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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Missing alt_ids in composite-metazoan #1259

Closed fbastian closed 3 years ago

fbastian commented 8 years ago

E.g., 

[Term]
id: EMAPA:27599
name: nephric duct, metanephric portion (mouse)

misses the alt_id EMAPA:17377 (see ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo)

Or 

[Term]
id: UBERON:0001264
name: pancreas
xref: xref: EMAPA:17503

misses the alt_id to EMAPA:18816 as xref.

Or

[Term]
id: UBERON:0000945
name: stomach
xref: EMAPA:17021

misses the alt_id to EMAPA:18889 as xref

uberon commented 8 years ago

I deliberately filtered alt_ids. Some ontologies like EHDAA2/AEO use alt_id to xref other ontologies. This creates huge problems as the official OWL interpretation of an alt_id according to the OBO spec is to treat it as an obsolete class... so EHDAA2/AEO would end up clobbering other ontologies

It looks like we have to selectively allow some alt_ids back in

On 29 Aug 2016, at 16:14, fbastian wrote:

E.g.,

[Term]
id: EMAPA:27599
name: nephric duct, metanephric portion (mouse)

misses the alt_id EMAPA:17377 (see ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAPA.obo)

Or

[Term]
id: UBERON:0001264
name: pancreas
xref: xref: EMAPA:17503

misses the alt_id to EMAPA:18816 as xref.

Or

[Term]
id: UBERON:0000945
name: stomach
xref: EMAPA:17021

misses the alt_id to EMAPA:18889 as xref

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gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.