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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Makefile should be referencing current or snapshot for db-xrefs #16981

Open kltm opened 5 years ago

kltm commented 5 years ago

Instead of grabbing database xref metadata from a possibly defunct S3 bucket, the Makefile should fetch the db-xrefs metadata from the current blessed sources, such as:

http://current.geneontology.org/metadata/GO.xrf_abbs http://snapshot.geneontology.org/metadata/GO.xrf_abbs

or even the high-protein and easily digestible:

http://current.geneontology.org/metadata/db-xrefs.json

See target https://github.com/geneontology/go-ontology/blob/master/src/ontology/Makefile#L148

Noting https://github.com/geneontology/go-ontology/issues/13837

kltm commented 3 years ago

@ValWood Somebody more familiar with the file and data flow should probably be making these changes.

ValWood commented 3 years ago

OK, I only assigned to you since it has been unassigned since March 2019 and I assumed you would know who to assign it to. Tickets won't be addressed unless assigned to somebody

balhoff commented 3 years ago

I assigned myself.

pgaudet commented 1 year ago

@balhoff needs to check how this is currently coded