PREFIX rdf: PREFIX rdfs: PREFIX sepio-model: PREFIX xsd: sepio-model:Qualifier a rdfs:Class ; rdfs:label "Qualifier" ; rdfs:comment "A key-value object used to capture additional piece of information that extends or refines the meaning of a Statement's core subject - predicate - object 'triple' - by providing additional detail, or constraining the statement to apply in a particular context." ; rdfs:subClassOf sepio-model:Utility . sepio-model:name a rdf:Property ; rdfs:comment "A descriptive name that describes the type of information captured in the Qualifier value." , "The given name of the Agent." , "A name for the Extension. Should be indicative of its meaning and/or the type of information it value represents." , "The type of the trait or role described by the trait (e.g. 'ethnicity', 'sex', 'age', 'disease status')." ; rdfs:range xsd:string . sepio-model:value a rdf:Property ; rdfs:comment "The value of the qualifier - holding information that refines/extends the meaning of the Statement." , "The value of the data item (could be quantitative or qualitative depending on the type of data item)." , "A free-text rendering of the expression used as a label for the entity" , "The value of the Extension - can be any primitive or structured object" ; rdfs:range xsd:string . sepio-model:DataItem a rdfs:Class ; rdfs:label "Data Item" ; rdfs:comment "An Information Entity representing an individual piece of data, generated or acquired through methods which reliably produce truthful information about something." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:date_authored a rdf:Property ; rdfs:comment "Indicates when the information content expressed in the Information Entity was generated." ; rdfs:range xsd:string . sepio-model:subtype a rdf:Property ; rdfs:comment "A specific type of data the DataItem instance represents (e.g. a 'specimen count', a 'patient weight', an 'allele frequency', a 'p-value')" , "A specific type of activity the Activity instance represents." , "A specific type of agent the Agent object represents. Must be one of {person, organization, software}" , "A specific type of method that a Method instance represents (e.g. 'Variant Interpretation Guideline', or 'Experimental Protocol')." , "A specific type of data set the DataSet instance represents (e.g. a 'clinical data set', a 'sequencing data set', a 'gene expression data set', a 'genome annotation data set')." , "A specific type of evidence the EvidenceLine instance represents (e.g. 'mutant phenotype evidence', 'evidence from manual interpretation', 'ACMG PM2 evidence')" , "A specific type of document that a Document instance represents (e.g. 'publication', 'patent', 'pathology report')" ; rdfs:range sepio-model:Coding , xsd:string . sepio-model:supporting_method_types a rdf:Property ; rdfs:comment "Types of methodological approaches that were executed to directly or indirectly support creation of the Information Entity." ; rdfs:range sepio-model:Coding . sepio-model:derived_from a rdf:Property ; rdfs:comment "Another Information Entity from which this Information Entity is derived, in whole or in part." ; rdfs:range sepio-model:InformationEntity . sepio-model:reported_in a rdf:Property ; rdfs:comment "A document in which the Information Entity is reported." ; rdfs:range xsd:string . sepio-model:specified_by a rdf:Property ; rdfs:comment "A specification that describes all or part of the process that led to creation of the Information Entity." , "A method that was followed in performing an Activity, that describes how it was executed." ; rdfs:range xsd:string , sepio-model:Method . sepio-model:identifiers a rdf:Property ; rdfs:comment "A globally-unique 'business' identifier or accession number for the real-world entity represented by a data object. These are typically assigned by an external system or authority, and used to connect entities and share content across different systems." ; rdfs:range xsd:string . sepio-model:alternative_labels a rdf:Property ; rdfs:comment "Alternative name(s) for the Entity." ; rdfs:range xsd:string . sepio-model:type a rdf:Property ; rdfs:comment "The name of the class that is instantiated by a data object representing the Entity." ; rdfs:range xsd:string . sepio-model:sources a rdf:Property ; rdfs:comment "A document or other informtion resource in which the information entity, or