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geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
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Implement gorule-0000038 gorule required: ISS annotations must refer to a sequence with an EXP annotation #1098

Open ValWood opened 5 years ago

ValWood commented 5 years ago

A- Any term which has ISS annotations but no EXP annotation (to term OR descendant)

Suggested by @cmungall in https://github.com/geneontology/go-ontology/issues/17435

B- We have also historically requested any ISS/ISO where the object in the with field does not have the annotation (term or descendant), which is similar, but slightly different. I think UniProt already includes this rule (@alexsign is that correct?) so it should be on the list somewhere anyway?

B might make A unnecessary, but B might be easier and quicker to implement?

@pgaudet do tickets already exist for all of the rules that GOA include but GO does not?

Caveat: Not all annotation will be incorrect- historically it was not mandated that the annotation must exist. MAny are made from alignments and cite specific publications. So in some cases the missing annotation will need adding rather than the unsupported annotation removing.

pgaudet commented 5 years ago

@pgaudet do tickets already exist for all of the rules that GOA include but GO does not?

Yes

kltm commented 4 years ago

Noting that this is not a "line-by-line" check, but requires access to all available annotations. Unlikely to be implemented directly in the python here, but deferred to SPARQL or other "global" query.