ga4gh-va-schema.yaml

name: GA4GH-VA-Spec
id: https://w3id.org/ga4gh-va
imports:
- linkml:types
prefixes:
  linkml:
    prefix_prefix: linkml
    prefix_reference: https://w3id.org/linkml/
  vaspec:
    prefix_prefix: vaspec
    prefix_reference: https://example.org/vaspec/
  FHIR:
    prefix_prefix: FHIR
    prefix_reference: http://example.org/FHIR/
  BFO:
    prefix_prefix: BFO
    prefix_reference: http://purl.obolibrary.org/obo/BFO_
  IAO:
    prefix_prefix: IAO
    prefix_reference: http://purl.obolibrary.org/obo/IAO_
  SEPIO:
    prefix_prefix: SEPIO
    prefix_reference: http://purl.obolibrary.org/obo/SEPIO_
  CAM:
    prefix_prefix: CAM
    prefix_reference: http://example.org/CAM/
  PROV:
    prefix_prefix: PROV
    prefix_reference: http://www.w3.org/ns/prov#
  xsd:
    prefix_prefix: xsd
    prefix_reference: http://www.w3.org/2001/XMLSchema#
default_prefix: vaspec
default_range: string
types:
  ga4ghString:
    name: ga4ghString
    description: A sequence of Unicode characters
    title: ga4ghString
    comments:
    - The ga4ghString data type represents free-text that is not constrained to some
      code set or associated with some semantic interpretation. It is the most generic
      form of free-text literal in the model, and conceptually subsumes other ga4ghString-based
      data types with more constrained interpretations (e.g. identifier, class, url).
    base: string
    uri: xsd:string
  url:
    name: url
    description: A string representing a Uniform Resource Locator (RFC 1738), specifying
      a web address where a resource can be found or information about the resource
      discovered.
    title: url
    comments:
    - 'Used in place of a plain string datatype when a resolvable web address for
      a resource is desired.  Common URL protocols are http{s}:, ftp:, mailto: and
      mllp:, though many others are defined.'
    base: ga4ghString
    uri: xsd:string
  class:
    name: class
    description: A string representing a class in a VA model used to type an object
      in the data.
    title: class
    comments:
    - This string must be the name of a concrete class from the core VA specification
      (e.g. 'Statement'), or a specialization of such a class in a profile defined
      by a particular implementation (e.g. TherapeuticEfficacyStatement').
    base: ga4ghString
    uri: xsd:string
  ga4ghDateTime:
    name: ga4ghDateTime
    description: A string value that specifies a date and time of day comprised of
      a year, month, day, hour, minute, and second, following the form “YYYY-MM-DDThh:mm:ss”
    title: ga4ghDateTime
    comments:
    - Conventions for representing date + time defined here are based on the ISO 8601
      standard. Hours of the day should use 24-hour time (e.g. 2PM = 14:00:00). A
      time zone can be specified as described for ‘dates’ above, e.g. "1978-01-20T05:15:00Z,
      and "1978-01-20T05:15:00+5:00".  If precision down to time of day is not possible
      or necessary, the hours, minutes, and seconds must still be provided due to
      schema constraints, but can all be set to “00” and ignored at the instruction
      of the message sender.
    base: ga4ghString
    uri: xsd:string
  identifier:
    name: identifier
    description: A string value that uniquely identifies a specific instance of an
      object in a dataset or document. Identifiers should be persistent, machine-resolvable,
      and unique within their intended scope of use.
    title: identifier
    comments:
    - We distinguish between two types of identifiers depending on their intended
      scope of use. ‘Logical identifiers’ are used to identify a data object within
      a given system, where it is used as a reference from other objects within the
      same system (i.e. primary and foreign keys). The same data object copied to
      a different system will likely have a different logical identifier in that new
      system. ‘Business identifiers’ are typically provided by an external system
      or authority, and are meant to be globally unique and persist across implementing
      systems. A given entity or concept may have many business identifiers associated
      with it, which can all be captured in a given data system. In the VA model,
      we follow FHIR naming conventions and use an  id  attribute to hold the logical
      identifier of a data object, and an identifier attribute to hold any business
      identifiers that the data creator may also want to provide. Use of the W3C Compact
      URI (CURIE) syntax to structure identifiers is strongly recommended, as a way
      to ensure that a given identifier is unique within its intended scope of use.
    base: ga4ghString
    uri: xsd:string
  ga4ghBoolean:
    name: ga4ghBoolean
    description: A binary data type that holds either a TRUE or FALSE value.
    title: ga4ghBoolean
    base: boolean
    uri: xsd:boolean
slots:
  extensionElement:
    name: extensionElement
    from_schema: https://w3id.org/ga4gh-va
  localId:
    name: localId
    from_schema: https://w3id.org/ga4gh-va
  globalIdentifier:
    name: globalIdentifier
    from_schema: https://w3id.org/ga4gh-va
  type:
    name: type
    from_schema: https://w3id.org/ga4gh-va
  label:
    name: label
    from_schema: https://w3id.org/ga4gh-va
  alternativeLabel:
    name: alternativeLabel
    from_schema: https://w3id.org/ga4gh-va
  description:
    name: description
    from_schema: https://w3id.org/ga4gh-va
  hasURL:
    name: hasURL
    from_schema: https://w3id.org/ga4gh-va
  reference:
    name: reference
    from_schema: https://w3id.org/ga4gh-va
  xref:
    name: xref
    from_schema: https://w3id.org/ga4gh-va
  thisRecordMeta:
    name: thisRecordMeta
    from_schema: https://w3id.org/ga4gh-va
  sourceRecordMeta:
    name: sourceRecordMeta
    from_schema: https://w3id.org/ga4gh-va
  isAbout:
    name: isAbout
    from_schema: https://w3id.org/ga4gh-va
  qualifiedContribution:
    name: qualifiedContribution
    from_schema: https://w3id.org/ga4gh-va
  dateAuthored:
    name: dateAuthored
    from_schema: https://w3id.org/ga4gh-va
  wasSpecifiedBy:
    name: wasSpecifiedBy
    from_schema: https://w3id.org/ga4gh-va
  derivedFrom:
    name: derivedFrom
    from_schema: https://w3id.org/ga4gh-va
  wasOutputOf:
    name: wasOutputOf
    from_schema: https://w3id.org/ga4gh-va
  hasPart:
    name: hasPart
    from_schema: https://w3id.org/ga4gh-va
  partOf:
    name: partOf
    from_schema: https://w3id.org/ga4gh-va
  isReportedIn:
    name: isReportedIn
    from_schema: https://w3id.org/ga4gh-va
  confidenceLevel:
    name: confidenceLevel
    from_schema: https://w3id.org/ga4gh-va
  confidenceScore:
    name: confidenceScore
    from_schema: https://w3id.org/ga4gh-va
  version:
    name: version
    from_schema: https://w3id.org/ga4gh-va
  license:
    name: license
    from_schema: https://w3id.org/ga4gh-va
  dataItemType:
    name: dataItemType
    from_schema: https://w3id.org/ga4gh-va
  value:
    name: value
    from_schema: https://w3id.org/ga4gh-va
  unit:
    name: unit
    from_schema: https://w3id.org/ga4gh-va
  variability:
    name: variability
    from_schema: https://w3id.org/ga4gh-va
  confidenceInterval:
    name: confidenceInterval
    from_schema: https://w3id.org/ga4gh-va
  componentDataItem:
    name: componentDataItem
    from_schema: https://w3id.org/ga4gh-va
  dataSetType:
    name: dataSetType
    from_schema: https://w3id.org/ga4gh-va
  dataSetLevel:
    name: dataSetLevel
    from_schema: https://w3id.org/ga4gh-va
  releaseDate:
    name: releaseDate
    from_schema: https://w3id.org/ga4gh-va
  previousVersion:
    name: previousVersion
    from_schema: https://w3id.org/ga4gh-va
  currentVersion:
    name: currentVersion
    from_schema: https://w3id.org/ga4gh-va
  format:
    name: format
    from_schema: https://w3id.org/ga4gh-va
  conformsTo:
    name: conformsTo
    from_schema: https://w3id.org/ga4gh-va
  documentType:
    name: documentType
    from_schema: https://w3id.org/ga4gh-va
  title:
    name: title
    from_schema: https://w3id.org/ga4gh-va
  statementType:
    name: statementType
    from_schema: https://w3id.org/ga4gh-va
  subject:
    name: subject
    from_schema: https://w3id.org/ga4gh-va
  predicate:
    name: predicate
    from_schema: https://w3id.org/ga4gh-va
  object:
    name: object
    from_schema: https://w3id.org/ga4gh-va
  qualifier:
    name: qualifier
    from_schema: https://w3id.org/ga4gh-va
  negated:
    name: negated
    from_schema: https://w3id.org/ga4gh-va
  assertedProposition:
    name: assertedProposition
    from_schema: https://w3id.org/ga4gh-va
  evidenceLevel:
    name: evidenceLevel
    from_schema: https://w3id.org/ga4gh-va
  evidenceScore:
    name: evidenceScore
    from_schema: https://w3id.org/ga4gh-va
  hasEvidenceLine:
    name: hasEvidenceLine
    from_schema: https://w3id.org/ga4gh-va
  hasEvidence:
    name: hasEvidence
    from_schema: https://w3id.org/ga4gh-va
  hasEvidenceOfType:
    name: hasEvidenceOfType
    from_schema: https://w3id.org/ga4gh-va
  hasEvidenceFromSource:
    name: hasEvidenceFromSource
    from_schema: https://w3id.org/ga4gh-va
  subjectDescriptor:
    name: subjectDescriptor
    from_schema: https://w3id.org/ga4gh-va
  objectDescriptor:
    name: objectDescriptor
