PREFIX rdf: PREFIX rdfs: PREFIX swo: PREFIX xsd: a rdfs:Class ; rdfs:label "OPL v1.0" ; rdfs:comment "OPL v1.0 is not a free software license according to the definition of the GNU Project because it requires sending every published modified version to a specific initial developer. " ; rdfs:subClassOf . a rdf:Property ; rdfs:label "is compatible license of"@en ; rdfs:comment "'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program." ; rdfs:domain swo:SWO_0000002 ; rdfs:range swo:SWO_0000002 . a rdf:Property ; rdfs:label "part of"@en ; rdfs:comment "a core relation that holds between a part and its whole"@en ; rdfs:seeAlso , , ; rdfs:range , , , , , ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causal relation between entities" ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "is about"@en ; rdfs:comment "A (currently) primitive relation that relates an information artifact to an entity."@en ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "is concretized as"@en ; rdfs:comment "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "participates in" ; rdfs:comment "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en ; rdfs:domain ; rdfs:range . swo:SWO_9001002 a rdf:Property ; rdfs:label "has clause" ; rdfs:comment "Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied." ; rdfs:domain ; rdfs:range swo:SWO_9000005 ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causally influences" ; rdfs:comment "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "is about" ; rdfs:comment "'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign." ; rdfs:domain ; rdfs:range . a rdfs:Class ; rdfs:label "obsolete Graph plot"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "MHAS Data Policy"@en ; rdfs:comment "The MHAS Data Policy is a vendor-specific license which requires that users attribute the data properly. The data is accessible free of charge to all commercial and non-commercial users. " ; rdfs:subClassOf . swo:SWO_0004006 a rdf:Property ; rdfs:label "has website homepage" ; rdfs:comment "The URL of the homepage for the resource this property is associated with." ; rdfs:range . a rdfs:Class ; rdfs:label "obsolete SNPRMA algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000516 a rdfs:Class ; rdfs:label ".data" ; rdfs:subClassOf . a rdf:Property ; rdfs:label "is alternative format of"@en ; rdfs:comment "With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data." ; rdfs:domain ; rdfs:range . swo:SWO_0004004 a rdf:Property ; rdfs:label "is published by" ; rdfs:comment "'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list." ; rdfs:range . swo:SWO_0000726 a rdfs:Class ; rdfs:label "weaver" ; rdfs:comment "This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdf:Property ; rdfs:label "has part"@en ; rdfs:comment "a core relation that holds between a whole and its part"@en ; rdfs:range ; rdfs:subPropertyOf . swo:SWO_0040005 a rdf:Property ; rdfs:label "is executed in" ; rdfs:comment "is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, " ; rdfs:domain swo:SWO_0000001 ; rdfs:range . swo:SWO_0000082 a rdf:Property ; rdfs:label "uses software"@en ; rdfs:comment "This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use." ; rdfs:domain swo:SWO_0000001 ; rdfs:range swo:SWO_0000001 . a rdf:Property ; rdfs:label "obsolete_is_published_by" ; rdfs:comment "The relationship between software and a software publisher." ; rdfs:domain swo:SWO_0000001 ; rdfs:range ; rdfs:subPropertyOf swo:SWO_0004007 . swo:SWO_0000150 a rdf:Property ; rdfs:label "uses platform"@en ; rdfs:comment "'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example." ; rdfs:domain swo:SWO_0000001 ; rdfs:range swo:SWO_0000021 . swo:SWO_0000087 a rdf:Property ; rdfs:label "has specified data output"@en ; rdfs:comment "The relationship between a piece of software and the data that it is possible to output."@en ; rdfs:domain swo:SWO_0000001 ; rdfs:range . swo:SWO_0000394 a rdf:Property ; rdfs:label "is developed by" ; rdfs:comment "The relationship between a software and software developer." ; rdfs:domain swo:SWO_0000001 ; rdfs:range . swo:SWO_0000740 a rdf:Property ; rdfs:label "implements" ; rdfs:comment "implements is the relationship between software and an algorithm that is defined for use within that software when executed. " ; rdfs:domain swo:SWO_0000001 ; rdfs:range . swo:SWO_0000086 a rdf:Property ; rdfs:label "has specified data input" ; rdfs:comment "The relationship between input data which is permitted to a piece of software." ; rdfs:domain swo:SWO_0000001 ; rdfs:range , , . swo:SWO_0000741 a rdf:Property ; rdfs:label "is encoded in" ; rdfs:comment "Is encoded in is an \"is about\" relationship which describes the type of encoding used for the referenced class." ; rdfs:domain ; rdfs:range , swo:SWO_0000118 ; rdfs:subPropertyOf . swo:SWO_0000157 a rdf:Property ; rdfs:label "is software for"@en ; rdfs:domain swo:SWO_0000001 ; rdfs:range swo:SWO_0000001 , swo:SWO_0000005 . swo:SWO_0000389 a rdfs:Class ; rdfs:label "Semantic Similarity Measures" ; rdfs:comment """Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath, 1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have presented to determine the semantic similarities of two GO terms based on the annotation statistics of their common ancestor terms. Wang [Wang et al., 2007] proposed a new method to measure the similarities based on the graph structure of GO.""" ; rdfs:subClassOf . swo:SWO_0000085 a rdf:Property ; rdfs:label "is implemented by"@en ; rdfs:comment "is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. " ; rdfs:domain ; rdfs:range swo:SWO_0000001 . swo:SWO_0000540 a rdfs:Class ; rdfs:label "flowQ" ; rdfs:comment "This package provides quality control and quality assessment tools for flow cytometry data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000523 a rdfs:Class ; rdfs:label "dyebias" ; rdfs:comment "Gene-specific dye-bias correction of two-color microarray data using the GASSCO method" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_9000018 a rdfs:Class ; rdfs:label "Derivatives not allowed" ; rdfs:comment "Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource." ; rdfs:subClassOf swo:SWO_9000007 . swo:SWO_0000171 a rdfs:Class ; rdfs:label "GSEAlm" ; rdfs:comment "Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000482 a rdfs:Class ; rdfs:label "bgafun" ; rdfs:comment "BGAfun is a method to identify specifity determining residues in protein families" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "MAGE-ML" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "LINCS Data Policy"@en ; rdfs:comment "The LINCS Data Policy is a license which allows redistribution and derivative works as long as the original data is attributed correctly. All investigators are encouraged, to publish results based on LINCS data. These results may include, but would not be limited to, integrating LINCS data with data from other sources. LINCS data are released with the sole restriction that they must be correctly cited so that others can establish provenance and access the original data; the correct citation will be released with each data set and will comprise either a PMID/PMCID reference or a unique LINCS identifier. " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Euteleostomi" ; rdfs:subClassOf . a rdf:Property ; rdfs:label "directly positively regulates activity of" ; rdfs:comment """The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.""" ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly negatively regulates activity of" ; rdfs:comment """The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.""" ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly regulates activity of" ; rdfs:comment """The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.""" ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "regulates activity of" ; rdfs:comment "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has_role" ; rdfs:comment "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "capable of"@en ; rdfs:comment "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has function"@en ; rdfs:comment "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causal relation between material entity and a process" ; rdfs:comment "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has disposition"@en ; rdfs:comment "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "interacts with" ; rdfs:comment "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." ; rdfs:seeAlso ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "is manufactured by" ; rdfs:comment """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.""" ; rdfs:domain ; rdfs:range xsd:string . swo:SWO_0000251 a rdfs:Class ; rdfs:label "Kolmogorov Smirnov rank-sum based algorithm" ; rdfs:comment "KS measures how biased the ranks of a subset of items are among the ranks of the entire set" ; rdfs:subClassOf . swo:SWO_0000640 a rdfs:Class ; rdfs:label "OMICS data" ; rdfs:subClassOf . swo:SWO_0000089 a rdf:Property ; rdfs:label "is specified data output of"@en ; rdfs:comment "The relationship between a data and the software which can possibly produce this data as output." ; rdfs:domain ; rdfs:range swo:SWO_0000001 . swo:SWO_0000088 a rdf:Property ; rdfs:label "is specified data input of"@en ; rdfs:comment "The relationship between a data and the software which can possibly take this data as input." ; rdfs:domain ; rdfs:range swo:SWO_0000001 . swo:SWO_0004002 a rdf:Property ; rdfs:label "has format specification" ; rdfs:comment "Has format specification is a type of \"is encoded in\" relationship which specifically describes the relationship between data and a data format specification." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf swo:SWO_0000741 . a rdfs:Class ; rdfs:label "material processing"@en ; rdfs:comment "A planned process which results in physical changes in a specified input material"@en ; rdfs:subClassOf . a rdf:Property ; rdfs:label "preceded by"@en ; rdfs:comment "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "precedes"@en ; rdfs:comment "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causal relation between processes" ; rdfs:comment "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "regulates characteristic" ; rdfs:comment "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "achieves_planned_objective" ; rdfs:comment "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." ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "has input"@en ; rdfs:comment "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "regulates"@en ; rdfs:comment "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has_specified_input"@en ; rdfs:comment "The inverse property of is_specified_input_of"@en ; rdfs:domain ; rdfs:range , , , ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has component process" ; rdfs:comment "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has_specified_output"@en ; rdfs:comment "The inverse property of is_specified_output_of"@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "realizes"@en ; rdfs:comment "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "has participant" ; 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." ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "temporally related to"@en ; rdfs:comment "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "regulated by"@en ; rdfs:comment "inverse of regulates" ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . swo:SWO_0000452 a rdfs:Class ; rdfs:label "affxparser" ; rdfs:comment "affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete MANOR"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Fischer's Exact Test"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000018 a rdfs:Class ; rdfs:label "MATLAB 7.12" ; rdfs:subClassOf swo:SWO_0000005 . swo:has_license a rdf:Property ; rdfs:label "has license" ; rdfs:comment "The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license." ; rdfs:domain ; rdfs:range , , , , ; rdfs:subPropertyOf . swo:SWO_0004000 a rdf:Property ; rdfs:label "has version" ; rdfs:comment "relationship between an entity and a version name or number" ; rdfs:range . a rdfs:Class ; rdfs:label "obsolete QuantArray version 2"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000460 a rdfs:Class ; rdfs:label "affyio" ; rdfs:comment "Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete RbcBook1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100001 a rdfs:Class ; rdfs:label "50-50 MANOVA" ; rdfs:comment "50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented." ; rdfs:subClassOf swo:SWO_1100075 , swo:SWO_1100115 . swo:SWO_0000029 a rdfs:Class ; rdfs:label "Microsoft developed software" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000191 a rdfs:Class ; rdfs:label "GeneSelectMMD" ; rdfs:comment "Gene selection based on a mixture of marginal distributions" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete qvalue"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "function"@en ; rdfs:subClassOf . a rdf:Property ; rdfs:label "concretizes"@en ; rdfs:comment "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en ; rdfs:domain ; rdfs:range . a rdf:Property ; rdfs:label "realized in"@en ; rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process" ; rdfs:domain ; rdfs:range , , . a rdf:Property ; rdfs:label "function of"@en ; rdfs:comment "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . swo:SWO_0000341 a rdfs:Class ; rdfs:label "RMA+" ; rdfs:subClassOf . swo:SWO_0000215 a rdfs:Class ; rdfs:label "Heterogeneous Error Model (HEM)" ; rdfs:subClassOf . swo:SWO_0000551 a rdfs:Class ; rdfs:label "geneRecommender" ; rdfs:comment "This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete panp"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete arrayWoRx 2.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100124 a rdfs:Class ; rdfs:label "'DynDoc'" ; rdfs:comment "A set of functions to create and interact with dynamic documents and vignettes." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "service provider role" ; rdfs:comment "is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "realizable entity"@en ; rdfs:comment "A specifically dependent continuant that inheres in 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."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MCR algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000072 a rdfs:Class ; rdfs:label "CRG TCoffee 9.02.r1228"@en ; rdfs:comment "The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface." ; rdfs:subClassOf swo:SWO_0000030 , swo:SWO_0000065 . swo:SWO_0000043 a rdf:Property ; rdfs:label "has documentation"@en ; rdfs:comment "Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class." ; rdfs:range xsd:string . swo:SWO_0004001 a rdf:Property ; rdfs:label "has interface" ; rdfs:comment "Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy." ; rdfs:range swo:SWO_9000050 , , . swo:SWO_0000418 a rdfs:Class ; rdfs:label "ScanArray" ; rdfs:comment "ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000129 a rdfs:Class ; rdfs:label "VHDL" ; rdfs:subClassOf . swo:SWO_0000475 a rdfs:Class ; rdfs:label "arrayWoRx 2.0" ; rdfs:subClassOf swo:SWO_0000476 . swo:SWO_1100093 a rdfs:Class ; rdfs:label "'DNAcopy'" ; rdfs:comment "Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ScanAlyze"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "XLS spreadsheet" ; rdfs:comment "A spreadsheet data format designed for Microsoft Excel." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Theodore Ts’o’s"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete flowUtils"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000007 a rdfs:Class ; rdfs:label "Derivatives clause" ; rdfs:comment "Derivatives clauses are license clauses which state what requirements on derivative resource, if any, are attached to a license. The license for a resource may or may not allow the creation of new resources derived from it. If it is allowed, such usage may be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "obsolete Sim method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Terms of Use for EMBL-EBI Services"@en ; rdfs:comment "The Terms of Use for EMBL-EBI Services reflect EMBL-EBI’s commitment to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the data owner.
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated on the appropriate web page. " ; rdfs:subClassOf , , . swo:SWO_0000352 a rdfs:Class ; rdfs:label "RbcBook1" ; rdfs:comment "Support for Springer monograph on Bioconductor" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100113 a rdfs:Class ; rdfs:label "GGBase" ; rdfs:comment "This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Rtreemix"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000213 a rdfs:Class ; rdfs:label "HELP" ; rdfs:comment "The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000159 a rdfs:Class ; rdfs:label "GNU Octave"@en ; rdfs:comment "GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "predictive model specification" ; rdfs:comment "Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "MIACA Full Copyright"@en ; rdfs:comment "MIACA Full Copyright is a vendor-specific license which allows the document it references to be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIACA Standards Initiative or other organizations, except as needed for the purpose of developing MIACA Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIACA Document process must be followed, or as required to translate it into languages other than English." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete TAS Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Locally Moderated Weighted-t (LMW) method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Textual format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete multtest"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ABarray"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BPMAP"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000118 a rdfs:Class ; rdfs:label "Python" ; rdfs:comment "Python is a widely used general-purpose, high-level programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles." ; rdfs:subClassOf . swo:SWO_9000034 a rdfs:Class ; rdfs:label "derivative code linked same license" ; rdfs:comment "Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license." ; rdfs:subClassOf swo:SWO_9000017 . a rdfs:Class ; rdfs:label "datum label"@en ; rdfs:comment "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 ; rdfs:subClassOf . swo:SWO_0000202 a rdfs:Class ; rdfs:label "GeneticsDesign" ; rdfs:comment "This package contains functions useful for designing genetics studies, including power and sample-size calculations." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete pickgene"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000696 a rdfs:Class ; rdfs:label "simpleaffy" ; rdfs:comment "Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000556 a rdfs:Class ; rdfs:label "genemeta" ; rdfs:comment "A collection of meta-analysis tools for analysing high throughput experimental data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "background correction" ; rdfs:comment "A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "PDDL v1.0"@en ; rdfs:comment "The ODC Public Domain Dedication and Licence is a document intended to allow you to freely share, modify, and use this work for any purpose and without any restrictions. This licence is intended for use on databases or their contents (“data”), either together or individually. The goal is to eliminate restrictions held by the original creator of the data and database on the use of it by others. Rightsholders will not be able to “dual license” their work by releasing the same work under different licences. This is because they have allowed anyone to use the work in whatever way they choose. Rightsholders therefore can’t re-license it under copyright or database rights on different terms because they have nothing left to license. " ; rdfs:subClassOf , , . swo:SWO_1100105 a rdfs:Class ; rdfs:label "Fischer's Exact Test" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "European Medicines Agency Copyright"@en ; rdfs:comment """The European Medicines Agency Copyright states that the Agency is the owner of copyright and other intellectual property rights for documents and other content published on their website. Information and documents made available on the Agency's webpages are public and may be reproduced and/or distributed, totally or in part, irrespective of the means and/or the formats used, for non-commercial and commercial purposes, provided that the Agency is always acknowledged as the source of the material. Such acknowledgement must be included in each copy of the material. Citations may be made from such material without prior permission, provided the source is always acknowledged. The above-mentioned permissions do not apply to content supplied by third parties. Therefore, for documents where the copyright vests in a third party, permission for reproduction must be obtained from this copyright holder.""" ; rdfs:subClassOf . swo:SWO_9000029 a rdfs:Class ; rdfs:label "Time for use unrestricted" ; rdfs:comment "Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the resource may be licensed for." ; rdfs:subClassOf swo:SWO_9000012 . a rdfs:Class ; rdfs:label "value specification" ; rdfs:comment "An information content entity that specifies a value within a classification scheme or on a quantitative scale." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete OLIN"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000148 a rdfs:Class ; rdfs:label "Firth's bias reduction procedure" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ImaGene 3.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000074 a rdfs:Class ; rdfs:label "Q 4.2"@en ; rdfs:subClassOf swo:SWO_0000073 . swo:SWO_0000691 a rdfs:Class ; rdfs:label "sagenhaft" ; rdfs:comment "This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100012 a rdfs:Class ; rdfs:label "AP-MS data" ; rdfs:subClassOf . swo:SWO_0000137 a rdfs:Class ; rdfs:label "NONMEM"@en ; rdfs:subClassOf swo:SWO_0000030 . a rdfs:Class ; rdfs:label "obsolete .rma format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MeasurementError.cor"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100082 a rdfs:Class ; rdfs:label "Non-linear functional regression model" ; rdfs:comment "non-linear functional regression model with both additive and multiplicative error terms" ; rdfs:subClassOf . swo:SWO_0000158 a rdfs:Class ; rdfs:label "libSBML"@en ; rdfs:comment "LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "REST service"@en ; rdfs:comment "A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of \"stateless\" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "PDE Algorithm"@en ; rdfs:comment "A partial differential equation (PDE) is a differential equation that contains unknown multivariable functions and their partial derivatives. This is in contrast to ordinary differential equations, which deal with functions of a single variable and their derivatives." ; rdfs:subClassOf . swo:SWO_0000103 a rdfs:Class ; rdfs:label "Eiffel" ; rdfs:subClassOf . swo:SWO_0000573 a rdfs:Class ; rdfs:label "Hierarchical clustering" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Attribution not required"@en ; rdfs:comment "Attribution not required is an attribution clause which states that no attribution need be provided whenever the resource is used." ; rdfs:subClassOf swo:SWO_9000006 . swo:SWO_0000710 a rdfs:Class ; rdfs:label "sscore" ; rdfs:comment "This package contains an implementation of the S-Score algorithm" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete nnNorm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete sizepower"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000374 a rdfs:Class ; rdfs:label "SAM" ; rdfs:comment "Note: It is unclear from just the label what is meant by a SAM algorithm. It may or may not be related to the SAM sequence alignment software described by the class SWO_0000077 (Allyson Lister)" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'CALIB'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data processing algorithm" ; rdfs:comment "A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "partitioning objective"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdf:Property ; rdfs:label "objective_achieved_by" ; rdfs:comment "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." ; rdfs:domain ; rdfs:range . a rdfs:Class ; rdfs:label "obsolete gaga"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000441 a rdfs:Class ; rdfs:label "Variance-stabilizing transformation (VST) algorithm" ; rdfs:subClassOf . swo:SWO_1100019 a rdfs:Class ; rdfs:label "'AffyExpress'" ; rdfs:comment "The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000534 a rdfs:Class ; rdfs:label "fdrame" ; rdfs:comment "This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "ORCID Terms of Use"@en ; rdfs:comment "The ORCID Terms of Use is a vendor-specific license for describing how the data in the ORCID resource may be used. ORCID data can be sublicensed, reproduced, stored, transmitted, distributed, publicly performed and publicly displayed for non-commercial and commercial uses." ; rdfs:subClassOf . swo:SWO_0000110 a rdfs:Class ; rdfs:label "Lisp" ; rdfs:subClassOf . swo:SWO_0000222 a rdfs:Class ; rdfs:label "Harshlight" ; rdfs:comment "The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000583 a rdfs:Class ; rdfs:label "iterativeBMAsurv" ; rdfs:comment "The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000160 a rdfs:Class ; rdfs:label "GWT"@en ; rdfs:subClassOf . swo:SWO_0000651 a rdfs:Class ; rdfs:label "pcot2" ; rdfs:comment "PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000721 a rdfs:Class ; rdfs:label "twilight" ; rdfs:comment "Estimation of local false discovery rate" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000233 a rdfs:Class ; rdfs:label "ILLUMINA data" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete keggorth"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete gtr"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000545 a rdfs:Class ; rdfs:label "'gaggle'" ; rdfs:comment "This package contains functions connecting R with the Gaggle" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'BioMVCClass'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "class prediction data transformation"@en ; rdfs:comment "A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction."@en ; rdfs:subClassOf . swo:SWO_1100000 a rdfs:Class ; rdfs:label "2-sample pooled t-test" ; rdfs:subClassOf . swo:SWO_0000505 a rdfs:Class ; rdfs:label "copa" ; rdfs:comment "COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete PAnnBuilder"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".mysql"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".class file" ; rdfs:comment "A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete chamber slide format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000180 a rdfs:Class ; rdfs:label "GenePix 5.0.1" ; rdfs:subClassOf swo:SWO_0000176 . a rdfs:Class ; rdfs:label "obsolete SBMLR format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete snapCGH"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000061 a rdfs:Class ; rdfs:label "EBI Muscle Web Tool"@en ; rdfs:subClassOf swo:SWO_0000060 . a rdfs:Class ; rdfs:label "newick" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "hierarchical clustering"@en ; rdfs:comment "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)."@en ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "UCSC Genome Browser Commercial Software License"@en ; rdfs:comment "The UCSC Genome Browser Commercial Software License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes under specific restrictions for a fee. The licensee shall not have the right to create Derivative Works of the Licensed Products, and the Licensee shall not have the right to sublicense, sell, transfer, or assign the Licensed Products. Non-commercial use does not require licensing or a fee, and is covered by a separate license." ; rdfs:subClassOf , . swo:SWO_0000002 a rdfs:Class ; rdfs:label "software license" ; rdfs:comment "A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ProDom Commercial License"@en ; rdfs:comment "The ProDom Commercial License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes for a fee. Non-commercial use does not require licensing or a fee, and is covered by a separate license." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete genomeIntervals"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "FreeBSD" ; rdfs:comment "This is the original BSD license with the advertising clause and another clause removed. (It is also sometimes called the “2-clause BSD license”.) It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL." ; rdfs:subClassOf . swo:SWO_0000367 a rdfs:Class ; rdfs:label "RpsiXML" ; rdfs:comment "Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000614 a rdfs:Class ; rdfs:label "'MAS5'" ; rdfs:subClassOf . swo:SWO_0000493 a rdfs:Class ; rdfs:label "cdt" ; rdfs:subClassOf . swo:SWO_1100023 a rdfs:Class ; rdfs:label "Agi4x44PreProcess" ; rdfs:comment "Preprocessing of Agilent 4x44 array data" ; rdfs:subClassOf swo:SWO_0000026 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Lognormal Normal with Modied Variance Model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000635 a rdfs:Class ; rdfs:label "nnNorm" ; rdfs:comment "This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete plgem"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GGtools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_FACS ( fluorescence-activated cell sorter)" ; rdfs:comment "This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method." ; rdfs:subClassOf . swo:SWO_1100102 a rdfs:Class ; rdfs:label "'FDR'" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Meta data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000013 a rdfs:Class ; rdfs:label "COPASI" ; rdfs:comment "COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. " ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100135 a rdfs:Class ; rdfs:label "Chromeleon" ; rdfs:comment "Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_9000031 a rdfs:Class ; rdfs:label "Usage restricted" ; rdfs:comment "Usage restricted is a usage clause which places restrictions on how the licensed resource may be used. These restrictions will vary according to the individual license." ; rdfs:subClassOf swo:SWO_9000013 . swo:SWO_0000356 a rdfs:Class ; rdfs:label "RefPlus" ; rdfs:comment "The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000471 a rdfs:Class ; rdfs:label "aroma.light" ; rdfs:comment "This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete SIM"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete sequence feature format"@en ; rdfs:comment "AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/16"@en ; rdfs:subClassOf . swo:SWO_0000527 a rdfs:Class ; rdfs:label "'edgeR'" ; rdfs:comment "Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000317 a rdfs:Class ; rdfs:label "PGSEA" ; rdfs:comment "Parametric Analysis of Gene Set Enrichment" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100096 a rdfs:Class ; rdfs:label "Expectation-Maximization(EM) algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete daMA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100008 a rdfs:Class ; rdfs:label "ALL/AML data set" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Xenbase Academic Conditions of Use"@en ; rdfs:comment """Data are to be used only for purposes of research and education. Commercial use is prohibited without written permission from Xenbase. The contributor(s) of unpublished data should be explicitly acknowledged in any publication that incorporates, or is based in part or entirely on these data. Xenbase should be explicitly acknowledged when data used in any publication, has been in part or solely derived from analysis of data from this website. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use).""" ; rdfs:subClassOf . swo:SWO_0000255 a rdfs:Class ; rdfs:label "Locally Moderated Weighted-t (LMW) method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_XML" ; rdfs:comment "5. SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. Please use SWO_3000005 instead." ; rdfs:subClassOf . swo:SWO_0000567 a rdfs:Class ; rdfs:label "graph" ; rdfs:comment "A package that implements some simple graph handling capabilities." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'CMA'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "dendrogram"@en ; rdfs:comment """A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm."""@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data normalization" ; rdfs:comment "A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons." ; rdfs:subClassOf . swo:SWO_9000081 a rdfs:Class ; rdfs:label "BioPerl" ; rdfs:subClassOf swo:SWO_0000001 . a rdf:Property ; rdfs:label "has declared status" ; rdfs:comment "'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information." ; rdfs:domain ; rdfs:range ; rdfs:subPropertyOf . swo:SWO_0000486 a rdfs:Class ; rdfs:label "'biocDatasets'" ; rdfs:comment "Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000429 a rdfs:Class ; rdfs:label "Spotfinder [TIGR]" ; rdfs:comment "TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete CSV data set"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000345 a rdfs:Class ; rdfs:label "RMAExpress quantification" ; rdfs:subClassOf swo:SWO_0000343 . a rdfs:Class ; rdfs:label "obsolete spkTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000209 a rdfs:Class ; rdfs:label "GraphAlignment" ; rdfs:comment "Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000338 a rdfs:Class ; rdfs:label "RLMM" ; rdfs:comment "A Genotype Calling Algorithm for Affymetrix SNP Arrays" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "web page specification" ; rdfs:subClassOf . swo:SWO_0000186 a rdfs:Class ; rdfs:label "GenePix Pro 6 [Axon Instruments]" ; rdfs:subClassOf swo:SWO_0000187 . a rdfs:Class ; rdfs:label "DWG" ; rdfs:comment "DWG (\"drawing\") is a binary file format used for storing two and three dimensional design data and metadata" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete occugene"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix Pro 6.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-SA 3.0"@en ; rdfs:comment "CC BY-SA 3.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." ; rdfs:subClassOf , . swo:SWO_0000024 a rdfs:Class ; rdfs:label "Adobe Illustrator 10" ; rdfs:comment "Adobe Illustrator is a graphics editor for creating and editing vector graphics." ; rdfs:subClassOf swo:SWO_0000026 . swo:SWO_0000598 a rdfs:Class ; rdfs:label "log file" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC-SA 2.5"@en ; rdfs:comment """CC BY-NC-SA 2.5 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete aroma.light"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete covdesc file"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "DbCL v1.0"@en ; rdfs:comment "The DbCL v1.0 allows a user of the database contents to share, create and adapt the contents. You must attribute any public use of the contents, or works produced from them. For redistribution or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original. If you publicly use any adapted version, or works produced from an adapted version, you must also offer it under the DbCL. If you redistribute the contents, or an adapted version of them, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. Users of the DbCL must comply with the ODbL v1.0." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Clustered data set"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete modelling" ; rdfs:comment "AL 18.9.2019: Redundant with EDAM 'Modelling and simulation'." ; rdfs:subClassOf . swo:SWO_0000512 a rdfs:Class ; rdfs:label "ctc" ; rdfs:comment "Tools for export and import classification trees and clusters to other programs" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete AIDA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000685 a rdfs:Class ; rdfs:label "reb" ; rdfs:comment "A set of functions to dentify regional expression biases" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_9000025 a rdfs:Class ; rdfs:label "Number of installations unrestricted" ; rdfs:comment "A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the resource may be installed by any given licensee." ; rdfs:subClassOf swo:SWO_9000010 . a rdfs:Class ; rdfs:label "obsolete Gene-Set Enrichment Analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000699 a rdfs:Class ; rdfs:label "xmapbridge" ; rdfs:comment "xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Euarchontoglires" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "tab delimited file format" ; rdfs:comment "Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Distribution unrestricted" ; rdfs:comment "Distribution unrestricted is a distribution clause which states that the licensed resource can be redistributed by a third party in whatever manner that party wishes." ; rdfs:subClassOf . swo:SWO_1100045 a rdfs:Class ; rdfs:label "'Biobase'" ; rdfs:comment "Functions that are needed by many other packages or which replace R functions" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ARACNE algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete timecourse"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RefPlus"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pdInfoBuilder"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000125 a rdfs:Class ; rdfs:label "Smalltalk" ; rdfs:subClassOf . swo:SWO_0000096 a rdfs:Class ; rdfs:label "C Sharp" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "statistical model validation" ; rdfs:comment "A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data construction algorithm" ; rdfs:subClassOf . swo:SWO_0000136 a rdfs:Class ; rdfs:label "NMTRAN"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affyio"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_Microarray data" ; rdfs:comment "Equivalent to EDAM class data_2603." ; rdfs:subClassOf . swo:SWO_1100109 a rdfs:Class ; rdfs:label "GEMTools 2.4" ; rdfs:comment "Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete GeneTraffic"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete widgetTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000288 a rdfs:Class ; rdfs:label "MantelCorr" ; rdfs:comment "Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data)" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete marray"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "JPEG 2000" ; rdfs:comment "JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia]" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affyImGUI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete vsn"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000266 a rdfs:Class ; rdfs:label "MAANOVA v1.2 package for MATLAB" ; rdfs:comment "Tools for analyzing Micro Array experiments" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete 'biocDatasets'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix 5.0.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Probe level Locally moderated Weighted median-t (PLW) method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000363 a rdfs:Class ; rdfs:label "Rnw" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GACK"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000603 a rdfs:Class ; rdfs:label "lumi" ; rdfs:comment "The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete made4"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MIcroarray Analysis Suite"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_png" ; rdfs:comment "SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'CGHbase'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "spreadsheet editing" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CEL binary format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000306 a rdfs:Class ; rdfs:label "Nonlinear Estimation by Iterative Partial Least Squares" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Affymetrix Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'MI'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000538 a rdfs:Class ; rdfs:label "flowCore" ; rdfs:comment "This package provides S4 data structures and basic functions to deal with flow cytometry data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "BioPAX RDF/XML format"@en ; rdfs:comment "AL 6.9.22: I would prefer to use the updated RO label 'has characteristic', but for some reason Protege only allows the use of the label RO deems older, 'bearer of'" ; rdfs:subClassOf . a rdf:Property ; rdfs:label "has characteristic"@en ; rdfs:comment "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence"@en ; rdfs:range . swo:SWO_1100060 a rdfs:Class ; rdfs:label "CARMAweb" ; rdfs:comment """CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages.""" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000328 a rdfs:Class ; rdfs:label "PLIER (Probe Logarithmic Error Intensity Estimate) method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Multinomial probit regression with Gaussian Process priors"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000277 a rdfs:Class ; rdfs:label "Markov Chain Monte Carlo" ; rdfs:subClassOf . swo:SWO_0000370 a rdfs:Class ; rdfs:label "Ruuid" ; rdfs:comment "A package to provide UUID values in R" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000457 a rdfs:Class ; rdfs:label "affyQCReport" ; rdfs:comment "This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000674 a rdfs:Class ; rdfs:label "Quantile regression techniques" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "manufacturing"@en ; rdfs:comment "Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'AnnotationDbi'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete limmaGUI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000114 a rdfs:Class ; rdfs:label "Pascal" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_OBO flat file format" ; rdfs:comment "Equivalence with EDAM term format_2549." ; rdfs:subClassOf . swo:SWO_0000646 a rdfs:Class ; rdfs:label "panp" ; rdfs:comment "A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Heat map" ; rdfs:comment "A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "processed material"@en ; rdfs:comment "Is a material entity that is created or changed during material processing."@en ; rdfs:subClassOf . a rdf:Property ; rdfs:label "is_specified_output_of"@en ; rdfs:comment "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:domain ; rdfs:range ; rdfs:subPropertyOf . a rdfs:Class ; rdfs:label "obsolete Resourcerer"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000594 a rdfs:Class ; rdfs:label "limmaGUI" ; rdfs:comment "A Graphical User Interface for the limma Microarray package" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000006 a rdfs:Class ; rdfs:label "Protege 4" ; rdfs:subClassOf swo:SWO_0000028 . swo:SWO_1100034 a rdfs:Class ; rdfs:label "Base-Pair-Distance Kernel" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete DFW"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000704 a rdfs:Class ; rdfs:label "spkTools" ; rdfs:comment "The package contains functions that can be used to compare expression measures on different array platforms." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete flagme"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Imagene v4.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Monte Carlo"@en ; rdfs:comment "Monte Carlo is a discrete stochastic simulation algorithm and an estimation procedure algorithm. If it is necessary to know the average value of some random variable and its distribution can not be stated, and if it is possible to take samples from the distribution, we can estimate it by taking the samples, independently, and averaging them. If there are sufficiently enough samples, then the law of large numbers says the average must be close to the true value. The central limit theorem says that the average has a Gaussian distribution around the true value." ; rdfs:subClassOf . swo:SWO_0000562 a rdfs:Class ; rdfs:label "gmt format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SAM"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Rnw"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete KCsmart"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete oligoClasses"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000070 a rdfs:Class ; rdfs:label "Microsoft Excel" ; rdfs:subClassOf swo:SWO_0000029 . a rdfs:Class ; rdfs:label "manufacturer" ; rdfs:comment "A person or organization that has a manufacturer role" ; rdfs:subClassOf . swo:SWO_0000587 a rdfs:Class ; rdfs:label "k-cores" ; rdfs:subClassOf . swo:SWO_0000314 a rdfs:Class ; rdfs:label "PAnnBuilder" ; rdfs:comment "Processing annotation data from public data repositories and building annoation data packages." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "citation management" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ecolitk"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000679 a rdfs:Class ; rdfs:label "rama" ; rdfs:comment "The rama package consists of several functions for robust estimation of two color microarray intensities with replicates" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete iterativeBMAsurv"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100071 a rdfs:Class ; rdfs:label "Feature Extraction Software" ; rdfs:subClassOf swo:SWO_1100021 . a rdfs:Class ; rdfs:label "GNU AGPL v3"@en ; rdfs:comment "This is a free software, copyleft license. Its terms effectively consist of the terms of GPLv3, with an additional paragraph in section 13 to allow users who interact with the licensed software over a network to receive the source for that program. It is recommended that developers consider using the GNU AGPL for any software which will commonly be run over a network." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete parse"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete FC"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000501 a rdfs:Class ; rdfs:label "'codelink'" ; rdfs:comment "This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000497 a rdfs:Class ; rdfs:label "chamber slide format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "classified data set"@en ; rdfs:comment "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels."@en ; rdfs:subClassOf . swo:SWO_0000639 a rdfs:Class ; rdfs:label "oligoClasses" ; rdfs:comment "This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_9000092 a rdfs:Class ; rdfs:label "EMBOSS package" ; rdfs:subClassOf swo:SWO_0000030 . a rdfs:Class ; rdfs:label "FCS3.0"@en ; rdfs:comment "FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter." ; rdfs:subClassOf . swo:SWO_0000333 a rdfs:Class ; rdfs:label "RBGL" ; rdfs:comment "A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000681 a rdfs:Class ; rdfs:label "Rank product non-parametric method" ; rdfs:subClassOf . swo:SWO_1100089 a rdfs:Class ; rdfs:label "'DFP'" ; rdfs:comment "This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100041 a rdfs:Class ; rdfs:label "Bayesian Model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:comment "The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools." ; rdfs:subClassOf . swo:SWO_0000381 a rdfs:Class ; rdfs:label "SDF format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete mdqc"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ICS-501 (version 2.3) Image Capture System"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BED format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Copyleft"@en ; rdfs:comment "Copyleft is a derivative code same license clause which says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. In other words, it requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, you first state that it is copyrighted; then the distribution terms described above are added. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable." ; rdfs:subClassOf swo:SWO_9000019 . swo:SWO_0000392 a rdfs:Class ; rdfs:label "software developer role" ; rdfs:comment "Software developer role is a role borne by an organization or individual in which they are responsible for authoring software." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Multiple testing"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'DynDoc'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100052 a rdfs:Class ; rdfs:label "'CALIB'" ; rdfs:comment "This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000035 a rdfs:Class ; rdfs:label "'AnnotationDbi'" ; rdfs:comment "This package provides user interface and database connection code for annotation data packages using SQLite data storage." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 50-50 MANOVA algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hidden Markov Model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Random effects model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete dyebias"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CRLMM algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete rda"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000657 a rdfs:Class ; rdfs:label "pickgene" ; rdfs:comment "Functions to Analyze Microarray (Gene Expression) Data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "University of Concordia Terms of Use"@en ; rdfs:comment "The University of Concordia Terms of Use is a vendor-specific license which states that no document appearing on this website or any other website owned, operated or controlled by Concordia may be copied, sold, reproduced, republished, downloaded, posted, transmitted or distributed by any means with the exception of downloading or printing the contents of the site for personal, non-commercial use. This use must bear in mind that Concordia reserves its copyright and its rights to exclusivity over the material." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete stepNorm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ChipSkipper V0.99"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000629 a rdfs:Class ; rdfs:label "Multivariate t mixture models" ; rdfs:subClassOf . swo:SWO_1100134 a rdfs:Class ; rdfs:label "ProteomicsTools" ; rdfs:comment "ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Hypergeometric enrichment"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BioConductor Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CDF binary format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affyQCReport"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data mining algorithm" ; rdfs:comment "A data mining algorithm is an algorithm that has as its objective a data mining task and outputs as a result a generalization specified by a generalization specification." ; rdfs:subClassOf . swo:SWO_0000020 a rdfs:Class ; rdfs:label "Unix" ; rdfs:subClassOf swo:SWO_0000021 , swo:SWO_0000030 . a rdfs:Class ; rdfs:label "obsolete_XML" ; rdfs:comment "Equivalence with EDAM http://edamontology.org/format_2332, please use that instead." ; rdfs:subClassOf . swo:SWO_0000725 a rdfs:Class ; rdfs:label "vsn" ; rdfs:comment "The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Concordance"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete globaltest"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Propagation of uncertainty in microarray analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000169 a rdfs:Class ; rdfs:label "Gene Recommender algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_ps" ; rdfs:comment "An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead. " ; rdfs:subClassOf . swo:SWO_0000490 a rdfs:Class ; rdfs:label "Bootstrap" ; rdfs:subClassOf . swo:SWO_0000489 a rdfs:Class ; rdfs:label "biomaRT" ; rdfs:comment "The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "JPEG" ; rdfs:comment "JPEG is a lossy file format for storing images" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MAQC data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "tex" ; rdfs:comment "tex is a format for documents written in the document markup language and document preparation system LaTeX." ; rdfs:subClassOf . swo:SWO_0000641 a rdfs:Class ; rdfs:label "oneChannelGUI" ; rdfs:comment "This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000628 a rdfs:Class ; rdfs:label "Multiple testing" ; rdfs:comment "multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BAR"@en ; rdfs:comment "BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BaldiLongT"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MicroArraySuite 4.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000205 a rdfs:Class ; rdfs:label "GenomeGraphs" ; rdfs:comment "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "GMTK parameter data"@en ; rdfs:comment "GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "SVG" ; rdfs:subClassOf . swo:SWO_9000021 a rdfs:Class ; rdfs:label "Source code unavailable" ; rdfs:comment "A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee." ; rdfs:subClassOf swo:SWO_9000008 . a rdfs:Class ; rdfs:label "obsolete RNAither"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000121 a rdfs:Class ; rdfs:label "SAS" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete oligo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000187 a rdfs:Class ; rdfs:label "GenePix Pro [Axon Instruments]" ; rdfs:subClassOf swo:SWO_0000182 . a rdfs:Class ; rdfs:label "class discovery" ; rdfs:comment "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." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete OutlierD"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "LPPL v1.3c" ; rdfs:comment "LPPL v1.3 is a free software license (by the defintion of the GNU Project), with less stringent requirements on distribution than LPPL 1.2. It is still incompatible with the GPL because some modified versions must include a copy of or pointer to an unmodified version.Software projects other than LaTeX rarely use it." ; rdfs:subClassOf . swo:SWO_0000692 a rdfs:Class ; rdfs:label "seqLogo" ; rdfs:comment "seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100145 a rdfs:Class ; rdfs:label "CutAdapt" ; rdfs:comment "Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100063 a rdfs:Class ; rdfs:label "'ChemmineR'" ; rdfs:comment "ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100030 a rdfs:Class ; rdfs:label "BGL" ; rdfs:comment "BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering" ; rdfs:subClassOf . swo:SWO_0000042 a rdfs:Class ; rdfs:label "ArrayVision" ; rdfs:comment "This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete bgafun"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data format specification"@en ; rdfs:comment """A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"""@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "predictive modeling task" ; rdfs:comment """Learning a (Probabilistic) Predictive Model. In this task, we are given a dataset that consists of examples of the form (d, c), where each d is of type Td and each c is of type Tc. We will refer to d as the description and c as the class or target. To learn a predictive model means to find a mapping from the description to the target, m :: Td → Tc, that fits the data closely. This means that the observed target values and the target values predicted by the model, i.e., c and ˆc = m(d), have to match closely.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Ruuid"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Mutual information matrix (MIM)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'affycoretools'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000143 a rdfs:Class ; rdfs:label "data storage" ; rdfs:comment "The storing of digital information. Often this is done for archiving and retrieval purposes." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "programming language format" ; rdfs:subClassOf . swo:SWO_0000210 a rdfs:Class ; rdfs:label "GridGrinder" ; rdfs:comment "Software for microarray image analysis." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete MAVI Pro"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000262 a rdfs:Class ; rdfs:label "Laplace mixture model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete FoxDimmicT"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY 3.0"@en ; rdfs:comment "CC BY 3.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete RMAExpress quantification"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Quantile normalization"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000467 a rdfs:Class ; rdfs:label "data annotation" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CLR algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000216 a rdfs:Class ; rdfs:label "Hubert’s gamma" ; rdfs:subClassOf . swo:SWO_1100035 a rdfs:Class ; rdfs:label "BPMAP" ; rdfs:comment "BPMAP is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The BPMAP format contains information relating to the design of the Affymetrix tiling arrays." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete twilight"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete gene2pathway"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "XGMML"@en ; rdfs:comment "XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML." ; rdfs:subClassOf . swo:SWO_0000067 a rdfs:Class ; rdfs:label "CRG RCoffee Web Tool"@en ; rdfs:comment "Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software." ; rdfs:subClassOf swo:SWO_0000064 . swo:SWO_0000219 a rdfs:Class ; rdfs:label "Hidden Variable Dynamic Modelling HVDM)" ; rdfs:comment "Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete QuantArray scanner software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Metazoa" ; rdfs:subClassOf . swo:SWO_0000322 a rdfs:Class ; rdfs:label "PROcess" ; rdfs:comment "A package for processing protein mass spectrometry data." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "data visualization task" ; rdfs:comment "data visualization task is information processing objective achieved by a data visualization algorithm execution process." ; rdfs:subClassOf . swo:SWO_1100127 a rdfs:Class ; rdfs:label "software before Microsoft 2007" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete GeneticsDesign"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ctc"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Bootstrap"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_BED format" ; rdfs:comment "Equivalence with EDAM term \"BED\" (format_3003)." ; rdfs:subClassOf . swo:SWO_0000311 a rdfs:Class ; rdfs:label "OrderedList" ; rdfs:comment "Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100142 a rdfs:Class ; rdfs:label "RSeQC" ; rdfs:comment "RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete BZScan"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000729 a rdfs:Class ; rdfs:label "xcms" ; rdfs:comment "Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'codelink'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000346 a rdfs:Class ; rdfs:label "RMAGEML" ; rdfs:comment "This package can be used to handle MAGEML documents in Bioconductor" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CC BY-NC-ND 3.0"@en ; rdfs:comment "CC BY-NC-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " ; rdfs:subClassOf , . swo:SWO_0000430 a rdfs:Class ; rdfs:label "Spotfire" ; rdfs:comment "Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete prada"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Library Search Algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000718 a rdfs:Class ; rdfs:label "tkWidgets" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100078 a rdfs:Class ; rdfs:label "F test" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "specimen collection objective" ; rdfs:comment "A objective specification to obtain a material entity for potential use as an input during an investigation." ; rdfs:subClassOf . swo:SWO_0000053 a rdfs:Class ; rdfs:label "ClustalW"@en ; rdfs:subClassOf swo:SWO_0000051 . a rdfs:Class ; rdfs:label "obsolete design file"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete AvgNRRs"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Artistic License" ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "obsolete maCorrPlot"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ontoTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".bw"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "NIDA NIH Data Access Policy"@en ; rdfs:comment "The NIDA NIH Data Access Policy specifies under what legal requirements NIDA NIH data may be accessed. Researchers may gain access to clinical data, genetic analysis data, and DNA by obtaining formal approval from the NIDA Genetic Data Access Request Committee. " ; rdfs:subClassOf . swo:software_before_Microsoft_2007 a rdfs:Class ; rdfs:label "obsolete software before Microsoft 2007"@en ; rdfs:comment "AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/18"@en ; rdfs:subClassOf . swo:SWO_1100085 a rdfs:Class ; rdfs:label "CodeLink Expression Scanning Software" ; rdfs:comment "Slides are scanned using CodeLink Expression Scanning Software" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000295 a rdfs:Class ; rdfs:label "MiPP" ; rdfs:comment "This package finds optimal sets of genes that seperate samples into two or more classes." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Heatplus"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete scanning software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete HELP"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PCMG"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete database creation"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "FlowRepository Open Access Terms of Use"@en ; rdfs:comment "The FlowRepository Open Access Terms of Use license allows any individual to access the licensed product (originally the Flow Cytometry Data Repository) for any purpose. There are no restrictions on the use or redistribution of the data associated with this license, though it makes the statement that some data covered may also be included under more restrictive licensing." ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "obsolete splicegear"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000385 a rdfs:Class ; rdfs:label "SMAP" ; rdfs:comment "Functions and classes for DNA copy number profiling of array-CGH data" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ScanArray"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete annotationTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Logit-t algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000707 a rdfs:Class ; rdfs:label "spotSegmentation" ; rdfs:comment "Spot segmentation via model-based clustering and gridding for blocks within microarray slides" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ANCOVA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "word processing" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete hexbin"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "tabix file format" ; rdfs:comment "Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format \"chr:beginPos-endPos\". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally." ; rdfs:subClassOf . swo:SWO_0000368 a rdfs:Class ; rdfs:label "Rredland" ; rdfs:comment "interface to redland RDF utilities" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000031 a rdfs:Class ; rdfs:label "Smultron" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete sscore"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000396 a rdfs:Class ; rdfs:label "software developer organization" ; rdfs:comment "An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-ND 4.0"@en ; rdfs:comment "CC BY-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation." ; rdfs:subClassOf . swo:SWO_1100120 a rdfs:Class ; rdfs:label "'CGHcall'" ; rdfs:comment "Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Kolmogorov Smirnov rank-sum based algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000165 a rdfs:Class ; rdfs:label "Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "multiple sequence alignment"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Rank-invariant set normalization"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete sagenhaft"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000280 a rdfs:Class ; rdfs:label "MEDME" ; rdfs:comment "MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000238 a rdfs:Class ; rdfs:label "ImaGene" ; rdfs:comment "ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "version name" ; rdfs:comment "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 ; rdfs:subClassOf . swo:SWO_0000081 a rdf:Property ; rdfs:label "is version of"@en ; rdfs:comment "'is version of' provides a link between a 'version name' and the entity with that version." ; rdfs:domain ; rdfs:range . swo:SWO_1100057 a rdfs:Class ; rdfs:label "'CORREP'" ; rdfs:comment "Multivariate correlation estimation and statistical inference." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete MergeMaid"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100138 a rdfs:Class ; rdfs:label "Supernovo" ; rdfs:comment "SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "IUPAC/InChI-Trust InChI Licence No. 1.0"@en ; rdfs:comment "IUPAC/InChI-Trust InChI Licence No. 1.0 is a vendor license which allows all users to make use of the resource, including the source code, for free, as long as its source is properly attributed. It is broadly compatible with the GNU GPL v3 and v2 in that it states in the license that you can change the license from this one to the GNU GPL if you wish." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Fixed effect model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "material information bearer"@en ; rdfs:comment "A material entity in which a concretization of an information content entity inheres."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GFF" ; rdfs:subClassOf . swo:SWO_0000176 a rdfs:Class ; rdfs:label "Gene Pix" ; rdfs:comment "GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete fdrame"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RMA+"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC-SA 3.0 US"@en ; rdfs:comment """CC BY-NC-SA 3.0 US is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . swo:SWO_9000030 a rdfs:Class ; rdfs:label "Usage unrestricted" ; rdfs:comment "Usage unrestricted is a usage clause which places no restrictions on how the licensed resource may be used." ; rdfs:subClassOf swo:SWO_9000013 . a rdfs:Class ; rdfs:label "biological sequence data" ; rdfs:comment "Data about primary biological sequence information, such as DNA neucleotide sequences." ; rdfs:subClassOf . swo:SWO_0000064 a rdfs:Class ; rdfs:label "TCoffee"@en ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class . swo:SWO_1100068 a rdfs:Class ; rdfs:label "affy" ; rdfs:comment "The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000249 a rdfs:Class ; rdfs:label "KGML" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete oneChannelGUI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Fee-Based Commercial License"@en ; rdfs:comment "Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee." ; rdfs:subClassOf swo:SWO_0000002 . swo:SWO_0000075 a rdfs:Class ; rdfs:label "SPSS"@en ; rdfs:comment "Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. " ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000378 a rdfs:Class ; rdfs:label "SBMLR format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".gz"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GlobalAncova"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000154 a rdfs:Class ; rdfs:label "COBRA"@en ; rdfs:comment "COBRA (COnstraint-Based Reconstruction and Analysis Toolbox) includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Semantic Similarity Measures"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'Needleman-Wunsch'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "regulatory agency"@en ; rdfs:comment "A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "OWL2-XML" ; rdfs:comment "Web Ontology Language version 2 in XML Serialization" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Modelling and simulation" ; rdfs:comment "Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete flowViz"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100116 a rdfs:Class ; rdfs:label "AtlasImage" ; rdfs:comment "Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "CGM" ; rdfs:comment "Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632." ; rdfs:subClassOf . swo:SWO_9000076 a rdfs:Class ; rdfs:label "software suite" ; rdfs:subClassOf swo:SWO_0000001 . a rdf:Property ; rdfs:label "has part" ; rdfs:comment "The inverse property. 'part of', contains the full official RO definition." ; rdfs:range . a rdfs:Class ; rdfs:label "obsolete Negative binomial distribution"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000478 a rdfs:Class ; rdfs:label "AvgNRRs" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CopasiML" ; rdfs:comment "An XML-based file format for use with the COPASI software." ; rdfs:subClassOf . swo:SWO_0000714 a rdfs:Class ; rdfs:label "stepNorm" ; rdfs:comment "Stepwise normalization functions for cDNA microarray data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000078 a rdfs:Class ; rdfs:label "SAM 3.5"@en ; rdfs:subClassOf swo:SWO_0000077 . a rdfs:Class ; rdfs:label "Archaea" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_SBML file" ; rdfs:comment "Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "audio format"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "partitioning data transformation"@en ; rdfs:comment "A partitioning data transformation is a data transformation that has objective partitioning."@en ; rdfs:subClassOf . swo:SWO_0000147 a rdfs:Class ; rdfs:label "Python 2.7"@en ; rdfs:comment "Version 2.7 of the Python programming language." ; rdfs:subClassOf swo:SWO_0000118 . a rdfs:Class ; rdfs:label "obsolete R interface to boost graph library algorithm (RBGL)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000104 a rdfs:Class ; rdfs:label "Forth" ; rdfs:subClassOf . swo:SWO_9000010 a rdfs:Class ; rdfs:label "Number of installations clause" ; rdfs:comment "A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "differential expression analysis" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete AtlasImage"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000549 a rdfs:Class ; rdfs:label "'genArise'" ; rdfs:comment "genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete OLINgui"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete gpls"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GMD Academic License"@en ; rdfs:comment "The GMD Academic License is a vendor-specific license which allows the access and use of the licensed data for non-commercial purposes, as long as the appropriate attribution is used and copyright notices retained. A separate license agreement is required for commercial users and as such, they are not covered by this license. Without written consent by the GMD, no part of the GMD - in its original or in any way processed or reformatted form - may be re-distributed in any way." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete mas5 format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY 2.0 UK"@en ; rdfs:comment "CC BY 2.0 UK is a UK-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "figure"@en ; rdfs:comment "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'PLM'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneSelectMMD"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete XDE"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete TargetSearch"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "spreadsheet format" ; rdfs:comment "A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "symbol"@en ; rdfs:comment "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "performance status value specification" ; rdfs:comment "A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life)." