id: https://w3id.org/kgcl
name: kgcl_schema
title: Knowledge Graph Change Language
description: 'A data model for describing change operations at a high level on an
  ontology or ontology-like artefact, such as a Knowledge Graph.

  * [Browse Schema](https://cmungall.github.io/knowledge-graph-change-language/)

  * [GitHub](https://github.com/cmungall/knowledge-graph-change-language)'
license: https://creativecommons.org/publicdomain/zero/1.0/
version: 0.0.1
prefixes:
  kgcl: http://w3id.org/kgcl/
  dcterms: http://purl.org/dc/terms/
  IAO: http://purl.obolibrary.org/obo/IAO_
  oio: http://www.geneontology.org/formats/oboInOwl#
  xml: http://www.w3.org/XML/1998/namespace#
  linkml: https://w3id.org/linkml/
  rdfs: http://www.w3.org/2000/01/rdf-schema#
default_prefix: kgcl
default_range: string
imports:
- linkml:types
- ontology_model
- prov
types:
  ChangeClassType:
    typeof: uriorcurie
    description: CURIE for a class within this data model. E.g. kgcl:NodeObsoletion
classes:
  ChangeLanguageElement:
    abstract: true
    description: A broad grouping for all elements of the change language
  Change:
    abstract: true
    is_a: ChangeLanguageElement
    description: Any change perform on an ontology or knowledge graph
    slots:
    - id
    - type
    - was_generated_by
    - see_also
    - pull_request
    - term_tracker_issue
    - creator
    - change_date
    - contributor
    - has_undo
    - change_description
    - associated_change_set
    slot_usage:
      was_generated_by:
        comments:
        - we use the PROV model to represent the agent making a change
      see_also:
        comments:
        - If this change is in relationship to an issue on a system like github, include
          the URL here
      pull_request:
        comments:
        - If this change has a pull request on a system like github, include the URL
          here
      term_tracker_issue:
        comments:
          - If this change has an issue on a system like github, include the URL
            here
      creator:
        slot_uri: dcterms:creator
        comments:
        - This should be the composition of 'was generated by' and 'was associated with'
      change_date:
        comments:
        - This should be the composition of 'was generated by' and 'ended at time'
  SimpleChange:
    abstract: true
    aliases:
    - atomic change
    is_a: Change
    description: A change that is about a single ontology element
    slots:
    - old_value
    - new_value
    - old_value_type
    - new_value_type
    - new_language
    - old_language
    - new_datatype
    - old_datatype
  ComplexChange:
    abstract: true
    is_a: Change
    description: A change that is is a composition of other changes
    slots:
    - change_set
  MultiNodeObsoletion:
    aliases:
    - multi node deprecation
    - multi class obsoletion
    - multi term obsoletion
    - multi concept obsoletion
    is_a: ComplexChange
    description: A complex change consisting of multiple obsoletions.
    see_also:
    - https://github.com/cmungall/obo-scripts/blob/master/obo-obsoletify.pl
    slot_usage:
      change_set:
        range: NodeObsoletion
      change_description:
        string_serialization: obsolete multiple {change set}
      associated_change_set:
        description: >-
          All changes associated with a set of obsoletions. This change
          set is the composed change set rather than the set of individual changes.
          For example, if previous state is:\n  `A subClassOf B subClassOf C subClassOf
          D` and we obsolete {B,C}, then the individual changes are `A moves from
          B to C` and `B moves from C to D`, but the composed change set is `A moves
          from B to D`"
          
  Transaction:
    is_a: Change
    description: A change that is a composition of a set of changes, where those changes
      are treated as a single unit. Could be a single change, or the results of an
      ontology diff
    slots:
    - change_set
  ChangeSetSummaryStatistic:
    is_a: ChangeLanguageElement
    description: A summary statistic for a set of changes of the same type, grouped
      by zero or more node properties
    slot_usage:
      #change type:
      #  range: ChangeClassType
      #count:
      #  range: integer
      #property_value_set:
      #  description: Summary statistic is grouped by these constraints
  ChangeMixin:
    mixin: true
    description: root class for all change mixins
    slots:
    - about
    - has_undo
    - old_value
    - new_value
  Obsoletion:
    aliases:
    - deprecation
    - retiring
    is_a: ChangeMixin
    mixin: true
    description: Obsoletion of an element deprecates usage of that element, but does
      not delete that element.
