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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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INtact complex portal (physical interaction between different species) #4241

Closed ValWood closed 1 year ago

ValWood commented 2 years ago

Could this annotation be deleted, it records a physical interaction between a pombe protein and human protein (these shouldn't get through to GO should they)?

INTA | P04910 | hta2 | enables | GO:0005515 | protein binding | ECO:0000353(IPI) | ECO:0000353 | (IPI) |   | PMID:21633354 |   | UniProtKB:Q15003

ECO:0000353 | (IPI)

ValWood commented 2 years ago

Assigning to @Antonialock to assign the right person, and check if this should be an annotation check

sandraorchard commented 2 years ago

The process is automatic so the only way of getting rid of this interaction at the IntAct end would be to add a filter so all cross-species interactions are removed from the IntAct2GO (and UniProt) exports. This has been discussed in the past, but would mean (a) all host-pathogen interactions and (b) all interactions designed to show sequence conservation are lost so it was always agreed the loss outweighed the gain. A data import filter at your end would be the other alternative.

ValWood commented 2 years ago

Hmm it would be a shame to use pathogen-host interactions from GO, as these are real interactions.

Is it possible to make a way to distinguish these ? It seems a shame that the pathogen-host interactions and the sequence conservation examples are not distinguishable. MAybe they could have a specific "qualifier" to distinguish them.

This would also enable the pathogen-host interaction pairs to be accessed as a set. I suspect PHI-base will be interested in this set as they are likely to be represent proteins that should be included in include . Is it possible to do a query to retrieve all interspecies physical interactions?

We can filter them locally from PomBase.

sandraorchard commented 1 year ago

Can this be closed now?

ValWood commented 1 year ago

Yes I guess (note to self add filter to PomBase)