Class: OntologyRelation

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.

URI: nmdc:OntologyRelation

classDiagram class OntologyRelation click OntologyRelation href "../OntologyRelation" OntologyRelation : object OntologyRelation --> "1" OntologyClass : object click OntologyClass href "../OntologyClass" OntologyRelation : predicate OntologyRelation --> "1" OntologyClass : predicate click OntologyClass href "../OntologyClass" OntologyRelation : subject OntologyRelation --> "1" OntologyClass : subject click OntologyClass href "../OntologyClass" OntologyRelation : type

Slots

Name	Cardinality and Range	Description	Inheritance
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct
subject	1 OntologyClass		direct
predicate	1 OntologyClass		direct
object	1 OntologyClass		direct

Usages

used by	used in	type	used
EnvironmentalMaterialTerm	relations	range	OntologyRelation
ChemicalEntity	relations	range	OntologyRelation
FunctionalAnnotationTerm	relations	range	OntologyRelation
Pathway	relations	range	OntologyRelation
OrthologyGroup	relations	range	OntologyRelation
OntologyClass	relations	range	OntologyRelation

Aliases

OntologyAssociation

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 stat∂ements 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.

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:OntologyRelation
native	nmdc:OntologyRelation

LinkML Source

Direct

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 stat∂ements 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

Induced

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 stat∂ements 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:
    - replaces legacy nmdc:type slot
    - 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
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: OntologyRelation
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:OntologyRelation