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Fix use of undefined slots in slot usage (#88)
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Fixes #88
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cmungall committed Nov 14, 2024
1 parent 0a37270 commit 3588269
Showing 1 changed file with 32 additions and 20 deletions.
52 changes: 32 additions & 20 deletions src/kgcl_schema/schema/kgcl.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand All @@ -103,15 +105,15 @@ 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.
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
Expand All @@ -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
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand All @@ -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
Expand All @@ -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:
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down

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