Class: OntologyRelation

name: OntologyRelation
description: A relationship between two ontology classes as specified either directly
  in the ontology in the form of axioms (statements or assertions that defines rules
  or constraints in an ontology) or inferred via reasoning.  The association object
  is defined by two terms (the subject and the object) and the relationship between
  them (the predicate). Because ontologies often have a plethora of relationships/axiom
  types and can have additional metadata on the relationship itself, these kinds of
  relationships are structured as a class instead of a simple set of slots on OntologyClass
  itself.
comments:
- 'For example, the relationship between ''soil'' and ''enriched soil'' in the Environmental
  Ontology (ENVO) is defined by the following axioms: ''enriched soil'' subclass_of
  ''soil'', and ''enriched soil'' has_increased_levels_of (some) ''material entity.''
  Converting these statements to OntologyAssociations so they can be used in the NMDC
  data stores, the subject of the first axiom or statement, would be ''soil'', the
  predicate would be ''subclass_of'', and the object would be ''enriched soil''. For
  the second axiom, the subject would be ''enriched soil'', the predicate would be
  ''has_increased_levels_of'', and the object would be ''material entity.'' (Note
  that text labels are used in this example for ease of understanding and the literal
  values of subject, predicate, and object in this class will be the id (curie) of
  the `OntologyClass` as defined below). Not all ontology axioms (associations) between
  terms need to be ingested into the NMDC data stores. In general, subclass_of and
  part_of relationships/axioms are often good default relations/associations to support
  ontology browsing in user interfaces.'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- OntologyAssociation
slots:
- type
attributes:
  subject:
    name: subject
    from_schema: https://w3id.org/nmdc/basic_classes
    domain_of:
    - FunctionalAnnotation
    - OntologyRelation
    range: OntologyClass
    required: true
  predicate:
    name: predicate
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    domain_of:
    - OntologyRelation
    range: OntologyClass
    required: true
  object:
    name: object
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    domain_of:
    - OntologyRelation
    range: OntologyClass
    required: true
class_uri: nmdc:OntologyRelation

name: OntologyRelation
description: A relationship between two ontology classes as specified either directly
  in the ontology in the form of axioms (statements or assertions that defines rules
  or constraints in an ontology) or inferred via reasoning.  The association object
  is defined by two terms (the subject and the object) and the relationship between
  them (the predicate). Because ontologies often have a plethora of relationships/axiom
  types and can have additional metadata on the relationship itself, these kinds of
  relationships are structured as a class instead of a simple set of slots on OntologyClass
  itself.
comments:
- 'For example, the relationship between ''soil'' and ''enriched soil'' in the Environmental
  Ontology (ENVO) is defined by the following axioms: ''enriched soil'' subclass_of
  ''soil'', and ''enriched soil'' has_increased_levels_of (some) ''material entity.''
  Converting these statements to OntologyAssociations so they can be used in the NMDC
  data stores, the subject of the first axiom or statement, would be ''soil'', the
  predicate would be ''subclass_of'', and the object would be ''enriched soil''. For
  the second axiom, the subject would be ''enriched soil'', the predicate would be
  ''has_increased_levels_of'', and the object would be ''material entity.'' (Note
  that text labels are used in this example for ease of understanding and the literal
  values of subject, predicate, and object in this class will be the id (curie) of
  the `OntologyClass` as defined below). Not all ontology axioms (associations) between
  terms need to be ingested into the NMDC data stores. In general, subclass_of and
  part_of relationships/axioms are often good default relations/associations to support
  ontology browsing in user interfaces.'
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- OntologyAssociation
attributes:
  subject:
    name: subject
    from_schema: https://w3id.org/nmdc/basic_classes
    alias: subject
    owner: OntologyRelation
    domain_of:
    - FunctionalAnnotation
    - OntologyRelation
    range: OntologyClass
    required: true
  predicate:
    name: predicate
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: predicate
    owner: OntologyRelation
    domain_of:
    - OntologyRelation
    range: OntologyClass
    required: true
  object:
    name: object
    from_schema: https://w3id.org/nmdc/basic_classes
    rank: 1000
    alias: object
    owner: OntologyRelation
    domain_of:
    - OntologyRelation
    range: OntologyClass
    required: true
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    structured_aliases:
      workflow_execution_class:
        literal_form: workflow_execution_class
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: OntologyRelation
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:OntologyRelation