explanations about xref abbreviations in Uberon

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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explanations about xref abbreviations in Uberon #1373

Closed ANiknejad closed 3 years ago

ANiknejad commented 7 years ago

sorry for this issue, but actually is there a place where to find meaning of all these xrefs abbreviation ? (even if I know most of them)

xref: Aortic:valve xref: BTO:0004628 xref: EFO:0003879 xref: EHDAA2:0000134 xref: EHDAA:4410 xref: EMAPA:17870 xref: FMA:7236 xref: GAID:563 xref: galen:AorticValve xref: http://linkedlifedata.com/resource/umls/id/C0003501 xref: http://www.snomedbrowser.com/Codes/Details/181287002 xref: MA:0000087 xref: MESH:D001021 xref: NCIT:C12670 xref: OpenCyc:Mx4rv5914JwpEbGdrcN5Y29ycA xref: UMLS:C0003501 {source="ncithesaurus:Aortic_Valve"} xref: VHOG:0000815

cmungall commented 7 years ago

For now, a combo of http://amigo.geneontology.org/xrefs and http://obofoundry.org

We expand some out to full URIs, but this seems to cause issues when roundtripping back to OBO. E.g. Aortic:valve is the roundtrip of the expanded URL for Wikipedia:Aortic_valve. After discussing with @SimonJupp I think best to retain as CURIEs in release (Simon did we have an OLS ticket discussing this, can't find it?).

The OpenCyc ones aren't maintained any more, could retire these.

GAID - should retire these. At one point someone cloned MESH and made an 'anatomy ontology' with new IDs. No longer used AFAICT.

simonjupp commented 7 years ago

I don't think so but I second keeping them as CURIEs in the releases.

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.