diff --git a/src/kgcl_schema/schema/kgcl.yaml b/src/kgcl_schema/schema/kgcl.yaml index d397151..a32d3e9 100644 --- a/src/kgcl_schema/schema/kgcl.yaml +++ b/src/kgcl_schema/schema/kgcl.yaml @@ -16,6 +16,7 @@ prefixes: 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: @@ -88,6 +89,7 @@ classes: description: A change that is is a composition of other changes slots: - change_set + - associated_change_set MultiNodeObsoletion: aliases: - multi node deprecation @@ -103,8 +105,7 @@ classes: range: NodeObsoletion change_description: string_serialization: obsolete multiple {change set} - associated change set: - is_a: 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. @@ -112,6 +113,7 @@ classes: 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 @@ -124,12 +126,12 @@ classes: 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 + #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 @@ -233,7 +235,7 @@ classes: - language - datatype slot_usage: - subject: + about_edge: comments: - if subject is empty, use the about field of the last node change todos: @@ -460,11 +462,11 @@ classes: 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_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 @@ -606,7 +608,7 @@ classes: string_serialization: removing {about_node} from {subset} about_node: description: The node that is removed from the subset - subset: + in_subset: description: The subset from which the node is to be removed NodeObsoletion: aliases: @@ -625,7 +627,7 @@ classes: slot_usage: change_description: string_serialization: obsoleting {about_node} - associated change set: + 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 @@ -645,13 +647,12 @@ classes: 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} - replaced by: - range: Node - consider: - range: Node see_also: - http://wiki.geneontology.org/index.php/Restoring_an_Obsolete_Ontology_Term NodeCreation: @@ -789,6 +790,9 @@ slots: 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 @@ -908,6 +912,14 @@ slots: 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