    comments:
    - In OWL, deprecation is handled by the deprecation axiom. In OBO, we use this,
      but place additional requirements and expectations on obsolete elements
    see_also:
    - http://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term
    - https://mondo.readthedocs.io/en/latest/editors-guide/merging-and-obsoleting/
    slot_usage:
      about:
        description: The element that is obsoleted by this change.
      has_undo:
        range: Obsoletion
  DatatypeOrLanguageTagChange:
    is_a: ChangeMixin
    mixin: true
    description: A change in a value assertion where the value remain unchanged but
      either the datatype or language changes
  LanguageTagChange:
    is_a: DatatypeOrLanguageTagChange
    slot_usage:
      old_value:
        multivalued: false
        range: LanguageTag
      new_value:
        multivalued: false
        range: LanguageTag
  DatatypeChange:
    is_a: DatatypeOrLanguageTagChange
  AllowsAutomaticReplacementOfEdges:
    is_a: Obsoletion
    mixin: true
    description: Applies to an obsoletion in which annotations or edges pointing at
      the obsoleted node can be automatically rewired to point to a target
  Unobsoletion:
    is_a: ChangeMixin
    mixin: true
    description: Opposite operation of obsoletion. Rarely performed.
    see_also:
    - http://wiki.geneontology.org/index.php/Restoring_an_Obsolete_Ontology_Term
    slot_usage:
      has_undo:
        range: Obsoletion
  Deletion:
    is_a: ChangeMixin
    mixin: true
    description: Removal of an element.
    comments:
    - In general, for OBO ontologies, node elements should never be deleted, always
      obsolete. However, edge deletion is more common.
  Creation:
    is_a: ChangeMixin
    mixin: true
    description: Creation of an element.
    slot_usage:
      has_undo:
        range: Deletion
  SubsetMembershipChange:
    is_a: ChangeMixin
    mixin: true
    description: A change in the membership status of a node with respect to a subset
      (view)
    slots:
    - in_subset
  AddToSubset:
    is_a: SubsetMembershipChange
    mixin: true
    description: placing an element inside a subset
    slot_usage:
      in_subset:
        description: subset that the element is being placed inside.
  RemoveFromSubset:
    is_a: SubsetMembershipChange
    mixin: true
    description: removing an element from a subset
    slot_usage:
      in_subset:
        description: subset that the element is being removed from
      has_undo:
        range: AddToSubset
  EdgeChange:
    abstract: true
    aliases:
    - axiom change
    - triple change
    is_a: SimpleChange
    description: A change in which the element that is the focus of the change is
      an edge.
    slots:
    - about_edge
    - object_type
    - language
    - datatype
    slot_usage:
      about_edge:
        comments:
        - if subject is empty, use the about field of the last node change
    todos:
    - decide on flat serialization, see https://github.com/cmungall/knowledge-graph-change-language/issues/7
  EdgeCreation:
    aliases:
    - relationship creation
    is_a: EdgeChange
    description: An edge change in which a de-novo edge is created. The edge is potentially
      annotated in the same action.
    mixins:
    - Creation
    slots:
    - subject
    - predicate
    - object
    - subject_type
    - predicate_type
    - object_type
    - annotation_set
    slot_usage:
      change_description:
        string_serialization: create edge {edge.subject} {edge.predicate} {edge.object}
    see_also:
    - http://wiki.geneontology.org/index.php/Guidelines_for_creating_relationships_between_terms
  PlaceUnder:
    is_a: EdgeCreation
    description: An edge creation where the predicate is owl:subClassOf
  EdgeDeletion:
    aliases:
    - relationship deletion
    is_a: EdgeChange
    description: An edge change in which an edge is removed. All edge annotations/properies
      are removed in the same action.
    mixins:
    - Deletion
    slots:
    - subject
    - predicate
    - object
    - subject_type
    - predicate_type
    - object_type
    - annotation_set
    slot_usage:
      change_description:
        string_serialization: delete edge {edge.subject} {edge.predicate} {edge.object}
  RemoveUnder:
    is_a: EdgeDeletion
    description: "An edge deletion where the predicate is owl:subClassOf\n  "
  EdgeObsoletion:
    aliases:
    - relationship obsoletion
    is_a: EdgeChange
    description: An edge change in which an edge is obsoleted.
    comments:
    - Note there is not yet consensus in how this should be done in rdf/owl implementations.
