ontology_model.yaml

id: https://w3id.org/kgcl/ontology
name: kgcl_schema-ontology-model
title: knowledge graph change language ontology model
description: A basic bare-bones model of an ontology or ontology-like structure. The
  purpose is not to provide a complete model, rather just sufficient structure for
  domain and range constraints in the ocl model
license: https://creativecommons.org/publicdomain/zero/1.0/
version: 0.0.1
prefixes:
  om: http://w3id.org/kgcl/om/
  dcterms: http://purl.org/dc/terms/
  linkml: https://w3id.org/linkml/
  oio: http://www.geneontology.org/formats/oboInOwl#
default_prefix: om
default_range: string
imports:
- linkml:types
- basics
classes:
  OntologyElement:
    aliases:
    - entity
    description: Any component of an ontology or knowledge graph
  PropertyValue:
    is_a: OntologyElement
    description: a property-value pair
    slots:
    - property
    - filler
  Annotation:
    is_a: PropertyValue
    description: owl annotations. Not to be confused with annotations sensu GO
    slots:
    - property
    - filler
    - annotation_set
    - property_type
    - filler_type
    mappings:
    - owl:Annotation
  Node:
    aliases:
    - entity
    - term
    is_a: OntologyElement
    description: Any named entity in an ontology. May be a class, individual, property
    slots:
    - id
    - name
    - annotation_set
    - owl_type
  ClassNode:
    aliases:
    - concept
    is_a: Node
    description: A node that is a class
    class_uri: owl:Class
  InstanceNode:
    aliases:
    - named individual
    is_a: Node
    description: A node that is an individual
    class_uri: owl:NamedIndividual
  Edge:
    aliases:
    - triple
    - axiom
    - relationship
    is_a: OntologyElement
    description: >-
      A relationship between two nodes.

      Currently the only kinds of edges supported in KGCL:

        * A subClassOf B <==> Edge(subject=A, predicate=owl:subClassOf, object=B)
        * A subClassOf P some B <==> Edge(subject=A, predicate=P, object=B)
        * P subPropertyOf Q <==> Edge(subject=P, predicate=owl:subPropertyOf, object=Q)

      These represent the most common kind of pairwise relationship between classes,
      and classes are the dominant node type in ontologies.

      In future a wider variety of OWL axiom types will be supportedn through the use
      of an additional edge property/slot to indicate the interpretation of the axiom,
      following owlstar (https://github.com/cmungall/owlstar).

      For example:
       * `A subClassOf R only B <==> Edge(subject=A, predicate=P, object=B, interpretation=AllOnly)`
       * `A Annotation(P,B) <==> Edge(subject=A, predicate=P, object=B, interpretation=annotationAssertion)`

      Note that not all axioms are intended to map to edges. Axioms/triples where the object is a literal
      would be represented as node properties. Complex OWL axioms involving nesting would have their own
      dedicated construct, or may be represented generically. These are out of scope for the current
      version of KGCL
      
    mappings:
    - owl:Axiom
    - rdf:Statement
    slots:
    - subject
    - predicate
    - object
    - subject_representation
    - predicate_representation
    - object_representation
    - annotation_set
  LogicalDefinition:
    is_a: OntologyElement
  OntologySubset:
    is_a: OntologyElement
slots:
  owl_type:
    range: OwlTypeEnum
  name: {}
  subject:
    range: Node
  object:
    range: Node
  predicate:
    range: Node
  annotation_set:
    range: Annotation
  property:
    range: Node
  filler: null
  property_type:
    deprecated: no longer required
  filler_type:
    deprecated: no longer required
  subject_representation:
    deprecated: no longer required
  predicate_representation:
    deprecated: no longer required
  object_representation:
    deprecated: no longer required
  property_value_set:
    range: PropertyValue
    multivalued: true
    inlined: true
enums:
  OwlTypeEnum:
    permissible_values:
      CLASS:
        meaning: owl:Class
      OBJECT_PROPERTY:
        meaning: owl:ObjectProperty
      NAMED_INDIVIDUAL:
        meaning: owl:NamedIndividual
  SynonymScopeEnum:
    permissible_values:
      related:
        meaning: oio:hasNarrowSynonym
      broad:
        meaning: oio:hasBroadSynonym
      narrow:
        meaning: oio:hasNarrowSynonym
      exact:
        meaning: oio:hasExactSynonym