    from_schema: https://w3id.org/ga4gh-va
  qualifierDescriptor:
    name: qualifierDescriptor
    from_schema: https://w3id.org/ga4gh-va
  studyResultType:
    name: studyResultType
    from_schema: https://w3id.org/ga4gh-va
  focus:
    name: focus
    from_schema: https://w3id.org/ga4gh-va
  data:
    name: data
    from_schema: https://w3id.org/ga4gh-va
  interpretation:
    name: interpretation
    from_schema: https://w3id.org/ga4gh-va
  sourceDataSet:
    name: sourceDataSet
    from_schema: https://w3id.org/ga4gh-va
  sourceStudy:
    name: sourceStudy
    from_schema: https://w3id.org/ga4gh-va
  sourceStudyType:
    name: sourceStudyType
    from_schema: https://w3id.org/ga4gh-va
  sourceStudyDate:
    name: sourceStudyDate
    from_schema: https://w3id.org/ga4gh-va
  sourceStudyMethod:
    name: sourceStudyMethod
    from_schema: https://w3id.org/ga4gh-va
  evidenceLineType:
    name: evidenceLineType
    from_schema: https://w3id.org/ga4gh-va
  targetProposition:
    name: targetProposition
    from_schema: https://w3id.org/ga4gh-va
  hasEvidenceItem:
    name: hasEvidenceItem
    from_schema: https://w3id.org/ga4gh-va
  evidenceDirection:
    name: evidenceDirection
    from_schema: https://w3id.org/ga4gh-va
  evidenceStrength:
    name: evidenceStrength
    from_schema: https://w3id.org/ga4gh-va
  evidenceItemSource:
    name: evidenceItemSource
    from_schema: https://w3id.org/ga4gh-va
  methodType:
    name: methodType
    from_schema: https://w3id.org/ga4gh-va
  activityType:
    name: activityType
    from_schema: https://w3id.org/ga4gh-va
  startDate:
    name: startDate
    from_schema: https://w3id.org/ga4gh-va
  endDate:
    name: endDate
    from_schema: https://w3id.org/ga4gh-va
  performedBy:
    name: performedBy
    from_schema: https://w3id.org/ga4gh-va
  hadInput:
    name: hadInput
    from_schema: https://w3id.org/ga4gh-va
  hadOutput:
    name: hadOutput
    from_schema: https://w3id.org/ga4gh-va
  researchStudyType:
    name: researchStudyType
    from_schema: https://w3id.org/ga4gh-va
  contributionMadeBy:
    name: contributionMadeBy
    from_schema: https://w3id.org/ga4gh-va
  contributionMadeTo:
    name: contributionMadeTo
    from_schema: https://w3id.org/ga4gh-va
  contributorRole:
    name: contributorRole
    from_schema: https://w3id.org/ga4gh-va
  organizationalContext:
    name: organizationalContext
    from_schema: https://w3id.org/ga4gh-va
  agentType:
    name: agentType
    from_schema: https://w3id.org/ga4gh-va
  softwareVersion:
    name: softwareVersion
    from_schema: https://w3id.org/ga4gh-va
  hasAffiliation:
    name: hasAffiliation
    from_schema: https://w3id.org/ga4gh-va
  parentOrganization:
    name: parentOrganization
    from_schema: https://w3id.org/ga4gh-va
  childOrganization:
    name: childOrganization
    from_schema: https://w3id.org/ga4gh-va
  propositionType:
    name: propositionType
    from_schema: https://w3id.org/ga4gh-va
  member:
    name: member
    from_schema: https://w3id.org/ga4gh-va
  organization:
    name: organization
    from_schema: https://w3id.org/ga4gh-va
  organizationalRole:
    name: organizationalRole
    from_schema: https://w3id.org/ga4gh-va
  affiliationStatus:
    name: affiliationStatus
    from_schema: https://w3id.org/ga4gh-va
  valueObjectId:
    name: valueObjectId
    from_schema: https://w3id.org/ga4gh-va
  valueObject:
    name: valueObject
    from_schema: https://w3id.org/ga4gh-va
  valueObjectName:
    name: valueObjectName
    from_schema: https://w3id.org/ga4gh-va
  valueObjectAlias:
    name: valueObjectAlias
    from_schema: https://w3id.org/ga4gh-va
  valueObjectExpression:
    name: valueObjectExpression
    from_schema: https://w3id.org/ga4gh-va
  valueObjectDescription:
    name: valueObjectDescription
    from_schema: https://w3id.org/ga4gh-va
  valueObjectXref:
    name: valueObjectXref
    from_schema: https://w3id.org/ga4gh-va
  moleculeContext:
    name: moleculeContext
    from_schema: https://w3id.org/ga4gh-va
  structuralType:
    name: structuralType
    from_schema: https://w3id.org/ga4gh-va
  code:
    name: code
    from_schema: https://w3id.org/ga4gh-va
  system:
    name: system
    from_schema: https://w3id.org/ga4gh-va
  systemURL:
    name: systemURL
    from_schema: https://w3id.org/ga4gh-va
  systemVersion:
    name: systemVersion
    from_schema: https://w3id.org/ga4gh-va
  name:
    name: name
    from_schema: https://w3id.org/ga4gh-va
  recordIdentifier:
    name: recordIdentifier
    from_schema: https://w3id.org/ga4gh-va
  partOfDataset:
    name: partOfDataset
    from_schema: https://w3id.org/ga4gh-va
  recordVersion:
    name: recordVersion
    from_schema: https://w3id.org/ga4gh-va
  dateRecordCreated:
    name: dateRecordCreated
    from_schema: https://w3id.org/ga4gh-va
  dateRecordLastModified:
    name: dateRecordLastModified
    from_schema: https://w3id.org/ga4gh-va
  recordURL:
    name: recordURL
    from_schema: https://w3id.org/ga4gh-va
  componentDisease:
    name: componentDisease
    from_schema: https://w3id.org/ga4gh-va
  componentPhenotype:
    name: componentPhenotype
    from_schema: https://w3id.org/ga4gh-va
  inheritancePattern:
    name: inheritancePattern
    from_schema: https://w3id.org/ga4gh-va
  contributingGene:
    name: contributingGene
    from_schema: https://w3id.org/ga4gh-va
  componentDrug:
    name: componentDrug
    from_schema: https://w3id.org/ga4gh-va
  componentProcedure:
    name: componentProcedure
    from_schema: https://w3id.org/ga4gh-va
  componentActivity:
    name: componentActivity
    from_schema: https://w3id.org/ga4gh-va
  drugOperator:
    name: drugOperator
    from_schema: https://w3id.org/ga4gh-va
  biotype:
    name: biotype
    from_schema: https://w3id.org/ga4gh-va
  symbol:
    name: symbol
    from_schema: https://w3id.org/ga4gh-va
  location:
    name: location
    from_schema: https://w3id.org/ga4gh-va
  strand:
    name: strand
    from_schema: https://w3id.org/ga4gh-va
classes:
  Element:
    name: Element
    exact_mappings:
    - FHIR:Element
    description: The base definition for all elements that comprise the model (classes,
      complex data types, value sets)
    title: Element
    comments:
    - This class is useful to reference as the range of attributes that can take instances
      of a class or a complex data type (e.g. a Coding) as their value (e.g. Statement.object)
    from_schema: https://w3id.org/ga4gh-va
    slots:
    - extensionElement
    slot_usage:
      extensionElement:
        name: extensionElement
        description: A key-value data structure that allows definition of custom fields
          to capture information not directly supported by the VA specification.
        comments:
        - The VA-Spec provides  implementers the ability to extend any model elements
          with new attributes using this flexible Extension element.
        multivalued: true
        range: Extension
        required: false
  Entity:
    name: Entity
    aliases:
    - Thing
    exact_mappings:
    - BFO:0000001
    description: Anything that exists, has existed, or will exist.
    title: Entity
    comments:
    - Entity is the root class of ‘core’ classes model - those that have identifiers
      and other general metadata like labels, xrefs, urls, descriptions, etc. All
      core classes descend from and inherit its attributes.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Element
    slots:
    - localId
    - globalIdentifier
    - type
    - label
    - alternativeLabel
    - description
    - hasURL
    - reference
    - xref
    - thisRecordMeta
    - sourceRecordMeta
    slot_usage:
      localId:
        name: localId
        exact_mappings:
        - FHIR:id
        description: The logical identifier of the entity in the system of record,
          e.g. a UUID.  This 'id' is unique within a given system. The identified
          entity may have a different 'id' in a different system.
        comments:
        - FHIR naming conventions are followed here, where an 'id' field holds logical
          identifiers which are unique only within a given system, and an 'identifier'
          field holds business identifiers, which are globally unique and used to
          connect entities and share content across systems.
        multivalued: false
        range: identifier
        required: true
      globalIdentifier:
        name: globalIdentifier
        exact_mappings:
        - FHIR:identifier
        description: A business identifier or accession number for the entity, typically
          as provided by an external system or authority, that is globally unique
          and persists across implementing systems.
        comments:
        - FHIR naming conventions are followed here, where an 'id' field holds logical
          identifiers which are unique only within a given system, and an 'identifier'
          field holds business identifiers, which are globally unique and used to
          connect entities and share content across systems.
        multivalued: true
        range: identifier
        required: false
      type:
        name: type
        description: The schema class that is instantiated by the data object.  Must
          be the name of a class from the VA schema.
