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Add 'composed entity' value to the EntityType enum.
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Add a new value 'composed entity' to the EntityType enumeration to
indicate that an ID is intended to represent a composed (aka "complex",
aka "post-coordinated") entity that involves several individual
entities.

closes #402
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gouttegd committed Dec 2, 2024
1 parent 1177d54 commit c32456e
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Showing 2 changed files with 18 additions and 1 deletion.
12 changes: 12 additions & 0 deletions examples/schema/composite-entities.sssom.tsv
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@@ -0,0 +1,12 @@
#curie_map:
# HP: http://purl.obolibrary.org/obo/HP_
# MONDO: http://purl.obolibrary.org/obo/MONDO_
# MP: http://purl.obolibrary.org/obo/MP_
# SCHEMA: http://example.org/schema
#mapping_set_id: https://w3id.org/sssom/commons/examples/composite-entities.sssom.tsv
#license: https://creativecommons.org/publicdomain/zero/1.0/
#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
subject_id predicate_id object_id mapping_justification subject_type
SCHEMA:0001/(disease:'MONDO:0005148',phenotype:'HP:0009124') skos:exactMatch MP:0000003 semapv:ManualMappingCuration composed entity
SCHEMA:0001/(disease:'MONDO:0005149',phenotype:'HP:0008551') skos:exactMatch MP:0000018 semapv:ManualMappingCuration composed entity
SCHEMA:0001/(disease:'MONDO:0005150',phenotype:'HP:0000411') skos:exactMatch MP:0000018 semapv:ManualMappingCuration composed entity
7 changes: 6 additions & 1 deletion src/sssom_schema/schema/sssom_schema.yaml
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Expand Up @@ -45,7 +45,7 @@ enums:
meaning: rdfs:Class
rdfs literal:
meaning: rdfs:Literal
description: This value indicate that the entity being mapped is not a semantic entity with a distinct identifier, but is instead represented entirely by its literal label. This value MUST NOT be used in the predicate_type slot.
description: This value indicates that the entity being mapped is not a semantic entity with a distinct identifier, but is instead represented entirely by its literal label. This value MUST NOT be used in the predicate_type slot.
see_also:
- https://mapping-commons.github.io/sssom/spec-model/#literal-mappings
- https://github.com/mapping-commons/sssom/issues/234
Expand All @@ -54,6 +54,11 @@ enums:
meaning: rdfs:Datatype
rdf property:
meaning: rdf:Property
composed entity:
description: This value indicates that the entity ID does not represent a single entity, but a composite involving several individual entities. This value MUST NOT be used in the predicate_type slot. This specifications does not prescribe how an ID representing a composite entity should be interpreted; this is left at the discretion of applications.
see_also:
- https://github.com/mapping-commons/sssom/issues/402
- https://github.com/mapping-commons/sssom/blob/master/examples/schema/composite-entities.sssom.tsv

predicate_modifier_enum:
permissible_values:
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