Skip to content

Class: NodeDeletion

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

URI: kgcl:NodeDeletion

classDiagram class NodeDeletion click NodeDeletion href "../NodeDeletion" Deletion <|-- NodeDeletion click Deletion href "../Deletion" NodeChange <|-- NodeDeletion click NodeChange href "../NodeChange" NodeDeletion : about NodeDeletion --> "0..1" OntologyElement : about click OntologyElement href "../OntologyElement" NodeDeletion : about_node NodeDeletion --> "0..1" Node : about_node click Node href "../Node" NodeDeletion : about_node_representation NodeDeletion : associated_change_set NodeDeletion --> "*" Change : associated_change_set click Change href "../Change" NodeDeletion : change_date NodeDeletion : change_description NodeDeletion : contributor NodeDeletion : creator NodeDeletion : has_undo NodeDeletion --> "0..1" Change : has_undo click Change href "../Change" NodeDeletion : id NodeDeletion : language NodeDeletion : new_datatype NodeDeletion : new_language NodeDeletion : new_value NodeDeletion : new_value_type NodeDeletion : old_datatype NodeDeletion : old_language NodeDeletion : old_value NodeDeletion : old_value_type NodeDeletion : pull_request NodeDeletion : see_also NodeDeletion : term_tracker_issue NodeDeletion : type NodeDeletion : was_generated_by NodeDeletion --> "0..1" Activity : was_generated_by click Activity href "../Activity"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
about_node 0..1
Node
NodeChange
about_node_representation 0..1
String
The representation of a node (URI, CURIE, label) NodeChange
language 0..1
LanguageTag
The language tag of a literal NodeChange
old_value 0..1
String
The value of a property held in the old instance of the ontology ChangeMixin, SimpleChange
new_value 0..1
String
The value of a property held in the new instance of the ontology ChangeMixin, SimpleChange
old_value_type 0..1
String
The type (IRI or Literal) of an old value SimpleChange
new_value_type 0..1
String
The type (IRI or Literal) of a new value SimpleChange
new_language 0..1
String
The new language tag of a literal SimpleChange
old_language 0..1
String
The old language tag of a literal SimpleChange
new_datatype 0..1
String
The new datatype of a literal SimpleChange
old_datatype 0..1
String
The old datatype of a literal SimpleChange
id 1
String
Change
type 0..1
String
Change
was_generated_by 0..1
Activity
Change
see_also 0..1
String
Change
pull_request 0..1
String
Change
term_tracker_issue 0..1
String
Change
creator 0..1
String
Change
change_date 0..1
String
Change
contributor 0..1
String
Change
has_undo 0..1
Change
A change that reverses this change ChangeMixin, Change
change_description 0..1
String
A string serialization of the change Change
associated_change_set *
Change
All changes forced as a result of this obsoletion Change
about 0..1
OntologyElement
The 'focus' entity on which the change operates ChangeMixin

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/kgcl

Mappings

Mapping Type Mapped Value
self kgcl:NodeDeletion
native kgcl:NodeDeletion

LinkML Source

Direct

name: NodeDeletion
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
from_schema: https://w3id.org/kgcl
is_a: NodeChange
mixins:
- Deletion
slot_usage:
  change_description:
    name: change_description
    string_serialization: delete {about_node}