      Simply marking the edge deprecated with render it visible to most clients. Care
      must be taken because simply adding a deprecation tag to an axiom does not silence
      it -- it is still asserted. It is therefore more common to obsolete an edge
      by shadowing the axiom as an annotation. See the Mondo docs for example
    see_also:
    - https://mondo.readthedocs.io/en/latest/editors-guide/g-logical-axioms/#excluded-subclassof
    mixins:
    - Obsoletion
    slots:
    - subject
    - predicate
    - object
    - annotation_set
    slot_usage:
      change_description:
        string_serialization: obsolete edge {edge.subject} {edge.predicate} {edge.object}
  EdgeRewiring:
    is_a: EdgeChange
    description: An edge change where one node is replaced with another, as in the
      case of obsoletion with replacement
    examples:
    - value: changing G1 annotated-to T1 to G1 annotated-to T2, after obsoletion of
        T1 and replacement with T2
  MappingCreation:
    deprecated: use NewMapping
    aliases:
    - xref creation
    is_a: EdgeCreation
    description: A specific kind of edge creation in which the created edge is a mapping.
    mixins:
    - Creation
    slots:
    - subject
    - predicate
    - object
    - annotation_set
    slot_usage:
      change_description:
        string_serialization: create mapping {subject} {predicate} {object}
      subject:
        description: This corresponds to subject_id in SSSOM
      predicate:
        description: This corresponds to predicate_id in SSSOM. The value of this
          is typically a predicate from SKOS
      object:
        description: This corresponds to object_id in SSSOM
    todos:
    - decide whether to make a corresponding change to the datamodel
  NodeMove:
    is_a: EdgeChange
    description: A node move is a combination of deleting a parent edge and adding
      a parent edge, where the predicate is preserved and the object/parent node changes
    slots:
    - old_object_type
    - new_object_type
    examples:
    - value: changing a is-a b to a is-a c
    slot_usage:
      change_description:
        string_serialization: move {about_edge.subject} {about_edge.predicate} {about_edge.object} from {old_value} to {new_value}
  NodeDeepening:
    is_a: NodeMove
    description: A node move in which a node where the destination is a proper descendant
      of the original location. Note that here descendant applied not just to subclass,
      but edges of any predicate in the relational graph
    examples:
    - value: changing a is-a b to a is-a c, where c is a subclass of b
    slot_usage:
      change_description:
        string_serialization: deepen {about_edge.subject} {about_edge.predicate} {about_edge.object} from {old_value} to {new_value}
  NodeShallowing:
    is_a: NodeMove
    description: The opposite of node deepening
    examples:
    - value: changing a is-a c to a is-a b, where c is a subclass of b
    slot_usage:
      change_description:
        string_serialization: lift {about_node} from {old_value} to {new_value}
  PredicateChange:
    is_a: EdgeChange
    description: An edge change where the predicate (relationship type) is modified.
    examples:
    - value: changing a is-a b to a part-of b
    slot_usage:
      change_description:
        string_serialization: change edge type between {about.subject} and {about.object}
          from {old_value} to {new_value}
  EdgeLogicalInterpretationChange:
    is_a: EdgeChange
    description: An edge change where the subject, object, and predicate are unchanged,
      but the logical interpretation changes
    examples:
    - value: changing a SubClassOf r some b to a subClassOf r only b
  LogicalAxiomChange:
    is_a: SimpleChange
    description: A simple change where a logical axiom is changed, where the logical
      axiom cannot be represented as an edge
  NodeChange:
    abstract: true
    is_a: SimpleChange
    description: A simple change where the change is about a node
    slots:
    - about_node
    - about_node_representation
    - language
  NodeRename:
    is_a: NodeChange
    description: A node change where the name (aka rdfs:label) of the node changes
    slots:
    - old_value
    - new_value
    - has_textual_diff
    - new_language
    - old_language
    slot_usage:
      old_value:
        multivalued: false
      new_value:
        multivalued: false
      change_description:
        string_serialization: rename {about_node} from {old_value} to {new_value}
    examples:
    - value: rename UBERON:0002398 from 'manus' to 'hand'
      description: replacing the rdfs:label of 'manus' on an uberon class with the
        rdfs:label 'hand'
  SetLanguageForName:
    is_a: NodeChange
    mixins:
    - LanguageTagChange
    description: A node change where the string value for the name is unchanged but
      the language tag is set
    slots:
    - old_value
    - new_value
    slot_usage:
      change_description:
        string_serialization: changed {about_node} name language from {old_value}
          to {new_value}
  NodeAnnotationChange:
    description: A node change where the change alters node properties/annotations.