        multivalued: false
        range: class
        required: true
      label:
        name: label
        description: A primary name for the Entity.
        multivalued: false
        range: string
        required: false
      alternativeLabel:
        name: alternativeLabel
        description: An alternative name for the Entity.
        multivalued: true
        range: string
        required: false
      description:
        name: description
        description: A free text description of the Entity.
        multivalued: false
        range: string
        required: false
      hasURL:
        name: hasURL
        description: The URL/web address of a digital resource representing the entity,
          or providing information about it.
        multivalued: true
        range: url
        required: false
      reference:
        name: reference
        description: A document or other Information Entity that describes the Entity.
        multivalued: true
        range: InformationEntity
        required: false
      xref:
        name: xref
        description: A cross-reference to database identifier(s) representing the
          same or a closely related entity or concept as the Entity.
        comments:
        - Preferred values for this field are CURIEs or URLs for database records
        multivalued: true
        range: string
        required: false
      thisRecordMeta:
        name: thisRecordMeta
        description: A reusable structure that encapsulates provenance metadata about
          the present record/data object  (as opposed to provenance information about
          the real world entity this record/data object represents).
        comments:
        - Record-level metadata applies to a specific concrete encoding/serialization
          of knowledge  (e.g as a record in a specific database, or an online digital
          resource). A RecordMetadata object can capture provenance and other metadata,
          including when, how, and by whom a specific record was generated or modified;
          what upstream resources it was derived/retrieved from; and record-level
          administrative information such as versioning and system / lifecycle status.
        multivalued: false
        range: RecordMetadata
        required: false
      sourceRecordMeta:
        name: sourceRecordMeta
        description: A reusable structure that encapsulates provenance metadata that
          applies to an upstream record/data objdct about the Entity, from which content
          of the present record was derived.
        comments:
        - The 'sourceRecordMeta' attribute holds a RecordMetadata object that carries
          information about a separate, upstream source record from which the present
          record derived its content.  This attribute is only used in edge cases where
          the data creator wants to caopture metadata about usptream source records.
        multivalued: true
        range: RecordMetadata
        required: false
  InformationEntity:
    name: InformationEntity
    aliases:
    - Information Content Entity, ICE
    exact_mappings:
    - IAO:0000030 | FRBR:Work
    description: An abstract (non-physical) entity that is about something.
    title: Information Entity
    comments:
    - Information Entities represent the abstract 'information content' encoded in
      physical or digital artifacts such as books, photographs, files, web pages,
      the neural connections of a human brain, etc. They are independent of any specific
      language, representational format, or physical/digital medium. In the FRBR model,
      this corresponds to the 'Works' level of representation.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - isAbout
    - qualifiedContribution
    - dateAuthored
    - wasSpecifiedBy
    - derivedFrom
    - wasOutputOf
    - hasPart
    - partOf
    - isReportedIn
    - confidenceLevel
    - confidenceScore
    - version
    - license
    slot_usage:
      isAbout:
        name: isAbout
        description: An entity or concept in the world that the information entity
          describes/is about.
        comments:
        - This field can be used to tag a Statement object with things it is about,
          in lieu of providing a more precise description of what the Statement asserts
          to be true using subject, predicate, object, and qualifier fields.
        multivalued: true
        range: Entity
        required: false
      qualifiedContribution:
        name: qualifiedContribution
        description: A specific contribution made by some Agent to the creation, modification,
          or validation of the information represented in the Information Entity.
        comments:
        - This attribute points to a Contribution object, which holds a structured
          description of the actions taken by a particular agent in contributing to
          an Information Entity.
        multivalued: true
        range: Contribution
        required: false
      dateAuthored:
        name: dateAuthored
        description: The date the information content expressed in this entity was
          generated.
        comments:
        - We use the term 'authored' to refer to the generation of information in
          the abstract - i.e. the information content expressed in a Statement, not
          a concrete encoding of it in a specific language or format.  The 'dateAuthored'
          attribute captures when this abstract information content was first created.  Information
          about when a particular concrete encoding of this information was created
          (e.g. as a VA-based json object) would live in a RecordMetadata object attached
          to the Information Entity).
        multivalued: false
        range: ga4ghDateTime
        required: false
      wasSpecifiedBy:
        name: wasSpecifiedBy
        description: A plan specification that describes all or part of the process
          through which the information was generated.
        comments:
        - Depending on the type of plan spcification, these may be called 'protocols',
          'guidelines', 'methods', 'rule sets', etc.
        multivalued: true
        range: Method
        required: false
      derivedFrom:
        name: derivedFrom
        exact_mappings:
        - DC:source
        description: An information resource from which the Information Entity is
          derived, in whole or in part
        multivalued: true
        range: InformationEntity
        required: false
      wasOutputOf:
        name: wasOutputOf
        description: An activity that generated the Entity.
        multivalued: true
        range: Activity
        required: false
      hasPart:
        name: hasPart
        description: Any part of the Information Entity (e.g. individual value or
          record from a larger data set, a section of a larger document)
        multivalued: true
        range: InformationEntity
        required: false
      partOf:
        name: partOf
        description: A larger Information Entity of which the present Information
          Entity is a part.
        multivalued: true
        range: InformationEntity
        required: false
      isReportedIn:
        name: isReportedIn
        description: A document in which the information content carried by the Information
          Entity is expressed
        comments:
        - This attribute is used specifically to reference documents/publications
          where the Information Entity is expressed or reported.  For a Statement,
          this might be a publication where the authors express the statement in text.  For
          a Data Item, this might be a publication with a table or figure that reports
          the value of the  data.   Note that the VA-Spec provide separate attributes
          for describing different types of 'references' from an Information Entity
          to a Document (e.g. hasEvidenceFromSource is used by a Statement to reference
          a Document that provided evidence for the knowldege the Statement expresses.
        multivalued: true
        range: Document
        required: false
      confidenceLevel:
        name: confidenceLevel
        description: A qualitative term describing the degree of confidence held by
          the creator of the information entity, that the information it represents
          is true (e.g. 'high confidence', 'likely true', 'low confidence').
        comments:
        - What a confidence level or score reflects may vary depending on the type
          of InformationEntity it describes. For Statements, it may reflect an agent's
          confidence that the statement asserts a proposition that is true. For a
          DataItem, its may reflect an agent's confidence that the value is an accurate
          reflection of the reality it measures or describes. For an Image, this may
          reflect the agent's confidence that it accurately represents the subject
          it depicts.
        multivalued: false
        range: Coding
        required: false
      confidenceScore:
        name: confidenceScore
        description: A quantitative score reflecting the degree of confidence held
          by the creator of the information entity, that the information it represents
          is true.
        multivalued: false
        range: DataItem
        required: false
      version:
        name: version
        description: The version of the Information Entity (to be used in cases where
          version is not reflected in the id or identifiers associated with the entity).
        comments:
        - Note that this attribute captures the version of the abstract information
          content that comproses the Information Entity - in cases where updated versions
          of the entity are released.  Versioning of specific concrete records/encodings
          of the information in a particular format/syntax are to be captured in the
          recordVersion field of a RecordMeadata object associated with the Information
          Entity.
        multivalued: false
        range: string
        required: false
      license:
        name: license
        description: The type of license that dictates legal permissions for how a
          resource (e.g. dataset, document, protocol) can be used - typically referenced
          by its URL.
        multivalued: false
        range: string
        required: false
  DataItem:
    name: DataItem
    exact_mappings:
    - IAO:0000027
    description: An InformationEntity representing an individual piece of data, generated/acquired
      through methods which reliably produce truthful information about something.
    title: Data Item
    comments:
    - Examples include raw observations or measurements such as an allele count, or
      patient's weight, derived calculations such as frequency or mean, and computed
      statistical scores/metrics such as p-values and z-scores.
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - dataItemType
    - value
    - unit
    - variability
    - confidenceInterval
    - componentDataItem
    slot_usage:
      dataItemType:
        name: dataItemType
        description: A specific type of data the DataItem object represents (e.g.
          a specimen count, a patient weight, an allele frequency, a p-value)
        multivalued: true
        range: Coding
        required: false
      value:
        name: value
        description: The value of the data item
        multivalued: false
        range: string
        required: true
      unit:
        name: unit
        description: A unit of measure for the value
        multivalued: false
        range: Coding
        required: false
      variability:
        name: variability
        description: A 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).
        comments:
        - Examples of statistical measures of variability include an Interquartile
          Range, Variance, Standard Deviation, Standard Error.
        multivalued: true
        range: DataItem
        required: false
      confidenceInterval:
        name: confidenceInterval
        description: 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.
        comments:
        - 'Confidence intervals reflect the degree of uncertainty in a sampling method.
          They may be bounded on one or both sides, and are  computed for a designated
          confidence level (most often 95% or 99%.  Example: A Hazard Ratio of 0.47
          might have a 95% confidence interval between 0.34 and 0.65, wiht a p-value
          of = 0.001.'
        multivalued: false
        range: DataItem
        required: false
      componentDataItem:
        name: componentDataItem
        description: A more foundational data item that is a logical component of
          a compound data item.
        comments:
        - Examples of 'compound' data items with componet parts include a confidence
          interval, which is comprised of data items representing its lower and upper
          bounds, and a blood pressure reading, which is comprised of separate systolic
          and diastolic measurements.
        multivalued: true
        range: DataItem
        required: false
  DataSet:
    name: DataSet
    exact_mappings:
    - IAO:0000100
    description: 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.
    title: Data Set
    comments:
    - Examples include the Broad ExAC dataset on allele population frequency, or a
      SIFT dataset of computational predictions functional impact for a set of variants,
      or the contents of a VCF file that describes variations observed in a particular
      patient and various annotations made on them.