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete cdt"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "NIH Genomic Data Sharing Policy"@en ; rdfs:comment """The NIH Genomic Data Sharing Policy specifies under what legal requirements NIH genomic data may be accessed. Access to human data is through a tiered model involving unrestricted- and controlled-data access mechanisms. Requests for controlled-access data are reviewed by NIH Data Access Committees (DACs).""" ; rdfs:subClassOf . swo:SWO_0000057 a rdfs:Class ; rdfs:label "ClustalX 2.1"@en ; rdfs:subClassOf swo:SWO_0000054 . a rdfs:Class ; rdfs:label "obsolete MCRestimate"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "material entity" ; rdfs:comment "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." ; rdfs:subClassOf . swo:SWO_1100074 a rdfs:Class ; rdfs:label "distance calculation" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Gene expression dataset"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000090 a rdfs:Class ; rdfs:label "Gene Expression Atlas at EBI R statistics package"@en ; rdfs:comment "R package for producing statistics that populate the Gene Expression Atlas. https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R " ; rdfs:subClassOf swo:SWO_0000001 . a rdf:Property ; rdfs:label "has support URL" ; rdfs:comment "A URL for a source of support information about software" ; rdfs:range . a rdfs:Class ; rdfs:subClassOf . swo:SWO_0000610 a rdfs:Class ; rdfs:label "maigesPack" ; rdfs:comment "This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "OWL-XML" ; rdfs:comment "The Web Ontology Language (OWL) in XML serialization" ; rdfs:subClassOf . swo:SWO_1100037 a rdfs:Class ; rdfs:label "'BSgenome'" ; rdfs:comment """This document describes the process of forging a BSgenome data package. It is intended for Bioconductor users who want to make a new BSgenome data package""" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100048 a rdfs:Class ; rdfs:label "'Biostrings'" ; rdfs:comment "Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000513 a rdfs:Class ; rdfs:label "dChip" ; rdfs:comment "Analysis and visualization of gene expression and SNP microarrays" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000621 a rdfs:Class ; rdfs:label "metahdep" ; rdfs:comment "Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000102 a rdfs:Class ; rdfs:label "Dylan" ; rdfs:subClassOf . swo:SWO_1100013 a rdfs:Class ; rdfs:label "ARACNE algorithm" ; rdfs:subClassOf . swo:SWO_0000149 a rdfs:Class ; rdfs:label "Mac OS"@en ; rdfs:comment "Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc." ; rdfs:subClassOf swo:SWO_0000021 . a rdfs:Class ; rdfs:label "obsolete_html" ; rdfs:comment "There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Jaccard’s index"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100050 a rdfs:Class ; rdfs:label "'BufferedMatrix'" ; rdfs:comment "This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "file rendering" ; rdfs:comment "Renders a file in such a way that its contents can be understood by users." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ODbL v1.0"@en ; rdfs:comment "The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures." ; rdfs:subClassOf , . swo:SWO_0000060 a rdfs:Class ; rdfs:label "MUSCLE"@en ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000703 a rdfs:Class ; rdfs:label "spikeLI" ; rdfs:comment "Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100114 a rdfs:Class ; rdfs:label "Gamma Gamma Model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Creative Commons" ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "obsolete Mfuzz"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "PDBML" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete tkWidgets"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ArrayExpress Bioconductor"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "MathML 2.0" ; rdfs:comment "MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages." ; rdfs:subClassOf . swo:SWO_0000632 a rdfs:Class ; rdfs:label "nem" ; rdfs:comment "Nested Effects Models to reconstruct phenotypic hierarchies" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Image" ; rdfs:comment "Biological or biomedical data has been rendered into an image, typically for display on screen." ; rdfs:subClassOf . swo:SWO_0000502 a rdfs:Class ; rdfs:label "dataset comparison" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ARR"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000287 a rdfs:Class ; rdfs:label "Mahalanobis distance" ; rdfs:subClassOf . swo:SWO_0000012 a rdfs:Class ; rdfs:label "Java" ; rdfs:subClassOf . swo:SWO_0000172 a rdfs:Class ; rdfs:label "Gamma-Gamma hierarchical model" ; rdfs:subClassOf . swo:SWO_0000161 a rdfs:Class ; rdfs:label "S language"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".java file" ; rdfs:comment "A source code file format which is specified to be used with the Java programming language." ; rdfs:subClassOf . swo:SWO_0000461 a rdfs:Class ; rdfs:label "affypdnn" ; rdfs:comment "The package contains functions to perform the PDNN method described by Li Zhang et al." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000673 a rdfs:Class ; rdfs:label "Quantile normalization" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_Image" ; rdfs:comment "Equivalence with EDAM data_2968" ; rdfs:subClassOf . swo:SWO_0000554 a rdfs:Class ; rdfs:label "Gene expression dataset" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete rbsurv"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Silicon Genetics Genespring"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-SA 3.0 US"@en ; rdfs:comment "CC BY-SA 3.0 US is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." ; rdfs:subClassOf , . swo:SWO_9000013 a rdfs:Class ; rdfs:label "Usage clause" ; rdfs:comment "A usage clause is a license clause which states the restrictions placed on how the licensed resource may be used. The license for a resource may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "Vendor-specific License"@en ; rdfs:comment "A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization." ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "obsolete ImageQuant"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "matrix manipulation" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete OCplus"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000284 a rdfs:Class ; rdfs:label "MMD" ; rdfs:comment "MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes)," ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data cleaning algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SMAP"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete xmapbridge"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete VanillaICE"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000662 a rdfs:Class ; rdfs:label "plw" ; rdfs:comment "Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW)." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Live" ; rdfs:comment "Live is a development status which is applied to software that has been designated as suitable for production environments by the developer/publisher. If a non-free product, software at this stage is available for purchase" ; rdfs:subClassOf . swo:SWO_0000650 a rdfs:Class ; rdfs:label "pcaMethods" ; rdfs:comment "A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete bioDist"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000591 a rdfs:Class ; rdfs:label "lapmix" ; rdfs:comment "lapmix is a software package for the identification of differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Category"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000472 a rdfs:Class ; rdfs:label "arrayMvout" ; rdfs:comment "This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "XML spreadsheet" ; rdfs:comment "A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete flowFlowJo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete TypeInfo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GBIF Data Sharing Agreement"@en ; rdfs:comment "GBIF Data Sharing Agreement is a simple vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SBMLR"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "diagram"@en ; rdfs:comment "A figure that expresses one or more propositions"@en ; rdfs:subClassOf . swo:SWO_0000298 a rdfs:Class ; rdfs:label "Mixed model equations" ; rdfs:subClassOf . swo:SWO_0000001 a rdfs:Class ; rdfs:label "software" ; rdfs:comment "Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ArrayNorm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000183 a rdfs:Class ; rdfs:label "GenePix Pro 3" ; rdfs:subClassOf swo:SWO_0000182 . swo:SWO_0000428 a rdfs:Class ; rdfs:label "Spot quantification" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Pearson correlation estimator"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000077 a rdfs:Class ; rdfs:label "Adobe Acrobat Reader" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "data set"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MAANOVA v1.2 package for MATLAB"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100024 a rdfs:Class ; rdfs:label "Agilent Feature Extraction 5.1.1" ; rdfs:subClassOf swo:SWO_1100104 . a rdfs:Class ; rdfs:label "obsolete RMA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000324 a rdfs:Class ; rdfs:label "Pathways 2.01 software" ; rdfs:comment "The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background)." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete microRNA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ArrayGauge"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete LPE"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000093 a rdfs:Class ; rdfs:label "AppleScript" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete xcms"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100099 a rdfs:Class ; rdfs:label "FACS data" ; rdfs:comment "FACS data is data which describes flow cytometry data sets." ; rdfs:subClassOf . swo:SWO_0000019 a rdfs:Class ; rdfs:label "STARLIMS" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "SAEM"@en ; rdfs:comment "A stochastic algorithm for population pharmacology modeling" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete distance calculation"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000388 a rdfs:Class ; rdfs:label "SPIA" ; rdfs:comment "This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000543 a rdfs:Class ; rdfs:label "flowViz" ; rdfs:comment "Provides visualization tools for flow cytometry data" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete QuantArray, PackaardBiochip technologies"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000377 a rdfs:Class ; rdfs:label "SBMLR" ; rdfs:comment "This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000221 a rdfs:Class ; rdfs:label "Hardy-Weinberg equilibrium" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "RIKEN Copyright"@en ; rdfs:comment "The RIKEN copyright is a vendor-specific license which states that all text, photographs, diagrams, and other materials on their website are copyrighted by RIKEN unless explicitly specified otherwise on the website. It is prohibited to use, reproduce, or modify any of the material without RIKEN's permission." ; rdfs:subClassOf . swo:SWO_0000250 a rdfs:Class ; rdfs:label "'KLD'" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "curve fitting" ; rdfs:comment "curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "SOAP service"@en ; rdfs:comment "A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations." ; rdfs:subClassOf . swo:SWO_0000528 a rdfs:Class ; rdfs:label "exonmap" ; rdfs:comment "This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete CBS algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000138 a rdfs:Class ; rdfs:label "Entrez" ; rdfs:comment "The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website." ; rdfs:subClassOf swo:SWO_0000140 . swo:SWO_0000330 a rdfs:Class ; rdfs:label "QuantArray, PackaardBiochip technologies" ; rdfs:subClassOf swo:SWO_0000329 . swo:SWO_0000487 a rdfs:Class ; rdfs:label "'biocGraph'" ; rdfs:comment "This package provides examples and code that make use of the different graph related packages produced by Bioconductor." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete BRB-ArrayTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000190 a rdfs:Class ; rdfs:label "GeneRfold" ; rdfs:comment "Package manipulating sequences with fold routines" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete CodeLink Expression Analysis Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000654 a rdfs:Class ; rdfs:label "pdmclass" ; rdfs:comment "This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "data processing task" ; rdfs:comment "A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset." ; rdfs:subClassOf . swo:SWO_1100094 a rdfs:Class ; rdfs:label "'EBImage'" ; rdfs:comment "EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000684 a rdfs:Class ; rdfs:label "rda" ; rdfs:subClassOf . swo:SWO_0000340 a rdfs:Class ; rdfs:label "RMA" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "role"@en ; rdfs:comment "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en ; rdfs:subClassOf . swo:SWO_0000214 a rdfs:Class ; rdfs:label "HEM" ; rdfs:comment "This package fits heterogeneous error models for analysis of microarray data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "PPDB Academic License"@en ; rdfs:comment "The PPDB Academic Licens specifies under what legal requirements PPDB data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of PPDB to exploit the data for commercial purposes. The resource will be used for teaching or not-for-profit research purposes only. The resource will not be further distributed to others. The recipient agrees to acknowledge the source of the material in any publication reporting its use. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use)." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete k-cores"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GEO data type"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000425 a rdfs:Class ; rdfs:label "Similarity score" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'apComplex'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Local-pooled-error"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100125 a rdfs:Class ; rdfs:label "FoxDimmicT" ; rdfs:subClassOf . swo:SWO_0000113 a rdfs:Class ; rdfs:label "Mathematica" ; rdfs:subClassOf . swo:SWO_0000506 a rdfs:Class ; rdfs:label "cosmo" ; rdfs:comment "cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete KEGGSOAP"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete rsbml"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Axon GenePix Pro 3"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "RDF" ; rdfs:comment "The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Recursive Feature Elimination (RFE)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "disposition"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GenBank format" ; rdfs:comment "Genbank entry format." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "single generalization specification" ; rdfs:comment "A single generalization specification is a generalization specification and denotes a type of generalization that is produced by a single generalization data mining algorithm. This algorithm produces only one generalization at its output." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "biological_process" ; rdfs:comment "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." . swo:SWO_0000565 a rdfs:Class ; rdfs:label "gpls" ; rdfs:comment "Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000546 a rdfs:Class ; rdfs:label "gcRMA quantification" ; rdfs:comment "Bioconductor package concerned with background adjustment using sequence information"@en ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete mrnet algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "HTML" ; rdfs:comment "html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web." ; rdfs:subClassOf . swo:SWO_0000465 a rdfs:Class ; rdfs:label "annaffy" ; rdfs:comment "This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000557 a rdfs:Class ; rdfs:label "geneplotter" ; rdfs:comment "Some basic functions for plotting genetic data" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100072 a rdfs:Class ; rdfs:label "Chi-square" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete exonmap"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000115 a rdfs:Class ; rdfs:label "Perl" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "application programming interface" ; rdfs:comment "An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact." ; rdfs:subClassOf swo:SWO_9000050 . a rdfs:Class ; rdfs:label "AI" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affyContam"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "SIF"@en ; rdfs:comment "SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). " ; rdfs:subClassOf . swo:SWO_0000243 a rdfs:Class ; rdfs:label "Jaccard’s index" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete cghMCR"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000362 a rdfs:Class ; rdfs:label "Rmagpie" ; rdfs:comment "Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "molecular_function" ; rdfs:comment "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." . swo:SWO_0000135 a rdfs:Class ; rdfs:label "PSI-BLAST" ; rdfs:comment "Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as \"hypothetical protein\" or \"similar to...\". " ; rdfs:subClassOf swo:SWO_1100032 . a rdfs:Class ; rdfs:label "Academic Free License version 3" ; rdfs:comment "The Academic Free License is a free software license under the definition of \"free\" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL." ; rdfs:subClassOf . swo:SWO_1100104 a rdfs:Class ; rdfs:label "Agilent Feature Extraction Software" ; rdfs:comment "The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment" ; rdfs:subClassOf swo:SWO_0000034 . swo:SWO_9000091 a rdfs:Class ; rdfs:label "Eclipse" ; rdfs:comment "The Eclipse IDE" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete GenePix Pro 3.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000026 a rdfs:Class ; rdfs:label "Number of users restricted" ; rdfs:comment "A Number of users restricted clause is a number of users clause which restricts the number of users the resource may have for a particular licensee. This may be number of total users, or number of concurrent users." ; rdfs:subClassOf swo:SWO_9000011 . swo:SWO_0000447 a rdfs:Class ; rdfs:label "XDotsReader" ; rdfs:comment "Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete GASSCO method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BlueFuse"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Agi4x44PreProcess"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Feature Extraction Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MEDME"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BCRANK"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete rHVDM"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ontology engineering" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "heatmap"@en ; rdfs:comment """A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map."""@en ; rdfs:subClassOf . swo:SWO_1100002 a rdfs:Class ; rdfs:label "ABarray" ; rdfs:comment "The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "software publishing process" ; rdfs:comment "The process of publishing software. Typically this process involves a software publisher performing acts such as licensing, marketing, publicising and/or providing support for a product." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GNU LGPL" ; rdfs:comment "The GNU Lesser General Public License (LGPL) is a free software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate LGPL software into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own software-parts. The license requires that only the LGPL software-parts be modifiable by end-users via source code availability. " ; rdfs:subClassOf , . swo:SWO_0000456 a rdfs:Class ; rdfs:label "affyPara" ; rdfs:comment "The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "MIT License" ; rdfs:comment """This is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. It is sometimes ambiguously referred to as the MIT License. For substantial programs it is better to use the Apache 2.0 license since it blocks patent treachery.""" ; rdfs:subClassOf . swo:SWO_0000276 a rdfs:Class ; rdfs:label "Multivariate correlation estimator" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GNU AGPL"@en ; rdfs:subClassOf swo:SWO_0000002 . swo:SWO_1100140 a rdfs:Class ; rdfs:label "HTSeq" ; rdfs:comment "HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "Gillespie's Stochastic Simulation Algorithm" ; rdfs:comment "Gillespie's Stochastic Simulation Algorithm is an algorithm which generates a statistically correct trajectory (possible solution) of a stochastic equation. It can be used to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. The algorithm is particularly useful for simulating reactions within cells where the number of reagents typically number in the tens of molecules (or less). Mathematically, it is a variety of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology" ; rdfs:subClassOf . swo:SWO_0000337 a rdfs:Class ; rdfs:label "Recursive Feature Elimination (RFE)" ; rdfs:comment "for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC)" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Absolute Expression Analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix Pro 6 [Axon Instruments]"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "document exchange format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CellFinder Copyright"@en ; rdfs:comment "The created contents and works provided under this license by CellFinder are subject to the German copyright law. Third-party contributions are marked as such. Reproduction, adaptation, dissemination and any kind of exploitation outside the limits of the copyright require the written consent of the author or creator. Downloads and copies of these pages are only permitted for private, non-commercial use. The operators of these pages aim to observe the copyright of others or will refer to their own or license-free works." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CARMAweb"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000355 a rdfs:Class ; rdfs:label "Rdisop" ; rdfs:comment "Decomposition of Isotopic Patterns" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000476 a rdfs:Class ; rdfs:label "arrayWoRx" ; rdfs:comment "Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "decision tree induction objective" ; rdfs:comment "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." ; rdfs:subClassOf . swo:SWO_0000071 a rdfs:Class ; rdfs:label "CRG PSICoffee Web Tool"@en ; rdfs:comment "Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software." ; rdfs:subClassOf swo:SWO_0000064 . a rdfs:Class ; rdfs:label "obsolete Rgraphviz"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "LOINC RELMA Terms of Use"@en ; rdfs:comment "LOINC RELMA Terms of Use is a vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. An unlimited number of copies of the licensed material may be used. " ; rdfs:subClassOf . swo:SWO_0000124 a rdfs:Class ; rdfs:label "Shell" ; rdfs:subClassOf . swo:SWO_0000015 a rdfs:Class ; rdfs:label "Microsoft Excel 2002" ; rdfs:subClassOf swo:SWO_9000070 . a rdfs:Class ; rdfs:label "obsolete SDF format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete siggenes"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "information content entity" ; rdfs:comment "An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete plw"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "OPML" ; rdfs:comment "OPML (Outline Processor Markup Language) is an XML format for outlines" ; rdfs:subClassOf . swo:SWO_0000126 a rdfs:Class ; rdfs:label "SQL" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete R data frame"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Global test"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'ACME'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ScISI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ALFRED Copyright"@en ; rdfs:comment "The ALFRED Copyright is a vendor-specific license which states that the resource is freely available to the scientific community for statistical analysis, the only condition being that attribution is required." ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "obsolete LMGene"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'DEDS'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000007 a rdfs:Class ; rdfs:label "OmniOutliner" ; rdfs:comment "OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000577 a rdfs:Class ; rdfs:label "hypergraph" ; rdfs:comment "A package that implements some simple capabilities for representing and manipulating hypergraphs." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GeneData Expressionist Analyst v4.0.5"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BLASTN" ; rdfs:comment "Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies." ; rdfs:subClassOf swo:SWO_1100032 . a rdfs:Class ; rdfs:label "Derivatives allowed" ; rdfs:comment "Derivatives allowed clauses are derivatives clauses which state that derivative resources are allowed using the licensed resource. Even when allowed, such a clause may or may not restrict the usage of the licensed resource in a variety of ways." ; rdfs:subClassOf swo:SWO_9000007 . a rdfs:Class ; rdfs:label "RegenBase Terms of Use"@en ; rdfs:comment "The RegenBase Terms of Use is a vendor-specific license which requires attribution and which does not meet the requirements for open source code, as there is a statement saying that the user will NOT translate, reverse engineer, decompile or disassemble the SYSTEM, or disclose the SYSTEM or any underlying information or technology to any third party." ; rdfs:subClassOf . swo:SWO_0000313 a rdfs:Class ; rdfs:label "Presence-Absence calls with Negative Probesets (PANP)" ; rdfs:subClassOf . swo:SWO_0000483 a rdfs:Class ; rdfs:label "bgx" ; rdfs:comment "Bayesian integrated analysis of Affymetrix GeneChips" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000097 a rdfs:Class ; rdfs:label "C++" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "correction" ; rdfs:comment "A correction is 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." ; rdfs:subClassOf . swo:SWO_0000576 a rdfs:Class ; rdfs:label "Hypergeometric enrichment" ; rdfs:subClassOf . swo:SWO_0000498 a rdfs:Class ; rdfs:label "cls" ; rdfs:comment "Categorical (e.g tumor vs normal) class file format" ; rdfs:subClassOf . swo:SWO_0000695 a rdfs:Class ; rdfs:label "Sim method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GLAD"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix Pro 4.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000033 a rdfs:Class ; rdfs:label "Academic use only" ; rdfs:comment "Academic use only is a usage restricted clause which restricts the use of the licensed resource to academic licensees only." ; rdfs:subClassOf swo:SWO_9000031 . swo:SWO_0000606 a rdfs:Class ; rdfs:label "maSigPro" ; rdfs:comment "maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Vertebrata " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete maSigPro"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "OmniOutline format" ; rdfs:comment "A proprietary format for documents created and edited using OmniOutliner outliner software," ; rdfs:subClassOf . swo:SWO_1100136 a rdfs:Class ; rdfs:label "AnalyzerPro" ; rdfs:comment "AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100083 a rdfs:Class ; rdfs:label "'CoCiteStats'" ; rdfs:comment "A collection of software tools for dealing with co-citation data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100007 a rdfs:Class ; rdfs:label "Average log expression across arrays (ALE)" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "First release" ; rdfs:comment "The first release of a piece of software. A first release does not imply any particular levels of maturity other than is this is the first instance of this software to be considered released." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ImmPort Conditions of Use"@en ; rdfs:comment "The ImmPort Conditions of Use is a vendor-specific license which allows the use of ImmPort data for any legal purpose except for those prohibited elsewhere in this agreement. There are very few prohibitions, and no requirement for attribution." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'CGHcall'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000254 a rdfs:Class ; rdfs:label "LMGene" ; rdfs:comment "LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000227 a rdfs:Class ; rdfs:label "Hypergeometric probability" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MicroArraySuite 5.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000618 a rdfs:Class ; rdfs:label "M-estimation regression" ; rdfs:subClassOf . swo:SWO_0000524 a rdfs:Class ; rdfs:label "Dynamic programming algorithm" ; rdfs:subClassOf . swo:SWO_0000373 a rdfs:Class ; rdfs:label "SAGx" ; rdfs:comment "A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000344 a rdfs:Class ; rdfs:label "RMAExpress 2.0" ; rdfs:subClassOf swo:SWO_0000343 . a rdfs:Class ; rdfs:label "manufacturing objective"@en ; rdfs:comment "is the objective to manufacture a material of a certain function (device)"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete F test"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete limma"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100131 a rdfs:Class ; rdfs:label "Graphpad Prism"@en ; rdfs:comment "GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers."@en ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000265 a rdfs:Class ; rdfs:label "Logic regression" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete arrayQualityMetrics"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "probability distribution specification" ; rdfs:comment "A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. This generalization is an output of a probability distribution estimation algorithm." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneticsPed"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000658 a rdfs:Class ; rdfs:label "pkgDepTools" ; rdfs:comment "This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000720 a rdfs:Class ; rdfs:label "tspair" ; rdfs:comment "Top Scoring Pairs for Microarray Classification" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000417 a rdfs:Class ; rdfs:label "ScanAlyze" ; rdfs:comment "Processes fluorescent images of microarrays" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000539 a rdfs:Class ; rdfs:label "flowFlowJo" ; rdfs:comment "FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the \"FlowJo Workspace\". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Harshlight"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:ontology a rdfs:Class ; rdfs:label "obsolete_ontology" ; rdfs:comment "Equivalence with EDAM data_0582." ; rdfs:subClassOf . swo:SWO_0000194 a rdfs:Class ; rdfs:label "GeneSpringGX" ; rdfs:subClassOf swo:SWO_0000193 . a rdfs:Class ; rdfs:label "feature extraction" ; rdfs:comment "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." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete fbat"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000019 a rdfs:Class ; rdfs:label "derivative code same license" ; rdfs:comment "Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license." ; rdfs:subClassOf swo:SWO_9000017 . a rdfs:Class ; rdfs:label "obsolete pamr"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000142 a rdfs:Class ; rdfs:label "PostgreSQL" ; rdfs:comment "PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "scatter plot"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "laboratory information management" ; rdfs:comment "Manage Laboratory information such is commonly performed by LIMS software." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'genArise'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100077 a rdfs:Class ; rdfs:label "Cosmo" ; rdfs:comment "cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture" ; rdfs:subClassOf . swo:SWO_1100088 a rdfs:Class ; rdfs:label "'DEDS'" ; rdfs:comment "This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GLEAMS software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100143 a rdfs:Class ; rdfs:label "SAMtools" ; rdfs:comment "SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete BasReader 3.01"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000179 a rdfs:Class ; rdfs:label "GenePix 4100A" ; rdfs:subClassOf swo:SWO_0000181 . a rdfs:Class ; rdfs:label "obsolete Rmagpie"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000024 a rdfs:Class ; rdfs:label "Number of installations restricted" ; rdfs:comment "A Number of installations restricted clause is a number of installations clause which restricts the number of times the resource may be installed by any given licensee." ; rdfs:subClassOf swo:SWO_9000010 . a rdfs:Class ; rdfs:label "entity"@en . swo:SWO_0000669 a rdfs:Class ; rdfs:label "puma" ; rdfs:comment "Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Cosmo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete sqlite"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000347 a rdfs:Class ; rdfs:label "RNAither" ; rdfs:comment "RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000521 a rdfs:Class ; rdfs:label "'domainsignatures'" ; rdfs:comment "Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CDF ASCII format"@en ; rdfs:comment "The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name." ; rdfs:subClassOf . swo:SWO_0000617 a rdfs:Class ; rdfs:label "mdqc" ; rdfs:comment "MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete altcdfenvs"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneR"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000217 a rdfs:Class ; rdfs:label "Hidden Markov Model" ; rdfs:subClassOf . swo:SWO_1100119 a rdfs:Class ; rdfs:label "'CGHbase'" ; rdfs:comment "Contains functions and classes that are needed by arrayCGH packages." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000052 a rdfs:Class ; rdfs:label "Clustal Omega"@en ; rdfs:comment "Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. " ; rdfs:subClassOf swo:SWO_0000051 . a rdfs:Class ; rdfs:label "regulatory role"@en ; rdfs:comment "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_FASTA" ; rdfs:comment "Equivalence with EDAM term format_1929. Please use this term instead." ; rdfs:subClassOf . swo:SWO_0000119 a rdfs:Class ; rdfs:label "REXX" ; rdfs:subClassOf . swo:SWO_1100029 a rdfs:Class ; rdfs:label "'BCRANK'" ; rdfs:comment "Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100108 a rdfs:Class ; rdfs:label "GC-RMA Quantification" ; rdfs:comment "Single-user desktop software package for analyzing microarray data from multiple microarray platforms." ; rdfs:subClassOf swo:SWO_0000034 . a rdfs:Class ; rdfs:label "obsolete Iteratively ReWeighted Least Squares"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Homo sapiens" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete iterativeBMA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "amino acid protein sequence data" ; rdfs:comment "Data which contains information about amino acid sequences of proteins." ; rdfs:subClassOf . swo:SWO_0000358 a rdfs:Class ; rdfs:label "Resourcerer" ; rdfs:comment "This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete MLInterfaces"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000730 a rdfs:Class ; rdfs:label "xps" ; rdfs:comment "Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Mozilla Public License Version 2.0" ; rdfs:comment "MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Multivariate t mixture models"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GNU GPL Compatible License Type" ; rdfs:comment "GNU GPL Compatible License Type is a GNU Project Free License Type which is also compatible with one or more versions of the GNU GPL" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "clustering algorithm" ; rdfs:comment "Clustering algorithm is a data mining algorithm that solves a clustering task and as a result produces a clustering." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Commercial use only"@en ; rdfs:comment "Commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are commercial entites." ; rdfs:subClassOf swo:SWO_9000031 . a rdfs:Class ; rdfs:label "obsolete multiscan"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete sproc"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'externalVector'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000339 a rdfs:Class ; rdfs:label "Regression model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Gene list"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Agilent Scan Control"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete AMDIS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Non-Commercial No-Fee License"@en ; rdfs:comment "Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost." ; rdfs:subClassOf swo:SWO_0000002 . swo:SWO_0000561 a rdfs:Class ; rdfs:label "globaltest" ; rdfs:comment "Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000272 a rdfs:Class ; rdfs:label "MicroArraySuite 5.0" ; rdfs:subClassOf swo:SWO_0000271 . swo:SWO_0000305 a rdfs:Class ; rdfs:label "Nested Effects Models" ; rdfs:comment "This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing" ; rdfs:subClassOf . swo:SWO_0000068 a rdfs:Class ; rdfs:label "CRG TCoffee Web Tool"@en ; rdfs:comment "Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode." ; rdfs:subClassOf swo:SWO_0000064 . a rdfs:Class ; rdfs:label "obsolete BGL"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "PNG" ; rdfs:comment "PNG is a bitmapped image format and video codec that employs lossless data compression." ; rdfs:subClassOf . swo:SWO_0000023 a rdfs:Class ; rdfs:label "Microsoft Word 2001" ; rdfs:subClassOf swo:SWO_0000025 . a rdfs:Class ; rdfs:label "PostScript" ; rdfs:comment "PostScript is a format used for describing documents." ; rdfs:subClassOf . swo:SWO_0000406 a rdfs:Class ; rdfs:label "Gene list" ; rdfs:subClassOf . swo:SWO_0000607 a rdfs:Class ; rdfs:label "maanova" ; rdfs:comment "Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ILLUMINA data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete log file"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete M-estimation regression"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ChipSkipper"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000168 a rdfs:Class ; rdfs:label "GOstats" ; rdfs:comment "A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete cosmo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'AffyExpress'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BiocCaseStudies'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000041 a rdfs:Class ; rdfs:label "'ArrayTools'" ; rdfs:comment "This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "action specification"@en ; rdfs:comment "A directive information entity that describes an action the bearer will take."