfs:label "4 cell stage"; rdfs:subClassOf ; "four-cell stage"; , . a owl:Class; rdfs:label "4-8 cell stage"; rdfs:subClassOf ; "four-eight cell stage"; , . a owl:Class; rdfs:label "8 cell stage"; rdfs:subClassOf ; "eight-cell stage"; , . a owl:Class; rdfs:label "echinopluteus larval stage"; rdfs:subClassOf ; "Larval stage in echinoderms characterized by a planktonic and feeding larval form that possesses limb-like outgrowths bearing ciliated bands."; "pluteus larval stage"; , . a owl:Class; rdfs:label "length unit"; rdfs:subClassOf ; "A unit which is a standard measure of the distance between two points."; . a owl:Class; rdfs:label "mass unit"; rdfs:subClassOf ; "A unit which is a standard measure of the amount of matter/energy of a physical object."; . a owl:Class; rdfs:label "time unit"; rdfs:subClassOf ; "A unit which is a standard measure of the dimension in which events occur in sequence."; "time derived unit"; . a owl:Class; rdfs:label "substance unit"; rdfs:subClassOf ; "A unit which is a standardised quantity of an element or compound with uniform composition."; . a owl:Class; rdfs:label "concentration unit"; rdfs:subClassOf ; "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance."; . a owl:Class; rdfs:label "volume unit"; rdfs:subClassOf ; "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas."; . a owl:Class; rdfs:label "frequency unit"; rdfs:subClassOf ; "A unit which is a standard measure of the number of repetitive actions in a particular time."; . a owl:Class; rdfs:label "pressure unit"; rdfs:subClassOf ; "A unit which is a standard measure of the force applied to a given area."; . a owl:Class; rdfs:label "volumetric flow rate unit"; rdfs:subClassOf ; "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ."; . a owl:Class; rdfs:subClassOf . a owl:Class; rdfs:subClassOf . a owl:Class . a owl:Class; owl:equivalentClass _:2f3019; rdfs:subClassOf . _:2f3019 a owl:Class; owl:oneOf _:2f3029 . _:2f3029 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:subClassOf . a owl:Class; rdfs:subClassOf . a owl:Class; rdfs:label "entity"; owl:equivalentClass _:2f3039 . _:2f3039 a owl:Class; owl:unionOf _:2f3049 . _:2f3049 rdf:first ; rdf:rest _:2f3059 . _:2f3059 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "continuant"; owl:equivalentClass _:2f3069; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.", "Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building", "Synonyms: endurant" . _:2f3069 a owl:Class; owl:unionOf _:2f3079 . _:2f3079 rdf:first ; rdf:rest _:2f3089 . _:2f3089 rdf:first ; rdf:rest _:2f3099 . _:2f3099 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "dependent_continuant"; owl:equivalentClass _:2f30a9; rdfs:subClassOf ; owl:disjointWith , ; rdfs:comment "Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities." . _:2f30a9 a owl:Class; owl:unionOf _:2f30b9 . _:2f30b9 rdf:first ; rdf:rest _:2f30c9 . _:2f30c9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "disposition"; rdfs:subClassOf ; owl:disjointWith , ; rdfs:comment "Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.", "Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity." . a owl:Class; rdfs:label "fiat_object_part"; rdfs:subClassOf ; owl:disjointWith , , , ; rdfs:comment "Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.", "Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso", "Synonyms: fiat substance part" . a owl:Class; rdfs:label "function"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.", "Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law" . a owl:Class; rdfs:label "generically_dependent_continuant"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.", "Examples: a certain PDF file that exists in different and in several hard drives" . a owl:Class; rdfs:label "independent_continuant"; owl:equivalentClass _:2f30d9; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.", "Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building", "Synonyms: substantial entity" . _:2f30d9 a owl:Class; owl:unionOf _:2f30e9 . _:2f30e9 rdf:first ; rdf:rest _:2f30f9 . _:2f30f9 rdf:first ; rdf:rest _:2f3109 . _:2f3109 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "material_entity"; owl:equivalentClass _:2f3119; rdfs:subClassOf , _:2f3159; owl:disjointWith , ; rdfs:comment "Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.", "Examples: collection of random bacteria, a chair, dorsal surface of the body"; "material entity" . _:2f3119 a owl:Class; owl:unionOf _:2f3129 . _:2f3129 rdf:first ; rdf:rest _:2f3139 . _:2f3139 rdf:first ; rdf:rest _:2f3149 . _:2f3149 rdf:first ; rdf:rest rdf:nil . _:2f3159 a owl:Restriction; owl:onProperty ; owl:someValuesFrom . a owl:Class; rdfs:label "object"; rdfs:subClassOf ; owl:disjointWith , , ; rdfs:comment "Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.", "Examples: an organism, a heart, a chair, a lung, an apple", "Synonyms: substance" . a owl:Class; rdfs:label "object_aggregate"; rdfs:subClassOf ; owl:disjointWith , ; rdfs:comment "Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.", "Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital", "Synonyms: substance aggregate" . a owl:Class; rdfs:label "object_boundary"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.", "Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.", "Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall", "Synonyms: substance boundary" . a owl:Class; rdfs:label "one_dimensional_region"; rdfs:subClassOf ; owl:disjointWith , , ; rdfs:comment "Definition: A spatial region [snap:SpatialRegion] with one dimension.", "Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space" . a owl:Class; rdfs:label "quality"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).", "Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee" . a owl:Class; rdfs:label "realizable_entity"; rdfs:subClassOf ; rdfs:comment "Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.", "Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.", "Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity" . a owl:Class; rdfs:label "role"; rdfs:subClassOf ; rdfs:comment "Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.", "Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university"; """In regards to use of roles, functions, and dispositions in ReO: Note that we use roles for the vast majority of dependent continuants inhering in our material entities, despite the fact that these roles always exploit more fundamental functions or dispositions. This is because we are concerned with the domain of scientific techniques and experimentation, where the intentions of researchers performing such processes is paramount. The more fundamental functions and dispositions that inhere in reagents, as a consequence of their inherent physical structures, are important in that they support the roles realized in experimental contexts according to researcher specifications. But to avoid overly complex and proliferative modeling, most of these dispositions and functions are considered out of scope for ReO, and left to other efforts to model. For example, most bearers of molecular effector roles in ReO additionally bear a more fundamental molecular binding function (as the bearers are often created for the purpose of binding some target . . . eg antibodies are created through biological processes for the purpose of recognizing/binding to antigens, probes are created typically through some synthetic process with the function to bind some target molecule). And this binding function could also be said to exploit an even more fundamental binding disposition. But because ReO is concerned primarily with human intention associated with the bearers of these dependent continuants, we concern ourselves primarily with modeling them as roles - as roles are borne in virtue of some agents intent or context (note that the binding disposition and function mentioned above are one example that is modeled in ReO) As an example of the issues that arise if we try to model functions and dispositions, consider the case of a ‘molecular activator’ reagent applied in an experiment. We could model this as a molecular entity that bears a reagent role and also bears a molecular activator function. But there are also cases where activators used in experiments activate some target not through realization of a function, but through realization of a disposition (e.g. certain salts or metals might be applied to activate ion channels, but certainly these chemicals were not created for the purpose of ion channel activation, and thus would have an activator disposition rather than function). So to model this in ReO,we would have to create both a molecular activator function and molecular activator disposition, and say that a molecular activator is a molecular entity that bears a reagent role and also bears a (molecular activator function or molecular activator disposition). Obviously, the creation, definition, and management of all these classes gets unwieldy. So to avoid such complexity, and represent the fact that we are concerned with intended applications of materials in experiments (ie roles they play) we simply say that molecular activators bear some molecular activator role, which is a subclass of reagent role. Functions and dispositions are used in some cases, however, when it is appropriate (ie DNA constructs bear a genetic vector function, because all members of this class are created with this purpose in mind). Functions are also seen in some cases to be used in defining equivalent classes, when all members of a defined class do clearly share a common function or disposition that is necessary and sufficient for membership in the class. For example, fluorescent reporter is defined as a molecular entity that bears a molecular reporter role and also a fluorescence disposition. """ . a owl:Class; rdfs:label "site"; rdfs:subClassOf ; rdfs:comment "Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of \"occupation\". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).", "Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.", "Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria." . a owl:Class; rdfs:label "spatial_region"; owl:equivalentClass _:2f3169; rdfs:subClassOf ; rdfs:comment "Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.", "Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].", "Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called \"absolutist\" or \"the container view\". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.", "Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.", "Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe" . _:2f3169 a owl:Class; owl:unionOf _:2f3179 . _:2f3179 rdf:first ; rdf:rest _:2f3189 . _:2f3189 rdf:first ; rdf:rest _:2f3199 . _:2f3199 rdf:first ; rdf:rest _:2f31a9 . _:2f31a9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "specifically_dependent_continuant"; owl:equivalentClass _:2f31b9; rdfs:subClassOf ; rdfs:comment "Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.", "Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.", "Synonyms: property, trope, mode" . _:2f31b9 a owl:Class; owl:unionOf _:2f31c9 . _:2f31c9 rdf:first ; rdf:rest _:2f31d9 . _:2f31d9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "three_dimensional_region"; rdfs:subClassOf ; owl:disjointWith , ; rdfs:comment "Definition: A spatial region [snap:SpatialRegion] with three dimensions.", "Examples: a cube-shaped part of space, a sphere-shaped part of space" . a owl:Class; rdfs:label "two_dimensional_region"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A spatial region [snap:SpatialRegion] with two dimensions.", "Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space" . a owl:Class; rdfs:label "zero_dimensional_region"; rdfs:subClassOf ; rdfs:comment "Definition: A spatial region [snap:SpatialRegion] with no dimensions.", "Examples: a point" . a owl:Class; rdfs:label "connected_spatiotemporal_region"; owl:equivalentClass _:2f31e9; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].", "Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus" . _:2f31e9 a owl:Class; owl:unionOf _:2f31f9 . _:2f31f9 rdf:first ; rdf:rest _:2f3209 . _:2f3209 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "connected_temporal_region"; owl:equivalentClass _:2f3219; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.", "Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis" . _:2f3219 a owl:Class; owl:unionOf _:2f3229 . _:2f3229 rdf:first ; rdf:rest _:2f3239 . _:2f3239 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "fiat_process_part"; rdfs:subClassOf ; owl:disjointWith , , , ; rdfs:comment "Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.", "Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life" . a owl:Class; rdfs:label "occurrent"; owl:equivalentClass _:2f3249; rdfs:subClassOf ; rdfs:comment "Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.", "Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor", "Synonyms: perdurant" . _:2f3249 a owl:Class; owl:unionOf _:2f3259 . _:2f3259 rdf:first ; rdf:rest _:2f3269 . _:2f3269 rdf:first ; rdf:rest _:2f3279 . _:2f3279 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "process"; rdfs:subClassOf ; owl:disjointWith , , ; rdfs:comment "Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.", "Examples: the life of an organism, the process of sleeping, the process of cell-division" . a owl:Class; rdfs:label "process_aggregate"; rdfs:subClassOf ; owl:disjointWith , ; rdfs:comment "Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.", "Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together" . a owl:Class; rdfs:label "process_boundary"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.", "Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery" . a owl:Class; rdfs:label "processual_context"; rdfs:subClassOf ; rdfs:comment "Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.", "Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.", "Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment." . a owl:Class; rdfs:label "processual_entity"; owl:equivalentClass _:2f3289; rdfs:subClassOf ; owl:disjointWith , ; rdfs:comment "Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.", "Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird" . _:2f3289 a owl:Class; owl:unionOf _:2f3299 . _:2f3299 rdf:first ; rdf:rest _:2f32a9 . _:2f32a9 rdf:first ; rdf:rest _:2f32b9 . _:2f32b9 rdf:first ; rdf:rest _:2f32c9 . _:2f32c9 rdf:first ; rdf:rest _:2f32d9 . _:2f32d9 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "scattered_spatiotemporal_region"; rdfs:subClassOf ; rdfs:comment "Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.", "Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair" . a owl:Class; rdfs:label "scattered_temporal_region"; rdfs:subClassOf ; rdfs:comment "Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.", "Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair" . a owl:Class; rdfs:label "spatiotemporal_instant"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.", "Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process" . a owl:Class; rdfs:label "spatiotemporal_interval"; rdfs:subClassOf ; rdfs:comment "Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.", "Examples: the spatiotemporal region occupied by a process or by a fiat processual part" . a owl:Class; rdfs:label "spatiotemporal_region"; owl:equivalentClass _:2f32e9; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.", "Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.", "Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called \"absolutist\" or \"the container view\". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.", "Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.", "Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis" . _:2f32e9 a owl:Class; owl:unionOf _:2f32f9 . _:2f32f9 rdf:first ; rdf:rest _:2f3309 . _:2f3309 rdf:first ; rdf:rest rdf:nil . a owl:Class; rdfs:label "temporal_instant"; rdfs:subClassOf ; owl:disjointWith ; rdfs:comment "Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.", "Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death" . a owl:Class; rdfs:label "temporal_interval"; rdfs:subClassOf ; rdfs:comment "Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.", "Examples: any continuous temporal duration during which a process occurs" . a owl:Class; rdfs:label "temporal_region"; owl:equivalentClass _:2f3319; rdfs:subClassOf ; rdfs:comment "Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].", "Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.", "Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called \"absolutist\" or \"the container view\" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].", "Definition: An occurrent [span:Occurrent] that is part of time.", "Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death" . _:2f3319 a owl:Class; owl:unionOf _:2f3329 . _:2f3329 rdf:first ; rdf:rest _:2f3339 . _:2f3339 rdf:first ; rdf:rest rdf:nil . a owl:NamedIndividual, ; rdfs:label "example to be eventually removed"@en . a owl:NamedIndividual, ; rdfs:label "failed exploratory term"@en; "Person:Alan Ruttenberg"; "The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en . a owl:NamedIndividual, ; rdfs:label "metadata complete"@en; "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en . a owl:NamedIndividual, ; rdfs:label "organizational term"@en; "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en . a owl:NamedIndividual, ; rdfs:label "ready for release"@en; "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en . a owl:NamedIndividual, ; rdfs:label "metadata incomplete"@en; "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en . a owl:NamedIndividual, ; rdfs:label "uncurated"@en; "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en . a owl:NamedIndividual, ; rdfs:label "pending final vetting"@en; "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en . a owl:NamedIndividual, ; rdfs:label "core"@en; "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en; "PERSON: Alan Ruttenberg"@en, "PERSON: Melanie Courtot"@en . a owl:NamedIndividual, ; rdfs:label "placeholder removed"@en . a owl:NamedIndividual, ; rdfs:label "terms merged"@en; "An editor note should explain what were the merged terms and the reason for the merge."@en . a owl:NamedIndividual, ; rdfs:label "term imported"@en; "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en . a owl:NamedIndividual, ; rdfs:label "term split"@en; "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en . a owl:NamedIndividual, ; rdfs:label "universal"; "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"; "Alan Ruttenberg"; "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." . a owl:NamedIndividual, ; rdfs:label "defined class"; "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."; "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal", "Alan Ruttenberg" . a owl:NamedIndividual, ; rdfs:label "named class expression"; "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."; "Alan Ruttenberg"; "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" . a owl:NamedIndividual, ; rdfs:label "to be replaced with external ontology term"@en; "Alan Ruttenberg"@en; "Terms with this status should eventually replaced with a term from another ontology."