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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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gorule-0000006 IEP and HEP restricted usage- small bug #2081

Closed pgaudet closed 1 year ago

pgaudet commented 1 year ago

Hello,

gorule-0000006 forbids IEP and HEP for non-BP annotations; however it looks like it is also picking up annotations to obsolete BP terms, for example here:

http://snapshot.geneontology.org/reports/assigned-by-cgd-report.html#gorule-0000006

ERROR - Violates GO Rule:GORULE:0000006: IEP and HEP usage is restricted to terms from the Biological Process ontology--CGD CAL0000186516 CDR1 GO:0035690 CGD_REF:CAL0141866|PMID:21474609 IEP P C3_05220W_A|orf19.13421|IPF21285.1|IPF9739.2|Contig4-1997_0005|CA6066|CaO19.6000|CaO19.13421|orf6.9037|orf19.6000|C3_05220W_B|C3_05220W|CAWG_02836 gene_product taxon:237561 20140625 CGD

GO:0035690 is an obsolete BP

To investigate (did I diagnose the issue correctly) and fix; this annotation should not be reported as an error for gorule-0000006

pgaudet commented 1 year ago

I will add tests for this

pgaudet commented 1 year ago

Added TEST-5 and TEST-6 TEST-5 tests an obsolete BP TEST-6 tests an altid

These terms should be ignored by this rule.

Thanks, Pascale

pgaudet commented 1 year ago

Looks good!