@en ; rdfs:subClassOf . swo:SWO_0000327 a rdfs:Class ; rdfs:label "Probe Cell Analysis" ; rdfs:subClassOf swo:SWO_0000272 . a rdfs:Class ; rdfs:label "obsolete Digital gene expression (DGE) datasets"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000120 a rdfs:Class ; rdfs:label "Ruby" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "FASTA format" ; rdfs:subClassOf . swo:SWO_1100132 a rdfs:Class ; rdfs:label "Salmon"@en ; rdfs:comment "Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data."@en ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000108 a rdfs:Class ; rdfs:label "JavaScript" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Beadstudio"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BMP" ; rdfs:comment "The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter)." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete safe"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RpsiXML"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GEMTools 2.4"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000494 a rdfs:Class ; rdfs:label "'cellHTS'" ; rdfs:comment "Bioconductor package concerned with analysis of cell-based RNA interference screens"@en ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete makecdfenv"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ROC"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "SciCrunch Terms and Conditions"@en ; rdfs:comment "The SciCrunch Terms and Conditions specifies under what legal requirements SciCrunch data may be accessed. Broadly speaking, the site conforms, both for data and for the site documents themselves, to the CC BY 3.0 license. However, particular details for this resource (other than attribution requirements) are unclear." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete yaqcaffy"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000719 a rdfs:Class ; rdfs:label "topGO" ; rdfs:comment "topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'KLD'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000127 a rdfs:Class ; rdfs:label "Turing" ; rdfs:subClassOf . swo:SWO_0000424 a rdfs:Class ; rdfs:label "Silicon Genetics Genespring" ; rdfs:comment "The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000532 a rdfs:Class ; rdfs:label "factDesign" ; rdfs:comment "This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "material supplier" ; rdfs:comment "A person or organization that provides material supplies to other people or organizations." ; rdfs:subClassOf . swo:SWO_0000261 a rdfs:Class ; rdfs:label "Langmuir Isotherm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Cyber-T"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000647 a rdfs:Class ; rdfs:label "parody" ; rdfs:comment "Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000602 a rdfs:Class ; rdfs:label "Logit-t algorithm" ; rdfs:subClassOf . swo:SWO_0000316 a rdfs:Class ; rdfs:label "PCpheno" ; rdfs:comment "Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000687 a rdfs:Class ; rdfs:label ".rma format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "independent continuant"@en ; rdfs:comment "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Multivariate correlation estimator"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY 3.0 AU"@en ; rdfs:comment "CC BY 3.0 AU is an Australia-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000708 a rdfs:Class ; rdfs:label "sproc" ; rdfs:subClassOf . swo:SWO_0000034 a rdfs:Class ; rdfs:label "Agilent Technologies Software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Spotfire"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000589 a rdfs:Class ; rdfs:label "k-nearest neighbour classification" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Not Free" ; rdfs:comment "Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "process"@en ; rdfs:comment "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en ; rdfs:subClassOf . swo:SWO_1100066 a rdfs:Class ; rdfs:label "ChipSkipper V0.99" ; rdfs:subClassOf swo:SWO_1100065 . swo:SWO_0000153 a rdfs:Class ; rdfs:label "VCell"@en ; rdfs:comment "VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete gcrma"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Opisthokonta" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "cross validation objective"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GOSemSim"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data selection algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Non-linear functional regression model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100126 a rdfs:Class ; rdfs:label "GEO Matrix Series format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete data visualization"@en ; rdfs:comment "AL 25.9.19: Redundant with http://purl.obolibrary.org/obo/OBI_0200111"@en ; rdfs:subClassOf . swo:SWO_0000283 a rdfs:Class ; rdfs:label "MLInterfaces" ; rdfs:comment "Uniform interfaces to machine learning code for data in Bioconductor containers" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100056 a rdfs:Class ; rdfs:label "CMA" ; rdfs:comment "CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting)" ; rdfs:subClassOf . swo:SWO_1100115 a rdfs:Class ; rdfs:label "matlab software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "CC BY-SA 2.0" ; rdfs:comment "CC BY-SA 2.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Mahalanobis distance"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Scanning software G2565AA version A6.3.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete tspair"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "word processing document format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Permission required for commercial use"@en ; rdfs:comment "Permission required for commercial use is a clause which restricts the use of the licensed resource only to licensees who are commercial entites which have received explicit permission in the manner stipulated by the resource." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Xba.CQV and Xba.regions"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'FDR'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100033 a rdfs:Class ; rdfs:label "Iterative Bayesian Model Averaging (BMA)" ; rdfs:subClassOf . swo:SWO_1100103 a rdfs:Class ; rdfs:label "Fixed effect model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "class prediction" ; rdfs:comment "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete gpr format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000509 a rdfs:Class ; rdfs:label "database creation" ; rdfs:comment "An objective in which the aim is to create a new database instance." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneRfold"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'beadarray'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000020 a rdfs:Class ; rdfs:label "Source code available" ; rdfs:comment "A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000008 . swo:SWO_0000665 a rdfs:Class ; rdfs:label "ppiStats" ; rdfs:comment "Tools for the analysis of protein interaction data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100110 a rdfs:Class ; rdfs:label "GEO data type" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Mixed model equations"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000208 a rdfs:Class ; rdfs:label "GraphAT" ; rdfs:comment "Functions and data used in Balasubramanian, et al. (2004)" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100044 a rdfs:Class ; rdfs:label "'BioMVCClass'" ; rdfs:comment "Creates classes used in model-view-controller (MVC) design that uses Biobase"@en ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000175 a rdfs:Class ; rdfs:label "GeneData Expressionist Analyst v4.0.5" ; rdfs:comment "Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000672 a rdfs:Class ; rdfs:label "qpgraph" ; rdfs:comment "Reverse engineering of molecular regulatory networks with qp-graphs" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "data transformation objective"@en ; rdfs:comment "An objective specification to transformation input data into output data"@en ; rdfs:subClassOf . swo:SWO_0000625 a rdfs:Class ; rdfs:label "minet" ; rdfs:comment "This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000056 a rdfs:Class ; rdfs:label "ClustalW 2.1"@en ; rdfs:subClassOf swo:SWO_0000053 . swo:SWO_0000676 a rdfs:Class ; rdfs:label "qvalue" ; rdfs:comment "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000613 a rdfs:Class ; rdfs:label "marray" ; rdfs:comment "Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete_Modified BSD License"@en ; rdfs:comment """This is the original BSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete HilbertVis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000636 a rdfs:Class ; rdfs:label "nudge" ; rdfs:comment "Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "data visualization algorithm" ; rdfs:subClassOf . swo:SWO_0000572 a rdfs:Class ; rdfs:label "hexbin" ; rdfs:comment "Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "miRTaBase Data License"@en ; rdfs:comment "miRTaBase Data License is a simple vendor license which allows academic users to make use of the data for free." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete logitT"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000453 a rdfs:Class ; rdfs:label "affyContam" ; rdfs:comment "affyContam is software which provides the in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics. In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "categorical value specification" ; rdfs:comment "A value specification that is specifies one category out of a fixed number of nominal categories" ; rdfs:subClassOf . swo:SWO_0000309 a rdfs:Class ; rdfs:label "OLINgui" ; rdfs:comment "Graphical user interface for the OLIN package" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Power Law Global Error Model (PLGEM) analysis method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Design Science License"@en ; rdfs:comment "The Design Science License is a license intended to be a general \"copyleft\" that can be applied to any kind of work that has protection under copyright. This license states those certain conditions under which a work published under its terms may be copied, distributed, and modified. Unlike other open source licenses, the DSL was intended to be used on any type of copyrightable work, including documentation and source code. It was the first \"generalized copyleft\" license. This is a free and copyleft license meant for general data. THe GNU Project does not recommend it for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL; however, they consider it appropriate for other kinds of data. The DSL was written by Michael Stutz. The DSL came out in the 1990s, before the formation of the Creative Commons. According to Wikipedia, once the Creative Commons arrived, Stutz considered the DSL experiment \"over\" and no longer recommended its use." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Statistical tests"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100061 a rdfs:Class ; rdfs:label "Category analysis" ; rdfs:subClassOf . swo:SWO_0000146 a rdfs:Class ; rdfs:label "Python 2.6"@en ; rdfs:comment "Version 2.6 of the Python programming language." ; rdfs:subClassOf swo:SWO_0000118 . a rdfs:Class ; rdfs:label "obsolete qpgraph"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000292 a rdfs:Class ; rdfs:label "MeasurementError.cor" ; rdfs:comment "Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000079 a rdfs:Class ; rdfs:label "Cytoscape"@en ; rdfs:comment "Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000105 a rdfs:Class ; rdfs:label "Fortran" ; rdfs:subClassOf . swo:SWO_0000510 a rdfs:Class ; rdfs:label "crlmm" ; rdfs:comment "Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete hypergraph"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000442 a rdfs:Class ; rdfs:label "VanillaICE" ; rdfs:comment "Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GenePix 3.0.6"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "probability distribution estimation task" ; rdfs:comment """Estimating the (Joint) Probability Distribution. A set of data (of type T) is often assumed to be a sample taken from a population according to a probability distribution. A probability distribution/density function assigns a non-negative probability/density to each object of type T. Probably the most general data mining task (Hand et al. 2001) is the task of estimating the (joint) probability distribution D over type T from a set of data items or a sample drawn from that distribution. As mentioned above, in the most typical case we would have T = Tuple(T1, . . ., Tk), where each of T1, . . ., Tk is Boolean, Discrete(S) or Real. We talk about the joint probability distribution to emphasize the difference to the marginal distributions of each of the variables of type T1, . . ., Tk: the joint distribution captures the interactions among the variables. Representing multi-variate distributions is a non-trivial task. Two approaches are commonly used in data mining. In the density-based clustering paradigm, mixtures of multi-variate Gaussian distributions are typically considered (Hand et al. 2001). Probabilistic graphical models, most notably Bayesian networks, represent graphically the (in)dependencies between the variables: Learning their structure and parameters is an important approach to the problem of estimating the joint probability distribution.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PLPE"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000550 a rdfs:Class ; rdfs:label "gene2pathway" ; rdfs:comment "The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100067 a rdfs:Class ; rdfs:label "multiscan" ; rdfs:comment "A multiscan is an R package for combining multiple scans" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'dualKS'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000384 a rdfs:Class ; rdfs:label "SLqPCR" ; rdfs:comment "Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'ArrayTools'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000030 a rdfs:Class ; rdfs:label "software with command line interface" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Expectation-Maximization(EM) algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "UCUM Terms of Use"@en ; rdfs:comment "The UCUM Terms of Use is a vendor-specific license which allows the resource it references to be used for commercial or non-commercial purposes without restriction of any kind, provided that appropriate attribution is given. However, the resource itself may not be modified in any way. Users may make and distribute an unlimited number of copies of the Licensed Materials. Each copy thereof must include the Copyright Notice and License." ; rdfs:subClassOf . swo:SWO_1100121 a rdfs:Class ; rdfs:label "'CGHregions'" ; rdfs:comment "Dimension Reduction for Array CGH Data with Minimal Information Loss" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "data mining task" ; rdfs:comment "A data mining task is an objective specification that specifies the objective that a data mining algorithm needs to achieve when executed on a dataset to produce as output a generalization." ; rdfs:subClassOf . swo:SWO_0000595 a rdfs:Class ; rdfs:label "Linear modelling" ; rdfs:subClassOf . swo:SWO_1100020 a rdfs:Class ; rdfs:label "Affymetrix GCOS v1.2" ; rdfs:subClassOf swo:SWO_1100021 . swo:SWO_0000045 a rdfs:Class ; rdfs:label "Array_vision_(Interfocus)" ; rdfs:subClassOf swo:SWO_0000042 . a rdfs:Class ; rdfs:label "obsolete 'Smith-Waterman'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000164 a rdfs:Class ; rdfs:label "GLAD" ; rdfs:comment "Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'betr'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BLAST"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000239 a rdfs:Class ; rdfs:label "Imagene v4.0" ; rdfs:subClassOf swo:SWO_0000238 . swo:SWO_0000584 a rdfs:Class ; rdfs:label "Iterative local regression and model selection" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MassSpecWavelet"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000281 a rdfs:Class ; rdfs:label "'MI'" ; rdfs:subClassOf . swo:SWO_1100137 a rdfs:Class ; rdfs:label "SWATH Software" ; rdfs:comment "SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "GNU LGPL v2.1"@en ; rdfs:comment "This is the previous version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv2 and GPLv3. We generally recommend the latest version of the LGPL, for special circumstances only." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete Laplace mixture model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ppiStats"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pgUtils"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000294 a rdfs:Class ; rdfs:label "Mfuzz" ; rdfs:comment "Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000420 a rdfs:Class ; rdfs:label "scanning software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete genefilter"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000184 a rdfs:Class ; rdfs:label "GenePix Pro 5.0" ; rdfs:subClassOf swo:SWO_0000182 . a rdfs:Class ; rdfs:label "obsolete SAGx"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GEOquery"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "plan specification"@en ; rdfs:comment "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "MPL" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete HEM"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Superseded" ; rdfs:comment "An updated version of the software is available." ; rdfs:subClassOf . swo:SWO_0000713 a rdfs:Class ; rdfs:label "Statistical tests" ; rdfs:comment "A statistical test is an algorithm for making quantitative decisions to determine which outcomes of a study would lead to a rejection of the null hypothesis for a pre-specified level of significance." ; rdfs:subClassOf . swo:SWO_0000334 a rdfs:Class ; rdfs:label "R interface to boost graph library algorithm (RBGL)" ; rdfs:subClassOf . swo:SWO_1100055 a rdfs:Class ; rdfs:label "'CMA'" ; rdfs:comment "This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete gene expression analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GEO Matrix Series format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000195 a rdfs:Class ; rdfs:label "GeneTac Analyser" ; rdfs:comment "Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "Gene expression data" ; rdfs:comment "Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC-ND 4.0"@en ; rdfs:comment "CC BY-NC-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " ; rdfs:subClassOf , . swo:SWO_1100018 a rdfs:Class ; rdfs:label "'AffyCompatible'" ; rdfs:comment "The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000369 a rdfs:Class ; rdfs:label "Rtreemix" ; rdfs:comment "Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete snpMatrix"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000680 a rdfs:Class ; rdfs:label "Rank-invariant set normalization" ; rdfs:subClassOf . swo:SWO_0000323 a rdfs:Class ; rdfs:label "Propagation of uncertainty in microarray analysis" ; rdfs:comment "Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_text file format" ; rdfs:comment "Equivalence with EDAM http://edamontology.org/format_2330, please use that class instead." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-ND 3.0"@en ; rdfs:comment "CC BY-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Interaction data"@en ; rdfs:comment "A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input." ; rdfs:subClassOf . swo:SWO_0000139 a rdfs:Class ; rdfs:label "web content search" ; rdfs:comment "Web content search is the searching for information on the World Wide Web." ; rdfs:subClassOf . swo:SWO_0000661 a rdfs:Class ; rdfs:label "Graph plot" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hexagon binning algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000518 a rdfs:Class ; rdfs:label "dcf" ; rdfs:subClassOf . swo:SWO_0000712 a rdfs:Class ; rdfs:label "stam" ; rdfs:comment "The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'cellHTS2'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000049 a rdfs:Class ; rdfs:label "Binning clustering method" ; rdfs:comment """binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory eciency by avoiding the calculation of an all-against-all distance matrix.""" ; rdfs:subClassOf . swo:SWO_0000058 a rdfs:Class ; rdfs:label "EBI Clustal W2 Web Tool"@en ; rdfs:subClassOf swo:SWO_0000051 . a rdfs:Class ; rdfs:label "obsolete_MAGE-ML" ; rdfs:comment "Equivalence with EDAM format_3161." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "document outlining" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "pattern discovery task" ; rdfs:comment """the task of pattern discovery is to find all local patterns from a given pattern language that satisfy the required conditions. A prototypical instantiation of this task is the task of finding frequent itemsets (sets of items, such as {bread, butter}), which are often found together in a transaction (e.g., a market basket) (Aggrawal et al 1993). The condition that a pattern (itemset) has to satisfy in this case is to appear in (hold true for) a sufficiently high proportion (called support and denoted by s) of the transactions in the input dataset. With the increasing interest in mining complex data, mining frequent patterns is also considered for structured data. We can thus talk about mining frequent subsequences or mining frequent subgraphs in sequence or graph data. We can consider as frequency the multiple occurrences of a pattern in a single data structure (e.g., sequence or graph) or the single occurrences of a pattern in multiple data structures.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affxparser"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000101 a rdfs:Class ; rdfs:label "Delphi" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "planned process"@en ; rdfs:comment "A process that realizes a plan which is the concretization of a plan specification."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete vbmp"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "desktop graphical user interface"@en ; rdfs:comment "A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete crlmm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100062 a rdfs:Class ; rdfs:label "Category" ; rdfs:comment "A collection of tools for performing category analysis." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ITALICS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000308 a rdfs:Class ; rdfs:label "OLIN" ; rdfs:comment "Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Category analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete lma"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Proprietary commercial software license" ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "obsolete qpcrNorm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000220 a rdfs:Class ; rdfs:label "HaarSeg algorithm" ; rdfs:subClassOf . swo:SWO_0000581 a rdfs:Class ; rdfs:label "impute" ; rdfs:comment "Imputation for microarray data (currently KNN only)" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Signaling Pathway Impact Analysis (SPIA) algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ODE Algorithm"@en ; rdfs:comment "In mathematics, an ordinary differential equation or ODE is an equation containing a function of one independent variable and its derivatives. The term \"ordinary\" is used in contrast with the term partial differential equation which may be with respect to more than one independent variable." ; rdfs:subClassOf . swo:SWO_0000112 a rdfs:Class ; rdfs:label "Maple" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "directive information entity"@en ; rdfs:comment "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en ; rdfs:subClassOf . swo:SWO_0000235 a rdfs:Class ; rdfs:label "ImaGene 3.0" ; rdfs:subClassOf swo:SWO_0000238 . a rdfs:Class ; rdfs:label "Knowledge representation"@en ; rdfs:comment "A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Nonlinear Estimation by Iterative Partial Least Squares"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "continuant"@en ; rdfs:comment "An 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."@en ; rdfs:subClassOf . swo:SWO_0000592 a rdfs:Class ; rdfs:label "Likelihood method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Bitmap object"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ASCII format" ; rdfs:subClassOf . swo:SWO_0000600 a rdfs:Class ; rdfs:label "logicFS dataset" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete flowCore"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CodeLink Expression Scanning Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "manage computer operations" ; rdfs:comment "the objective of performing the actions of an operation system such as managing the software running a computer and the interactions with the system resources and hardware." ; rdfs:subClassOf . swo:SWO_1100025 a rdfs:Class ; rdfs:label "Agilent Feature Extraction software version 7.1" ; rdfs:subClassOf swo:SWO_1100104 . a rdfs:Class ; rdfs:label "Free" ; rdfs:comment "Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".csv"@en ; rdfs:subClassOf . swo:SWO_1100036 a rdfs:Class ; rdfs:label "BRB-ArrayTools" ; rdfs:comment "BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000182 a rdfs:Class ; rdfs:label "GenePix Pro" ; rdfs:subClassOf swo:SWO_0000176 . a rdfs:Class ; rdfs:label "processed specimen" ; rdfs:comment "A specimen that has been intentionally physically modified." ; rdfs:subClassOf , . swo:SWO_0000620 a rdfs:Class ; rdfs:label "Meta data" ; rdfs:subClassOf . swo:SWO_0000055 a rdfs:Class ; rdfs:label "Clustal Omega 1.1"@en ; rdfs:subClassOf swo:SWO_0000052 . a rdfs:Class ; rdfs:label "obsolete GenePix Pro"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000503 a rdfs:Class ; rdfs:label "Concordance" ; rdfs:subClassOf . swo:SWO_0000677 a rdfs:Class ; rdfs:label "rHVDM" ; rdfs:comment "Hidden Variable Dynamic Modeling" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete miRNApath"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000092 a rdfs:Class ; rdfs:label "Ada" ; rdfs:subClassOf . swo:SWO_0000446 a rdfs:Class ; rdfs:label "XDE" ; rdfs:comment "XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "support vector machine" ; rdfs:comment "A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space." ; rdfs:subClassOf . swo:SWO_0000637 a rdfs:Class ; rdfs:label "occugene" ; rdfs:comment "Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete MMD"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PROcess"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100006 a rdfs:Class ; rdfs:label "AIDA" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete R software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete gxl format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Similarity score"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Gamma-Gamma hierarchical model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000207 a rdfs:Class ; rdfs:label "GOSemSim" ; rdfs:comment "Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000178 a rdfs:Class ; rdfs:label "GenePix 4.1" ; rdfs:subClassOf swo:SWO_0000176 . a rdfs:Class ; rdfs:label "genomedata format"@en ; rdfs:comment "Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Latest release" ; rdfs:comment "The latest release of a piece of software. This does not imply any levels of maturity other than indicating this is the most recent release." ; rdfs:subClassOf . swo:SWO_0000130 a rdfs:Class ; rdfs:label "Visual Basic" ; rdfs:subClassOf . swo:SWO_0000257 a rdfs:Class ; rdfs:label "Lognormal Normal with Modied Variance Model" ; rdfs:subClassOf . swo:SWO_0000319 a rdfs:Class ; rdfs:label "PLPE" ; rdfs:comment "This package performs tests for paired high-throughput data." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GSEAlm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000008 a rdfs:Class ; rdfs:label "Source code clause" ; rdfs:comment "A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000005 . swo:SWO_1100122 a rdfs:Class ; rdfs:label "CHP binary format" ; rdfs:comment "CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications." ; rdfs:subClassOf . swo:SWO_9000050 a rdfs:Class ; rdfs:label "software interface" ; rdfs:comment "The mode of interaction with a piece of software." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "SBML" ; rdfs:comment "Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time." ; rdfs:subClassOf . swo:SWO_0000398 a rdfs:Class ; rdfs:label "50-50 MANOVA algorithm" ; rdfs:comment "Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GOstats"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Agilent Feature Extraction Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000016 a rdfs:Class ; rdfs:label "MATLAB 7" ; rdfs:subClassOf swo:SWO_0000005 . a rdfs:Class ; rdfs:label "obsolete CBS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GridGrinder"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'domainsignatures'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000590 a rdfs:Class ; rdfs:label "keggorth" ; rdfs:comment "Test package for a pathway 'ontology'" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000343 a rdfs:Class ; rdfs:label "RMAExpress" ; rdfs:comment "RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000655 a rdfs:Class ; rdfs:label "pedigree data file" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "kinase activity" ; rdfs:comment "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." ; rdfs:subClassOf . swo:SWO_0000553 a rdfs:Class ; rdfs:label "gene expression analysis" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete .raw files"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "algorithm" ; rdfs:comment "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." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-SA 4.0"@en ; rdfs:comment "CC BY-SA 4.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete matlab software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100051 a rdfs:Class ; rdfs:label "'BufferedMatrixMethods'" ; rdfs:comment "This package involves microarray Data related methods that utlize BufferedMatrix objects" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "pdf" ; rdfs:comment "PDF is an open standard for document exchange. " ; rdfs:subClassOf . swo:SWO_0000008 a rdfs:Class ; rdfs:label "Racket" ; rdfs:comment "Racket is a Scheme-based language interpreter and programming environment" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Agilent Feature Extraction software version 7.5"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hardy-Weinberg equilibrium"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000193 a rdfs:Class ; rdfs:label "GeneSpring" ; rdfs:comment "Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects" ; rdfs:subClassOf swo:SWO_0000034 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete SVDimpute algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'ChemmineR'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Open Data Commons"@en ; rdfs:subClassOf swo:SWO_0000002 . swo:SWO_0000473 a rdfs:Class ; rdfs:label "arrayQuality" ; rdfs:comment "This package functions for performing print-run and array level quality assessment." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "annotation editing" ; rdfs:subClassOf . swo:SWO_9000005 a rdfs:Class ; rdfs:label "clause" ; rdfs:comment "A licence clause is a component of a licence which defines some aspect of a restriction or conversely permission in how something corresponding to a licence may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Matlab .m file" ; rdfs:subClassOf . swo:SWO_0000350 a rdfs:Class ; rdfs:label "RankProd" ; rdfs:comment "Rank Product method for identifying differentially expressed genes with application in meta-analysis" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_9000023 a rdfs:Class ; rdfs:label "Platform unrestricted" ; rdfs:comment "Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for." ; rdfs:subClassOf swo:SWO_9000009 . swo:SWO_0000269 a rdfs:Class ; rdfs:label "MANOR" ; rdfs:comment "We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "GNU GPL v3"@en ; rdfs:comment "The GNU GPL v3 is the latest version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination." ; rdfs:subClassOf . swo:SWO_0000631 a rdfs:Class ; rdfs:label "Negative binomial distribution" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete topGO"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000123 a rdfs:Class ; rdfs:label "Scheme" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete AWS algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000671 a rdfs:Class ; rdfs:label "qpcrNorm" ; rdfs:comment "The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Distribution clause" ; rdfs:comment "Distribution clauses are license clauses which state the requirements on how the licensed resource is redistributed. The license for a resource may or may not allow the redistribution of that resource. If it is allowed, such usage may be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "obsolete SPIA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000246 a rdfs:Class ; rdfs:label "KCsmart" ; rdfs:comment "Multi sample aCGH analysis package using kernel convolution" ; rdfs:subClassOf swo:SWO_0000026 , swo:SWO_1100075 . swo:SWO_0000514 a rdfs:Class ; rdfs:label "daMA" ; rdfs:comment "This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'CGHregions'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneSpringGX"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100038 a rdfs:Class ; rdfs:label "BZScan" ; rdfs:comment "BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic \"batch mode\" or at different levels of manual operation." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete goTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000605 a rdfs:Class ; rdfs:label "maDB" ; rdfs:comment "maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "EPL v1" ; rdfs:comment "The Eclipse Public License is similar to the Common Public License. This is a free software license. Unfortunately, its weak copyleft and choice of law clause make it incompatible with the GNU GPL. The only change is that the EPL removes the broader patent retaliation language regarding patent infringement suits specifically against Contributors to the EPL'd program." ; rdfs:subClassOf . swo:SWO_0000622 a rdfs:Class ; rdfs:label "miRNApath" ; rdfs:comment "This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100047 a rdfs:Class ; rdfs:label "BioConductor Software" ; rdfs:comment "Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete rtracklayer"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100130 a rdfs:Class ; rdfs:label "Seurat"@en ; rdfs:comment "Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data."