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - dataSetType
    - dataSetLevel
    - releaseDate
    - license
    - version
    - previousVersion
    - currentVersion
    - format
    - conformsTo
    slot_usage:
      dataSetType:
        name: dataSetType
        description: A specific type of data set the DataSet object represents.
        comments:
        - The recorded type is typically based on the nature of the data in the dataset,
          and what it describes (e.g. genomic sequence dataset, genome feature annotation
          dataset) .
        multivalued: true
        range: Coding
        required: false
      dataSetLevel:
        name: dataSetLevel
        description: The level at which the Data Set is considered and described ('Summary'
          level, 'Version' level, or 'Distribution' level - see https://www.w3.org/TR/hcls-dataset/#datasetdescriptionlevels)
        comments:
        - 'The VA model adopts the W3C HCLS DataSet Model view that DataSets can be
          considered and described at three levels: - The ''Summary'' level considers
          the Data Set at the most abstract/general level, independent of a specific
          version or format. - The ''Version'' level considers a specific version
          of a Data Set, which may acquire version-specific characteristics (e.g.
          a release date). - The ''Distribution'' level considers a specific format/encoding
          of a dataset version, which may acquire distribution-specific characteristics
          (e.g. a format, or downloadURL). Attributes defined for the DataSet class
          may apply at all or only some of the ‘levels’ described above. Guidance
          in this regard is provided in comments on each attribute, and should be
          followed when creating DataSet objects.'
        multivalued: false
        range: Coding
        required: false
      releaseDate:
        name: releaseDate
        description: The date when a version-level Data Set was released.
        comments:
        - This attribute may apply to version and distribution-level Data Set representations.
        multivalued: false
        range: ga4ghDateTime
        required: false
      license:
        name: license
        description: The type of license that dictates legal permissions for how the
          Data Set can be used - typically referenced by its URL.
        comments:
        - The VA Model can record license information for resources such as Data Sets
          and Documents that get published and released as a unit for community use.
          This attribute may apply to summary, version, and distribution-level Data
          Set representations.
        multivalued: false
        range: string
        required: false
      version:
        name: version
        description: The version of the Data Set (use this field used in cases where
          version is not reflected in an identifier associated with the Data Set)
        comments:
        - The VA Model can record version information for resources such as Data Sets
          and Documents that get published and released as a unit for community use.
          These may go through rounds of revisions that add or modify content, but
          don’t change the identity of the resource.  This attribute may apply to
          version and distribution-level Data Set representations.
        multivalued: false
        range: string
        required: false
      previousVersion:
        name: previousVersion
        description: A version-level Data Set representing the version described here.
        comments:
        - This attribute may apply to version and distribution-level Data Set representations.
        multivalued: false
        range: DataSet
        required: false
      currentVersion:
        name: currentVersion
        description: A version-level Data Set representing the most current version
          at the time of recording.
        comments:
        - This attribute may apply to version and distribution-level Data Set representations.
        multivalued: false
        range: DataSet
        required: false
      format:
        name: format
        description: A specific representational format used to encode a distribution-level
          Dataset.
        comments:
        - This attribute may apply to  distribution-level Data Set representations.
        multivalued: false
        range: string
        required: false
      conformsTo:
        name: conformsTo
        description: A community standard that is used in representing any of the
          data in the Data Set (e.g. an ontology or code system from which enumerated
          values are drawn, a standard data model used to structure the representation).
        comments:
        - This attribute may apply to summary, version, and distribution-level Data
          Set representations.
        multivalued: true
        range: string
        required: false
  Document:
    name: Document
    exact_mappings:
    - IAO:0000310
    description: A collection of information, usually in human-readable form, intended
      to be read and understood together as a whole.
    title: Document
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - documentType
    - title
    - license
    - version
    slot_usage:
      documentType:
        name: documentType
        description: The specific type of the document (e.g.  'publication', 'patent',
          'pathology report')
        multivalued: true
        range: Coding
        required: false
      title:
        name: title
        description: The given title of the document.
        multivalued: false
        range: string
        required: false
      license:
        name: license
        description: The type of license that dictates legal permissions for how the
          Document can be used - typically referenced by its URL.
        comments:
        - The VA Model can record license information for resources such as Data Sets
          and Documents that get published and released as a unit for community use.
        multivalued: false
        range: string
        required: false
      version:
        name: version
        description: The version of the Document (use this field used in cases where
          version is not reflected in an identifier associated with the Document)
        comments:
        - The VA Model can record version information for resources such as Data Sets
          and Documents that get published and released as a unit for community use.
          These may go through rounds of revisions that add or modify content, but
          don’t change the identity of the resource.
        multivalued: false
        range: string
        required: false
  Statement:
    name: Statement
    aliases:
    - Assertion; Claim
    exact_mappings:
    - SEPIO:0000174
    description: An information entity expressing a declarative sentence that is either
      true or false.
    title: Statement
    comments:
    - In the VA model, each assertion of knowledge about a variant is captured in
      a self-contained Statement object. The semantics of what is asserted to be true
      is explicitly structured in terms of a subject, predicate, object, and qualifier(s).
      Organization of variant knowledge into discrete Statement objects allows clear
      and precise tracking of the evidence and provenance that supports each.
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - statementType
    - subject
    - predicate
    - object
    - qualifier
    - negated
    - assertedProposition
    - evidenceLevel
    - evidenceScore
    - hasEvidenceLine
    - hasEvidence
    - hasEvidenceOfType
    - hasEvidenceFromSource
    - subjectDescriptor
    - objectDescriptor
    - qualifierDescriptor
    slot_usage:
      statementType:
        name: statementType
        description: A specific type of statement the Statement object represents
          (e.g. a 'Variant Pathogenicity Statement', or 'Molecular Consequence Statement')
        multivalued: true
        range: Coding
        required: false
      subject:
        name: subject
        description: The Entity about which the Statement is made.
        comments:
        - The VA Core model is domain-agnsotic, and supports Statements/Propositions
          about any tyep of Entity.  Typically this will be a genetic varition - but
          data creators may want to make Statements/Propositions about other entities
          that represent evidence for a Statement about variation (e.g. a statement
          that a gene is valid for some disease is one type of evidence that may support
          the pathogenicity of a variant that affects that gene).
        multivalued: false
        range: Entity
        required: true
      predicate:
        name: predicate
        description: The relationship asserted to hold between the subject and the
          object of the Statement.
        comments:
        - The VA-Spec uses value sets to hold the types of relationships that may
          be described in a particular type of Statement. The core specification itself
          is domain agnostic, and does not define Codings for any specific types of
          relationships.  When applied to represent a particular type of Statement
          (via 'Profiling'), implementers can define predicates for the relationships
          relevant in the domain. For example, in a Statement about the pathogenicity
          of a variant, the predicate value set might include codings for 'pathogenic
          for', 'benign for', and 'uncertain significance for' relationships.
        multivalued: false
        range: Coding
        required: true
      object:
        name: object
        description: An Entity, concept, or value that is related to the subject of
          a Statement via its predicate.
        comments:
        - The object of a Statement can be an Entity that describes or is related
          to the subject Variation (e.g. a Drug, a Genetic Condition, a Study Result),
          a Coding from a value set representing some concept in the domain of discourse,
          or some quantitative value about the Variation.  'Element' covers any type
          of element in the model.
        multivalued: false
        range: Element
        required: true
      qualifier:
        name: qualifier
        description: A value or concept that extends or refines the meaning of the
          claim expressed in the core subject - predicate - object 'triple' - e.g.
          by providing additional information/detail, or constraining the claim to
          apply in a particular context.
        comments:
        - The qualifier attribute allows representation of more complex, n-ary expressions
          that may not be accommodated by a simple subject-predicate-object triple.
          For example, if this triple asserts that 'Variant X' - predicts sensitivity
          to - 'Drug Y', a qualifier can be used to indicate that this applies in
          the context of a particular 'Disease Z'.  Qualifiers can also add information
          that 'quantifies' a Statement - e.g. for a Statement triple asserting that
          a 'Variant X'- causes - 'Phenotype Y', a qualifier can be used to add penetrance
          information that quantifies the percentage of carriers in which the phenotype
          is observed to manifest.
        multivalued: true
        range: Element
        required: false
      negated:
        name: negated
        description: A boolean flag set to 'true' if the statement expressed by the
          subject, predicate, object, and qualifier(s) is explicitly asserted to be
          false.
        comments:
        - Along with the 'subject', predicate', 'object', and 'qualifier' attributes,
          the 'negated' element contributes to the semantics of what a Statement asserts
          to be true.  Accordingly, it would get encapsulsted in a Proposition object
          with these other other attributes in a Proposition-based approach.
        multivalued: false
        range: boolean
        required: false
      assertedProposition:
        name: assertedProposition
        description: The possible fact (proposition) that the Statement puts forth
          as true.
        comments:
        - This attribute provides the option of representing the semantics of what
          a Statement asserts to be true (its 'proposition') in a separate 'Proposition'
          object.  With this alternative modeling pattern, the subject, predicate,
          object, and any qualifier attributes are encapsulated inside a separate
          Proposition object. This Proposition can be referenced from from a Statements
          that assert it to be true, or an Evidence Line that weighs evidence against
          it).
        multivalued: false
        range: Proposition
        required: false
      evidenceLevel:
        name: evidenceLevel
        description: A term indicating the overall strength of support for the Statement
          based on all evidence assessed.