@en; "group:OBI"@en . a owl:NamedIndividual, ; rdfs:label "requires discussion"@en; "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en; "Alan Ruttenberg"@en; "group:OBI"@en . a owl:NamedIndividual, ; rdfs:label "example defined class"; "To be used as a value for a 'curation status specification' annotation property that marks a class that is an example of a defined class that can be constructed using the relations and design patterns provided by ReO" . a owl:NamedIndividual, ; rdfs:label "example particular class"; "To be used as a value for a 'curation status specification' annotation property that marks a class that is an example of a granular class to illlustrate types of particular reagents that qualify as a type of a ReO class, and to illustrate the axiomitization that is applied to such classes to enable its inferred classification." . a owl:NamedIndividual, ; rdfs:label "out of scope class"; "To be used as a value for a 'curation status specification' annotation property that marks classes/modeling that I dont want/need in ReO, but want to keep as it may be in scope for related ontologies such as OBI of ERO (or i may want to put it in ReO at some point)." . a owl:NamedIndividual, ; rdfs:label "example to live in new layer"; "To be used as a value for a 'curation status specification' annotation property that marks a class or axiom that is to be moved to a different 'layer'/file in the ReO stack" . a owl:NamedIndividual, ; rdfs:label "nucleotides"; "nt"; "an instance of a length unit used to measure the length of single stranded nucleic acids according to the number of nucleotide residues they contain" . a owl:NamedIndividual, ; rdfs:label "exploratory class"; rdfs:comment "Note that many such classes are remain exploratory because they are out of scope for ReO and thus not a priority here, but may be valuable as recorded ideas for another ontology in thel OBO community"; "To be used as a value for a 'curation status specification' annotation property that marks a class or axiom that is exploratory in nature but not yet ready for release . . . used to test or record some new modeling approach/pattern, but requires further review and consideration regarding its necessity/utility in the ontology." . a owl:NamedIndividual, ; rdfs:label "base pairs"; "bp"; "an instance of a length unit used to measure the length of double stranded nucleic acids according to the number of nucleotide base pairs they contain" . a owl:NamedIndividual, ; rdfs:label "amino acids"; "aa" . a owl:NamedIndividual, ; rdfs:label "shortcut relation" . a owl:NamedIndividual, ; rdfs:label "reference dictionary"; rdfs:comment "used to annotate classes such as 'genetic material' that are created to provide a reference definitions for terms/concepts that are used in textual descriptions of other classes in ReO (but where the class itself is not used logically in class axioms)"; "term clarification" . a owl:NamedIndividual, ; rdfs:label "primary classification axis"; rdfs:comment """All siblings with 'primary axis classification' tags should be disjoint from each other (but not necessarily disjoint from sibling classes with 'secondary classificaiton axis' or 'example defined class' tags). This tag is included only wehre there exist one or more defined or secondary axes of classification, which could obscure the primary axis. In hierarchies where these tags are not applied, all siblings should be considered as representing a primary axis of classification, and thus be disjoint from each other."""; "Indicates that a class is conceived to represent the primary axis of classification in the hierarchy of which it is a part (as opposed to secondary axes of classification implemented through the definition of defined classes that provide alternate approaches for partitioning a parent class)." . a owl:NamedIndividual, ; rdfs:label "secondary classification axis"; rdfs:comment """indicates that a class is conceived to represent a secondray axis of classification in the hierarchy of which it is a part, implemented through the definition of defined classes that provide alternate approaches for partitioning a parent class (relative to the primary axis of classification) Classes flagged as 'secondary classification axes' are intended to be retained in a 'ReO core' ontology, as they are considered generally useful (and not just an example of a defined class that can be created using ReO constructs - such classes are flagged with the individual 'example defined class')""" . _:2f3349 _:2f3359 . _:2f3369 _:2f3379 . _:2f3389 _:2f3399 . _:2f33a9 _:2f33b9, _:2f33c9 . _:2f33d9 _:2f33e9 . _:2f33f9 _:2f3409 . _:2f3419 _:2f3429 . _:2f3439 _:2f3449 . _:2f3459 _:2f3469 . "obsolete_role_of"; _:2f3479 . _:2f3479 _:2f3489 . rdfs:isDefinedBy . rdfs:isDefinedBy . rdfs:isDefinedBy . rdfs:isDefinedBy . "obsolete_quality_of"; _:2f3499; _:2f34a9 . _:2f34a9 _:2f34b9 . rdfs:isDefinedBy . "obsolete_function_of"; _:2f34c9 . _:2f34c9 _:2f34d9 . . _:2f34e9 a owl:AllDifferent; owl:distinctMembers _:2f34f9 . _:2f34f9 rdf:first ; rdf:rest _:2f3509 . _:2f3509 rdf:first ; rdf:rest _:2f3519 . _:2f3519 rdf:first ; rdf:rest _:2f3529 . _:2f3529 rdf:first ; rdf:rest rdf:nil . _:2f3539 a owl:AllDifferent; owl:distinctMembers _:2f3549 . _:2f3549 rdf:first ; rdf:rest _:2f3559 . _:2f3559 rdf:first ; rdf:rest _:2f3569 . _:2f3569 rdf:first ; rdf:rest _:2f3579 . _:2f3579 rdf:first ; rdf:rest _:2f3589 . _:2f3589 rdf:first ; rdf:rest _:2f3599 . _:2f3599 rdf:first ; rdf:rest _:2f35a9 . _:2f35a9 rdf:first ; rdf:rest _:2f35b9 . _:2f35b9 rdf:first ; rdf:rest rdf:nil . _:2f35c9 a owl:AllDifferent; owl:distinctMembers _:2f35d9 . _:2f35d9 rdf:first ; rdf:rest rdf:nil .