      TODO
    is_a: NodeChange
    slots:
    - annotation_property
    - annotation_property_type
  NodeAnnotationReplacement:
    is_a: NodeAnnotationChange
    description: A node annotation change where the change replaces a particular property
      value. TODO
  NodeSynonymChange:
    is_a: NodeChange
  NewSynonym:
    description: A node synonym change where a de-novo synonym is created
    is_a: NodeSynonymChange
    slots:
    - new_value
    - language
    - qualifier
    - predicate
    aliases:
    - new alias
    - create synonym
    - add synonym
  NameBecomesSynonym:
    is_a: NodeSynonymChange
    description: A node synonym where the name NAME of an node NODE moves to a synonym,
      and NODE receives a new name. This change consists of compose of (1) a node
      rename where NAME is replaced by a different name (2) a new synonym
    slot_usage:
      #change_1:
      #  range: NodeRename
      #change 2:
      #  range: NewSynonym
      #  description: ''
      change_description:
        string_serialization: synonym {synonym} becomes new name of {about_node},
          and name {name} becomes a synonym
  RemoveSynonym:
    description: A node synonym change where a synonym is deleted
    is_a: NodeSynonymChange
    slots:
    - old_value
  SynonymReplacement:
    description: A node synonym change where the text of a synonym is changed
    is_a: NodeSynonymChange
    slots:
    - old_value
    - new_value
    - qualifier
    - has_textual_diff
  SynonymPredicateChange:
    aliases:
    - node scope change
    description: 'A node synonym change where the predicate of a synonym is changed.
      Background: synonyms can be represented by a variety of predicates. For example,
      many OBO ontologies make use of predicates such as oio:hasExactSynonym, oio:hasRelatedSynonym,
      etc'
    is_a: NodeSynonymChange
    slots:
    - old_value
    - new_value
    - has_textual_diff
    - target
  NodeMappingChange:
    description: A node change where the mappings for that node are altered
    is_a: NodeChange
    aliases:
    - xref change
  NewMapping:
    description: A node mapping change where a mapping is added to a node
    is_a: NodeMappingChange
    slots:
    - object
    - predicate
    aliases:
    - xref change
  RemoveMapping:
    description: A node mapping change where a mapping is deleted
    is_a: NodeMappingChange
    slots:
    - object
    - predicate
  MappingReplacement:
    description: A node mapping change where the object of a mapping is changed
    is_a: NodeMappingChange
    slots:
    - old_value
    - new_value
  MappingPredicateChange:
    aliases:
    - node scope change
    description: A node mapping change where the predicate of a mapping is changed.
    is_a: NodeMappingChange
    slots:
    - old_value
    - new_value
  NodeMetadataAssertionChange:
    description: A node change where the metadata assertion (OWL annotations) for
      that node are altered
    is_a: NodeChange
    aliases:
    - NodeAnnotationChange
  NewMetadataAssertion:
    description: A node metadata assertion change where a metadata assertion is added
      to a node
    is_a: NodeMetadataAssertionChange
    slots:
    - object
    - predicate
    aliases:
    - xref change
  RemoveMetadataAssertion:
    description: A node metadata assertion change where a metadata assertion is deleted
    is_a: NodeMetadataAssertionChange
    slots:
    - object
    - predicate
  MetadataAssertionReplacement:
    description: A node metadata assertion change where the object of a metadata assertion
      is changed
    is_a: NodeMetadataAssertionChange
    slots:
    - old_value
    - new_value
  MetadataAssertionPredicateChange:
    aliases:
    - node scope change
    description: A node metadata assertion change where the predicate of a metadata
      assertion is changed.