        multivalued: false
        range: Coding
        required: false
      evidenceScore:
        name: evidenceScore
        description: A quantitative score reflecting the overall strength of support
          for the Statement based on all evidence assessed.
        multivalued: false
        range: DataItem
        required: false
      hasEvidenceLine:
        name: hasEvidenceLine
        description: A discrete, independent argument relevant to the validity of
          the Proposition put forth as true in the Statement, that is based on the
          interpretation of one or more pieces of information as evidence.
        comments:
        - Evidence Lines result from the interpretation of one or more pieces of information
          to build an argument for or against a particular Proposition. These arguments
          have direction (supporting / disputing) and strength (e.g. strong, moderate,
          weak) relative to the Proposition they are evaluated against. For example,
          ExaC allele counts and frequency calculations for the BRCA2 c.8023A>G variant
          in different populations may be collectively assessed to provide an argument
          of moderate strength in support of a Proposition that the variant is pathogenicity
          for breast cancer.
        multivalued: true
        range: EvidenceLine
        required: false
      hasEvidence:
        name: hasEvidence
        description: A piece of information that represents or contributes to an argument
          for or against the validity of a Statement.
        comments:
        - Evidence is any information that is interpreted in assessing the truth of  the
          proposition a Statement puts forth as true.  A piece of information only
          becomes evidence when it is interpreted in this way. Different types and
          scales of information entity can be used and cited as evidence, including
          direct observation or measurement data, derived statistical calculations,
          data tables or figures in a publication, conclusions/findings from a particular
          study, or prior assertions of knowledge  that themselves are based on their
          own set of evidence.  This is a shortcut relation that links a Statement
          directly to a piece of evidnece supporting it, to be used data creators
          cannot or do not wich to create an Evidence Line between them.
        multivalued: true
        range: InformationEntity
        required: false
      hasEvidenceOfType:
        name: hasEvidenceOfType
        description: A term describing a type of evidence used to support a Statement
          (e.g. 'sequence similarity evidence', 'in vitro assay evidence') - as opposed
          to an instance of evidence information such as a particular data item, study
          result, or prior assertions, etc.
        comments:
        - The VA-Spec recommends the use of terms from ontologies such as the Evidence
          and Conclusion Ontology (ECO) to describe specific types of evidence.
        multivalued: true
        range: Coding
        required: false
      hasEvidenceFromSource:
        name: hasEvidenceFromSource
        description: An Information Entity (typically a publication, dataset, or database)
          that reports information interpreted as evidence to make the Statement.
        comments:
        - This is a 'shortcut relation' that can be used to directly link a Statement
          to sources that provided evidence supporting/disputing it, without having
          to represent those Evidence Items directly.
        multivalued: true
        range: InformationEntity
        required: false
      subjectDescriptor:
        name: subjectDescriptor
        description: A collection of additional metadata about the subject of the
          Statement's proposition, that cannot represented in its value object based
          representation, but may be useful for understanding and use of the subject
          entity (e.g. labels, xrefs, aliases, and other subjective/context specific
          information)
        comments:
        - 'See the VRSATILE Value Object Descriptor Specification for more detail
          about this modeling approach: https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/index.html'
        multivalued: false
        range: Descriptor
        required: false
      objectDescriptor:
        name: objectDescriptor
        description: A collection of additional metadata about the object of the Statement's
          proposition, that cannot represented in its value object based representation,
          but may be useful for understanding and use of the subject entity (e.g.
          labels, xrefs, aliases, and other subjective/context specific information)
        comments:
        - 'See the VRSATILE Value Object Descriptor Specification for more detail
          about this modeling approach: https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/index.html'
        multivalued: false
        range: Descriptor
        required: false
      qualifierDescriptor:
        name: qualifierDescriptor
        description: A collection of additional metadata about an entity/concept that
          qualifies the Statement's proposition. This additional metadata cannot represented
          in its value object based representation, but may be useful for understanding
          and use of the subject entity (e.g. labels, xrefs, aliases, and other subjective/context
          specific information)
        comments:
        - 'See the VRSATILE Value Object Descriptor Specification for more detail
          about this modeling approach: https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/index.html'
        multivalued: true
        range: Descriptor
        required: false
  StudyResult:
    name: StudyResult
    description: A collection of select data items from a single study that are about
      a particular subject or experimental unit -  and may include provenance metadata
      describing how these data were generated.
    title: Study Result
    comments:
    - StudyResult objects end up being a very flexible and useful way to summarize
      the salient data/metadata from a larger study that is specifically useful as
      evidence in curation workflows aimed at generating higher order knowledge about
      a particular variant or other entity. For example, a specific subset of allele
      frequency data/metadata concerning a particular variant of interest in the Gnomad
      dataset can be summarized in a Study Result object, and referenced as evidence
      for a higher-order Statement about the variant's pathogenicity that relied on
      this frequency data for support.
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - studyResultType
    - focus
    - data
    - interpretation
    - sourceDataSet
    - sourceStudy
    - sourceStudyType
    - sourceStudyDate
    - sourceStudyMethod
    slot_usage:
      studyResultType:
        name: studyResultType
        description: A specific type of result the StudyResult object represents (e.g.
          an 'Allele Frequency Study Result')
        multivalued: true
        range: Coding
        required: false
      focus:
        name: focus
        description: The specific subject, concept, or experimental unit in the Research
          Study that data in the Result is about. The focus guides the selection of
          data that is included within a single Study Result object.
        comments:
        - The value of this field explains why the sleected data as included in the
          Study Result - because it all pertains to the 'focus' of the curator when
          creating it.
        multivalued: true
        range: Entity
        required: false
      data:
        name: data
        description: A piece of data from the source Study that is included in the
          Result, and pertains to the entity that is the 'focus'. Can be data directly
          about the focus, or metadata relevant to how this data was generated.
        multivalued: true
        range: DataItem
        required: false
      interpretation:
        name: interpretation
        description: A qualitative interpretation of the lower-level data item(s)
          included in the result (e.g. that a result is high, normal, or low).
        comments:
        - This field allows basic interpretations / classifications to be included
          in a Study Result, such as binning a result as in or out of normal range.
        multivalued: false
        range: Coding
        required: false
      sourceDataSet:
        name: sourceDataSet
        description: A larger Data Set from which the content of the Result was derived.
        multivalued: true
        range: DataSet
        required: false
      sourceStudy:
        name: sourceStudy
        description: The Study that generated the date reported in the Result.
        multivalued: false
        range: ResearchStudy
        required: false
      sourceStudyType:
        name: sourceStudyType
        description: The type of study that produced the result (e.g. 'allele population
          frequency study', 'computational functional impact prediction', 'protein
          functional assay', 'randomized clinical trial')
        comments:
        - This is a shortcut relationship that can be used to capture the type of
          source study in models that don't represent the Study itself as an object
          in the data.
        multivalued: false
        range: Coding
        required: false
      sourceStudyDate:
        name: sourceStudyDate
        description: The date the study from which the Result was derived was performed.
        comments:
        - This is a shortcut relationship that can be used to capture the date of
          the source study in models that don't represent the Study itself as an object
          in the data.
        multivalued: false
        range: ga4ghDateTime
        required: false
      sourceStudyMethod:
        name: sourceStudyMethod
        description: A plan specification that describes all or part of the process
          that created the information (e.g. interpretation guidelines, rule sets,
          etc.).
        comments:
        - This is a shortcut relationship that can be used to capture methods applied
          in the source study in models that don't represent the Study itself as an
          object in the data.
        multivalued: true
        range: Method
        required: false
  EvidenceLine:
    name: EvidenceLine
    exact_mappings:
    - SEPIO:0000002
    description: A discrete, independent argument relevant to the validity of the
      Proposition put forth as true in the Statement,  that is based on the interpretation
      of one or more pieces of information as evidence.
    title: Evidence Line
    comments:
    - 'Evidence Lines result from the interpretation of one or more pieces of information
      (Evidence Items) to build an argument for or against a particular Proposition
      (possible fact). The Evidence Line that results can be considered a special
      kind of Statement that asserts the direction and strength such an argument provides
      for some target Proposition. For example, The various allele counts and frequency
      calculations for the BRCA2 c.8023A>G variant found in the ExAC database are
      Evidence Items  that might be collectively assessed by a ClinGen curator to
      build an Evidence Line that is deemed to ''support'' with ''moderate'' strength
      a target proposition that the variant is pathogenic for Breast Cancer.  The
      narrative form of the Statement represented by this Evidence Line is roughly:
      "ExAC allele frequency data for BRCA2 c.8023A>G {0.0000021, 0.0000034, ...}
      provides evidence of moderate strength supporting the proposition that BRCA2
      c.8023A>G is pathogenic for Breast Cancer".'