Induced

name: NodeDeletion
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
from_schema: https://w3id.org/kgcl
is_a: NodeChange
mixins:
- Deletion
slot_usage:
  change_description:
    name: change_description
    string_serialization: delete {about_node}
attributes:
  about_node:
    name: about_node
    from_schema: https://w3id.org/kgcl
    rank: 1000
    is_a: about
    alias: about_node
    owner: NodeDeletion
    domain_of:
    - NodeChange
    range: Node
    multivalued: false
  about_node_representation:
    name: about_node_representation
    description: 'The representation of a node (URI, CURIE, label) '
    deprecated: no longer required
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: about_node_representation
    owner: NodeDeletion
    domain_of:
    - NodeChange
    range: string
  language:
    name: language
    description: The language tag of a literal
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: language
    owner: NodeDeletion
    domain_of:
    - EdgeChange
    - NodeChange
    - NewSynonym
    - NodeCreation
    range: LanguageTag
  old_value:
    name: old_value
    description: The value of a property held in the old instance of the ontology
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: old_value
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    - ChangeMixin
    - NodeRename
    - SetLanguageForName
    - RemoveSynonym
    - SynonymReplacement
    - SynonymPredicateChange
    - MappingReplacement
    - MappingPredicateChange
    - MetadataAssertionReplacement
    - MetadataAssertionPredicateChange
    - RemoveTextDefinition
    - TextDefinitionReplacement
    range: string
  new_value:
    name: new_value
    description: The value of a property held in the new instance of the ontology
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: new_value
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    - ChangeMixin
    - NodeRename
    - SetLanguageForName
    - NewSynonym
    - SynonymReplacement
    - SynonymPredicateChange
    - MappingReplacement
    - MappingPredicateChange
    - MetadataAssertionReplacement
    - MetadataAssertionPredicateChange
    - NewTextDefinition
    - TextDefinitionReplacement
    range: string
  old_value_type:
    name: old_value_type
    description: The type (IRI or Literal) of an old value
    deprecated: no longer required
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: old_value_type
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    range: string
  new_value_type:
    name: new_value_type
    description: The type (IRI or Literal) of a new value
    deprecated: no longer required
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: new_value_type
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    range: string
  new_language:
    name: new_language
    description: The new language tag of a literal
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: new_language
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    - NodeRename
    range: string
  old_language:
    name: old_language
    description: The old language tag of a literal
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: old_language
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    - NodeRename
    range: string
  new_datatype:
    name: new_datatype
    description: The new datatype of a literal
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: new_datatype
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    range: string
  old_datatype:
    name: old_datatype
    description: The old datatype of a literal
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: old_datatype
    owner: NodeDeletion
    domain_of:
    - SimpleChange
    range: string
  id:
    name: id
    from_schema: https://w3id.org/kgcl
    rank: 1000
    identifier: true
    alias: id
    owner: NodeDeletion
    domain_of:
    - Change
    - Node
    - Activity
    - Agent
    range: string
    required: true
  type:
    name: type
    from_schema: https://w3id.org/kgcl
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  was_generated_by:
    name: was_generated_by
    comments:
    - we use the PROV model to represent the agent making a change
    from_schema: https://w3id.org/kgcl
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: NodeDeletion
    domain_of:
    - Change
    range: Activity
  see_also:
    name: see_also
    comments:
    - If this change is in relationship to an issue on a system like github, include
      the URL here
    from_schema: https://w3id.org/kgcl
    rank: 1000
    slot_uri: rdfs:seeAlso
    alias: see_also
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  pull_request:
    name: pull_request
    comments:
    - If this change has a pull request on a system like github, include the URL here
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: pull_request
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  term_tracker_issue:
    name: term_tracker_issue
    comments:
    - If this change has an issue on a system like github, include the URL here
    from_schema: https://w3id.org/kgcl
    exact_mappings:
    - IAO:0000233
    rank: 1000
    alias: term_tracker_issue
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  creator:
    name: creator
    comments:
    - This should be the composition of 'was generated by' and 'was associated with'
    from_schema: https://w3id.org/kgcl
    rank: 1000
    slot_uri: dcterms:creator
    alias: creator
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  change_date:
    name: change_date
    comments:
    - This should be the composition of 'was generated by' and 'ended at time'
    from_schema: https://w3id.org/kgcl
    rank: 1000
    slot_uri: dcterms:date
    alias: change_date
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  contributor:
    name: contributor
    from_schema: https://w3id.org/kgcl
    rank: 1000
    slot_uri: dcterms:creator
    alias: contributor
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  has_undo:
    name: has_undo
    description: A change that reverses this change
    from_schema: https://w3id.org/kgcl
    rank: 1000
    domain: Change
    alias: has_undo
    owner: NodeDeletion
    domain_of:
    - Change
    - ChangeMixin
    range: Change
    multivalued: false
  change_description:
    name: 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'
    from_schema: https://w3id.org/kgcl
    rank: 1000
    string_serialization: delete {about_node}
    alias: change_description
    owner: NodeDeletion
    domain_of:
    - Change
    range: string
  associated_change_set:
    name: associated_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'
    from_schema: https://w3id.org/kgcl
    rank: 1000
    is_a: change_set
    alias: associated_change_set
    owner: NodeDeletion
    domain_of:
    - Change
    range: Change
    multivalued: true
    inlined: true
    inlined_as_list: true
  about:
    name: about
    description: The 'focus' entity on which the change operates
    from_schema: https://w3id.org/kgcl
    rank: 1000
    alias: about
    owner: NodeDeletion
    domain_of:
    - ChangeMixin
    range: OntologyElement
    multivalued: false