From f4358b53585ab9d59b36be382c329572fba43d1e Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 2 Dec 2024 19:56:07 +0000 Subject: [PATCH 1/2] Add 'composed entity' value to the EntityType enum. 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 --- CHANGELOG.md | 1 + examples/schema/composite-entities.sssom.tsv | 12 ++++++++++++ src/sssom_schema/schema/sssom_schema.yaml | 7 ++++++- 3 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 examples/schema/composite-entities.sssom.tsv diff --git a/CHANGELOG.md b/CHANGELOG.md index 54d7ccdb..0f505713 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ## Next +- Add `composed entity` as a new value in the `EntityType` enumeration ([issue](https://github.com/mapping-commons/sssom/issues/402)). - TBD ## SSSOM version 1.0.0 diff --git a/examples/schema/composite-entities.sssom.tsv b/examples/schema/composite-entities.sssom.tsv new file mode 100644 index 00000000..1e6ff624 --- /dev/null +++ b/examples/schema/composite-entities.sssom.tsv @@ -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 diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 7303fe0b..060fead1 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -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 @@ -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: From 8c10cda145b0ae814709b6dab5e1df96ec947dec Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 5 Dec 2024 11:38:00 +0000 Subject: [PATCH 2/2] Rename 'composed entity' to 'composed entity expression'. It is believed that 'composed entity expression' better conveys the idea that the entity being referred to is a composite entity, compared to 'composed entity' alone. --- CHANGELOG.md | 2 +- examples/schema/composite-entities.sssom.tsv | 6 +++--- src/sssom_schema/schema/sssom_schema.yaml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0f505713..94b6da62 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,7 @@ ## Next -- Add `composed entity` as a new value in the `EntityType` enumeration ([issue](https://github.com/mapping-commons/sssom/issues/402)). +- Add `composed entity expression` as a new value in the `EntityType` enumeration ([issue](https://github.com/mapping-commons/sssom/issues/402)). - TBD ## SSSOM version 1.0.0 diff --git a/examples/schema/composite-entities.sssom.tsv b/examples/schema/composite-entities.sssom.tsv index 1e6ff624..8550ec0d 100644 --- a/examples/schema/composite-entities.sssom.tsv +++ b/examples/schema/composite-entities.sssom.tsv @@ -7,6 +7,6 @@ #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 +SCHEMA:0001/(disease:'MONDO:0005148',phenotype:'HP:0009124') skos:exactMatch MP:0000003 semapv:ManualMappingCuration composed entity expression +SCHEMA:0001/(disease:'MONDO:0005149',phenotype:'HP:0008551') skos:exactMatch MP:0000018 semapv:ManualMappingCuration composed entity expression +SCHEMA:0001/(disease:'MONDO:0005150',phenotype:'HP:0000411') skos:exactMatch MP:0000018 semapv:ManualMappingCuration composed entity expression diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 060fead1..6bae0362 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -54,7 +54,7 @@ enums: meaning: rdfs:Datatype rdf property: meaning: rdf:Property - composed entity: + composed entity expression: 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