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - evidenceLineType
    - targetProposition
    - hasEvidenceItem
    - evidenceDirection
    - evidenceStrength
    - evidenceItemSource
    slot_usage:
      evidenceLineType:
        name: evidenceLineType
        description: A specific type of evidence the EvidenceLine object represents
          (e.g. 'mutant phenotype evidence', 'evidence from manual interpretation',
          'ACMG PM2 evidence')
        comments:
        - Data creators may choose to define specific types of evidence lines relevant
          for their domain/use case, based on the type of evidence items that comprise
          it, the methodology that guided evidence interpretation, or the type of
          statement the evidence line supports.  Terms from ontologies like the Evidence
          and Conclusion Ontology (ECO) can be used as values here.
        multivalued: true
        range: Coding
        required: false
      targetProposition:
        name: targetProposition
        description: The proposition against which the evidence items were evaluated,
          in determining the overall strength and direction of evidence they provide
          (as captured in the Evidence Line)
        comments:
        - 'An example based on the ACMG Guidelines for germline variant pathogenicity
          interpretation: consider a curator assessing the evidence provided by population
          frequency data for a specific variant based on the ACMG criteria.  In order
          to assign a strength (e.g. moderate, strong) and direction (PM2 or  BS1)
          to this data as evidence, there must be some ''target proposition'' toward
          which the evidence is assessed. If the PM2 criteria is deemed ''met'', this
          indicates that the population frequency evidence supports with moderate
          strength the target proposition that the variant is pathogenic for the disease
          of interest.'
        multivalued: false
        range: Proposition
        required: false
      hasEvidenceItem:
        name: hasEvidenceItem
        description: An Information Entity that was evaluated in making the argument
          represented by the Evidence Lines.
        comments:
        - A given Evidence Line might be suported by one or many individual pieces
          of evidence. Different types or scales of information entity can serve as
          evidence - but only when it realizes this role do we call it an 'Evidence
          Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G  becomes
          an Evidence Item when it is assessed as evidence (e.g. for the variant’s
          pathogenicity - and thus contributes to an argument for (or against) this
          target proposition.
        multivalued: true
        range: InformationEntity
        required: false
      evidenceDirection:
        name: evidenceDirection
        description: The direction of support that the Evidence Line is determined
          to provide for its target Proposition (can be supporting, disputing, or
          neutral)
        multivalued: false
        range: Coding
        required: false
      evidenceStrength:
        name: evidenceStrength
        description: The strength of support that an Evidence Line is determined to
          provide for or against its target Proposition.
        multivalued: false
        range: Coding
        required: false
      evidenceItemSource:
        name: evidenceItemSource
        description: An information resource (e.g. document, dataset, knowledgebase)
          that provided information interpreted as evidence in building an Evidence
          Line.
        comments:
        - This is a 'shortcut relation' that can be used to directly link an Evidence
          Line to sources of its supporting Evidence Items, without having to represent
          those Evidence Items directly.
        multivalued: true
        range: InformationEntity
        required: false
  Method:
    name: Method
    exact_mappings:
    - IAO:0000104
    description: A set of instructions that specify how to achieve some objective
      (e.g. study/experimental protocols, curation guidelines, rule sets, etc.)
    title: Method
    comments:
    - Methods guide human or computational agents by specifying what actions to perform
      and how to do so.  Examples include research protocols specifying how to execute
      studies or experiments to generate data, and guidelines for data curation or
      interpretation that specify how information can be organized, evaluated, and
      interpreted to generate evidence-based assertions.
    from_schema: https://w3id.org/ga4gh-va
    is_a: InformationEntity
    slots:
    - methodType
    slot_usage:
      methodType:
        name: methodType
        description: A specific type of method that the Method object represents (e.g.
          'Variant Interpretation Guideline', 'Experimental Protocol')
        multivalued: true
        range: Coding
        required: false
  Activity:
    name: Activity
    exact_mappings:
    - PROV:Activity | OBI:0000011
    description: 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.
    title: Activity
    comments:
    - Activities relevant to scientific knowledge generation including things like
      designing and performing experiments, data analysis and transfomration, publishing
      research results, data curation and interpretation, observations of the natural
      world, and assessment and treatment of patients in clinical settings.  These
      activities produce information that gets encoded in sharable artifacts used
      to generate scientific knowledge. Agents can play different types of roles in
      the generation and use of such artifacts.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - activityType
    - startDate
    - endDate
    - performedBy
    - hadInput
    - hadOutput
    - wasSpecifiedBy
    - hasPart
    - partOf
    slot_usage:
      activityType:
        name: activityType
        description: A specific type of activity this Activity object may represent
        multivalued: true
        range: Coding
        required: false
      startDate:
        name: startDate
        description: The date that the Activity started
        comments:
        - The model provides startDate and endDate attributes to allow precise reporting
          of the time an Activity occurred. Implementations wishing to specify a single
          time should simply report the date and/or time that the contribution ended.
          An empty startDate means that the start time is unknown or unspecified.
        multivalued: false
        range: ga4ghDateTime
        required: false
      endDate:
        name: endDate
        description: The date that the Activity ended
        multivalued: false
        range: ga4ghDateTime
        required: false
      performedBy:
        name: performedBy
        description: An Agent taking part in executing the Activity.
        multivalued: true
        range: Agent
        required: false
      hadInput:
        name: hadInput
        description: An entity that was input into the Activity (could be material
          or information)
        multivalued: true
        range: Entity
        required: false
      hadOutput:
        name: hadOutput
        description: An entity that was output from the Activity (could be material
          or information)
        multivalued: true
        range: Entity
        required: false
      wasSpecifiedBy:
        name: wasSpecifiedBy
        description: A directive specification followed in performing an Activity,
          that describes how it should be executed.
        multivalued: true
        range: Method
        required: false
      hasPart:
        name: hasPart
        description: A smaller, discrete Activity that is part of this larger Activity
        multivalued: true
        range: Activity
        required: false
      partOf:
        name: partOf
        description: A larger Activity of which this Activity is a part (i.e. it was
          performed during the larger Activity)
        multivalued: true
        range: Activity
        required: false
  ResearchStudy:
    name: ResearchStudy
    exact_mappings:
    - SEPIO:0000125
    description: An activity that applies a defined methodological approach to interrogate
      a specific set of subjects, and generate data that is analyzed and interpreted
      to answer a particular research question (typically the validation or generation
      of hypothesis)
    title: Research Study
    comments:
    - This is a stub for a basic model of a Study that will be developed in future
      iterations of the specification.  At present, adopters can plug their own model
      of research studies in here.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Activity
    slots:
    - researchStudyType
    slot_usage:
      researchStudyType:
        name: researchStudyType
        description: A specific type of study this ResearchStudy object represents.
        is_a: Activity
        multivalued: true
        range: Coding
        required: false
  Contribution:
    name: Contribution
    exact_mappings:
    - CAM:Contribution
    description: The actions taken by a particular agent in the creation, modification,
      assessment, or deprecation of some entity (e.g. a Statement, Evidence Line,
      Data Item, Publication, etc.)
    title: Contribution
    comments:
    - The scope of a given Contribution instance includes only the actions of a single
      agent in contributing to a single artifact.  The agent can be an individual,
      or a group or organization of individuals acting together to make the contribution.
      Contribution instances are used to organize information about when, where, how
      (e.g. what roles were played), and on whose behalf these actions were performed.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Activity
    slots:
    - contributionMadeBy
    - contributionMadeTo
    - contributorRole
    - organizationalContext
    slot_usage:
      contributionMadeBy:
        name: contributionMadeBy
        description: The agent that made the contribution.
        multivalued: false
        range: Agent
        required: false
      contributionMadeTo:
        name: contributionMadeTo
        description: The artifact toward which the contribution was made.
        multivalued: false
        range: InformationEntity
        required: false
      contributorRole:
        name: contributorRole
        description: A role indicating the nature of the contribution made by the
          Agent - i.e. the specific type of contribution that was made.
        comments:
        - Data creators can define terms for the specific roles relevant to their
          use case/application, and/or re-use roles defined in the Contribution Role
          Ontology (CRO).  Note that if the same Agent played multiple roles in contibuting
          to some artifact, they may all be captured in a single Contribution object.
          However, if data creators want to provide metadata specific to each role
          (e.g. when or how each role was played), then a separate Contribution object
          should be created for each role.
        multivalued: true
        range: Coding
        required: false
      organizationalContext:
        name: organizationalContext
        description: An organization whose resources and/or directives supported the
          contribution made by an Agent.
        comments:
        - The Affiliation object holds details about an Agent's status/position in
          a particular Organization on whose behalf they were acting when they made
          the Contribution.
        multivalued: true
        range: Affiliation
        required: false
  Agent:
    name: Agent
    exact_mappings:
    - CAM:Agent
    description: An autonomous actor (person, organization, or computational agent)
      that bears some form of responsibility for an activity taking place, for the
      existence of an entity, or for another agent’s activity.
    title: Agent
    comments:
    - This is a stub for a basic model of an Agent that may be developed in future
      iterations of the specification.  At present, adopters can plug their own model
      of Agents in here.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - agentType
    - softwareVersion
    - hasAffiliation
    - parentOrganization
    - childOrganization
    slot_usage:
      agentType:
        name: agentType
        description: A specific type of agent the Agent object represents. Must be
          one of {Person, Organization, Software Agent}
        comments:
        - At present, there are no named subtypes representing the three high level
          subtypes of Agent (Person, Organization, or Software Agent). If it is determined
          that there are enough unique properties that need to be defined for these
          subtypes, separate classes may be created.
        multivalued: false
        range: Coding
        required: false
      softwareVersion:
        name: softwareVersion
        description: For software/computational agents, the specific version of the
          software it represents.
        multivalued: false
        range: string
        required: false
      hasAffiliation:
        name: hasAffiliation
        description: A membership relation between the Agent and an Organization to
          which they belong or at one time belonged.
        multivalued: true
        range: Affiliation
        required: false
      parentOrganization:
        name: parentOrganization
        description: A larger Organization of which this Organization is a part
        comments:
        - The agentType of the referenced Agent should be set to 'Organization'
        multivalued: true
        range: Agent
        required: false
      childOrganization:
        name: childOrganization
        description: A smaller Organization that is a part of this larger one
        comments:
        - The agentType of the referenced Agent should be set to 'Organization'
        multivalued: true
        range: Agent
        required: false
  Proposition:
    name: Proposition
    exact_mappings:
    - SEPIO:0000000
    description: An abstract entity representing the sharable meaning that can be
      put forth as true in a Statement made by an Agent.