@en ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete KEGGgraph"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000484 a rdfs:Class ; rdfs:label "Bitmap object" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Variance-stabilizing transformation (VST) algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete maanova"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RWebServices"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000228 a rdfs:Class ; rdfs:label "ICS-501 (version 2.3) Image Capture System" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000644 a rdfs:Class ; rdfs:label "pair file" ; rdfs:subClassOf . swo:SWO_1100129 a rdfs:Class ; rdfs:label "shinyNGS"@en ; rdfs:comment "Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools."@en ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100084 a rdfs:Class ; rdfs:label "CodeLink Expression Analysis Software" ; rdfs:comment "This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000694 a rdfs:Class ; rdfs:label "siggenes" ; rdfs:comment "Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM)." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000312 a rdfs:Class ; rdfs:label "OutlierD" ; rdfs:comment "This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_9000027 a rdfs:Class ; rdfs:label "Number of users unrestricted" ; rdfs:comment "A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource." ; rdfs:subClassOf swo:SWO_9000011 . swo:SWO_0000575 a rdfs:Class ; rdfs:label "HTML report" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "organism"@en ; rdfs:comment "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 ; rdfs:subClassOf . swo:SWO_0000014 a rdfs:Class ; rdfs:label "Microsoft Excel 2003" ; rdfs:comment "Microsoft Excel 2003 is a spreadsheet editing and viewing tool." ; rdfs:subClassOf swo:SWO_1100127 , swo:SWO_9000070 . swo:SWO_0000224 a rdfs:Class ; rdfs:label "Heatplus" ; rdfs:comment "Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000372 a rdfs:Class ; rdfs:label "Serial Analysis of Gene Expression (SAGE)" ; rdfs:subClassOf . swo:SWO_0000156 a rdfs:Class ; rdfs:label "COBRA Toolbox"@en ; rdfs:comment "COBRA Toolbox is the version of the COBRA software for Matlab." ; rdfs:subClassOf swo:SWO_0000154 . swo:SWO_0000065 a rdfs:Class ; rdfs:label "CRG TCoffee"@en ; rdfs:comment "TCoffee is a multiple sequence alignment program with a number of different modes. " ; rdfs:subClassOf swo:SWO_0000064 . a rdfs:Class ; rdfs:label "obsolete Rosetta Resolver"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GNU LGPL v3" ; rdfs:comment """This is the latest version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv3. It is therefore recommend for special circumstances only. Please note that LGPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination.""" ; rdfs:subClassOf , . swo:SWO_0000459 a rdfs:Class ; rdfs:label "'affycoretools'" ; rdfs:comment "Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete gcRMA quantification"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100017 a rdfs:Class ; rdfs:label "Absolute Expression Analysis" ; rdfs:subClassOf swo:SWO_0000272 . swo:SWO_0000145 a rdfs:Class ; rdfs:label "Segway 1.2"@en ; rdfs:comment "The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100069 a rdfs:Class ; rdfs:label "affycomp" ; rdfs:comment "The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000709 a rdfs:Class ; rdfs:label "sqlite" ; rdfs:subClassOf . swo:SWO_9000012 a rdfs:Class ; rdfs:label "Time clause" ; rdfs:comment "A time clause is a license clause which states the restrictions placed on the length of time the licensed resource may be used, if any. The license for a resource may or may not allow access to the resource for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "obsolete 'explorase'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Likelihood method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Spotfinder [TIGR]"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000072 a rdfs:Class ; rdfs:label "Microsoft Windows" ; rdfs:comment "The Windows Operating System" ; rdfs:subClassOf swo:SWO_0000021 , swo:SWO_0000029 . a rdfs:Class ; rdfs:label "obsolete 'biocViews'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000723 a rdfs:Class ; rdfs:label "vbmp" ; rdfs:comment "Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000076 a rdfs:Class ; rdfs:label "SPSS 20.0"@en ; rdfs:subClassOf swo:SWO_0000075 . swo:SWO_0000046 a rdf:Property ; rdfs:label "has download location"@en ; rdfs:comment "The location from where the software can be downloaded." ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004006 . a rdfs:Class ; rdfs:label "dot plot"@en ; rdfs:comment "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 ; rdfs:subClassOf . swo:SWO_0000564 a rdfs:Class ; rdfs:label "goTools" ; rdfs:comment "Wraper functions for description/comparison of oligo ID list using Gene Ontology database" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label ".zip"@en ; rdfs:subClassOf . swo:SWO_0000547 a rdfs:Class ; rdfs:label "gcrma" ; rdfs:comment "Background adjustment using sequence information" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'DFP'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete OrderedList"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000466 a rdfs:Class ; rdfs:label "'annotate'" ; rdfs:comment "Using R enviroments for annotation." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "GNU Project Free License Type" ; rdfs:comment """A licensed is a free license according to GNU if the users have the four essential freedoms: The freedom to run the program, for any purpose (freedom 0). The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. The freedom to redistribute copies so you can help your neighbor (freedom 2). The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. “Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies. """ ; rdfs:subClassOf , swo:SWO_0000002 . swo:SWO_0000616 a rdfs:Class ; rdfs:label "matchprobes" ; rdfs:comment "Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "image"@en ; rdfs:comment "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 ; rdfs:subClassOf . swo:SWO_1100118 a rdfs:Class ; rdfs:label "CBS algorithm" ; rdfs:subClassOf . swo:SWO_1100073 a rdfs:Class ; rdfs:label "Annotation-Driven Clustering" ; rdfs:comment "adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GGBase"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Empirical Bayes rule"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'edgeR'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Logic regression"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "manufacturer role" ; rdfs:comment "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process." ; rdfs:subClassOf . swo:SWO_0000633 a rdfs:Class ; rdfs:label "Neural networks models" ; rdfs:subClassOf . swo:SWO_0000499 a rdfs:Class ; rdfs:label "'clusterStab'" ; rdfs:comment "This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100049 a rdfs:Class ; rdfs:label "BlueFuse" ; rdfs:comment "BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100014 a rdfs:Class ; rdfs:label "ARR" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC 3.0"@en ; rdfs:comment """CC BY-NC 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete 'bridge'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000529 a rdfs:Class ; rdfs:label "'explorase'" ; rdfs:comment "This package explores and analyzes *omics data with R and GGobi" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000361 a rdfs:Class ; rdfs:label "Rintact" ; rdfs:comment "Queries and data structures for protein interactions" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete LPEadj"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "regulator role"@en ; rdfs:comment "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BicARE'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "RDF-XML" ; rdfs:comment "A serialisation of RDF into an XML format." ; rdfs:subClassOf , . swo:SWO_0000435 a rdfs:Class ; rdfs:label "TargetSearch" ; rdfs:comment "This packages provides a targeted pre-processing method for GC-MS data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete rMAT"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete LC-MS data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "XML" ; rdfs:comment "Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete HTML report"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000016 a rdfs:Class ; rdfs:label "No restrictions on derivatives" ; rdfs:comment "No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created." ; rdfs:subClassOf . swo:SWO_0000098 a rdfs:Class ; rdfs:label "COBOL" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete .data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000542 a rdfs:Class ; rdfs:label "flowUtils" ; rdfs:comment "This package provides utilities for flow cytometry data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000387 a rdfs:Class ; rdfs:label "SNPchip" ; rdfs:comment "This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ArrayVision 6.0 (Imaging Research Inc.)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000134 a rdfs:Class ; rdfs:label "MLXTRAN"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Modified BSD" ; rdfs:comment """The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery.""" ; rdfs:subClassOf . swo:SWO_0000569 a rdfs:Class ; rdfs:label "gtr" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneticsBase"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000253 a rdfs:Class ; rdfs:label "LC-MS data" ; rdfs:subClassOf . swo:SWO_1100058 a rdfs:Class ; rdfs:label "CRLMM algorithm" ; rdfs:comment "This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data visualization"@en ; rdfs:comment "An planned process that creates images, diagrams or animations from the input data."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Chi-square"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RBGL"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000050 a rdfs:Class ; rdfs:label "Ensembl"@en ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Heterogeneous Error Model (HEM)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000488 a rdfs:Class ; rdfs:label "'biocViews'" ; rdfs:comment "Categorized views of R package repositories" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000027 a rdfs:Class ; rdfs:label "OBO-Edit" ; rdfs:comment "OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities." ; rdfs:subClassOf swo:SWO_0000028 . a rdfs:Class ; rdfs:label "Development status" ; rdfs:comment "Development status is an information content entity which indicates the maturity of a software entity within the context of the software life cycle." ; rdfs:subClassOf . swo:SWO_1100003 a rdfs:Class ; rdfs:label "'ACME'" ; rdfs:comment "The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe." ; rdfs:subClassOf . swo:SWO_1100141 a rdfs:Class ; rdfs:label "RNA-SeQC" ; rdfs:comment "RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete arrayQuality"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "quality"@en ; rdfs:subClassOf . swo:SWO_0000683 a rdfs:Class ; rdfs:label "rbsurv" ; rdfs:comment "This package selects genes associated with survival." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000336 a rdfs:Class ; rdfs:label "Random effects model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MAGE-TAB inputting software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000507 a rdfs:Class ; rdfs:label "cosmoGUI" ; rdfs:comment "cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CC BY 2.0"@en ; rdfs:comment "CC BY 2.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete k-means"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100095 a rdfs:Class ; rdfs:label "'EBarrays'" ; rdfs:comment "EBarrays provides tools for the analysis of replicated/unreplicated microarray data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000004 a rdfs:Class ; rdfs:label "Microsoft Excel 2007" ; rdfs:comment "Microsoft Excel 2007 is a spreadsheet editing and viewing tool." ; rdfs:subClassOf swo:SWO_9000070 . swo:SWO_0000132 a rdf:Property ; rdfs:label "directly followed by"@en ; rdfs:comment "'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s." ; rdfs:range ; rdfs:subPropertyOf swo:SWO_0000300 . a rdf:Property ; rdfs:label "has release date" ; rdfs:comment "The official date of release of software" ; rdfs:range xsd:string . swo:SWO_0000477 a rdfs:Class ; rdfs:label "Associative T method" ; rdfs:subClassOf . swo:SWO_0000659 a rdfs:Class ; rdfs:label "plgem" ; rdfs:comment "PLGEM is useful for detecting differential expression in microarray and proteomics datasets." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete ImageReader"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000070 a rdfs:Class ; rdfs:label "CRG Expresso Web Tool"@en ; rdfs:comment "Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software." ; rdfs:subClassOf swo:SWO_0000064 . a rdfs:Class ; rdfs:label "obsolete RMAExpress 2.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete flowQ"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete R language"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete sigPathway"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CTD Legal Notice and Terms of Data Use"@en ; rdfs:comment "The CTD Legal Notice and Terms of Data Use specifies under what legal requirements the CTD data may be accessed. Data is available for use for non-commercial purposes as long as the data is properly attributed, but users must get express written consent of CTD to exploit the data for commercial purposes. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). Additionally,You must notify CTD and describe your use of their data. For quality control purposes, you must provide CTD with periodic access to your publication of their data." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'AffyCompatible'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MiPP"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000578 a rdfs:Class ; rdfs:label "Icens" ; rdfs:comment "Many functions for computing the NPMLE for censored and truncated data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000270 a rdfs:Class ; rdfs:label "MAQC data" ; rdfs:subClassOf . swo:SWO_0000558 a rdfs:Class ; rdfs:label "genomeIntervals" ; rdfs:comment "Tools for operation on genomic intervals." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Iterative Bayesian Model Averaging (BMA)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000200 a rdfs:Class ; rdfs:label "GenePix Pro 3.0" ; rdfs:subClassOf swo:SWO_0000182 . a rdfs:Class ; rdfs:label "obsolete rama"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000116 a rdfs:Class ; rdfs:label "PHP" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Binning clustering method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'Biostrings'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100090 a rdfs:Class ; rdfs:label "Discriminant Fuzzy Pattern Algorithm" ; rdfs:comment "A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High'" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BufferedMatrix'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Obsolete Class" . swo:SWO_1100065 a rdfs:Class ; rdfs:label "ChipSkipper" ; rdfs:comment "ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000326 a rdfs:Class ; rdfs:label "Power Law Global Error Model (PLGEM) analysis method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix 4.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ScanArray v3.1 software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100076 a rdfs:Class ; rdfs:label "BCRANK" ; rdfs:comment "BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Rdisop"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete impute"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "beta" ; rdfs:comment "Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers. " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Tetrapoda" ; rdfs:subClassOf . swo:SWO_0000141 a rdfs:Class ; rdfs:label "Weka" ; rdfs:comment "Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete_Heatmap" ; rdfs:comment "Equivalence with EDAM data_1636." ; rdfs:subClassOf . swo:SWO_0000648 a rdfs:Class ; rdfs:label "parse" ; rdfs:subClassOf . swo:SWO_0000601 a rdfs:Class ; rdfs:label "logitT" ; rdfs:comment "The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Complex Estimation Algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000688 a rdfs:Class ; rdfs:label "rsbml" ; rdfs:comment "R support for SBML, using libsbml" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CC BY 2.5"@en ; rdfs:comment "CC BY 2.5 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "image compression" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_MAGE tab format" ; rdfs:comment "Equivalent with EDAM format_3162." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "FieldML"@en ; rdfs:comment """FieldML is an XML-based language for describing time-varying and spatially-varying fields. The aims of the language design process are to keep the language concise, consistent, intuitive and flexible.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GC-RMA Quantification"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000247 a rdfs:Class ; rdfs:label "KEGGSOAP" ; rdfs:comment "A package that provides a client interface to the KEGG SOAP server" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100040 a rdfs:Class ; rdfs:label "BasReader 3.01" ; rdfs:comment "This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000)." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000152 a rdfs:Class ; rdfs:label "iBioSim"@en ; rdfs:comment "iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. " ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete ArrayVision"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneRegionScan"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000588 a rdfs:Class ; rdfs:label "k-means" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "web service" ; rdfs:comment "A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services." ; rdfs:subClassOf swo:SWO_9000050 . a rdfs:Class ; rdfs:label "TCGA Data Use Certification"@en ; rdfs:comment "The TCGA Data Use Certification is a vendor-specific license which specifies the certification which must be officially agreed to before data may be accessed. There are a number of requirements in this license including attribution, non-transferability, annual progress updates, and a number of security measures." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label ".sql"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "decision tree building data transformation"@en ; rdfs:comment "A decision tree building data transformation is a data transformation that has objective decision tree induction."@en ; rdfs:subClassOf . swo:SWO_0000519 a rdfs:Class ; rdfs:label "design file" ; rdfs:subClassOf . swo:SWO_0000536 a rdfs:Class ; rdfs:label "flagme" ; rdfs:comment "Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000275 a rdfs:Class ; rdfs:label "MAVI Pro" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000469 a rdfs:Class ; rdfs:label "Annotation data packages" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Neural networks models"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000260 a rdfs:Class ; rdfs:label "publisher role" ; rdfs:comment "A publisher role is a role borne by an organization or individual in which they are responsible for making software available to a particular consumer group. Such organizations or individuals do need to be involved in the development of the software." ; rdfs:subClassOf . swo:SWO_0000095 a rdfs:Class ; rdfs:label "C" ; rdfs:subClassOf . swo:SWO_0000037 a rdfs:Class ; rdfs:label "Applied Biosystems 1700 Expression Array System Software" ; rdfs:comment """Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are: Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA. Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated. Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results.""" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000106 a rdfs:Class ; rdfs:label "Groovy" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "alpha" ; rdfs:comment "Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete WilcEbam"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000508 a rdfs:Class ; rdfs:label "covdesc file" ; rdfs:subClassOf . swo:SWO_0000348 a rdfs:Class ; rdfs:label "ROC" ; rdfs:comment "utilities for ROC, with uarray focus" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000520 a rdfs:Class ; rdfs:label "'diffGeneAnalysis'" ; rdfs:comment "Analyze microarray data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "ensemble specification" ; rdfs:comment "A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Rintact"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Langmuir Isotherm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "License without restrictions on derivatives" ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "programming language" ; rdfs:comment "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." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete FARMS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "binary format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete logicFS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete xps"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100010 a rdfs:Class ; rdfs:label "ANCOVA" ; rdfs:comment "The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR" ; rdfs:subClassOf . swo:SWO_0000599 a rdfs:Class ; rdfs:label "logicFS" ; rdfs:comment "Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_9000074 a rdfs:Class ; rdfs:label "Windows XP" ; rdfs:subClassOf swo:SWO_9000072 . swo:SWO_0000365 a rdfs:Class ; rdfs:label "Rosetta Resolver" ; rdfs:comment "The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100028 a rdfs:Class ; rdfs:label "ArrayVision 6.0 (Imaging Research Inc.)" ; rdfs:subClassOf swo:SWO_0000042 . swo:SWO_0000531 a rdfs:Class ; rdfs:label "f-test" ; rdfs:subClassOf . swo:SWO_0000236 a rdfs:Class ; rdfs:label "ImageQuant" ; rdfs:comment "This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000109 a rdfs:Class ; rdfs:label "LabVIEW" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete genemeta"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000495 a rdfs:Class ; rdfs:label "'cellHTS2'" ; rdfs:comment "Analysis of cell-based RNA interference screens" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000612 a rdfs:Class ; rdfs:label "makecdfenv" ; rdfs:comment "This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "NLM Open License with Attribution"@en ; rdfs:comment "The NLM Open License with Attribution is a vendor-specific license which is similar to public domain, but which requests attribution. Government information at NLM Web sites is in the public domain. Public domain information may be freely distributed and copied, but it is requested that in any subsequent use the National Library of Medicine (NLM) be given appropriate acknowledgement. When using NLM Web sites, you may encounter documents, illustrations, photographs, or other information resources contributed or licensed by private individuals, companies, or organizations that may be protected by U.S. and foreign copyright laws. Transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the written permission of the copyright owners. Specific NLM Web sites containing protected information provide additional notification of conditions associated with its use." ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "source code module"@en ; rdfs:comment "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en ; rdfs:subClassOf . swo:SWO_0000069 a rdfs:Class ; rdfs:label "CRG MCoffee Web Tool"@en ; rdfs:comment "Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software." ; rdfs:subClassOf swo:SWO_0000064 . a rdfs:Class ; rdfs:label "material supplier role"@en ; rdfs:comment "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Jaguar"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ALL/AML data set"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Icens"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Agilent Feature Extraction software version A.5.1.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000163 a rdfs:Class ; rdfs:label "GGtools" ; rdfs:comment "This package deals with hapmap SNP reports, GWAS, etc." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000188 a rdfs:Class ; rdfs:label "GeneR" ; rdfs:comment "Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100087 a rdfs:Class ; rdfs:label "Cyber-T" ; rdfs:comment "Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_9000090 a rdfs:Class ; rdfs:label "Dropbox" ; rdfs:subClassOf swo:SWO_0000030 . a rdfs:Class ; rdfs:label "obsolete RLMM"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pair file"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000022 a rdfs:Class ; rdfs:label "Linux" ; rdfs:subClassOf swo:SWO_0000021 , swo:SWO_0000030 . swo:SWO_0000383 a rdfs:Class ; rdfs:label "SLGI" ; rdfs:comment "A variety of data files and functions for the analysis of genetic interactions" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000525 a rdfs:Class ; rdfs:label "ecolitk" ; rdfs:comment "Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100054 a rdfs:Class ; rdfs:label "CDF binary format" ; rdfs:comment "The CDF binary format is a binary data format specification created by Affymetrix was created for faster access and smaller file size in comparison to the CDF ASCII format. The values in the file are stored in little-endian format. CDF binary format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name." ; rdfs:subClassOf . swo:SWO_0000454 a rdfs:Class ; rdfs:label "affyImGUI" ; rdfs:comment "A Graphical User Interface for affy analysis using the limma Microarray package" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'CORREP'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000048 a rdfs:Class ; rdfs:label "BAC" ; rdfs:comment "This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete spotSegmentation"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hidden Variable Dynamic Modelling HVDM)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete f-test"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "free to use license"@en ; rdfs:comment "A license which allows any form of usage of the artifact." ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "obsolete software developer role"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affy"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete puma"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "specifically dependent continuant"@en ; rdfs:comment "A 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."@en ; rdfs:subClassOf . swo:SWO_0000170 a rdfs:Class ; rdfs:label "GSEABase" ; rdfs:comment "This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA)." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000560 a rdfs:Class ; rdfs:label "Global test" ; rdfs:comment "global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments." ; rdfs:subClassOf . swo:SWO_1100091 a rdfs:Class ; rdfs:label "DFW" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete metaArray"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "dataset creating"@en ; rdfs:comment "A planned process that has a data set as its specified output."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CAS Information Use Policy" ; rdfs:comment "The CAS Information Use Policy specifies under what legal requirements CAS Information may be accessed. Attribution to ACS must be included whenever creating derivatives or redistributing data covered under this license.Each User is permitted to download and retain a maximum of 5,000 Records and a maximum of 5,000 Molfiles at any given time for personal use or to share within a Project team for the life of the Project. There are also limits on how long records may be stored with the licensee, and how records may be linked." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix Pro [Axon Instruments]"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100107 a rdfs:Class ; rdfs:label "GASSCO method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "averaging" ; rdfs:comment "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation." ; rdfs:subClassOf . swo:SWO_0000199 a rdfs:Class ; rdfs:label "GenePix Pro 4.0" ; rdfs:subClassOf swo:SWO_0000182 . a rdfs:Class ; rdfs:label "obsolete Average log expression across arrays (ALE)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Algorithms for Calculating Microarray Enrichment"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100059 a rdfs:Class ; rdfs:label "Continuous Wavelet Transform (CWT)-based peak detection algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Affymetrix GeneChip Operating Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete factDesign"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RMAExpress"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000297 a rdfs:Class ; rdfs:label "MicroArraySuite 4.0" ; rdfs:subClassOf swo:SWO_0000271 . a rdfs:Class ; rdfs:label "obsolete makePlatformDesign"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Eukaryota" ; rdfs:subClassOf . swo:SWO_0000390 a rdfs:Class ; rdfs:label "SSPA" ; rdfs:comment "Sample size and power analysis for microarray data, where two groups are analysed." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000003 a rdfs:Class ; rdfs:label "obsolete information processing" ; rdfs:comment "Information processing is a process in which input information is analysed or transformed in order to produce information as output." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ImaGene4.1 software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000608 a rdfs:Class ; rdfs:label "macat" ; rdfs:comment "This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_9000032 a rdfs:Class ; rdfs:label "Non-commercial use only" ; rdfs:comment "Non-commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are not commercial entites." ; rdfs:subClassOf swo:SWO_9000031 . swo:SWO_0000359 a rdfs:Class ; rdfs:label "Rgraphviz" ; rdfs:comment "Provides plotting capabilities for R graph objects" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete HilbertVisGUI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BioPAX Manchester OWL Syntax format"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "NONMEM data format"@en ; rdfs:subClassOf . swo:SWO_0000416 a rdfs:Class ; rdfs:label "ScISI" ; rdfs:comment "Package to create In Silico Interactomes" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000279 a rdfs:Class ; rdfs:label "MCRestimate" ; rdfs:comment "This package includes a function for combining preprocessing and classification methods to calculate misclassification errors" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000203 a rdfs:Class ; rdfs:label "GeneticsPed" ; rdfs:comment "Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000044 a rdfs:Class ; rdfs:label "BLAST+ 2.2.26"@en ; rdfs:comment "The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763)" ; rdfs:subClassOf swo:SWO_0000030 , swo:SWO_1100032 . swo:SWO_0000026 a rdfs:Class ; rdfs:label "software with image input" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "organization" ; rdfs:comment "An entity that can bear 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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'diffGeneAnalysis'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "WordStar format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Obsolete" ; rdfs:comment "Sofware is no longer being supplied by the developers/publishers" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pcaMethods"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000264 a rdfs:Class ; rdfs:label "Loess algorithm" ; rdfs:subClassOf . swo:SWO_0000011 a rdfs:Class ; rdfs:label "IntelliJ IDEA" ; rdfs:comment "IntelliJ IDEA is a commercial Java IDE for developing software." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Agilent Feature Extraction 5.1.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Markov Chain Monte Carlo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000196 a rdfs:Class ; rdfs:label "GeneTraffic" ; rdfs:comment "Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw)" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Gene array analysis algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000212 a rdfs:Class ; rdfs:label "Hexagon binning algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Probe Cell Analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Lognormal Normal Model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000320 a rdfs:Class ; rdfs:label "Probe level Locally moderated Weighted median-t (PLW) method" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BGmix'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GraphAT"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000432 a rdfs:Class ; rdfs:label "TAS Software" ; rdfs:comment "Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics." ; rdfs:subClassOf swo:SWO_1100022 . swo:SWO_0000596 a rdfs:Class ; rdfs:label "lma" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'beadarraySNP'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000231 a rdfs:Class ; rdfs:label "ITALICS" ; rdfs:comment "A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CC BY-NC-ND 2.5"@en ; rdfs:comment "CC BY-NC-ND 2.5 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete 'Biobase'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100032 a rdfs:Class ; rdfs:label "BLAST" ; rdfs:comment "BLAST, or Basic Local Alignment Search Tool in full, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete_.java file" ; rdfs:comment "The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of 'Programming language format' this class was retained and SWO_0000585 deemed obsolete. The usages of SWO_0000585 were refactored to reference 3. SWO_3000034, and SWO_0000585 was marked as obsolete. Please use SWO_3000034 instead." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete graph"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Acuity"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CopasiML" ; rdfs:comment "CopasiML, the native format of COPASI." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Gene Recommender algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PCpheno"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneSpring"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY 2.1 JP" ; rdfs:comment "CC BY 2.1 JP is a Japan-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . swo:SWO_9000083 a rdfs:Class ; rdfs:label "DNDC" ; rdfs:comment "Soil Chemistry Model" ; rdfs:subClassOf swo:SWO_0000030 . a rdfs:Class ; rdfs:label "DXF" ; rdfs:comment "DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Serial Analysis of Gene Expression (SAGE)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Apache License Version 2.0" ; rdfs:comment "This is a free software license under the definition of \"free\" by the GNU Project, and is compatible with version 3 of the GNU GPL." ; rdfs:subClassOf , . swo:SWO_1100100 a rdfs:Class ; rdfs:label "FARMS" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MantelCorr"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GEOmetadb"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Purchase cost" ; rdfs:comment "Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a resource." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "obsolete Position weight matrix (PWM )"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100098 a rdfs:Class ; rdfs:label "Expert 2100" ; rdfs:comment "Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools." ; rdfs:subClassOf swo:SWO_0000034 . a rdfs:Class ; rdfs:label "obsolete stam"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC-ND 2.5 CH"@en ; rdfs:comment "CC BY-NC-ND 2.5 CH is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. " ; rdfs:subClassOf , . swo:SWO_0000293 a rdfs:Class ; rdfs:label "MergeMaid" ; rdfs:comment "The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000167 a rdfs:Class ; rdfs:label "GMS" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete copa"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "cross validation" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SLqPCR"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000421 a rdfs:Class ; rdfs:label "Scanning software G2565AA version A6.3.1" ; rdfs:comment "High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results" ; rdfs:subClassOf swo:SWO_0000420 . a rdfs:Class ; rdfs:label "Attribution required"@en ; rdfs:comment "Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the resource is used." ; rdfs:subClassOf swo:SWO_9000006 . a rdfs:Class ; rdfs:label "raster image format" ; rdfs:comment "A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel." ; rdfs:subClassOf . swo:SWO_9000094 a rdfs:Class ; rdfs:label "Grimoires" ; rdfs:subClassOf swo:SWO_0000030 . swo:SWO_0000450 a rdfs:Class ; rdfs:label "Array Comparative Genomic Hybridization" ; rdfs:comment "The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "SABIO-RK Non-Commercial Purpose License"@en ; rdfs:comment "The SABIO-RK Non-Commercial Purpose License covers use of the Database for Non-Commercial Purpose only, and appropriate attribution must be given. Non-Commercial Purpose means the use of the Database solely for internal non-commercial research and academic purposes. As consent must be aquired for commercial use, a separate agreement must be entered into for commercial use and is not covered here." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete software developer organization"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "measurement unit label"@en ; rdfs:comment "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ensemble algorithm" ; rdfs:comment """Ensemble algorithms are algorithms that generate an ensemble when executed on a dataset. The ensemble algorithms include a specification of single generalization algorithms which are executed in oreder to produce the single generalizations that compose the ensemble. Examples of ensemble algorithms include bagging, boosting, stacking, random forests, random subspaces,bagging of random subspaces etc. For example, bagging of decision trees algorithm includes the specification of a bagging algorithm and having a decision tree algorithm for generating the base models composing the ensemble.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete logicFS dataset"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GNU GPL v2"@en ; rdfs:comment "The GNU GPL v2 is an earlier version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv2 is, by itself, not compatible with GPLv3. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'CoCiteStats'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000331 a rdfs:Class ; rdfs:label "QuantArray version 2" ; rdfs:subClassOf swo:SWO_0000329 . a rdfs:Class ; rdfs:label "obsolete 'EBarrays'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RankProd"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "DrugBank Academic License"@en ; rdfs:comment "DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes (including internal use) requires a license. We ask that users who download significant portions of the database cite the DrugBank paper in any resulting publications. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use)." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "graphical user interface" ; rdfs:comment "https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013." ; rdfs:subClassOf swo:SWO_9000050 . a rdfs:Class ; rdfs:label "dimensionality reduction"@en ; rdfs:comment "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m."@en ; rdfs:subClassOf , . swo:SWO_0000258 a rdfs:Class ; rdfs:label "LPE" ; rdfs:comment "This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000201 a rdfs:Class ; rdfs:label "GeneticsBase" ; rdfs:comment "This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "GIF" ; rdfs:comment "The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia]" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ChipReader 3.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "simulation and analysis of biochemical networks" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix Pro 3"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'affyPLM'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC-SA 4.0"@en ; rdfs:comment """CC BY-NC-SA 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . swo:SWO_0000405 a rdfs:Class ; rdfs:label "ArrayExpress Bioconductor" ; rdfs:comment "ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects." ; rdfs:subClassOf swo:SWO_1100075 , swo:SWO_1100079 . a rdfs:Class ; rdfs:label "obsolete goProfiles"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "sequence alignment"@en ; rdfs:subClassOf . swo:SWO_0000354 a rdfs:Class ; rdfs:label "RdbiPgSQL" ; rdfs:comment "Provides methods for accessing data stored in PostgreSQL tables." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete gct"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000009 a rdfs:Class ; rdfs:label "Platform clause" ; rdfs:comment "A Platform clause is a license clause which states the platform restrictions for the licensed resource, if any. The license for a resource may or may not allow the use of any platform. If it is allowed, such usage may be restricted in a variety of ways." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "image format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Bayesian Model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000225 a rdfs:Class ; rdfs:label "HilbertVis" ; rdfs:comment "Functions to visualize long vectors of integer data by means of Hilbert curves" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000282 a rdfs:Class ; rdfs:label "Mutual information matrix (MIM)" ; rdfs:subClassOf . swo:SWO_0000666 a rdfs:Class ; rdfs:label "prada" ; rdfs:comment "Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy)." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GMS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000073 a rdfs:Class ; rdfs:label "Windows Vista" ; rdfs:subClassOf swo:SWO_9000072 . swo:SWO_0000131 a rdf:Property ; rdfs:label "directly preceded by" ; rdfs:comment "Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software." ; rdfs:range ; rdfs:subPropertyOf swo:SWO_0000301 . a rdfs:Class ; rdfs:label "obsolete Gene Pix"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pedigree data file"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000174 a rdfs:Class ; rdfs:label "Gene-Set Enrichment Analysis" ; rdfs:subClassOf . swo:SWO_0000626 a rdfs:Class ; rdfs:label "mrnet algorithm" ; rdfs:subClassOf . swo:SWO_1100043 a rdfs:Class ; rdfs:label "'BicARE'" ; rdfs:comment "This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000304 a rdfs:Class ; rdfs:label "'Needleman-Wunsch'" ; rdfs:subClassOf . swo:SWO_0000185 a rdfs:Class ; rdfs:label "GenePix Pro 6.0" ; rdfs:subClassOf swo:SWO_0000182 . swo:SWO_0000731 a rdfs:Class ; rdfs:label "yaqcaffy" ; rdfs:comment "Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Affymetrix-compliant data"@en ; rdfs:comment "Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "DAE Algorithm" ; rdfs:comment "Differential Algebraic equations (DAEs) are a general form of (systems of) differential equations for vector–valued functions in one independent variable. In practical terms, the distinction between DAEs and ODEs is often that the solution of a DAE system depends on the derivatives of the input signal and not just the signal itself as in the case of ODEs." ; rdfs:subClassOf . swo:SWO_0000470 a rdfs:Class ; rdfs:label "'apComplex'" ; rdfs:comment "This package functions to estimate a bipartite graph of protein complex membership using AP-MS data." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Gaussian locally weighted regression"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Distribution with notices" ; rdfs:comment "Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices)." ; rdfs:subClassOf . swo:SWO_0000409 a rdfs:Class ; rdfs:label "R data frame" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PPC algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000481 a rdfs:Class ; rdfs:label "'betr'" ; rdfs:comment "betr is a software package which implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000315 a rdfs:Class ; rdfs:label "Pearson correlation estimator" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete k-nearest neighbour classification"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100092 a rdfs:Class ; rdfs:label "Digital gene expression (DGE) datasets" ; rdfs:subClassOf . swo:SWO_1100080 a rdfs:Class ; rdfs:label "Text data set" ; rdfs:subClassOf . swo:SWO_0000419 a rdfs:Class ; rdfs:label "ScanArray v3.1 software" ; rdfs:subClassOf swo:SWO_0000418 . swo:SWO_9000006 a rdfs:Class ; rdfs:label "Attribution clause" ; rdfs:comment "An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the resource." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "graph"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete plier"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000408 a rdfs:Class ; rdfs:label "Clustered data set" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 50-50 MANOVA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SSPA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000071 a rdfs:Class ; rdfs:label "Microsoft Excel for Windows 2010" ; rdfs:subClassOf swo:SWO_9000070 . swo:SWO_0000181 a rdfs:Class ; rdfs:label "GenePix" ; rdfs:subClassOf swo:SWO_0000176 . a rdfs:Class ; rdfs:label "obsolete SNPchip"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "k-means clustering"@en ; rdfs:comment "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)."@en ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "data about an ontology part"@en ; rdfs:comment "Data about an ontology part is a data item about a part of an ontology, for example a term"@en ; rdfs:subClassOf . swo:SWO_0000122 a rdfs:Class ; rdfs:label "Scala" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ORCID MIT-Style License (MIT)"@en ; rdfs:comment "The ORCID MIT-style license is identical to the MIT License, except for the addition of the following two clauses: 1. \"The above license does not apply to the branding or the \"look and feel\" of the websites located at the orcid.org URL even if elements thereof are contained in the Software.\"; 2. \"Except to provide the copyright notice required above or as allowed under ORCID Inc.'s Trademark Use Policy (available at http://orcid.org, under \"Policies\"), you may not use the name of ORCID, Inc., ORCID, its marks and logo, to advertise, promote or suggest any affiliation with or endorsement by ORCID, Inc. in connection with your use of the Software.\". The MIT License is is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. " ; rdfs:subClassOf , . swo:SWO_0000690 a rdfs:Class ; rdfs:label "safe" ; rdfs:comment "SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "clustered data set"@en ; rdfs:comment "A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Distribution restricted" ; rdfs:comment "Distribution restricted is a distribution clause which places restrictions on how the licensed resource may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "error correction" ; rdfs:comment "An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete metahdep"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000256 a rdfs:Class ; rdfs:label "Lognormal Normal Model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete CHP binary format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000017 a rdfs:Class ; rdfs:label "MATLAB 6" ; rdfs:subClassOf swo:SWO_0000005 . swo:SWO_1100005 a rdfs:Class ; rdfs:label "Affymetrix Expression Console" ; rdfs:comment "Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000541 a rdfs:Class ; rdfs:label "flowStats" ; rdfs:comment "This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000689 a rdfs:Class ; rdfs:label "rtracklayer" ; rdfs:comment "R interface to genome browsers and their annotation tracks" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100081 a rdfs:Class ; rdfs:label "CSV data set" ; rdfs:subClassOf . swo:SWO_0000649 a rdfs:Class ; rdfs:label "pathRender" ; rdfs:comment "build graphs from pathway databases, render them by Rgraphviz" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete GSEABase"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000522 a rdfs:Class ; rdfs:label "'dualKS'" ; rdfs:comment "This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the \"multiclass\" problem. That is, it can discriminate between more than 2 classes." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "LPPL" ; rdfs:subClassOf . swo:SWO_0000670 a rdfs:Class ; rdfs:label "qPCR data" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "clustered data visualization" ; rdfs:comment "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "text editing" ; rdfs:comment "Text editing is the objective of editing plain text files." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data integration algorithm" ; rdfs:subClassOf . swo:SWO_1100139 a rdfs:Class ; rdfs:label "PEAKS DB" ; rdfs:comment "Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete HaarSeg algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000329 a rdfs:Class ; rdfs:label "QuantArray scanner software" ; rdfs:comment """QuantArray® is a powerful microarray analysis software that enables researchers to easily and accurately visualize and quantitate gene expression data.""" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000342 a rdfs:Class ; rdfs:label "RMA++" ; rdfs:subClassOf . swo:SWO_0000192 a rdfs:Class ; rdfs:label "GeneSelector" ; rdfs:comment "The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "RIFF"@en ; rdfs:subClassOf . swo:SWO_0000533 a rdfs:Class ; rdfs:label "fbat" ; rdfs:comment "This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000111 a rdfs:Class ; rdfs:label "Lua" ; rdfs:subClassOf . swo:SWO_0000579 a rdfs:Class ; rdfs:label "idiogram" ; rdfs:comment "A package for plotting genomic data by chromosomal location" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100123 a rdfs:Class ; rdfs:label "CLR algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Text data set"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000040 a rdfs:Class ; rdfs:label "ArrayNorm" ; rdfs:comment "ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete GenomeGraphs"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete lapmix"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "plain text file format" ; rdfs:subClassOf . swo:SWO_9000089 a rdfs:Class ; rdfs:label "DROID" ; rdfs:comment "Digital Record Object Identification" ; rdfs:subClassOf swo:SWO_0000030 . a rdfs:Class ; rdfs:label ".mgf"@en ; rdfs:subClassOf . swo:SWO_0000054 a rdfs:Class ; rdfs:label "ClustalX"@en ; rdfs:subClassOf swo:SWO_0000051 . swo:SWO_0000555 a rdfs:Class ; rdfs:label "genefilter" ; rdfs:comment "Some basic functions for filtering genes" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000700 a rdfs:Class ; rdfs:label "snapCGH" ; rdfs:comment "Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete nudge"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Rdbi"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete quantsmooth"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100075 a rdfs:Class ; rdfs:label "R software" ; rdfs:comment "Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Robust likelihood-based survival modeling"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000705 a rdfs:Class ; rdfs:label "splicegear" ; rdfs:comment "A set of tools to work with alternative splicing" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000039 a rdfs:Class ; rdfs:label "ArrayGauge" ; rdfs:comment """Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis. Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop.""" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "pattern discovery algorithm" ; rdfs:comment "Pattern discovery algorithm is a data mining algorithm that solves a pattern discovery task and as a result produces a set of patterns." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BSgenome'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000022 a rdfs:Class ; rdfs:label "Platform restricted" ; rdfs:comment "Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on." ; rdfs:subClassOf swo:SWO_9000009 . a rdfs:Class ; rdfs:label "obsolete cls"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000062 a rdfs:Class ; rdfs:label "MUSCLE 3.8.31"@en ; rdfs:subClassOf swo:SWO_0000030 , swo:SWO_0000063 . a rdfs:Class ; rdfs:label "obsolete flowStats"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "GNU GPL" ; rdfs:subClassOf . swo:SWO_0000711 a rdfs:Class ; rdfs:label "ssize" ; rdfs:comment "Functions for computing and displaying sample size information for gene expression arrays." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete edd"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000615 a rdfs:Class ; rdfs:label "mas5 format" ; rdfs:subClassOf . swo:SWO_1100070 a rdfs:Class ; rdfs:label "PCMG" ; rdfs:comment "PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneTac Analyser"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MVCClass"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000245 a rdfs:Class ; rdfs:label "Jaguar" ; rdfs:comment "Image analysis software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete_newick" ; rdfs:comment "Equivalence with EDAM format_1910." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "quality" ; rdfs:comment "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_Clustering algorithm" ; rdfs:comment "The original label for this class, 'Clustering algorithm', was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM (OntoDM_170075). As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. Please use OntoDM_170075 instead." ; rdfs:subClassOf . swo:SWO_0000133 a rdfs:Class ; rdfs:label "DAVID" ; rdfs:comment "DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000609 a rdfs:Class ; rdfs:label "made4" ; rdfs:comment "Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Absolute Expression Analysis"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000630 a rdfs:Class ; rdfs:label "multtest" ; rdfs:comment "Resampling-based multiple hypothesis testing" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Expert 2100"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000727 a rdfs:Class ; rdfs:label "webbioc" ; rdfs:comment "An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Array_vision_(Interfocus)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Genome annotation" ; rdfs:comment "Annotate a genome sequence with terms from a controlled vocabulary." ; rdfs:subClassOf . swo:SWO_9000017 a rdfs:Class ; rdfs:label "Restrictions on derivative software" ; rdfs:comment "Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "software"@en ; rdfs:comment """Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit."""@en ; rdfs:subClassOf . swo:SWO_0000059 a rdfs:Class ; rdfs:label "EBI Clustal Omega Web Tool"@en ; rdfs:subClassOf swo:SWO_0000051 . swo:SWO_0000415 a rdfs:Class ; rdfs:label "R language" ; rdfs:subClassOf . swo:SWO_0000100 a rdfs:Class ; rdfs:label "D" ; rdfs:subClassOf . swo:SWO_0000574 a rdfs:Class ; rdfs:label "hopach" ; rdfs:comment "The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering)." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete simulatorAPMS"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000117 a rdfs:Class ; rdfs:label "Prolog" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Artistic License 1.0" ; rdfs:comment "The Artistic License v1.0 is not considered a free software license by the definition of the GNU Project because it is too vague; some passages are "too clever for their own good", and their meaning is not clear. The GNU Project recommends that it is not used except as part of the disjunctive license of Perl." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Annotation-Driven Clustering"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000335 a rdfs:Class ; rdfs:label "RBioinf" ; rdfs:comment "Functions and datasets and examples to accompany the monograph R For Bioinformatics." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Array Comparative Genomic Hybridization"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ShortRead"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000552 a rdfs:Class ; rdfs:label "Gene array analysis algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "dynamic Bayesian network model"@en ; rdfs:comment "A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps." ; rdfs:subClassOf swo:SWO_1100041 . swo:SWO_0000563 a rdfs:Class ; rdfs:label "goProfiles" ; rdfs:comment "The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100112 a rdfs:Class ; rdfs:label "GEOquery" ; rdfs:comment "The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete XDotsReader"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete parody"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000353 a rdfs:Class ; rdfs:label "Rdbi" ; rdfs:comment "Generic database methods" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Nested Effects Models"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000073 a rdfs:Class ; rdfs:label "Q"@en ; rdfs:comment """Q is a set of tools tailored for some specific kinds of free energy calculations, namely: (I) Free energy perturbation (FEP) simulations. (II) Empirical valence bond (EVB) calculations of reaction free energies. (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities."""@en ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000234 a rdfs:Class ; rdfs:label "ImaGene4.1 software" ; rdfs:subClassOf swo:SWO_0000238 . a rdfs:Class ; rdfs:label "clustering specification" ; rdfs:comment "Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data." ; rdfs:subClassOf . swo:SWO_0000128 a rdfs:Class ; rdfs:label "Verilog" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix Pro 5.0"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "single generalization algorithm" ; rdfs:comment "single generalization algorithms are data mining algorithms that given a dataset on input produce a generalization at the output." ; rdfs:subClassOf . swo:SWO_0000028 a rdfs:Class ; rdfs:label "ontology engineering software" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000474 a rdfs:Class ; rdfs:label "arrayQualityMetrics" ; rdfs:comment "This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete_jpeg" ; rdfs:comment "SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label 'JPEG', is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_ 0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead." ; rdfs:subClassOf . swo:SWO_0000496 a rdfs:Class ; rdfs:label "cghMCR" ; rdfs:comment "Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000155 a rdfs:Class ; rdfs:label "COBRApy"@en ; rdfs:comment "COBRA Toolbox is the version of the COBRA software for Python." ; rdfs:subClassOf swo:SWO_0000154 . swo:SWO_0000656 a rdfs:Class ; rdfs:label "pgUtils" ; rdfs:comment "Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Spot quantification"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000005 a rdfs:Class ; rdfs:label "MATLAB" ; rdfs:comment "MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000593 a rdfs:Class ; rdfs:label "limma" ; rdfs:comment "Data analysis, linear models and differential expression for microarray data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete flowClust"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Discriminant Fuzzy Pattern Algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete biomaRT"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'biocGraph'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SAS/STAT Software, Version 8"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000077 a rdfs:Class ; rdfs:label "Sequence Alignment and Modeling System"@en ; rdfs:comment "Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "histologic grade for ovarian tumor" ; rdfs:comment "A categorical value specification that is a histologic grade assigned to a ovarian tumor." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Presence-Absence calls with Negative Probesets (PANP)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000716 a rdfs:Class ; rdfs:label "tilingArray" ; rdfs:comment "Transcript mapping with high-density oligonucleotide tiling arrays" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete pathRender"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Affymetrix Expression Console"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000271 a rdfs:Class ; rdfs:label "MIcroarray Analysis Suite" ; rdfs:comment "Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Base-Pair-Distance Kernel"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Loess algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "SBGN Open License with Attribution"@en ; rdfs:comment "The SBGN Open License with Attribution is a very simple statement of openness for the SBGN standard and related resources available on its website. No one—not the principal investigators, nor the SBGN Editors, nor the members of the SBGN Scientific Committee, nor the funding agencies or anyone else—owns SBGN; it is a free and open community effort that extends beyond any single group, and they view themselves only as organizers and fellow developers." ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "molecular sequence analysis" ; rdfs:subClassOf . swo:SWO_0000697 a rdfs:Class ; rdfs:label "simulatorAPMS" ; rdfs:comment "Functions to computationally simulate the AP-MS technology based on wet-lab data." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100026 a rdfs:Class ; rdfs:label "Agilent Feature Extraction software version 7.5" ; rdfs:subClassOf swo:SWO_1100104 . a rdfs:Class ; rdfs:label "obsolete Gamma Gamma Model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "software development"@en ; rdfs:comment "A planned process that has specified output a software product and that involves the creation of source code."@en ; rdfs:subClassOf . swo:SWO_0000099 a rdfs:Class ; rdfs:label "ColdFusion" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pkgDepTools"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete MATLAB language"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000526 a rdfs:Class ; rdfs:label "edd" ; rdfs:comment "This package provides tools for evaluating cohort distributions of gene expression levels" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "specimen role"@en ; rdfs:comment "a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete macat"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100097 a rdfs:Class ; rdfs:label "Empirical Bayes rule" ; rdfs:subClassOf . swo:SWO_0000318 a rdfs:Class ; rdfs:label "'PLM'" ; rdfs:comment "it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis" ; rdfs:subClassOf . swo:SWO_0000604 a rdfs:Class ; rdfs:label "maCorrPlot" ; rdfs:comment "Graphically displays correlation in microarray data that is due to insufficient normalization" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000386 a rdfs:Class ; rdfs:label "SNPRMA algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Permission required for derivative work"@en ; rdfs:comment "Permission required for derivative work is a clause which restricts the production of derivative work based on the licensed resource only to licensees who have received explicit permission in the manner stipulated by the resource." ; rdfs:subClassOf swo:SWO_9000017 . swo:SWO_0000664 a rdfs:Class ; rdfs:label "Position weight matrix (PWM )" ; rdfs:subClassOf . swo:SWO_1100021 a rdfs:Class ; rdfs:label "Affymetrix GeneChip Operating Software" ; rdfs:comment "The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000566 a rdfs:Class ; rdfs:label "gpr format" ; rdfs:subClassOf . swo:SWO_0000051 a rdfs:Class ; rdfs:label "Clustal"@en ; rdfs:comment "Multiple alignment program for nucleic acid or protein sequences." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "MAGE-TAB" ; rdfs:comment "MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files." ; rdfs:subClassOf . swo:SWO_0000371 a rdfs:Class ; rdfs:label "S-Score algorithm" ; rdfs:subClassOf . swo:SWO_9000079 a rdfs:Class ; rdfs:label "BioJava" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000252 a rdfs:Class ; rdfs:label "LBE" ; rdfs:comment "LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Radial basis function"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000485 a rdfs:Class ; rdfs:label "bioDist" ; rdfs:comment "The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "decision tree induction" ; rdfs:comment "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." ; rdfs:subClassOf . swo:SWO_0000084 a rdfs:Class ; rdfs:label "CEL binary format" ; rdfs:comment "CEL binary format is a binary data format specification created by Affymetrix where values are stored in little-endian format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hubert’s gamma"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'gaggle'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000537 a rdfs:Class ; rdfs:label "flowClust" ; rdfs:comment "Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete spikeLI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100016 a rdfs:Class ; rdfs:label "Absolute Expression Analysis" ; rdfs:subClassOf swo:SWO_0000297 . a rdfs:Class ; rdfs:label "CC0 1.0" ; rdfs:comment "CC0 is a public domain dedication from Creative Commons. A work released under CC0 is dedicated to the public domain to the fullest extent permitted by law. If that is not possible for any reason, CC0 also provides a lax, permissive license as a fallback. Both public domain works and the lax license provided by CC0 are compatible with the GNU GPL." ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "obsolete Linear modelling"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Facebase Data Access Policy"@en ; rdfs:comment "The Facebase Data Access Policy specifies under what legal requirements Facebase data may be accessed. Non-sensitive data is available for use for all purposes and usages. As consent must be aquired for sensitive (or closed) data, this license only covers the use of the open data (a separate agreement must be entered into for restricted access data)." ; rdfs:subClassOf . swo:SWO_0000686 a rdfs:Class ; rdfs:label "rflowcyt" ; rdfs:comment "Statistical tools and data structures for analytic flow cytometry" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000423 a rdfs:Class ; rdfs:label "Signaling Pathway Impact Analysis (SPIA) algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_pdf" ; rdfs:comment "SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_0000652 were transferred to SWO_3000015. Please use SWO_3000015 instead. " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete arrayWoRx"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000645 a rdfs:Class ; rdfs:label "pamr" ; rdfs:comment "Some functions for sample classification in microarrays" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "UMLS Metathesaurus License"@en ; rdfs:comment "The UMLS Metathesaurus License is a vendor-specific license which allows redistribution (as part of a larger computer application) as long as the original data is attributed correctly and a summary of data use provided each year. There is no cost to use the service, and may be used both commercially and non-commercially. Users must inform the resource if it is redistributed within a computer application." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete cosmoGUI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000722 a rdfs:Class ; rdfs:label "Two-stage measurement error model" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "predictive modeling algorithm" ; rdfs:comment "Predictive modeling algorithm is a data mining algorithm that solves a predictive modeling task and as a result produces a predictive model." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "biological data processing" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "EMBLEM ELM Academic License"@en ; rdfs:comment """The EMBLEM ELM Academic LIcense was developed as the license for the ELM (Eukaryotic Linear Motif) resource. Non-commerical use is allowed under this license, an additional commercial license is also available. This license makes the Licensed Software available free of charge for the licensee, which is a non-profit educational, academic and/or research institution. The software can only be used for academic research projects. This explicitly excludes projects which charge a fee, or projects that are done in collaboration with a third party that is funding the research in whole or in part in exchange for commercial rights on the results and/or possible delay in publication of any relevant results to the academic community. The user and any research assistants, co-workers or other workers who may use the Software agree to not grant licenses on any software that includes the Licensed Software, alone or integrated into other software, to third parties. Modification of the Licensed Software code is prohibited without the prior written consent of EMBLEM.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "pattern specification" ; rdfs:comment "A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T." ; rdfs:subClassOf . swo:SWO_0000698 a rdfs:Class ; rdfs:label "sizepower" ; rdfs:comment "This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete KGML"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete hopach"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100117 a rdfs:Class ; rdfs:label "CBS" ; rdfs:comment "The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm." ; rdfs:subClassOf . swo:SWO_1100015 a rdfs:Class ; rdfs:label "AWS algorithm" ; rdfs:subClassOf . swo:SWO_0000623 a rdfs:Class ; rdfs:label "microRNA" ; rdfs:comment "microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete rflowcyt"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Bilateria" ; rdfs:subClassOf . swo:SWO_0000397 a rdfs:Class ; rdfs:label "software publisher organization" ; rdfs:comment "An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Firth's bias reduction procedure"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Optiquant"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ImaGene"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Misclassification-Penalized Posteriors (MiPP)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "TIFF" ; rdfs:comment "TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete dataset comparison"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "class discovery data transformation"@en ; rdfs:comment "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "occurrent"@en ; rdfs:comment "An entity that has temporal parts and that happens, unfolds or develops through time."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Rredland"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000678 a rdfs:Class ; rdfs:label "rMAT" ; rdfs:comment "R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete tilingArray"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100046 a rdfs:Class ; rdfs:label "'BiocCaseStudies'" ; rdfs:comment "Software and data to support the case studies." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete AP-MS data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100039 a rdfs:Class ; rdfs:label "BaldiLongT" ; rdfs:subClassOf . swo:SWO_0000445 a rdfs:Class ; rdfs:label "Wilcoxon" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affypdnn"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000289 a rdfs:Class ; rdfs:label "MassSpecWavelet" ; rdfs:comment "Processing Mass Spectrometry spectrum by using wavelet based algorithm" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000360 a rdfs:Class ; rdfs:label "Ringo" ; rdfs:comment "The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000638 a rdfs:Class ; rdfs:label "oligo" ; rdfs:comment "A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete webbioc"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hypergeometric probability"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "ODC-By v1.0"@en ; rdfs:comment "The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures." ; rdfs:subClassOf , . swo:SWO_0000241 a rdfs:Class ; rdfs:label "Initial microarray data processing (data filtering, local normalisation and quality control)" ; rdfs:comment "These scripts are for primer design and initial microarray data processing and are available as .zip files:" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_9000028 a rdfs:Class ; rdfs:label "Time for use restricted" ; rdfs:comment "Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used." ; rdfs:subClassOf swo:SWO_9000012 . a rdfs:Class ; rdfs:label "class discovery objective"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_TIFF image" ; rdfs:comment "SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label 'TIFF', is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BRENDA License"@en ; rdfs:comment "The BRENDA License is a vendor-specific license which allows access to the official website and its data free of charge. Any inclusion of BRENDA components into other data bases, or redistribution of BRENDA requires a license. To obtain commercial in-house versions please contact our distributor Biobase GmbH ( http://www.biobase-international.com). In-house versions for academic users are available from Enzymeta GmbH (http://www.enzymeta.de). The copyright of the printed version is held by Springer publishers. Users of the website may retrieve a copy of the data but must not alter the BRENDA data or charge money for a copy of it, and must not distribute any BRENDA data without prior permission of the copyright holder. As there are separate licenses for in-house versions of BRENDA, please note that this license only describes the website-accessible version of BRENDA." ; rdfs:subClassOf . swo:SWO_0000675 a rdfs:Class ; rdfs:label "quantsmooth" ; rdfs:comment "Quantile smoothing and genomic visualization of array data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Agilent Technologies Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000458 a rdfs:Class ; rdfs:label "affyTiling" ; rdfs:comment "This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000307 a rdfs:Class ; rdfs:label "OCplus" ; rdfs:comment "This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes)." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100004 a rdfs:Class ; rdfs:label "Algorithms for Calculating Microarray Enrichment" ; rdfs:comment "ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing \"enrichment\". It does not rely on a specific array technology (although the array should be a \"tiling\" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "GeneNetwork Conditions of Use"@en ; rdfs:comment "The GeneNetwork Conditions of Use describes the data licensing for the resource covered. Commercial and non-commercial use is allowed, though attribution is requested via either acknowledgement or co-authorship. Further restrictions on the bulk download of as-yet unpublished data is also described. (While mentioned in the document, software licensing is not the focus of this conditions of use and therefore is not modelled here.)" ; rdfs:subClassOf . swo:SWO_0000582 a rdfs:Class ; rdfs:label "iterativeBMA" ; rdfs:comment "The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402)." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000066 a rdfs:Class ; rdfs:label "EBI TCoffee Web Tool"@en ; rdfs:comment "Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. Currently only the Web service interface is modelled in OWL." ; rdfs:subClassOf swo:SWO_0000064 . a rdfs:Class ; rdfs:label "obsolete 'annotate'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "sequence feature format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_FCS" ; rdfs:comment "Obsoleted as it was a generic term where there was no way of knowing for sure which format it was - or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class." ; rdfs:subClassOf . swo:SWO_9000011 a rdfs:Class ; rdfs:label "Number of users clause" ; rdfs:comment "A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the resource." ; rdfs:subClassOf swo:SWO_9000005 . a rdfs:Class ; rdfs:label "Query and retrieval" ; rdfs:comment "Search or query a data resource and retrieve entries and / or annotation." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-SA 2.1 JP" ; rdfs:comment "CC BY-SA 2.1 JP is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete bgx"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000189 a rdfs:Class ; rdfs:label "GeneRegionScan" ; rdfs:comment "A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Wilcoxon"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Applied Biosystems 1700 Expression Array System Software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000229 a rdfs:Class ; rdfs:label "Iteratively ReWeighted Least Squares" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_SBML" ; rdfs:comment "Equivalence with the EDAM SBML class format_2585." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete dChip"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete gmt format"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "pairwise sequence alignment"@en ; rdfs:subClassOf . swo:SWO_0000009 a rdfs:Class ; rdfs:label "Kakadu" ; rdfs:subClassOf swo:SWO_0000026 . a rdfs:Class ; rdfs:label "obsolete LBE"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000162 a rdfs:Class ; rdfs:label "Excel"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete seqLogo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100022 a rdfs:Class ; rdfs:label "Affymetrix Software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete Affymetrix GCOS v1.2"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Labome Copyright"@en ; rdfs:comment """The Labome copyright makes the contents of their resource freely available for browsing. Any redistribution or reproduction of part or all of the contents in any form is prohibited other than the following: you may print or download to a local hard disk extracts for your use only, with a daily limit of 50 webpages; and you may copy the content to individual third parties for their use, but only if you acknowledge the website as the source of the material. You may not, except with our express written permission, distribute or commercially exploit the content.""" ; rdfs:subClassOf . swo:SWO_0000083 a rdfs:Class ; rdfs:label "Plugin"@en ; rdfs:comment "This role can be borne by any software which is a plugin for another piece of software. It can be used, for example, with an axiom such as \"ParentSoftware 'uses software' some (PluginSoftware has_role some Plugin)\"" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PGSEA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete publisher role"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000422 a rdfs:Class ; rdfs:label "ShortRead" ; rdfs:comment "Base classes, functions, and methods for representation of high-throughput, short-read sequencing data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000717 a rdfs:Class ; rdfs:label "timecourse" ; rdfs:comment "Functions for data analysis and graphical displays for developmental microarray time course data." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete pdmclass"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete preprocessCore"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000296 a rdfs:Class ; rdfs:label "Misclassification-Penalized Posteriors (MiPP)" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "specimen"@en ; rdfs:comment "A material entity that has the specimen role."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete dcf"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RMAGEML"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_9000075 a rdfs:Class ; rdfs:label "Microsoft Office 2001" ; rdfs:subClassOf swo:SWO_9000076 . a rdfs:Class ; rdfs:label "obsolete maDB"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete S-Score algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000653 a rdfs:Class ; rdfs:label "pdInfoBuilder" ; rdfs:comment "Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_0000619 a rdfs:Class ; rdfs:label "metaArray" ; rdfs:comment "1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'MAS5'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000382 a rdfs:Class ; rdfs:label "SIM" ; rdfs:comment "Finds associations between DNA copy number and gene expression." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100128 a rdfs:Class ; rdfs:label "bcbio"@en ; rdfs:comment "bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology."@en ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000080 a rdfs:Class ; rdfs:label "Cytoscape 2.8"@en ; rdfs:subClassOf swo:SWO_0000079 . swo:SWO_0000693 a rdfs:Class ; rdfs:label "sigPathway" ; rdfs:comment "Conducts pathway analysis by calculating the NT_k and NE_k statistics" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CC BY 3.0 US"@en ; rdfs:comment "CC BY 3.0 US is a US-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software." ; rdfs:subClassOf , . swo:SWO_0000375 a rdfs:Class ; rdfs:label "SAS/STAT Software, Version 8" ; rdfs:comment "Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000263 a rdfs:Class ; rdfs:label "Library Search Algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "JSON web service" ; rdfs:comment "A web service in which calls invoked return JSON." ; rdfs:subClassOf . swo:SWO_0000391 a rdfs:Class ; rdfs:label "SVDimpute algorithm" ; rdfs:subClassOf . swo:SWO_0000715 a rdfs:Class ; rdfs:label "'t-test'" ; rdfs:subClassOf . swo:SWO_0000151 a rdfs:Class ; rdfs:label "OS X"@en ; rdfs:comment "OS X is a Mac OS operating system which succeeds the original Mac OS, which had been Apple's primary operating system since 1984. Unlike the earlier Macintosh operating system, OS X is a Unix-based operating system." ; rdfs:subClassOf swo:SWO_0000149 . swo:SWO_1100053 a rdfs:Class ; rdfs:label "'CAMERA'" ; rdfs:comment "Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_1100144 a rdfs:Class ; rdfs:label "FastQC" ; rdfs:comment "FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "Maintained" ; rdfs:comment "Software has developers actively maintaining it (fixing bugs)" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Taverna workflow format" ; rdfs:comment "Format of Taverna workflows." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete geneRecommender"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Dynamic programming algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000332 a rdfs:Class ; rdfs:label "Radial basis function" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'EBImage'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000682 a rdfs:Class ; rdfs:label ".raw files" ; rdfs:subClassOf . swo:SWO_0000480 a rdfs:Class ; rdfs:label "'beadarraySNP'" ; rdfs:comment "Importing data from Illumina SNP experiments and performing copy number calculations and reports." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "material transformation objective"@en ; rdfs:comment "an objective specifiction that creates an specific output object from input materials."@en ; rdfs:subClassOf . swo:SWO_1100064 a rdfs:Class ; rdfs:label "ChipReader 3.1" ; rdfs:comment "Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime." ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000032 a rdfs:Class ; rdfs:label "Agilent Scan Control" ; rdfs:comment "Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions" ; rdfs:subClassOf swo:SWO_0000034 . a rdfs:Class ; rdfs:label "obsolete convert"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete arrayMvout"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Clustered gene expression profiles" ; rdfs:comment "Groupings of gene expression profiles according to a clustering algorithm." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "CC BY-NC-SA 3.0"@en ; rdfs:comment """CC BY-NC-SA 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . swo:SWO_0000597 a rdfs:Class ; rdfs:label "Local-pooled-error" ; rdfs:subClassOf . swo:SWO_1100133 a rdfs:Class ; rdfs:label "Stavrox" ; rdfs:comment "StavroX software identifies cross-linked peptides." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "CC BY-NC 4.0" ; rdfs:comment """CC BY-NC 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . swo:SWO_0000642 a rdfs:Class ; rdfs:label "ontoTools" ; rdfs:comment "tools for working with ontologies and graphs" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100042 a rdfs:Class ; rdfs:label "Beadstudio" ; rdfs:comment "BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100101 a rdfs:Class ; rdfs:label "FC" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BufferedMatrixMethods'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "WKn"@en ; rdfs:comment "WKn is a collective name for a spreadsheet format created for Lotus 1-2-3." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affyTiling"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100106 a rdfs:Class ; rdfs:label "GACK" ; rdfs:comment "Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "generalization specification" ; rdfs:comment "Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'DNAcopy'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000667 a rdfs:Class ; rdfs:label "preprocessCore" ; rdfs:comment "A library of core preprocessing routines" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "descriptive statistical calculation" ; rdfs:comment "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." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "class prediction objective"@en ; rdfs:comment """A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data."""@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete BAC"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000548 a rdfs:Class ; rdfs:label "gct" ; rdfs:comment "Gene Cluster Text file format " ; rdfs:subClassOf . swo:SWO_0000627 a rdfs:Class ; rdfs:label "Multinomial probit regression with Gaussian Process priors" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Iterative local regression and model selection"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100011 a rdfs:Class ; rdfs:label "'ANOVA'" ; rdfs:comment "ANOVA or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "software development" ; rdfs:comment "The process of developing software, typically involving the design, implementation and testing of software." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RdbiPgSQL"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Associative T method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete annaffy"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000173 a rdfs:Class ; rdfs:label "Gaussian locally weighted regression" ; rdfs:subClassOf . swo:SWO_0000364 a rdfs:Class ; rdfs:label "Robust likelihood-based survival modeling" ; rdfs:subClassOf . swo:SWO_1100027 a rdfs:Class ; rdfs:label "Agilent Feature Extraction software version A.5.1.1" ; rdfs:subClassOf swo:SWO_1100104 . a rdfs:Class ; rdfs:label "center calculation" ; rdfs:comment "A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set." ; rdfs:subClassOf . swo:SWO_0000237 a rdfs:Class ; rdfs:label "ImageReader" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "LPPL v1.2"@en ; rdfs:comment "LPPL v1.2 is a free software license (by the defintion of the GNU Project), This license is an incomplete statement of the distribution terms for LaTeX. While it is a free software license, it is incompatible with the GPL because it has many requirements that are not in the GPL. Software projects other than LaTeX rarely use it." ; rdfs:subClassOf . swo:SWO_0000285 a rdfs:Class ; rdfs:label "MVCClass" ; rdfs:comment "Creates classes used in model-view-controller (MVC) design" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "DNA nucleotide sequence"@en ; rdfs:comment "A nucleic acid sequence that indicate the order of nucleotides within some DNA." ; rdfs:subClassOf . swo:SWO_0000140 a rdfs:Class ; rdfs:label "search engine" ; rdfs:comment "A search engine is a software system that is designed to search for information on the World Wide Web." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete CMA"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000021 a rdfs:Class ; rdfs:label "operating system" ; rdfs:comment "An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete_SBML model" ; rdfs:comment "'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Quantile regression techniques"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000449 a rdfs:Class ; rdfs:label "Xba.CQV and Xba.regions" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete data annotation"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Regression model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000455 a rdfs:Class ; rdfs:label "'affyPLM'" ; rdfs:comment "A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools." ; rdfs:subClassOf swo:SWO_0000461 . a rdfs:Class ; rdfs:label "GeneProf Academic License"@en ; rdfs:comment "The GeneProf Academic License is a vendor-specific license which allows the access and use of the licensed resource for non-commercial purposes." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete pcot2"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete weaver"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "command-line interface" ; rdfs:comment "A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines)." ; rdfs:subClassOf swo:SWO_9000050 . swo:SWO_0000349 a rdfs:Class ; rdfs:label "RWebServices" ; rdfs:comment "This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete_Information processing" ; rdfs:comment "Information processing is a process in which input information is analysed or transformed in order to produce information as output." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete software development"@en ; rdfs:comment "AL 24.9.2019: Duplicate of http://www.ebi.ac.uk/swo/organization/SWO_9000056"@en ; rdfs:subClassOf . swo:SWO_0000274 a rdfs:Class ; rdfs:label "MATLAB language" ; rdfs:subClassOf . swo:SWO_0000218 a rdfs:Class ; rdfs:label "Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete reb"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "generically dependent continuant"@en ; rdfs:comment "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'BCRANK'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 't-test'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000094 a rdfs:Class ; rdfs:label "Assembly" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete idiogram"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GenePix 4100A"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Pathways 2.01 software"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Addgene Terms of Use"@en ; rdfs:comment "The Addgene Terms of Use specifies under what legal requirements Addgene data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of Addgene to exploit the data for commercial purposes. All copyright, trademark and other proprietary notices must be retained on the data. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use)." ; rdfs:subClassOf . swo:SWO_0000107 a rdfs:Class ; rdfs:label "Haskell" ; rdfs:subClassOf . a rdfs:Class ; rdfs:comment "An unconstrained type or object" . a rdfs:Class ; rdfs:label "outline document format" ; rdfs:comment "A format specification for data used or produced by outliner software" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "objective specification"@en ; rdfs:comment "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 ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete SLGI"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete minet"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "clustering task" ; rdfs:comment """Clustering. Clustering in general is concerned with grouping objects into classes of similar objects (Kaufman and Rousseeuw 1990). Given a set of examples (object descriptions), the task of clustering is to partition these examples into subsets, called clusters.""" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'CAMERA'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affyPara"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000166 a rdfs:Class ; rdfs:label "GLEAMS software" ; rdfs:comment "Microarray image quantification is performed using GLEAMS software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "obsolete simpleaffy"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000491 a rdfs:Class ; rdfs:label "'bridge'" ; rdfs:comment """The bridge package consists of several functions for testing for dierential expression among mul- tiple samples""" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000025 a rdfs:Class ; rdfs:label "Microsoft Word" ; rdfs:subClassOf swo:SWO_0000029 . swo:SWO_0000437 a rdfs:Class ; rdfs:label "Theodore Ts’o’s" ; rdfs:subClassOf . swo:SWO_9000078 a rdfs:Class ; rdfs:label "Annotare" ; rdfs:subClassOf swo:SWO_1100079 . a rdfs:Class ; rdfs:label "data transformation"@en ; rdfs:comment "A planned process that produces output data from input data."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete geneplotter"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000438 a rdfs:Class ; rdfs:label "TypeInfo" ; rdfs:comment "A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete RMA++"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Annotation data packages"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "k-nearest neighbors"@en ; rdfs:comment "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned."@en ; rdfs:subClassOf , , . a rdfs:Class ; rdfs:label "CC BY-NC-SA 2.5 IN"@en ; rdfs:comment """CC BY-NC-SA 2.5 IN is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. """ ; rdfs:subClassOf , . swo:SWO_0000530 a rdfs:Class ; rdfs:label "'externalVector'" ; rdfs:comment "Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete maigesPack"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000091 a rdfs:Class ; rdfs:label "ActionScript" ; rdfs:subClassOf . swo:SWO_0000426 a rdfs:Class ; rdfs:label "'Smith-Waterman'" ; rdfs:subClassOf . swo:SWO_0000479 a rdfs:Class ; rdfs:label "'beadarray'" ; rdfs:comment "The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000267 a rdfs:Class ; rdfs:label "Median Average Difference Algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "specimen collection process" ; rdfs:comment "A planned process with the objective of collecting a specimen." ; rdfs:subClassOf . swo:SWO_1100009 a rdfs:Class ; rdfs:label "AMDIS" ; rdfs:subClassOf . swo:SWO_0000706 a rdfs:Class ; rdfs:label "splots" ; rdfs:comment "The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete software publisher organization"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "web user interface"@en ; rdfs:comment "A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'clusterStab'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000248 a rdfs:Class ; rdfs:label "KEGGgraph" ; rdfs:comment "KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000226 a rdfs:Class ; rdfs:label "HilbertVisGUI" ; rdfs:comment "An interactive tool to visualize long vectors of integer data by means of Hilbert curves" ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000259 a rdfs:Class ; rdfs:label "LPEadj" ; rdfs:comment "Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "GML"@en ; rdfs:comment "GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GraphAlignment"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000321 a rdfs:Class ; rdfs:label "PPC algorithm" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "histogram"@en ; rdfs:comment """A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes."""@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete GeneSelector"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 2-sample pooled t-test"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000278 a rdfs:Class ; rdfs:label "MCR algorithm" ; rdfs:comment "minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples." ; rdfs:subClassOf . swo:SWO_0000444 a rdfs:Class ; rdfs:label "WilcEbam" ; rdfs:subClassOf . swo:SWO_0000544 a rdfs:Class ; rdfs:label "gaga" ; rdfs:comment "This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling)." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Release candidate" ; rdfs:comment "A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Median Average Difference Algorithm"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_1100086 a rdfs:Class ; rdfs:label "Complex Estimation Algorithm" ; rdfs:subClassOf . swo:SWO_0000701 a rdfs:Class ; rdfs:label "snpMatrix" ; rdfs:comment "Implements classes and methods for large-scale SNP association studies" ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . swo:SWO_1100031 a rdfs:Class ; rdfs:label "'BGmix'" ; rdfs:comment "Bayesian models for differential gene expression" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Rank product non-parametric method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000728 a rdfs:Class ; rdfs:label "widgetTools" ; rdfs:comment "This packages contains tools to support the construction of tcltk widgets" ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "Mammalia" ; rdfs:subClassOf . swo:SWO_0000504 a rdfs:Class ; rdfs:label "convert" ; rdfs:comment "Define coerce methods for microarray data objects." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete Ringo"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000310 a rdfs:Class ; rdfs:label "Optiquant" ; rdfs:comment "Computer software for image acquisition, analysis and reporting, for use in the life sciences" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "CEL ASCII format"@en ; rdfs:comment "CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Initial microarray data processing (data filtering, local normalisation and quality control)"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Hierarchical clustering"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000206 a rdfs:Class ; rdfs:label "GlobalAncova" ; rdfs:comment "GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete matchprobes"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete OMICS data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Viruses" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete FACS data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "BedGraph"@en ; rdfs:comment "The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "data item"@en ; rdfs:comment "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 ; rdfs:seeAlso ; rdfs:subClassOf . swo:SWO_1100079 a rdfs:Class ; rdfs:label "MAGE-TAB inputting software" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_0000177 a rdfs:Class ; rdfs:label "GenePix 3.0.6" ; rdfs:subClassOf swo:SWO_0000176 . a rdfs:Class ; rdfs:label "OBO Flat File Format" ; rdfs:comment "OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. " ; rdfs:subClassOf . swo:SWO_0000660 a rdfs:Class ; rdfs:label "plier" ; rdfs:comment "The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete 'cellHTS'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete_gff format" ; rdfs:comment "Equivalence with EDAM format_2305." ; rdfs:subClassOf . swo:SWO_0000010 a rdfs:Class ; rdfs:label "WordStar" ; rdfs:subClassOf swo:SWO_0000001 . swo:SWO_1100111 a rdfs:Class ; rdfs:label "GEOmetadb" ; rdfs:comment "The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata." ; rdfs:subClassOf swo:SWO_1100075 . swo:SWO_0000611 a rdfs:Class ; rdfs:label "makePlatformDesign" ; rdfs:comment "makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "CC BY 4.0"@en ; rdfs:comment """The CC BY 4.0 license is a Creative Commons license. This is a non-copyleft free license that is good for art and entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. People are free to: Share — copy and redistribute the material in any medium or format; Adapt — remix, transform, and build upon the material for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. But they must conform to the following terms: Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.""" ; rdfs:subClassOf , . swo:SWO_0000063 a rdfs:Class ; rdfs:label "Drive5 MUSCLE"@en ; rdfs:subClassOf swo:SWO_0000060 . a rdfs:Class ; rdfs:label "Open source software license" ; rdfs:subClassOf swo:SWO_0000002 . a rdfs:Class ; rdfs:label "Data File Standard for Flow Cytometry"@en ; rdfs:comment "The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type." ; rdfs:subClassOf . swo:SWO_9000093 a rdfs:Class ; rdfs:label "Endnote" ; rdfs:comment "Citation management software" ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "Artistic License 2.0" ; rdfs:comment "The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0)." ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "vector image format" ; rdfs:comment "A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Microsoft Word doc" ; rdfs:comment "A file format for word processing documents for Microsoft Word. " ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Bacteria" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete RBioinf"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "collection of specimens"@en ; rdfs:comment "A material entity that has two or more specimens as its parts."@en ; rdfs:subClassOf . a rdf:Property ; rdfs:label "has member"@en ; rdfs:comment "has member is a mereological relation between a collection and an item." ; rdfs:range ; rdfs:subPropertyOf . a rdfs:Class ; rdfs:label "probability distribution estimation algorithm" ; rdfs:subClassOf . swo:SWO_0000570 a rdfs:Class ; rdfs:label "gxl format" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Agilent Feature Extraction software version 7.1"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000047 a rdfs:Class ; rdfs:label "Axon GenePix Pro 3" ; rdfs:subClassOf swo:SWO_0000187 . swo:SWO_0000468 a rdfs:Class ; rdfs:label "annotationTools" ; rdfs:comment "This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files)." ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete lumi"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete splots"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "Amniota" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete Two-stage measurement error model"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete affycomp"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000451 a rdfs:Class ; rdfs:label "Acuity" ; rdfs:comment "Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security." ; rdfs:subClassOf swo:SWO_0000001 . a rdfs:Class ; rdfs:label "Ontology" ; rdfs:comment "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete ssize"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000463 a rdfs:Class ; rdfs:label "altcdfenvs" ; rdfs:comment "altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs. " ; rdfs:subClassOf swo:SWO_1100047 , swo:SWO_1100075 . a rdfs:Class ; rdfs:label "document"@en ; rdfs:comment "A collection of information content entities intended to be understood together as a whole"@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete 'ANOVA'"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete qPCR data"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "MPL v1.1" ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "obsolete nem"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . swo:SWO_0000230 a rdfs:Class ; rdfs:label "IRanges" ; rdfs:comment "The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions." ; rdfs:subClassOf swo:SWO_1100075 . a rdfs:Class ; rdfs:label "obsolete IRanges"@en ; rdfs:comment "AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information."@en ; rdfs:subClassOf . a rdfs:Class ; rdfs:label "OME Software Conditons of Use"@en ; rdfs:comment """All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under GNU public \"copyleft\" licenses or through commercial license from Glencoe Software. FLIMfit is also now available under a GNU public \"copyleft\" license. For questions about the GNU license refer to the Frequently Asked Questions about the GNU Licenses page. Bio-Formats - under the terms of the GNU public \"copyleft\" license, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive BSD-2 license which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the supported formats table. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from Glencoe Software; please contact them at bioformats@glencoesoftware.com to discuss your requirements. The core OME Model Schema files (.XSD) use the Creative Commons Attribution 4.0 International License, and as such you are free to share or adapt them as long as you attribute the OME consortium as follows; \"This work is derived in part from the OME specification. Copyright (C) 2002-2016 Open Microscopy Environment\". See further information about using OME-XML in your work. This website is also covered by the Creative Commons Attribution 4.0 International License - you are free to share or adapt content as long as you credit the Open Microscopy Environment. The exception to this is the screenshots and videos which can only be used for non-commercial purposes, see Attributions below. """ ; rdfs:subClassOf , . a rdfs:Class ; rdfs:label "obsolete_PSI-MI format" ; rdfs:comment "Equivalence with EDAM format_3158." ; rdfs:subClassOf . a rdf:Property ; rdfs:label "editor preferred label" ; rdfs:comment "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "example of usage" ; rdfs:comment "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." ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "textual definition" ; rdfs:comment "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 ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "term editor"@en ; rdfs:comment "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 ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "alternative term" ; rdfs:comment "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "definition source" ; rdfs:comment "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 ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "term tracker item"@en ; rdfs:comment "An IRI or similar locator for a request or discussion of an ontology term."@en ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "imported from"@en ; rdfs:comment "For external terms/classes, the ontology from which the term was imported"@en ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "term replaced by" ; rdfs:comment "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "is_specified_input_of"@en ; rdfs:comment "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 ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "inheres in"@en ; rdfs:comment "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "quality of"@en ; rdfs:comment "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "role of"@en ; rdfs:comment "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has quality"@en ; rdfs:comment "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en ; rdfs:range ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "disposition of"@en ; rdfs:comment "inverse of has disposition" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has regulatory component activity" ; rdfs:comment "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "has negative regulatory component activity" ; rdfs:comment "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "has positive regulatory component activity" ; rdfs:comment "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "has component activity" ; rdfs:comment "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly regulated by" ; rdfs:comment "Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly negatively regulated by" ; rdfs:comment "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly positively regulated by" ; rdfs:comment "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has effector activity" ; rdfs:comment "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "ends after"@en ; rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "immediately preceded by"@en ; rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "immediately precedes"@en ; rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "overlaps"@en ; rdfs:comment "x overlaps y if and only if there exists some z such that x has part z and z part of y" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "has component"@en ; rdfs:comment "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "negatively regulates"@en ; rdfs:comment "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "positively regulates"@en ; rdfs:comment "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "capable of part of"@en ; rdfs:comment "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "has output"@en ; rdfs:comment "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "acts upstream of" ; rdfs:comment "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "acts upstream of or within" ; rdfs:comment "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causally upstream of, positive effect" ; rdfs:comment "p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "causally upstream of, negative effect" ; rdfs:comment "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "characteristic of part of"@en ; rdfs:comment "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "mereotopologically related to"@en ; rdfs:comment "A mereological relationship or a topological relationship" ; rdfs:range . a rdf:Property ; rdfs:label "enables"@en ; rdfs:comment "c enables p iff c is capable of p and c acts to execute p." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "functionally related to"@en ; rdfs:comment "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." ; rdfs:range . a rdf:Property ; rdfs:label "part of structure that is capable of"@en ; rdfs:comment "this relation holds between c and p when c is part of some c', and c' is capable of p." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "involved in"@en ; rdfs:comment "c involved_in p if and only if c enables some process p', and p' is part of p" ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "enabled by"@en ; rdfs:comment "inverse of enables" ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "negatively regulated by"@en ; rdfs:comment "inverse of negatively regulates" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "positively regulated by"@en ; rdfs:comment "inverse of positively regulates" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "member of"@en ; rdfs:comment "is member of is a mereological relation between a item and a collection." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "input of" ; rdfs:comment "inverse of has input" ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "output of" ; rdfs:comment "inverse of has output" ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "causally downstream of"@en ; rdfs:comment "inverse of upstream of" ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "immediately causally downstream of"@en ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "indirectly positively regulates"@en ; rdfs:comment "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "indirectly negatively regulates"@en ; rdfs:comment "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "causally related to"@en ; rdfs:comment "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." ; rdfs:range . a rdf:Property ; rdfs:label "causally upstream of"@en ; rdfs:comment "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "immediately causally upstream of"@en ; rdfs:comment "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "causally upstream of or within" ; rdfs:comment "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causally downstream of or within" ; rdfs:comment "inverse of causally upstream of or within" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "involved in regulation of" ; rdfs:comment "c involved in regulation of p if c is involved in some p' and p' regulates some p" ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "involved in positive regulation of" ; rdfs:comment "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "involved in negative regulation of" ; rdfs:comment "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "involved in or involved in regulation of" ; rdfs:comment "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" ; rdfs:range xsd:string ; rdfs:subPropertyOf , , . a rdf:Property ; rdfs:label "molecularly interacts with" ; rdfs:comment "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "phosphorylates" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "helper property (not for use in curation)" ; rdfs:range . a rdf:Property ; rdfs:label "is kinase activity" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causal agent in process" ; rdfs:comment "A relationship between a material entity and a process where the material entity has some causal role that influences the process" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "depends on" ; rdfs:seeAlso ; rdfs:range . a rdf:Property ; rdfs:label "causally influenced by" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "interaction relation helper property" ; rdfs:seeAlso , ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "molecular interaction relation helper property" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly regulates" ; rdfs:comment "p directly regulates q iff p is immediately causally upstream of q and p regulates q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "is a defining property chain axiom" ; rdfs:comment "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "is a defining property chain axiom where second argument is reflexive" ; rdfs:comment "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "has part structure that is capable of" ; rdfs:comment "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "capable of regulating" ; rdfs:comment "Holds between c and p if and only if c is capable of some activity a, and a regulates p." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "capable of negatively regulating" ; rdfs:comment "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "capable of positively regulating" ; rdfs:comment "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "process has causal agent" ; rdfs:comment "Inverse of 'causal agent in process'" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "directly positively regulates" ; rdfs:comment "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "directly negatively regulates" ; rdfs:comment "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "enables subfunction" ; rdfs:comment "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "acts upstream of or within, positive effect" ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "acts upstream of or within, negative effect" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "acts upstream of, positive effect" ; rdfs:comment "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "acts upstream of, negative effect" ; rdfs:comment "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" ; rdfs:seeAlso ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "causally upstream of or within, negative effect" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "causally upstream of or within, positive effect" ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "indirectly causally upstream of"@en ; rdfs:comment "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "indirectly regulates"@en ; rdfs:comment "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." ; rdfs:range xsd:string ; rdfs:subPropertyOf , . a rdf:Property ; rdfs:label "device utilizes material"@en ; rdfs:comment "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." ; rdfs:range . a rdf:Property ; rdfs:label "positively regulates characteristic" ; rdfs:comment "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "negatively regulates characteristic" ; rdfs:comment "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:range xsd:string . a rdf:Property ; rdfs:range xsd:string . a rdf:Property ; rdfs:range xsd:string . a rdf:Property ; rdfs:range xsd:string . a rdf:Property ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "obsoleted in version" ; rdfs:comment "The version in which a class or property has been made obsolete" ; rdfs:range xsd:string . a rdf:Property ; rdfs:label "obsolete reason_for_obsolescence"@en ; rdfs:comment "AL 2023-03-05: Replaced by rdfs:comment as no longer within the EFO release files."@en ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . a rdf:Property ; rdfs:label "obsolete is developed by"@en ; rdfs:comment "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs."@en ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . a rdf:Property ; rdfs:label "has legal status" ; rdfs:comment "This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage." ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . a rdf:Property ; rdfs:label "obsolete implements"@en ; rdfs:comment "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs."@en ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . a rdf:Property ; rdfs:label "obsolete is encoded in"@en ; rdfs:comment "AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs."@en ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . swo:SWO_0000300 a rdf:Property ; rdfs:label "followed by" ; rdfs:comment "AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' (which was the original parent for 'directly followed by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class that performs a similar function to BFO 'precedes' but without the domain/range restrictions." ; rdfs:range . swo:SWO_0000301 a rdf:Property ; rdfs:label "follows" ; rdfs:comment "AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' and 'preceded by' (which was the original parent for 'directly preceded by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class (and this, its inverse) that performs a similar function to BFO 'precedes' but without the domain/range restrictions." ; rdfs:range . swo:SWO_0004003 a rdf:Property ; rdfs:label "obsolete_is developed by" ; rdfs:comment "is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead." ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . swo:SWO_0004007 a rdf:Property ; rdfs:label "obsolete object property" ; rdfs:comment "Stores those object properties which are no longer appropriate for use within SWO." ; rdfs:range . swo:SWO_9000058 a rdf:Property ; rdfs:label "obsolete_is specified output of" ; rdfs:comment "There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead." ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . swo:is_license_for a rdf:Property ; rdfs:label "is license for"@en ; rdfs:comment "The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it." ; rdfs:range xsd:string ; rdfs:subPropertyOf . a rdf:Property ; rdfs:label "obsolete_has_participant" ; rdfs:comment "Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class." ; rdfs:range xsd:string ; rdfs:subPropertyOf swo:SWO_0004007 . a rdf:Property ; rdfs:label "part of" ; rdfs:comment "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.)" ; rdfs:range . a rdfs:Class ; rdfs:label "pathologic lymph node stage for colon and rectum according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." ; rdfs:subClassOf . a ; rdfs:label "pN0 (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis." . a ; rdfs:label "pN1 (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes." . a ; rdfs:label "pN1a (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node." . a ; rdfs:label "pN1b (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes." . a ; rdfs:label "pN1c (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis." . a ; rdfs:label "pN2 (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes." . a ; rdfs:label "pN2a (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes." . a ; rdfs:label "pN2b (colon)" ; rdfs:comment "A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes." . a rdfs:Class ; rdfs:label "pathologic distant metastases stage for ovary according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "cM0 (ovary)" ; rdfs:comment "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis." . a ; rdfs:label "cM1 (ovary)" ; rdfs:comment "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment." . a ; rdfs:label "pM1 (ovary)" ; rdfs:comment "A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed." . a rdfs:Class ; rdfs:label "clinical tumor stage group according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems." ; rdfs:subClassOf . a ; rdfs:label "Occult Carcinoma (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma." . a ; rdfs:label "Stage 0 (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. " . a ; rdfs:label "Stage I (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes." . a ; rdfs:label "Stage IIA (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC." . a ; rdfs:label "Stage IIB (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC." . a ; rdfs:label "Stage IIC (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB." . a ; rdfs:label "Stage IIIA (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC." . a ; rdfs:label "Stage IIIB (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC." . a ; rdfs:label "Stage IIIC (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB." . a ; rdfs:label "Stage IVA (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB." . a ; rdfs:label "Stage IVB (AJCC 7th)" ; rdfs:comment "A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA." . a rdfs:Class ; rdfs:label "concentration unit" ; rdfs:subClassOf . a ; rdfs:label "molar" ; rdfs:comment "A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L)." . a ; rdfs:label "millimolar" ; rdfs:comment "A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M." . a ; rdfs:label "micromolar" ; rdfs:comment "A unit of molarity which is equal to one millionth of a molar or 10^[-6] M." . a ; rdfs:label "nanomolar" ; rdfs:comment "A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M." . a ; rdfs:label "picomolar" ; rdfs:comment "A unit of molarity which is equal to 10^[-12] M." . a ; rdfs:label "mass percentage" ; rdfs:comment "A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture." . a ; rdfs:label "mass volume percentage" ; rdfs:comment "A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture." . a ; rdfs:label "volume percentage" ; rdfs:comment "A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution." . a ; rdfs:label "gram per liter" ; rdfs:comment "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." . a ; rdfs:label "milligram per milliliter" ; rdfs:comment "A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters." . a ; rdfs:label "pH" ; rdfs:comment "A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+)." . a ; rdfs:label "milliliter per liter" ; rdfs:comment "A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution." . a ; rdfs:label "gram per deciliter" ; rdfs:comment "A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters." . a ; rdfs:label "colony forming unit per volume" ; rdfs:comment "A concentration unit which a measure of viable bacterial numbers in a given volume." . a ; rdfs:label "microgram per liter" ; rdfs:comment "A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters." . a rdfs:Class ; rdfs:label "International Federation of Gynecology and Obstetrics ovarian cancer stage value specification" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system." ; rdfs:subClassOf . a ; rdfs:label "Stage 1 (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0." . a ; rdfs:label "Stage 1A (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0." . a ; rdfs:label "Stage 1B (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0." . a ; rdfs:label "Stage 1C (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0." . a ; rdfs:label "Stage 2 (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0." . a ; rdfs:label "Stage 2A (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0." . a ; rdfs:label "Stage 2B (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0." . a ; rdfs:label "Stage 2C (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0." . a ; rdfs:label "Stage 3 (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0)." . a ; rdfs:label "Stage 3A (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 ." . a ; rdfs:label "Stage 3B (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 ." . a ; rdfs:label "Stage 3C (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0)." . a ; rdfs:label "Stage 4 (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1." . a ; rdfs:label "Stage Unknown (FIGO)" ; rdfs:comment "A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0)." . a rdfs:Class ; rdfs:label "pathologic lymph node stage for ovary according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." ; rdfs:subClassOf . a ; rdfs:label "pN0 (ovary)" ; rdfs:comment "A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis." . a ; rdfs:label "pN1 (ovary)" ; rdfs:comment "A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis." . a rdfs:Class ; rdfs:label "frequency unit" ; rdfs:subClassOf . a ; rdfs:label "hertz" ; rdfs:comment "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." . a rdfs:Class ; rdfs:label "pathologic primary tumor stage for colon and rectum according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "pT0 (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor." . a ; rdfs:label "pTis (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria)." . a ; rdfs:label "pT1 (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa." . a ; rdfs:label "pT2 (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria." . a ; rdfs:label "pT3 (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues." . a ; rdfs:label "pT4a (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum." . a ; rdfs:label "pT4b (colon)" ; rdfs:comment "A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures." . a rdfs:Class ; rdfs:label "Eastern Cooperative Oncology Group score value specification" ; rdfs:comment "A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient." ; rdfs:subClassOf . a ; rdfs:label "3: symptomatic in bed more than 50% of the day but not bed ridden" ; rdfs:comment "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden." . a ; rdfs:label "2: symptomatic but in bed less than 50% of the day" ; rdfs:comment "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day." . a ; rdfs:label "4: bed ridden" ; rdfs:comment "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden." . a ; rdfs:label "0: asymptomatic" ; rdfs:comment "An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic." . a ; rdfs:label "1: symptomatic but fully ambulatory" ; rdfs:comment "An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory." . a rdfs:Class ; rdfs:label "pathologic distant metastases stage for colon according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "cM0 (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis." . a ; rdfs:label "cM1 (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases." . a ; rdfs:label "cM1a (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment." . a ; rdfs:label "cM1b (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment." . a ; rdfs:label "pM1 (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease." . a ; rdfs:label "pM1a (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed." . a ; rdfs:label "pM1b (colon)" ; rdfs:comment "A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed." . a rdfs:Class ; rdfs:label "temperature unit" ; rdfs:subClassOf . a ; rdfs:label "degree Celsius" ; rdfs:comment "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." . a ; rdfs:label "degree Fahrenheit" ; rdfs:comment "A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius." . a rdfs:Class ; rdfs:label "categorical label" ; rdfs:comment "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale." ; rdfs:subClassOf . a ; rdfs:label "right handed" . a ; rdfs:label "ambidexterous" . a ; rdfs:label "left handed" . a rdfs:Class ; rdfs:label "pathologic lymph node stage for lung according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." ; rdfs:subClassOf . a ; rdfs:label "pN0 (lung)" ; rdfs:comment "A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis." . a ; rdfs:label "pN1 (lung)" ; rdfs:comment "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension." . a ; rdfs:label "pN2 (lung)" ; rdfs:comment "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s)." . a ; rdfs:label "pN3 (lung)" ; rdfs:comment "A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s)." . a rdfs:Class ; rdfs:label "histologic grade for ovarian tumor according to the World Health Organization" ; rdfs:comment "A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO)." ; rdfs:subClassOf . a ; rdfs:label "G1 (WHO)" ; rdfs:comment "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated." . a ; rdfs:label "G2 (WHO)" ; rdfs:comment "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated." . a ; rdfs:label "G3 (WHO)" ; rdfs:comment "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated." . a ; rdfs:label "G4 (WHO)" ; rdfs:comment "A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated." . a rdfs:Class ; rdfs:label "pathologic distant metastases stage for kidney according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "cM0 (kidney)" ; rdfs:comment "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis." . a ; rdfs:label "cM1 (kidney)" ; rdfs:comment "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment." . a ; rdfs:label "pM1 (kidney)" ; rdfs:comment "A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed." . a rdfs:Class ; rdfs:label "pathologic primary tumor stage for kidney according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "pT0 (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor." . a ; rdfs:label "pT1 (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney." . a ; rdfs:label "pT1a (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less." . a ; rdfs:label "pT1b (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm." . a ; rdfs:label "pT2 (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney." . a ; rdfs:label "pT2a (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm." . a ; rdfs:label "pT2b (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney." . a ; rdfs:label "pT3 (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia." . a ; rdfs:label "pT3a (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia." . a ; rdfs:label "pT3b (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm." . a ; rdfs:label "pT3c (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava." . a ; rdfs:label "pT4 (kidney)" ; rdfs:comment "A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland)." . a rdfs:Class ; rdfs:label "rate unit" ; rdfs:subClassOf . a ; rdfs:label "count per nanomolar second" ; rdfs:comment "A rate unit which is equal to one over one nanomolar second." . a ; rdfs:label "count per molar second" ; rdfs:comment "A rate unit which is equal to one over one molar second." . a ; rdfs:label "count per nanomolar" ; rdfs:comment "A rate unit which is equal to one over one nanomolar." . a ; rdfs:label "count per molar" ; rdfs:comment "A rate unit which is equal to one over one molar." . a rdfs:Class ; rdfs:label "substance unit" ; rdfs:subClassOf . a ; rdfs:label "micromole" ; rdfs:comment "A substance unit equal to a millionth of a mol or 10^[-6] mol." . a ; rdfs:label "nanomole" ; rdfs:comment "A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol." . a ; rdfs:label "picomole" ; rdfs:comment "A substance unit equal to 10^[-12] mol." . a rdfs:Class ; rdfs:label "denotator type"@en ; rdfs:comment "A denotator type indicates how a term should be interpreted from an ontological perspective."@en ; rdfs:subClassOf . a ; rdfs:label "universal"@en . a ; rdfs:label "defined class"@en ; rdfs:comment "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en . a ; rdfs:label "named class expression"@en ; rdfs:comment "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en . a rdfs:Class ; rdfs:label "histologic grade for ovarian tumor according to a two-tier grading system" ; rdfs:comment "A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. " ; rdfs:subClassOf . a ; rdfs:label "Low grade ovarian tumor" ; rdfs:comment "A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade." . a ; rdfs:label "High grade ovarian tumor" ; rdfs:comment "A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade." . a rdfs:Class ; rdfs:label "GenePattern software" ; rdfs:comment "a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks." ; rdfs:subClassOf . a ; rdfs:label "GenePattern module SVM" ; rdfs:comment "GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation." . a ; rdfs:label "GenePattern module KMeansClustering" ; rdfs:comment "GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation." . a ; rdfs:label "GenePattern module CARTXValidation" ; rdfs:comment "GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations." . a ; rdfs:label "GenePattern module KNNXValidation" ; rdfs:comment "GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations." . a ; rdfs:label "GenePattern module PeakMatch" . a ; rdfs:label "GenePattern module KNN" ; rdfs:comment "GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation." . a ; rdfs:label "GenePattern module HierarchicalClustering" ; rdfs:comment "GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation." . a ; rdfs:label "GenePattern module PCA" ; rdfs:comment "GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation." . a ; rdfs:label "GenePattern module HeatMapViewer" ; rdfs:comment "A GenePattern software module which is used to generate a heatmap view of data." . a ; rdfs:label "GenePattern module HierarchicalClusteringViewer" ; rdfs:comment "A GenePattern software module which is used to generate a view of data that has been hierarchically clustered." . a rdfs:Class ; rdfs:label "histologic grade according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system." ; rdfs:subClassOf . a ; rdfs:label "G1: Well differentiated" ; rdfs:comment "A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal." . a ; rdfs:label "G2: Moderately differentiated" ; rdfs:comment "A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade." . a ; rdfs:label "G3: Poorly differentiated" ; rdfs:comment "A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue." . a ; rdfs:label "G4: Undifferentiated" ; rdfs:comment "A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue." . a rdfs:Class ; rdfs:label "time unit" ; rdfs:comment "A unit which is a standard measure of the dimension in which events occur in sequence." ; rdfs:subClassOf . a ; rdfs:label "second" ; rdfs:comment "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." . a ; rdfs:label "minute" ; rdfs:comment "A time unit which is equal to 60 seconds." . a ; rdfs:label "hour" ; rdfs:comment "A time unit which is equal to 3600 seconds or 60 minutes." . a ; rdfs:label "day" ; rdfs:comment "A time unit which is equal to 24 hours." . a ; rdfs:label "week" ; rdfs:comment "A time unit which is equal to 7 days." . a ; rdfs:label "month" ; rdfs:comment "A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days." . a ; rdfs:label "year" ; rdfs:comment "A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days." . a rdfs:Class ; rdfs:label "pathologic distant metastases stage for lung according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "cM0 (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis." . a ; rdfs:label "cM1 (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment." . a ; rdfs:label "cM1a (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion." . a ; rdfs:label "cM1b (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment." . a ; rdfs:label "pM1 (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed." . a ; rdfs:label "pM1a (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion." . a ; rdfs:label "pM1b (lung)" ; rdfs:comment "A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis." . a rdfs:Class ; rdfs:label "volume unit" ; rdfs:subClassOf . a ; rdfs:label "cubic centimeter" ; rdfs:comment "A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml." . a ; rdfs:label "milliliter" ; rdfs:comment "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." . a ; rdfs:label "liter" ; rdfs:comment "A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter." . a ; rdfs:label "cubic decimeter" ; rdfs:comment "A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L." . a ; rdfs:label "microliter" ; rdfs:comment "A volume unit which is equal to one millionth of a liter or 10^[-6] L." . a ; rdfs:label "nanoliter" ; rdfs:comment "A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L." . a ; rdfs:label "picoliter" ; rdfs:comment "A volume unit which is equal to 10^[-12] L." . a rdfs:Class ; rdfs:label "questionnaire" ; rdfs:comment "A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study."@en ; rdfs:subClassOf . a ; rdfs:label "Edingburgh handedness inventory" ; rdfs:comment "The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. "@en . a rdfs:Class ; rdfs:label "length unit" ; rdfs:comment "A unit which is a standard measure of the distance between two points." ; rdfs:subClassOf . a ; rdfs:label "meter" ; rdfs:comment "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." . a ; rdfs:label "centimeter" ; rdfs:comment "A length unit which is equal to one hundredth of a meter or 10^[-2] m." . a ; rdfs:label "millimeter" ; rdfs:comment "A length unit which is equal to one thousandth of a meter or 10^[-3] m." . a ; rdfs:label "micrometer" ; rdfs:comment "A length unit which is equal to one millionth of a meter or 10^[-6] m." . a ; rdfs:label "nanometer" ; rdfs:comment "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." . a ; rdfs:label "angstrom" ; rdfs:comment "A length unit which is equal to 10 [-10] m." . a rdfs:Class ; rdfs:label "principal components analysis dimensionality reduction"@en ; rdfs:comment "A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones."@en ; rdfs:subClassOf . a ; rdfs:label "GenePattern PCA" . a rdfs:Class ; rdfs:label "International Federation of Gynecology and Obstetrics cervical cancer stage value specification" ; rdfs:comment "A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems." ; rdfs:subClassOf . a ; rdfs:label "Stage IA (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm." . a ; rdfs:label "Stage IA1 (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm." . a ; rdfs:label "Stage IA2 (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm." . a ; rdfs:label "Stage IB (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA" . a ; rdfs:label "Stage IB1 (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension." . a ; rdfs:label "Stage IB2 (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension." . a ; rdfs:label "Stage IIA (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. " . a ; rdfs:label "Stage IIA1 (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. " . a ; rdfs:label "Stage IIA2 (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. " . a ; rdfs:label "Stage IIB (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. " . a ; rdfs:label "Stage IIIA (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall." . a ; rdfs:label "Stage IIIB (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney." . a ; rdfs:label "Stage IVA (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs." . a ; rdfs:label "Stage IVB (FIGO)" ; rdfs:comment "An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs." . a rdfs:Class ; rdfs:label "pathologic lymph node stage for kidney according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." ; rdfs:subClassOf . a ; rdfs:label "pN0 (kidney)" ; rdfs:comment "A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis." . a ; rdfs:label "pN1 (kidney)" ; rdfs:comment "A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis." . a rdfs:Class ; rdfs:label "peak matching" ; rdfs:comment "Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold" ; rdfs:subClassOf . a ; rdfs:label "GenePattern peak matching" . a rdfs:Class ; rdfs:label "Karnofsky score vaue specification" ; rdfs:comment "A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment." ; rdfs:subClassOf . a ; rdfs:label "100: asymptomatic" ; rdfs:comment "A Karnofsky score vaue specification indicating that a patient is asymptomatic." . a ; rdfs:label "80-90: symptomatic but fully ambulatory" ; rdfs:comment "A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory." . a ; rdfs:label "60-70: symptomatic but in bed less than 50% of the day" ; rdfs:comment "A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day." . a ; rdfs:label "40-50: symptomatic, in bed more than 50% of the day, but not bed ridden" ; rdfs:comment "A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden." . a rdfs:Class ; rdfs:label "volumetric flow rate unit" ; rdfs:subClassOf . a ; rdfs:label "microliters per minute" ; rdfs:comment "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." . a rdfs:Class ; rdfs:label "CART"@en ; rdfs:comment "A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure."@en ; rdfs:subClassOf . a ; rdfs:label "GenePattern CART" . a rdfs:Class ; rdfs:label "histologic grade according to the Fuhrman Nuclear Grading System" ; rdfs:comment "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System." ; rdfs:subClassOf . a ; rdfs:label "G1 (Fuhrman)" ; rdfs:comment "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent." . a ; rdfs:label "G2 (Fuhrman)" ; rdfs:comment "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident." . a ; rdfs:label "G3 (Fuhrman)" ; rdfs:comment "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent." . a ; rdfs:label "G4 (Fuhrman)" ; rdfs:comment "A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped." . a rdfs:Class ; rdfs:label "mass unit" ; rdfs:comment "A unit which is a standard measure of the amount of matter/energy of a physical object." ; rdfs:subClassOf . a ; rdfs:label "kilogram" ; rdfs:comment "A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France." . a ; rdfs:label "gram" ; rdfs:comment "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." . a ; rdfs:label "milligram" ; rdfs:comment "A mass unit which is equal to one thousandth of a gram or 10^[-3] g." . a ; rdfs:label "microgram" ; rdfs:comment "A mass unit which is equal to one millionth of a gram or 10^[-6] g." . a ; rdfs:label "nanogram" ; rdfs:comment "A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g." . a ; rdfs:label "picogram" ; rdfs:comment "A mass unit which is equal to 10^[-12] g." . a rdfs:Class ; rdfs:label "leave one out cross validation method"@en ; rdfs:comment "is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data" ; rdfs:subClassOf . a ; rdfs:label "GenePattern LOOCV" . a rdfs:Class ; rdfs:label "obsolescence reason specification"@en ; rdfs:comment "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 ; rdfs:subClassOf . a ; rdfs:label "failed exploratory term"@en ; rdfs:comment "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en . a ; rdfs:label "placeholder removed"@en . a ; rdfs:label "terms merged"@en . a ; rdfs:label "term imported"@en . a ; rdfs:label "term split"@en . a rdfs:Class ; rdfs:label "curation status specification"@en ; rdfs:comment "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 ; rdfs:subClassOf . a ; rdfs:label "example to be eventually removed"@en . a ; rdfs:label "metadata complete"@en ; rdfs:comment "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 ; rdfs:label "organizational term"@en ; rdfs:comment "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en . a ; rdfs:label "ready for release"@en ; rdfs:comment "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 ; rdfs:label "metadata incomplete"@en ; rdfs:comment "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en . a ; rdfs:label "uncurated"@en ; rdfs:comment "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en . a ; rdfs:label "pending final vetting"@en ; rdfs:comment "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 ; rdfs:label "to be replaced with external ontology term"@en ; rdfs:comment "Terms with this status should eventually replaced with a term from another ontology."@en . a ; rdfs:label "requires discussion"@en ; rdfs:comment "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 . a rdfs:Class ; rdfs:label "pathologic primary tumor stage for ovary according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "pT0 (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor." . a ; rdfs:label "pT1 (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both)." . a ; rdfs:label "pT1a (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings." . a ; rdfs:label "pT1b (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings." . a ; rdfs:label "pT1c (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings." . a ; rdfs:label "pT2 (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension." . a ; rdfs:label "pT2a (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings." . a ; rdfs:label "pT2b (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings." . a ; rdfs:label "pT2c (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings." . a ; rdfs:label "pT3 (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis." . a ; rdfs:label "pT3a (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis." . a ; rdfs:label "pT3b (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension." . a ; rdfs:label "pT3c (ovary)" ; rdfs:comment "A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis." . a rdfs:Class ; rdfs:label "pathologic primary tumor stage for lung according to AJCC 7th edition" ; rdfs:comment "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." ; rdfs:subClassOf . a ; rdfs:label "pT0 (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor." . a ; rdfs:label "pTis (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ." . a ; rdfs:label "pT1 (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus)." . a ; rdfs:label "pT1a (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension." . a ; rdfs:label "pT1b (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension." . a ; rdfs:label "pT2 (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung." . a ; rdfs:label "pT2a (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension." . a ; rdfs:label "pT2b (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension." . a ; rdfs:label "pT3 (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary." . a ; rdfs:label "pT4 (lung)" ; rdfs:comment "A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary." .