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pombase / pombase-chado

PomBase code for accessing Chado
MIT License
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filter Complex portal protein binding annotations with non-pombe IDs in the "with"field #1053

Closed ValWood closed 6 months ago

ValWood commented 1 year ago

I don't think these should be in GO, since GO is representing normal, actual biology. The only inter-species protein-protein interactions should be between host and pathogen proteins.

https://github.com/geneontology/go-annotation/issues/4241

so, we should filter any annotation with a non pombe uniprot Id in the with filed.

Not urgent

ValWood commented 6 months ago

This is a small task that can be slotted in some time, but I don't know if there are any, so maybe they are filtered anyway (do we filter protein binding from Complex Portal? I think we might? in which case this can close)

ValWood commented 6 months ago

this is largely a duplicate (because I think Complex Portal is the only source) https://github.com/pombase/pombase-chado/issues/1001

kimrutherford commented 6 months ago

There are only 35 pombe annotations that are assigned by ComplexPortal. Are those the ones you're thinking of here?

Only 5 of those have a with/from and in those 5 cases the value is "ComplexPortal:CPX-565".

ValWood commented 6 months ago

OK do we load those?

kimrutherford commented 6 months ago

OK do we load those?

Yep, those numbers were from Chado queries.

Although now when I query again I see only 23 annotations assigned_by ComplexPortal and 4 annotations have a "with" value that's a ComplexPortal ID.

These are the 4 annotations with a "with":

 SPAC140.01   | mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone)
 SPAC140.01   | tricarboxylic acid cycle
 SPCC330.12c  | tricarboxylic acid cycle
 SPAC1556.02c | tricarboxylic acid cycle