    title: Proposition
    comments:
    - Propositions are taken to represent the semantic content of sentences or larger
      lexical entities formulated in some natural or artificial language. As primary
      bearers of truth, they are either true or false. They are abstract entities
      whose identity and existence are independent of space and time, and of whether
      they are ever asserted to be true by some agent. Propositions are ‘sharable’
      in the sense that the same Proposition instance can be expressed in many different
      Statements, as made by different Agents and/or on different occasions.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - propositionType
    - subject
    - predicate
    - object
    - qualifier
    - negated
    slot_usage:
      propositionType:
        name: propositionType
        description: A specific type of proposition the Proposition object represents
          (e.g. a 'Variant Pathogenicity Proposition', or 'Molecular Consequence Proposition')
        multivalued: true
        range: Coding
        required: false
      subject:
        name: subject
        description: The Entity about which the Proposition is made.
        comments:
        - The VA Core model is domain-agnostic, and supports statements about any
          type of Entity.  For most VA use cases, the subject will be a genetic variation
          - but data creators may want to make statements about other entities that
          represent evidence for a Statement about variation (e.g. a statement that
          a gene is valid for some disease is one type of evidence that may support
          the pathogenicity of a variant that affects that gene).
        multivalued: false
        range: Entity
        required: true
      predicate:
        name: predicate
        description: The relationship asserted to hold between the subject and the
          object of the Proposition.
        comments:
        - The VA-Spec uses value sets to hold the types of relationships that may
          be described in a particular type of Statement. The core specification itself
          is domain agnostic, and does not define Codings for any specific types of
          relationships.  When applied to represent a particular type of Proposition
          (via 'Profiling'), implementers can define predicates for the relationships
          relevant in the domain. For example, in a Proposition concerning the pathogenicity
          of a variant, the predicate value set might include codings for 'pathogenic
          for', 'benign for', and 'uncertain significance for' relationships.
        multivalued: false
        range: Coding
        required: true
      object:
        name: object
        description: An Entity, concept, or value that is related to the subject of
          a Proposition via its predicate.
        comments:
        - The object of a Proposition can be an Entity that describes or is related
          to the subject Variation (e.g. a Drug, a Genetic Condition, a Study Result),
          a Coding from a value set representing some concept in the domain of discourse,
          or some quantitative value about the Variation.  'Element' covers any type
          of element in the model.
        multivalued: false
        range: Element
        required: true
      qualifier:
        name: qualifier
        description: A value or concept that extends or refines the meaning of the
          Proposition expressed by the core subject - predicate - object 'triple'
          - e.g. by providing additional information/detail, or constraining the claim
          to apply in a particular context.
        comments:
        - Qualifiers allow representation of more complex, n-ary expressions that
          may not be accommodated by a simple S-P-O triple. For example, if a triple
          asserts that Variant X - is associated with sensitivity to - Drug Y, a qualifier
          can be used to indicate that this applies in the context of a particular
          treated Condition Z.
        multivalued: true
        range: Element
        required: false
      negated:
        name: negated
        description: A boolean flag set to 'true' if the statement expressed by the
          subject, predicate, object, and qualifier(s) is explicitly asserted to be
          false.
        comments:
        - Along with the 'subject', predicate', 'object', and 'qualifier' attributes,
          the 'negated' element contributes to the semantics of the 'possible fact'
          that a Proposition expresses.
        multivalued: false
        range: boolean
        required: false
  Affiliation:
    name: Affiliation
    description: A relationship between an Agent and a Group or Organization to which
      they belong or belonged.
    title: Affiliation
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - member
    - organization
    - organizationalRole
    - affiliationStatus
    - startDate
    - endDate
    slot_usage:
      member:
        name: member
        description: The Agent participating in the Affiliation
        comments:
        - The Affiliation object is scoped to define the relationship between one
          Agent and one Organization, over a specified period of time.  A given Agent
          may participate in more than on Affiliation with the same Organization,
          if they held different roles/positions/statuses at different times.
        multivalued: false
        range: Agent
        required: true
      organization:
        name: organization
        description: The Organization to which the Agent belongs or belonged.
        comments:
        - Here the Agent referenced should be an Organization (Agent.agentType = 'Organization')
        multivalued: false
        range: Agent
        required: true
      organizationalRole:
        name: organizationalRole
        description: An official position or role held by the Agent in the Organization
          during the span of the defined Affiliation (e.g. graduate student, principle
          investigator, curator, physician, expert panel member)
        multivalued: true
        range: Coding
        required: false
      affiliationStatus:
        name: affiliationStatus
        description: The status of the Agent's affiliation at the time the Affiliation
          record was created  or last updated (e.g. active, pending, probation, inactive)
        multivalued: false
        range: Coding
        required: false
      startDate:
        name: startDate
        description: The date that the Affiliation described here began (where a organizational
          role is provided, this is the date when this role in the organization began)
        comments:
        - If a specific organizational role and/or status are reported, the startDate
          indicates when this particular role/status began.
        multivalued: false
        range: ga4ghDateTime
        required: false
      endDate:
        name: endDate
        description: The date that the Affiliation described here ended (where a organizational
          role is provided, this is the date when this role in the organization ended)
        comments:
        - If a specific organizational role and/or status are reported, the endDate
          indicates when this particular role/status ended.
        multivalued: false
        range: ga4ghDateTime
        required: false
  Descriptor:
    name: Descriptor
    description: An object that wraps a value object in order to transfer additional,
      non-definitional information about it.
    title: Descriptor
    comments:
    - Value Object Descriptors are constructs created and used for message passing,
      and provide a means to separate immutable elements that define an entity, from
      other descriptors that are often passed along to improve the useability of the
      object (e.g. labels, identifiers, xrefs, aliases, etc.).
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - valueObjectId
    - valueObject
    - valueObjectName
    - valueObjectAlias
    - valueObjectExpression
    - valueObjectDescription
    - valueObjectXref
    slot_usage:
      valueObjectId:
        name: valueObjectId
        description: The computed identifier of the value object described/wrapped
          by the Descriptor
        comments:
        - 'Condition:  either the valueObjectId or the valueObject field is Required'
        multivalued: false
        range: identifier
        required: false
      valueObject:
        name: valueObject
        description: An in-lined representation of the wrapped value object
        comments:
        - 'Condition:  either the valueObjectId or the valueObject field is Required'
        multivalued: false
        range: Entity
        required: false
      valueObjectName:
        name: valueObjectName
        description: The preferred name for the wrapped value object as assigned by
          the creator of the VOD
        multivalued: false
        range: string
        required: false
      valueObjectAlias:
        name: valueObjectAlias
        description: Other labels that exist for the wrapped value object.
        comments:
        - 'Guidance: The primary purpose of this field is to capture simple, informal
          names. Labels based on systematically-generated expressions from formal
          nomenclatures can be included here, but are best captured using the valueObjectExpression
          field.'
        multivalued: true
        range: string
        required: false
      valueObjectExpression:
        name: valueObjectExpression
        description: Systematic expressions that describe the wrapped object, as generated
          by formal nomenclature systems (e.g. HGVS, ISCN, HLA).
        comments:
        - 'Guidance:  For Variations, itis strongly recommended that a HGVS or ISCN
          expression is captured in this field (even if it is the same as the preferred
          or an alias).'
        multivalued: true
        range: Expression
        required: false
      valueObjectDescription:
        name: valueObjectDescription
        description: A free text description of the entity represented by the wrapped
          value object.
        multivalued: false
        range: string
        required: false
      valueObjectXref:
        name: valueObjectXref
        description: Points to an external database record for an entity that is equivalent
          to or closely related to the entity represented by the wrapped value object.
        multivalued: true
        range: string
        required: false
  VariationDescriptor:
    name: VariationDescriptor
    description: A Descriptor that describes a value object representation of a molecular
      variation.
    title: Variation Descriptor
    from_schema: https://w3id.org/ga4gh-va
    is_a: Descriptor
    slots:
    - moleculeContext
    - structuralType
    slot_usage:
      moleculeContext:
        name: moleculeContext
        description: The type of macromolecule on which the variation exists (e.g.
          genomic, transcript, protein)
        multivalued: false
        range: Coding
        required: false
      structuralType:
        name: structuralType
        description: The high-level structural type of the Variation (e.g. SNV, CNV,
          insertion, duplication, etc)
        multivalued: true
        range: Coding
        required: false
  Coding:
    name: Coding
    exact_mappings:
    - FHIR:Coding
    description: A structured representation of a coded/enumerated data value, that
      includes additional metadata about the code and code system.
    title: Coding
    from_schema: https://w3id.org/ga4gh-va
    is_a: Element
    slots:
    - code
    - label
    - system
    - systemURL
    - systemVersion
    slot_usage:
      code:
        name: code
        description: The value of the code itself.
        comments:
        - Either a code, label, or both must be provided.
        multivalued: false
        range: string
        required: false
      label:
        name: label
        description: A human-readable name for the code.
        comments:
        - Either a code, label, or both must be provided.
        multivalued: false
        range: string
        required: false
      system:
        name: system
        description: The code system where the code is defined.
        multivalued: false
        range: string
        required: false
      systemURL:
        name: systemURL
        description: A URL where the code system can be found.
        multivalued: false
        range: url
        required: false
      systemVersion:
        name: systemVersion
        description: The version of the code system.
        multivalued: false
        range: string
        required: false
  Expression:
    name: Expression
    description: 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).
