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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
36 stars 13 forks source link

Adding UniProt IDs? #799

Open moghelab opened 1 year ago

moghelab commented 1 year ago

Newbie here. I followed an older discussion here: https://github.com/geneontology/noctua/issues/471 that suggests that adding data about at least some UniProt IDs should be possible. However, I tried retrieving this entry using the Noctua Form Editor (https://www.uniprot.org/uniprotkb/A0A193BL32/entry) but it doesn't load in the GP cell. From what I understand from the discussions here, the entry has to be in the Neo database and I am not sure which aspects of Uniprot entries have been loaded into Neo. I work in plants and I can retrieve proteins from Arabidopsis using their TAIR-assigned IDs (ATxGXXXXX) but I am not sure how to add MF/BP annotations to other proteins not from model organisms?

Are only UniProtKB entries enabled? Am I not able to add because the above entry is in TrEMBL (unreviewed)? If the latter, is this functionality under consideration? Ability to add GOs for TrEMBL entries would be super-useful because it would reduce the curation bottleneck at UniprotKB for plants. A lot of the TrEMBL entries have been experimentally characterized and have a published manuscript associated with them, but have not had the chance to be reviewed yet, which can take a very long time.

vanaukenk commented 1 year ago

Hi @moghelab

Thanks for your questions about UniProtKB entries in Noctua. You are correct in that, right now, the entities need to be available in the NEO ontology for annotation in Noctua. And currently, we include the reviewed Swiss-Prot entries in NEO, but not the TrEMBL entries.

We'll discuss with the GO PIs (hopefully tomorrow) what would be needed to bring more TrEMBL entries into NEO to facilitate curation of other organisms that may not have their proteins reviewed yet. We don't want this to be a bottleneck for your curation.

Thanks, --Kimberly

moghelab commented 1 year ago

Hi, @vanaukenk I wonder if you have any suggestions on how to proceed on this (assuming this was discussed at the PI meeting)? Thanks!

vanaukenk commented 1 year ago

Hi @moghelab thanks for checking back in. Would you be able to supply us with a list of TrEMBL accessions that you'd like to have available, at least in the near term?

moghelab commented 1 year ago

Yes, I can! Should I email them somewhere?

vanaukenk commented 1 year ago

Hi @moghelab I just sent you an email so you can send me the list of accessions and I'll forward them on to the GO software team. Thx.