    is_a: NodeMetadataAssertionChange
    slots:
    - old_value
    - new_value
  NodeTextDefinitionChange:
    abstract: true
    is_a: NodeChange
    description: A node change where the text definition is changed
  NewTextDefinition:
    description: A node change where a de-novo text definition is created
    is_a: NodeTextDefinitionChange
    slots:
    - new_value
  RemoveTextDefinition:
    description: A node change where a text definition is deleted
    is_a: NodeTextDefinitionChange
    slots:
    - old_value
  TextDefinitionReplacement:
    description: A node change where a text definition is modified
    is_a: NodeTextDefinitionChange
    slots:
    - old_value
    - new_value
    - has_textual_diff
  AddNodeToSubset:
    aliases:
    - add term to slim
    is_a: NodeChange
    mixins:
    - AddToSubset
    description: Places a node inside a subset, by annotating that node
    see_also:
    - http://wiki.geneontology.org/index.php/Adding_a_Term_to_a_GO_Subset_(Slim)
  RemoveNodeFromSubset:
    aliases:
    - remove term from slim
    is_a: NodeChange
    mixins:
    - RemoveFromSubset
    description: Removes a node from a subset, by removing an annotation
    slot_usage:
      change_description:
        string_serialization: removing {about_node} from {subset}
      about_node:
        description: The node that is removed from the subset
      in_subset:
        description: The subset from which the node is to be removed
  NodeObsoletion:
    aliases:
    - node deprecation
    - class obsoletion
    - term obsoletion
    - concept obsoletion
    is_a: NodeChange
    mixins:
    - Obsoletion
    description: Obsoletion of a node deprecates usage of that node, but does not
      delete it.
    slots:
    - has_direct_replacement
    - has_nondirect_replacement
    slot_usage:
      change_description:
        string_serialization: obsoleting {about_node}
      associated_change_set:
        is_a: change_set
        description: 'All changes forced as a result of this obsoletion. For example,
          starting with `A subClassOf B subClassOf C`, if we obsolete node B, then
          we may decide to bundle in a node move change of A from B to C. Note: this
          change set is not considered a part of the obsoletion, as obsoletion is
          considered atomic/simple. Instead this is a reference to a change set that
          may exist elsewhere'
    see_also:
    - http://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term
  NodeUnobsoletion:
    aliases:
    - node undeprecation
    - class unobsoletion
    - term unobsoletion
    - concept unobsoletion
    is_a: NodeChange
    mixins:
    - Unobsoletion
    description: unobsoletion of a node deprecates usage of that node. Rarely applied.
    slots:
    - has_direct_replacement
    - has_nondirect_replacement
    slot_usage:
      change_description:
        string_serialization: unobsoleting {about_node}
    see_also:
    - http://wiki.geneontology.org/index.php/Restoring_an_Obsolete_Ontology_Term
  NodeCreation:
    is_a: NodeChange
    mixins:
    - Creation
    description: a node change in which a new node is created
    slots:
    - node_id
    - name
    - owl_type
    - annotation_set
    - language
    slot_usage:
      change_description:
        string_serialization: creating node {id} {label} with {annotation set}
    todos:
    - allow this for the creation of an instance from a class. This may include metaclasses
      (templates)
    see_also:
    - http://wiki.geneontology.org/index.php/Guidelines_for_creating_a_GO_term
  ClassCreation:
    is_a: NodeCreation
    description: A node creation where the owl type is 'owl:Class'
    slots:
    - superclass
    slot_usage:
      change_description:
        string_serialization: create class {about_node}
  ObjectPropertyCreation:
    is_a: NodeCreation
    description: A node creation where the owl type is 'ObjectProperty'
    slot_usage:
      change_description:
        string_serialization: create object property {about_node}
  NodeDeletion:
    is_a: NodeChange
    mixins:
    - Deletion
    description: Deletion of a node from the graph. Note it is recommended nodes are
      obsoleted and never merged, but this operation exists to represent deletions
      in ontologies, accidental or otherwise
    slot_usage:
      change_description:
        string_serialization: delete {about_node}
  NodeDirectMerge:
    is_a: NodeObsoletion
    mixins:
    - AllowsAutomaticReplacementOfEdges
    description: An obsoletion change in which all metadata (including name/label)
      from the source node is deleted and added to the target node, and edges can
      automatically be rewired to point to the target node
    comments:
    - In the OBO format serialization of the graph, the source node vanishes from
      the file as a distinct entry and is retained only as an alt_id
    slot_usage:
      has_direct_replacement:
        required: true
      about_node:
        aliases:
        - alt_id
      change_description:
        string_serialization: merge {about_node} into {has_direct_replacement}
    see_also:
    - http://wiki.geneontology.org/index.php/Merging_Ontology_Terms
    - http://wiki.geneontology.org/index.php/Principles_for_merging_terms
  NodeObsoletionWithDirectReplacement:
    is_a: NodeObsoletion
    mixins:
    - AllowsAutomaticReplacementOfEdges
    description: An obsoletion change in which information from the obsoleted node
      is selectively copied to a single target, and edges can automatically be rewired
      to point to the target node
    slot_usage:
      has_direct_replacement:
        required: true
      change_description:
        string_serialization: obsolete {about_node} with replacement {has_direct_replacement}
    see_also:
    - http://wiki.geneontology.org/index.php/Merging_Ontology_Terms
    - http://wiki.geneontology.org/index.php/Principles_for_merging_terms
  NodeObsoletionWithNoDirectReplacement:
    is_a: NodeObsoletion
    description: An obsoletion change in which there is no direct replacement
    slot_usage:
      has_nondirect_replacement:
        required: true
      change_description:
        string_serialization: obsolete {about_node} with alternative {has_nondirect_replacement}
  TextualDiff:
    is_a: ChangeLanguageElement
    description: A summarizing of a change on a piece of text. This could be rendered
      in a number of different ways
  Configuration:
    is_a: ChangeLanguageElement
    description: The meaning of operations can be configured
    attributes:
      name_predicate: null
      definition_predicate: null
      main_synonym_predicate: null
      synonym_predicates: null
      creator_predicate: null
      contributor_predicate: null
      obsolete_node_label_prefix:
        range: string
        description: A prefix to add to the label of an obsolete node. This may include
          a space at the end.
      obsoletion_workflow: null
      obsoletion_policies:
        multivalued: true
        range: ObsoletionPolicyEnum
      obsolete_subclass_of_shadow_property:
        range: uriorcurie
        description: >-
          specifies the annotation property to be used to create a shadow annotation assertion triple when
          a subclass edge is deleted.
  Session:
    is_a: ChangeLanguageElement
    description: A session consists of a set of change sets bundled with the activities
      that generated those change sets
    tree_root: true
    slots:
    - change_set
    - activity_set
slots:
  type:
    designates_type: true
    slot_uri: rdf:type
  pull_request: null
  see_also:
    slot_uri: rdfs:seeAlso
  creator:
    slot_uri: dcterms:creator
  contributor:
    slot_uri: dcterms:creator
  change_date:
    slot_uri: dcterms:date
  term_tracker_issue:
    exact_mappings:
      - IAO:0000233
  has_undo:
    domain: Change
    description: A change that reverses this change
    range: Change
    multivalued: false
  node_id:
    description: id of a node to be created
    todos:
    - consider using 'about' instead
    range: Node
  superclass:
    range: Node
  language:
    range: LanguageTag
    description: The language tag of a literal
  about:
    description: The 'focus' entity on which the change operates
    multivalued: false
    range: OntologyElement
  about_node:
    is_a: about
    multivalued: false
    range: Node
  about_edge:
    is_a: about
    multivalued: false
    range: Edge
  about_node_representation:
    deprecated: no longer required
    description: 'The representation of a node (URI, CURIE, label) '
  target:
    description: The secondary entity on which the change operates
  old_value:
    description: The value of a property held in the old instance of the ontology
  new_value:
    description: The value of a property held in the new instance of the ontology
  datatype:
    description: The datatype of a literal
  new_datatype:
    description: The new datatype of a literal
  old_datatype:
    description: The old datatype of a literal
  new_language:
    description: The new language tag of a literal
  old_language:
    description: The old language tag of a literal
  qualifier:
    description: The qualifier of a change operation
  subclass:
    description: The subclass of a subsumption axiom
  new_subclass:
    description: The new subclass of a subsumption axiom
  new_property:
    description: The new property of an OWL restriction
  new_filler:
    description: The new filler of an OWL restriction
  object_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of an object
  new_object_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of a new object
  old_object_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of an old object
  new_value_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of a new value
  old_value_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of an old value
  subject_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of an edge's subject
  subclass_type:
    deprecated: no longer required
    description: The type of a subclass
  superclass_type:
    deprecated: no longer required
    description: The type of a superclass
  predicate_type:
    deprecated: no longer required
    description: The type (IRI or Literal) of an edge's subject
  in_subset:
    description: The subset that pertains to this change
    range: OntologySubset
  annotation_property:
    description: An annotation property
  annotation_property_type:
    deprecated: no longer required
    description: 'The type of a property (URI, CURIE, label) '
  change_description:
    description: A string serialization of the change. This should be both human-readable,
      and parseable.
