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Standardise annotation property: abbreviation (UBERON) #3079

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ghost opened this issue Sep 25, 2023 · 0 comments · Fixed by #3082
Closed

Standardise annotation property: abbreviation (UBERON) #3079

ghost opened this issue Sep 25, 2023 · 0 comments · Fixed by #3082
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synonym tech

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ghost commented Sep 25, 2023 •
edited by ghost
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Related issue: obophenotype/cell-ontology#2150
Depends on/Prerequisite: OMO import added to UBERON

There are several variations of the synonym_type_property abbreviation in CL and UBERON:

http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION with no asserted rdfs:label in CL
http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION with label 'abbreviation' in UBERON
http://purl/obolibrary.org/obo/cl#abbreviation with label 'abbreviation' in CL
http://purl/obolibrary.org/obo/cl#abbreviation with no asserted rdfs:label in UBERON

As part of an effort to standardise synonym_type_properties in OBO ontologies (like obophenotype/cell-ontology#2143), this ticket proposes to delete the above annotation properties and replace all with the OMO term OMO:0003000 abbreviation.

This ticket will address native instances of the property in UBERON.
A separate PR addresses native instances in CL: obophenotype/cell-ontology#2159
@ghost ghost added synonym tech labels Sep 25, 2023
@ghost ghost mentioned this issue Sep 25, 2023
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@cthoyt cthoyt mentioned this issue Oct 1, 2023
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cthoyt added a commit to cthoyt/uberon that referenced this issue Oct 1, 2023
@cthoyt
Replace type definition for abbreviation synonyms
af87363 
Closes obophenotype#3079 by replacing the ad-hod "abbreviation" synonym type definition with the equivalent, externally defined OMO:0003000
@cthoyt cthoyt mentioned this issue Oct 1, 2023
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anitacaron added a commit that referenced this issue Oct 26, 2023
@cthoyt @anitacaron
Replace type definition for abbreviation synonyms (#3082)
276ae33 
* Replace type definition for abbreviation synonyms

Closes #3079 by replacing the ad-hod "abbreviation" synonym type definition with the equivalent, externally defined OMO:0003000

* Update uberon-edit.obo

* update abbreviation annotation in sparql_test check

* normalize uberon-edit

* remove `synonymtypedef: ABBREVIATION` in uberon-edit

* lower missing_synonymtype_declaration's severity to WARN

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Co-authored-by: Anita Caron <[email protected]>
Co-authored-by: Anita Caron <[email protected]>
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Replace type definition for abbreviation synonyms cthoyt/uberon
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