evidence supporting it, is reported." ; rdfs:range xsd:string . sepio-model:variability_measures a rdf:Property ; rdfs:comment "A statistical score describing the variability inherent in a data item representing a statistical summary of a set of observations/measurements (e.g. the standard deviation associated with a statistical mean calculated across several experimental replicates)." ; rdfs:range sepio-model:DataItem . sepio-model:description a rdf:Property ; rdfs:comment "A free text description of the Entity." ; rdfs:range xsd:string . sepio-model:contributions a rdf:Property ; rdfs:comment "Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity." , "describes specific contributions made by an human or software agent to the creation, modification, or administrative management of a data record or object." ; rdfs:range sepio-model:Contribution . sepio-model:label a rdf:Property ; rdfs:comment "A primary name for the Entity." , "The human-readable name for the coded concept, as defined by the code system." ; rdfs:range xsd:string . sepio-model:supporting_methods a rdf:Property ; rdfs:comment "Specific methods that were executed to directly or indirectly support creation of the Information Entity." ; rdfs:range xsd:string . sepio-model:extensions a rdf:Property ; rdfs:comment "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model." ; rdfs:range sepio-model:Extension . sepio-model:record_metadata a rdf:Property ; rdfs:comment "Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries)." ; rdfs:range sepio-model:RecordMetadata . sepio-model:component_data_item a rdf:Property ; rdfs:comment "A more foundational data item that is a logical component of a compound data item." ; rdfs:range sepio-model:DataItem . sepio-model:id a rdf:Property ; rdfs:comment "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference one object from another." ; rdfs:range xsd:string . sepio-model:information_quality a rdf:Property ; rdfs:comment "A qualitative term indicating the scientific rigor or reliability with which the information was generated/collected." ; rdfs:range sepio-model:Coding . sepio-model:is_about a rdf:Property ; rdfs:comment "An entity or concept in the world that the information entity describes/is about." ; rdfs:range xsd:string . sepio-model:confidence_interval a rdf:Property ; rdfs:comment "A measure of the probability that a parameter of interest will fall within a defined range of values around a mean or other statistical calculation." ; rdfs:range sepio-model:DataItem . sepio-model:unit a rdf:Property ; rdfs:comment "A unit of measure for the value (e.g. meters, grams, fluorescent units, seconds, mg/ml, etc.)" ; rdfs:range sepio-model:Coding . sepio-model:Entity a rdfs:Class ; rdfs:label "Entity" ; rdfs:comment "Anything that exists, has existed, or will exist." . sepio-model:Expression a rdfs:Class ; rdfs:label "Expression" ; rdfs:comment "A structure for labels representing systematic expressions that describe an entity, as generated by formal nomenclatures (e.g. HGVS for genetic variants, ISCN for karyotypes, HLA nomenclature for HLA genes/alleles)." ; rdfs:subClassOf sepio-model:Utility . sepio-model:system_url a rdf:Property ; rdfs:comment "A URL for the nomenclature system" ; rdfs:range xsd:anyURI . sepio-model:system_version a rdf:Property ; rdfs:comment "The version of the nomenclature system." , "Version of the terminology or code system that provided the code." ; rdfs:range xsd:string . sepio-model:Activity a rdfs:Class ; rdfs:label "Activity" ; rdfs:comment "An action or set of actions performed by an agent, that occurs over a period of time. Activities may use, generate, modify, move, or destroy one or more entities." ; rdfs:subClassOf sepio-model:Entity . sepio-model:performed_by a rdf:Property ; rdfs:comment "An Agent who participated in executing the Activity." ; rdfs:range sepio-model:Agent . sepio-model:date a rdf:Property ; rdfs:comment "The date that the Activity was completed." ; rdfs:range xsd:date . sepio-model:input a rdf:Property ; rdfs:comment "An entity that was input into the Activity (could be material or information)" ; rdfs:range sepio-model:Entity . sepio-model:output a rdf:Property ; rdfs:comment "An entity that was output from the Activity (could be material or information)" ; rdfs:range sepio-model:Entity . sepio-model:Agent a rdfs:Class ; rdfs:label "Agent" ; rdfs:comment "An autonomous actor (person, organization, or software agent) that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity." ; rdfs:subClassOf sepio-model:Entity . sepio-model:Method a rdfs:Class ; rdfs:label "Method" ; rdfs:comment "A set of instructions that specify how to achieve some objective." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:urls a rdf:Property ; rdfs:comment "The URL/web address from which the Method can be retrieved." , "One or more URLs from which the content of the Document can be retrieved." ; rdfs:range xsd:string . sepio-model:Coding a rdfs:Class ; rdfs:label "Coding" ; rdfs:comment "A structured representation of a code for a defined concept in a terminology or code system." ; rdfs:subClassOf sepio-model:Utility . sepio-model:code a rdf:Property ; rdfs:comment "A symbol uniquely identifying the concept, as in a syntax defined by the code system. CURIE format is preferred where possible (e.g. ‘SO:0000704’ is the CURIE form of the Sequence Ontology code for 'gene')." ; rdfs:range xsd:string . sepio-model:system a rdf:Property ; rdfs:comment "The terminology/code system that defined the code. May be reported as a free-text name (e.g. ‘Sequence Ontology’), but it is preferable to provide a uri/url for the system. When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the Sequence Ontology)." ; rdfs:range xsd:string . sepio-model:Extension a rdfs:Class ; rdfs:label "Extension" ; rdfs:comment "A data structure that allows custom attributes to be defined for an Entity, to capture information unique to a given content provider, or not currently supported by the core specification." ; rdfs:subClassOf sepio-model:Utility . sepio-model:extension_description a rdf:Property ; rdfs:comment "A free text description of the intended meaning and use of the extension element, which may include the types of values it takes, and how to interpret these values in the context of the parent Class." ; rdfs:range xsd:string . sepio-model:InformationEntity a rdfs:Class ; rdfs:label "Information Entity" ; rdfs:comment "An abstract (non-physical) entity that is about something - representing the underlying 'information content' conveyed by physical or digital information artifacts like books, web pages, data tables, or photographs." ; rdfs:subClassOf sepio-model:Entity . sepio-model:StudyResult a rdfs:Class ; rdfs:label "Study Result" ; rdfs:comment "A collection of data items from a single study that pertain to a particular subject or experimental unit in the study, along with optional provenance information describing how these data items were generated." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:interpretation a rdf:Property ; rdfs:comment "The outcome of an interpretation of lower-level data item(s) in a StudyResult, that express some broader conclusion or insight that was made (e.g. that data indicates a result to be is high, normal, or low)." ; rdfs:range sepio-model:Coding . sepio-model:source_data_set a rdf:Property ; rdfs:comment "A larger DataSet from which the content of the StudyResult was derived." ; rdfs:range sepio-model:DataSet . sepio-model:data_items a rdf:Property ; rdfs:comment "One or more data items that are included in the StudyResult because it pertains to the 'focus' of the result. This can be data that directly describes this 'focus' (e.g. the population frequency of an allele focus), or be metadata about how data about the 'focus' were generated (e.g the quality measures for the sequencing run used to determine this allele frequency)." ; rdfs:range sepio-model:DataItem . sepio-model:component_result a rdf:Property ; rdfs:comment "Another StudyResult comprised of data items about the same focus as its parent Result, but based on a more narrowly scoped analysis of the foundational data (e.g. an analysis based on data about a subset of the parent Results full study population)." ; rdfs:range sepio-model:StudyResult . sepio-model:focus a rdf:Property ; rdfs:comment "A specific subject or experimental unit in a Study, that data in the StudyResult object is about - e.g. a particular variant in a population allele frequency dataset like ExAC or gnomAD." ; rdfs:range xsd:string . sepio-model:study_group a rdf:Property ; rdfs:comment "A description of a specific group or population of subjects interrogated in the ResearchStudy that produced the data captured in the StudyResult." ; rdfs:range sepio-model:StudyGroup . sepio-model:DataSet a rdfs:Class ; rdfs:label "Data Set" ; rdfs:comment "A collection of related data items or records that are organized together in a common format or structure, to enable their computational manipulation as a unit." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:release_date a rdf:Property ; rdfs:comment "Indicates when a version of a DataSet was formally released." ; rdfs:range xsd:string . sepio-model:license a rdf:Property ; rdfs:comment "A specific license that dictates legal permissions for how a data set can be used (by whom, where, for what purposes, with what additional requirements, etc.)." , "A specific license that dictates legal permissions for how a document can be used (by whom, where, for what purposes, with what additional requirements, etc.)" ; rdfs:range xsd:string . sepio-model:version a rdf:Property ; rdfs:comment "The version of the DataSet, as assigned by its creator." ; rdfs:range xsd:string . sepio-model:Proposition a rdfs:Class ; rdfs:label "Proposition" ; rdfs:comment "An abstract entity representing a possible fact that is either true or false." ; rdfs:subClassOf sepio-model:Entity . sepio-model:predicate a rdf:Property ; rdfs:comment "The relationship declared to hold between the subject and the object of the Proposition." , "The relationship declared to hold between the subject and the object of the Statement." ; rdfs:range sepio-model:Coding . sepio-model:qualifier a rdf:Property ; rdfs:comment "An additional piece of information that extends or refines the meaning of a Propositions's core subject - predicate - object 'triple' - by providing additional detail, or constraining the statement to apply in a particular context." , "An additional piece of information that extends or refines the meaning of a Statement's core subject - predicate - object 'triple' - by providing additional detail, or constraining the statement to apply in a particular context." ; rdfs:range sepio-model:Qualifier . sepio-model:subject a rdf:Property ; rdfs:comment "The Entity or concept about which the Proposition is made." , "The Entity or concept about which the Statement is made." ; rdfs:range xsd:string . sepio-model:proposition_text a rdf:Property ; rdfs:comment "A natural-language expression of the Proposition's meaning (i.e. the 'possible fact' it expresses)." ; rdfs:range xsd:string . sepio-model:object a rdf:Property ; rdfs:comment "An Entity or concept that is related to the subject of a Proposition via its predicate." , "An Entity or concept that is related to the subject of a Statement via its predicate." ; rdfs:range xsd:string . sepio-model:negated a rdf:Property ; rdfs:comment "A boolean flag set to 'true' to represent a negation of the proposition expressed by the subject, predicate, object, and qualifier(s) (e.g. that \"Variant X is NOT pathogenic for Disease Y\")" ; rdfs:range xsd:boolean . sepio-model:Characteristic a rdfs:Class ; rdfs:label "Characteristic" ; rdfs:comment "An object holding a name-value pair used to describe a trait or role of an individual member of a StudyGroup." ; rdfs:subClassOf sepio-model:Utility . sepio-model:values a rdf:Property ; rdfs:comment "The specific value(s) that the indicated traitor role holds in all population members (e.g. 'east asian', 'female', 'adolescent', 'cancer')." ; rdfs:range xsd:string . sepio-model:value_operator a rdf:Property ; rdfs:comment "An operation that defines how to logically interpret a set of more than one Characteristic values ('AND', 'OR', 'NOT')." ; rdfs:range xsd:string . sepio-model:EvidenceLine a rdfs:Class ; rdfs:label "Evidence Line" ; rdfs:comment "An independent, evidence-based argument that may support or refute the validity of a specific proposition. The strength and direction of this argument is based on an interpretation of one or more pieces of information as evidence for or against the target proposition." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:target_proposition a rdf:Property ; rdfs:comment "The possible fact against which evidence items contained in an Evidence Line were collectively evaluated, in determining the overall strength and direction of support they provide. For example, in an ACMG Guideline-based assessment of variant pathogenicity, the support provided by distinct lines of evidence are assessed against a target proposition that some variant is pathogenic for a specific disease." ; rdfs:range sepio-model:Proposition . sepio-model:strength_of_evidence_provided a rdf:Property ; rdfs:comment "The strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided." ; rdfs:range xsd:string . sepio-model:direction_of_evidence_provided a rdf:Property ; rdfs:comment "The direction of support that the Evidence Line is determined to provide toward its target Proposition (supports, disputes, neutral)." ; rdfs:range xsd:string . sepio-model:score_of_evidence_provided a rdf:Property ; rdfs:comment "A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value." ; rdfs:range xsd:float . sepio-model:has_evidence_items a rdf:Property ; rdfs:comment "An individual piece of information that was evaluated as evidence in building the argument represented by an Evidence Line." ; rdfs:range sepio-model:InformationEntity . sepio-model:evidence_item_sources a rdf:Property ; rdfs:comment "An information resource (e.g. document, dataset, digital resource such as a database or knowledgebase) that provides information interpreted as evidence in building an Evidence Line." ; rdfs:range xsd:string . sepio-model:Statement a rdfs:Class ; rdfs:label "Statement" ; rdfs:comment "A claim of purported truth as made by a particular agent, on a particular occasion. Statements may be used to simply put forth a possible fact (i.e. a 'proposition') as true, or to provide a more nuanced assessment of the level of confidence or evidence supporting a particular proposition." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:direction a rdf:Property ; rdfs:comment "A term indicating whether the Statement supports, disputes, or remains neutral w.r.t. the validity of the Proposition it evaluates." ; rdfs:range xsd:string . sepio-model:strength a rdf:Property ; rdfs:comment "A term used to report the strength of a Proposition's assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Implementers may choose to frame a strength assessment in terms of how *confident* an agent is that the Proposition is true or false, or in terms of the *strength of all evidence* they believe supports or disputes it." ; rdfs:range xsd:string . sepio-model:proposition a rdf:Property ; rdfs:comment "A possible fact that the Statement assesses or puts forth as true." ; rdfs:range sepio-model:Proposition . sepio-model:has_evidence_from_sources a rdf:Property ; rdfs:comment "An Information Entity (typically a publication, dataset, or database) that provided information used as evidence to generate the knowledge expressed in a Statement." ; rdfs:range sepio-model:InformationEntity . sepio-model:has_evidence_lines a rdf:Property ; rdfs:comment "An evidence-based argument that supports or disputes the validity of the proposition that a Statement assesses or puts forth as true. The strength and direction of this argument (whether it supports or disputes the proposition, and how strongly) is based on an interpretation of one or more pieces of information as evidence (i.e. 'Evidence Items)." ; rdfs:range sepio-model:EvidenceLine . sepio-model:has_evidence_of_types a rdf:Property ; rdfs:comment "A term describing a type of evidence used to assess the validity of Statement's proposition (e.g. 'sequence similarity evidence', 'in vitro assay evidence')." ; rdfs:range xsd:string . sepio-model:score a rdf:Property ; rdfs:comment "A quantitative score that indicates the strength of a Proposition's validity assessment in the direction indicated (i.e. how strongly supported or disputed the Proposition is believed to be). Depending on its implementation, a score may reflect how *confident* that agent is that the Proposition is true or false, or the *strength of evidence* they believe supports or disputes it." ; rdfs:range xsd:float . sepio-model:has_evidence a rdf:Property ; rdfs:comment "A piece of information that represents or contributes to an argument for or against the validity of the Proposition put forth in a Statement. This is a shortcut relation that links a Statement directly to a piece of evidence supporting it, bypassing the Evidence Line class when used data creators do not utilize an Evidence Line object." ; rdfs:range sepio-model:InformationEntity . sepio-model:statement_text a rdf:Property ; rdfs:comment "A natural-language expression of what a Statement asserts to be true." ; rdfs:range xsd:string . sepio-model:subject_classification a rdf:Property ; rdfs:comment "A single term or phrase summarizing the outcome of direction and strength assessments of a Statement's proposition, in terms of a classification of its subject." ; rdfs:range sepio-model:Coding . sepio-model:Contribution a rdfs:Class ; rdfs:label "Contribution" ; rdfs:comment "An action or actions taken by a particular agent in the creation, modification, assessment, or deprecation of some entity (e.g. a Statement, Evidence Line, DataSet, Publication, etc.)