    comments:
    - Form 1: IRIs are denoted by CURIEs, optionally followed by label in parenthesis
    - Form 2: IRIs are denoted by the rdfs:label in single quotes, e.g. 'nervous system'
    examples:
    - value: rename UBERON:0002398 from 'manus' to 'hand'
    - value: move 'hand' from 'part of' 'hindlimb' to 'part of' 'forelimb'
    - value: merge 'cellular metabolic process' into 'metabolic process'
    - value: search and replace 'metabolic process' with 'metabolism' in all labels
        under 'biological process'
    - value: search and replace 'metabolic process' with 'metabolism' in all labels
        under 'biological process' retaining as 'exact synonym'
  has_textual_diff:
    description: A representation of character-level changes on a textual literal
      property. For example, if a text definition may change by only a single character
      such as addition of a period, it is useful to be able to see this visually.
    comments:
    - this is NOT for representing the diff of the change as a whole.
    domain: Change
    range: TextualDiff
  change_set:
    description: A collection of changes
    range: Change
    multivalued: true
    inlined: true
    inlined_as_list: true
  associated_change_set:
    is_a: change_set
    description: 'All changes forced as a result of this obsoletion. For example,
      starting with `A subClassOf B subClassOf C`, if we obsolete node B, then
      we may decide to bundle in a node move change of A from B to C. Note: this
      change set is not considered a part of the obsoletion, as obsoletion is
      considered atomic/simple. Instead this is a reference to a change set that
      may exist elsewhere'
  has_replacement:
    domain: NodeObsoletion
    range: Node
    abstract: true
    is_a: target
    description: A single node obsoletion event may be accompanied by one or more
      suggested replacement nodes
    comments:
    - In OBO, the replacement term is indicated using IAO:nnnnnn
  has_direct_replacement:
    range: Node
    multivalued: false
    close_mappings:
    - IAO:0100001
    description: An obsoletion replacement where it IS valid to automatically update
      annotations/edges pointing at the node with its direct replacement
    comments:
    - if a node obsoletion C, C about N1, and C has direct replacement N2, and there
      exists an edge with an edge property referencing N1, it is possible to replace
      with N2
    - if a node obsoletion C C about N1, and Chas direct replacement N2, then N1 IAO:0100001
      N2
  has_nondirect_replacement:
    range: Node
    multivalued: true
    description: An obsoletion replacement where it is NOT valid to automatically
      update annotations/edges pointing at the node with its direct replacement
    close_mappings:
    - oio:consider
    comments:
    - if a node obsoletion C, C about N1, and C has direct replacement N2, and there
      exists an edge with an edge property referencing N1, it is possible to replace
      with N2
    - if a node obsoletion C C about N1, and Chas direct replacement N2, then N1 oio:consider
      N2
enums:
  ObsoletionPolicyEnum:
    permissible_values:
      NoLogicalAxiomsOnObsoletes:
        description: The obsoletion policy is that there MUST NOT be logical axioms about an obsolete node
      ObsoleteLabelsArePrefixed:
        description: The obsoletion policy is that any label on an obsolete node MUST be prefixed with 'obsolete' or similar