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Add OMO import to UBERON #3058

Closed
Tracked by #3083
, #3077 ,  #3082
...
ghost opened this issue Sep 6, 2023 · 2 comments · Fixed by #3092
Closed
Tracked by #3083
, #3077 ,  #3082
...

Add OMO import to UBERON #3058

ghost opened this issue Sep 6, 2023 · 2 comments · Fixed by #3092
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@anitacaron
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synonym update-imports-required Imports need to be refreshed before this PR can be merged.

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@ghost
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ghost commented Sep 6, 2023

Context: obophenotype/cell-ontology#2045

Depends on importing OMO (@anitacaron).

Once OMO is imported, edit all plural term annotation properties to OMO:0003004 'plural form'.
@ghost ghost added synonym blocked blocked by another issue update-imports-required Imports need to be refreshed before this PR can be merged. labels Sep 6, 2023
@ghost ghost self-assigned this Sep 6, 2023
@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 plural form synonyms
1cf4e49 
Closes obophenotype#3058 and closes obophenotype#3080 (duplicate of obophenotype#3058) by replacing the ad-hod "plural" synonym type definition with the equivalent, externally defined OMO:0003004
@cthoyt cthoyt mentioned this issue Oct 1, 2023
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@ghost
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ghost commented Oct 2, 2023

#3080 details the ontology edits required.

@anitacaron, can we re-appropriate this issue to track adding the OMO import to Uberon? If so, I will assign this ticket to you and, once completed, follow up in #3080.

@anitacaron
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Ok, can you change the title, too, please?

@ghost ghost changed the title Update all plural term annotations to OMO 'plural form' Add OMO import to UBERON Oct 5, 2023
This was referenced Oct 10, 2023
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@anitacaron anitacaron assigned anitacaron and unassigned ghost Oct 13, 2023
@anitacaron anitacaron removed the blocked blocked by another issue label Oct 13, 2023
@anitacaron anitacaron mentioned this issue Oct 13, 2023
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anitacaron added a commit that referenced this issue Oct 27, 2023
@cthoyt @anitacaron
Replace type definition for plural form synonyms (#3083)
c5b5a32 
* Replace type definition for plural form synonyms

Closes #3058 and closes #3080 (duplicate of #3058) by replacing the ad-hod "plural" synonym type definition with the equivalent, externally defined OMO:0003004

* Update uberon-edit.obo

* Update uberon-edit.obo

* replace remaining case after merge from master

* normalize uberon-edit

* remove `synonymtypedef: PLURAL` from edit file

* add back plural synonymtypedef to uberon-edit

* add abbreviation synonymtypedef

* fix abbreviation annotation curie

* add label to the synonymtypedef

---------

Co-authored-by: Anita Caron <[email protected]>
Co-authored-by: Anita Caron <[email protected]>
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Import OMO terms obophenotype/uberon
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