    title: Expression
    comments:
    - Similar to the 'Coding' data type, which provides the same fields but for coded
      values, as opposed to human-readable names.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Element
    slots:
    - value
    - system
    - systemURL
    - systemVersion
    slot_usage:
      value:
        name: value
        description: A free-text rendering of the expression used as a label for the
          entity
        multivalued: false
        range: string
        required: true
      system:
        name: system
        description: The nomenclature system that created and assigned the expression.
        comments:
        - This should be provided whenever the expression comes from a formal nomenclature
          system.
        multivalued: false
        range: string
        required: true
      systemURL:
        name: systemURL
        description: A URL for the nomenclature system
        multivalued: false
        range: url
        required: false
      systemVersion:
        name: systemVersion
        description: The version of the nomenclature system.
        multivalued: false
        range: string
        required: false
  Extension:
    name: Extension
    exact_mappings:
    - FHIR.Extension
    description: A data structure that allows implementations to define and create
      custom fields within an Entity to capture information not supported by the core
      specification.
    title: Extension
    comments:
    - The modeling pattern and use of Extensions is based on that defined by the FHIR
      Speciufication - see https://build.fhir.org/extensibility.html
    from_schema: https://w3id.org/ga4gh-va
    is_a: Element
    slots:
    - description
    - name
    - value
    slot_usage:
      description:
        name: description
        description: A free text description of the intended semantics and use of
          this extension element (i.e. they types of values it takes, and how to interpret
          these values in the context of the parent Class)
        multivalued: false
        range: string
        required: false
      name:
        name: name
        description: A name that captures the meaning of the extension element
        multivalued: false
        range: string
        required: true
      value:
        name: value
        description: The value of the extension element
        multivalued: false
        range: Element
        required: true
  RecordMetadata:
    name: RecordMetadata
    description: A re-usable structure that encapsulates provenance metadata that
      applies to a specific concrete record/encoding of information, as opposed to
      provenance of the abstract information content/knowledge the record represents.
    title: Record Metadata
    comments:
    - Record-level metadata applies to a specific concrete encoding/serialization
      of knowledge  (e.g as a record in a specific database, or an online digital
      resource). A RecordMetadata object can capture provenance and other metadata,
      including when, how, and by whom a specific record was generated or modified;
      what upstream resources it was derived/retrieved from; and record-level administrative
      information such as versioning and system / lifecycle status.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Element
    slots:
    - description
    - recordIdentifier
    - partOfDataset
    - recordVersion
    - previousVersion
    - dateRecordCreated
    - dateRecordLastModified
    - qualifiedContribution
    - recordURL
    - xref
    slot_usage:
      description:
        name: description
        description: A free text description of the RecordMetadata object.
        comments:
        - It be helpful to describe in free text what specific record the object describes,
          and the type of metadata it contains, to assist consumers in understanding/using
          this information.
        multivalued: false
        range: string
        required: false
      recordIdentifier:
        name: recordIdentifier
        description: The business identifier of the record described in the RecordMetadata
          object (required when the record described is not the one in the present
          system)
        comments:
        - This is needed only when the RecordMetadata object describes an upstream
          source record, as opposed to the record in the present system, so it is
          clear what the metadata it contains is about.  e.g. when ClinGen ingests
          and transfroms ClinVar data, it wants to maintain a record of when the source
          ClinVar record was submitted and by whom.  A RecordMetadata object could
          be created that describes this upstream source recrod, including infromation
          about its submission to ClinVar.
        multivalued: false
        range: identifier
        required: false
      partOfDataset:
        name: partOfDataset
        description: The dataset of which the described record is a part (releveant
          when the record described is not the one in the present system)
        comments:
        - Can provide important context for understanding record-level metadata, in
          cases where it describes records from upstream datasets/systems.
        multivalued: false
        range: DataSet
        required: false
      recordVersion:
        name: recordVersion
        description: The version number of the record-level artifact the object describes
        multivalued: false
        range: string
        required: false
      previousVersion:
        name: previousVersion
        description: The version of a record in the same system that the current record
          replaces/follows.
        comments:
        - 'Value should be a string representing the identifier of the previous record.
          Consider renaming: ''previousRecord'', ''replaces'''
        multivalued: false
        range: identifier
        required: false
      dateRecordCreated:
        name: dateRecordCreated
        description: The date the record was initially created.
        multivalued: false
        range: ga4ghDateTime
        required: false
      dateRecordLastModified:
        name: dateRecordLastModified
        description: The date the record was last edited/updated/modified to its present
          concrete form.
        multivalued: false
        range: ga4ghDateTime
        required: false
      qualifiedContribution:
        name: qualifiedContribution
        description: Links to a 'Contribution' object allowing richer representation
          of specific types of contributions made by an agent to the creation, modification,
          or administrative management of a record.
        multivalued: true
        range: Contribution
        required: false
      recordURL:
        name: recordURL
        description: A web address where the entity is found or described.
        multivalued: true
        range: url
        required: false
      xref:
        name: xref
        description: A cross-reference linking to an identifier for an entity/record
          that represents the same or a closely related concepts or knowledge as the
          present record.
        comments:
        - Preferred values for this field are CURIEs or URLs for database records
        multivalued: true
        range: string
        required: false
  Variation:
    name: Variation
    description: A representation of the state of one or more biomolecules.
    title: Variation
    comments:
    - This is a placeholder for the root class of the VRS hierarchy of Variation classes,
      which we will use to represent the subjects of Statements in the VA model. See
      https://vrs.ga4gh.org/en/stable/terms_and_model.html#variation
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
  GeneticCondition:
    name: GeneticCondition
    description: A disease, or a set of one or more co-occurring phenotypes, controlled
      by genetic factors with a defined inheritance pattern.
    title: Genetic Condition
    comments:
    - A Genetic Condition object can be used to compose a condition description based
      on component diseases and phenotypes, contributing genes, and an inheritance
      pattern. For now it is a simple/loose collection of features.  We can define
      a more complex model to support more precise and nuanced characterizations,
      as needed in future iterations.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - componentDisease
    - componentPhenotype
    - inheritancePattern
    - contributingGene
    slot_usage:
      componentDisease:
        name: componentDisease
        description: A disease that is manifest in the genetic condition
        multivalued: true
        range: Coding
        required: false
      componentPhenotype:
        name: componentPhenotype
        description: A phenotype that is manifest in the genetic condition
        multivalued: true
        range: Coding
        required: false
      inheritancePattern:
        name: inheritancePattern
        description: The pattern in which the condition is passed from one generation
          to the next.
        multivalued: false
        range: Coding
        required: false
      contributingGene:
        name: contributingGene
        description: Genes implicated in the condition
        multivalued: true
        range: Gene
        required: false
  TherapeuticIntervention:
    name: TherapeuticIntervention
    description: A type of treatment administered/prescribed to a patient to prevent,
      ameliorate, or cure a medical condition.
    title: Therapeutic Intervention
    comments:
    - This class is meant to describe a higher level class/type of therapeutic intervention,
      which may be composed of one or more drugs, procedures, or therapeutic activities
      -  as opposed to a specific instance that occurs on specific occasions toward
      particular patients.
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - componentDrug
    - componentProcedure
    - componentActivity
    - drugOperator
    slot_usage:
      componentDrug:
        name: componentDrug
        description: A chemical or biological substance administered or consumed to
          alleviate or prevent a condition
        multivalued: true
        range: Coding
        required: false
      componentProcedure:
        name: componentProcedure
        description: A medical procedure underwent to alleviate or prevent a condition
        multivalued: true
        range: Coding
        required: false
      componentActivity:
        name: componentActivity
        description: An activity participated in to alleviate or prevent a condition
        multivalued: true
        range: Coding
        required: false
      drugOperator:
        name: drugOperator
        description: Allows specification of how the drugs captured in the drug field
          should be considered in relation to each other (e.g. co-treatment, sequential
          treatment, alternates)
        multivalued: false
        range: Coding
        required: false
  Gene:
    name: Gene
    description: A region (or regions) that includes all of the sequence elements
      necessary to encode a functional transcript. A gene may include regulatory regions,
      transcribed regions and/or other functional sequence regions.
    title: Gene
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity
    slots:
    - biotype
    - symbol
    - location
    - strand
    slot_usage:
      biotype:
        name: biotype
        description: A classification of the gene according to the Ensembl Biotypes
          (e.g. Protein coding, ncRNA, Pseudogene, IG gene, etc).
        comments:
        - See http://uswest.ensembl.org/info/genome/genebuild/biotypes.html.
        multivalued: false
        range: string
        required: false
      symbol:
        name: symbol
        description: Abbreviated symbol for the gene (e.g. 'BRCA2', 'FGF8')
        comments:
        - Use the 'label' attribute to hold the full name of the gene.
        multivalued: false
        range: string
        required: false
      location:
        name: location
        description: Location of the gene on a reference.
        comments:
        - Use the VRS SequenceLocation class to describe the location of the gene.
        multivalued: true
        range: SequenceLocation
        required: false
      strand:
        name: strand
        description: The strand on which the gene is located (positive, negative)
        multivalued: false
        range: Coding
        required: false
  SequenceLocation:
    name: SequenceLocation
    description: A specified subsequence of a reference Sequence. The reference is
      typically a chromosome, transcript, or protein sequence.
    title: Sequence Location
    comments:
    - 'This is a stub for a class defined by the VRS specification:  https://vrs.ga4gh.org/en/stable/terms_and_model.html?highlight=curie#sequencelocation'
    from_schema: https://w3id.org/ga4gh-va
    is_a: Entity