." ; rdfs:subClassOf sepio-model:Activity . sepio-model:contributor a rdf:Property ; rdfs:comment "The Agent that made the contribution." ; rdfs:range sepio-model:Agent . sepio-model:contribution_made_to a rdf:Property ; rdfs:comment "The artifact toward which the contribution was made." ; rdfs:range sepio-model:InformationEntity . sepio-model:activity_type a rdf:Property ; rdfs:comment "The specific type of activity performed or role played by an agent in making the contribution (e.g. for a publication, agents may contribute as a primary author, editor, figure designer, data generator, etc. . Values of this property may be framed as activities or as contribution roles (e.g. using terms from the Contribution Role Ontology (CRO))." ; rdfs:range sepio-model:Coding . sepio-model:Utility a rdfs:Class ; rdfs:comment "An abstract organizational class that groups classes acting as complex datatypes in the model - providing reusable collections of fields that can be plugged into other objects to capture sets of related information." . sepio-model:StudyGroup a rdfs:Class ; rdfs:label "Study Group" ; rdfs:comment "A collection of individuals or specimens from the same taxonomic class, selected for analysis in a scientific study based on their exhibiting one or more common characteristics (e.g. species, race, age, gender, disease state, income). May be referred to as a 'cohort' or 'population' in specific research settings." ; rdfs:subClassOf sepio-model:Entity . sepio-model:is_subset_of a rdf:Property ; rdfs:comment "A larger StudyGroup of which this StudyGroup represents a subset." ; rdfs:range sepio-model:StudyGroup . sepio-model:member_count a rdf:Property ; rdfs:comment "The total number of individual members in the StudyGroup." ; rdfs:range xsd:integer . sepio-model:characteristics a rdf:Property ; rdfs:comment "A feature or role shared by all members of the StudyGroup, representing a criterion for membership in the group." ; rdfs:range sepio-model:Characteristic . sepio-model:RecordMetadata a rdfs:Class ; rdfs:label "Record Metadata" ; rdfs:comment "A reusable structure that encapsulates provenance metadata about a serialized data record or object in a particular dataset (as opposed to provenance of the real world entity this record or object represents)." ; rdfs:subClassOf sepio-model:Utility . sepio-model:record_version a rdf:Property ; rdfs:comment "The version number of the record-level artifact the object describes." ; rdfs:range xsd:string . sepio-model:date_record_created a rdf:Property ; rdfs:comment "The date the record was initially created." ; rdfs:range xsd:string . sepio-model:derived_from_record a rdf:Property ; rdfs:comment "Another data record from which the record described here was derived, through a data ingest and/or transformation process." ; rdfs:range xsd:string . sepio-model:record_identifier a rdf:Property ; rdfs:comment "The identifier of the record described in the RecordMetadata object (required when the record described is not the one in the present system)." ; rdfs:range xsd:string . sepio-model:Document a rdfs:Class ; rdfs:label "Document" ; rdfs:comment "A collection of information, usually in a text-based or graphic human-readable form, intended to be read and understood together as a whole." ; rdfs:subClassOf sepio-model:InformationEntity . sepio-model:doi a rdf:Property ; rdfs:comment "A `Digital Object Identifier _` for the document." ; rdfs:range xsd:string . sepio-model:pmid a rdf:Property ; rdfs:comment "A `PubMed unique identifier `_ for the document." ; rdfs:range xsd:string . sepio-model:title a rdf:Property ; rdfs:comment "The official title given to the document by its authors." ; rdfs:range xsd:string .