search

intermine / pombemine

0 stars 1 forks source link

Question: How to access protein domain beginning from gene? #61

Closed ValWood closed 2 years ago

ValWood commented 2 years ago

I can't see how to do this. I also can't access gene from domain due to an apparent bug: https://github.com/intermine/bluegenes/issues/799

danielabutano commented 2 years ago

@ValWood I think that you can quey Gene -> UniProtEntry->ProteinDomainRegion->ProteinDomain

ValWood commented 2 years ago

So protein domains are loaded from secondary source (UniProt) rather than primary source (InterPro)? (this will make them quite out of data. as UniProt only updates every 6 months or so). Also it in not clear if this will include protein families as well as domains.

It's OK for now. This is just an observation.

danielabutano commented 2 years ago

@ValWood Protein domain and ProteinDomainRegion are loaded from InterPro. Gene -> UniProtEntry->ProteinDomainRegion->ProteinDomain was only a way to show you how the relation between gene and protein domain has been implemented in the intermine model. It might be helpful to look at the template Gene -> Protein + Domains defined in humanmine. Let me know if I have I 've misundersdood your question.

ValWood commented 2 years ago

THANKS!