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DDB IDs in IPI With not valid on 2nd leg (reciprocal) #25

Open pfey03 opened 5 years ago

pfey03 commented 5 years ago

dictyBase gene IDs (DDB_Gxxxxxxx) have been available for a while in extensions and when doing the first leg WITH in IPI annotations.

However, when doing the reciprocal WITH, the DDB_G IDs are not recognized and I then have to go and find the UniProt ID to add those on the reciprocal annotations.

Could you please make the DDB_G IDs also work on this leg?

examples are on this annotation and when you go to their reciprocal partners: https://www.ebi.ac.uk/internal-tools/protein2go/dynamic.html?database=production#ac=Q54L90

Thanks! Petra

alexsign commented 5 years ago

@pfey03 If I understand this correctly, when you press the Make reciprocal button on the P2GO interface it automatically create and fill the form for you. However, this form is automatically invalid because "Entity ID" has DDB_G identifier and you have to change it to UniProt accession in order to add the annotation. If that what it is I'll look into it and let you know how complex the changes will be.

pfey03 commented 5 years ago

@alexsign Yes you got it! And thanks for looking into it. happy holidays!

pfey03 commented 5 years ago

@alexsign I got this in the error report yesterday. So in the first part of the WITH I have DDB IDs and obviously those are now not recognized as reciprocal to the matching UniProt IDs. I don't have time to fix this now as I travel to the UK christmas Dicty meeting tomorrow, but obviously the tool allows something that results in an error. I'll replace the DDB Ids when I get a chance next week.

Thanks!

Here is what I got:

Hello,

We have identified the following annotation(s) with the ECO:0000353 (IPI) evidence code by the DictyBase group to GO:0005515 (protein binding), GO:0003723 (RNA binding), GO:0044877 (macromolecular complex binding), GO:0042277 (peptide binding), or one of their descendant terms, and for which we are unable to locate a reciprocal annotation.

If you have any concerns regarding the contents of this email, please contact goa@ebi.ac.uk; please DO NOT REPLY to this email - it is sent from an unmonitored account.

Thanks, The GOA team.

Curator Entity ID GO ID Reference With_string Petra Fey P15064 GO:0005515 PMID:27009206 UniProtKB:Q54L90 Petra Fey P32253 GO:0005515 PMID:27009206 UniProtKB:Q54L90 Petra Fey P34144 GO:0005515 PMID:27009206 UniProtKB:Q54L90 Petra Fey P34148 GO:0005515 PMID:27009206 UniProtKB:Q54L90 Petra Fey Q23862 GO:0005515 PMID:27009206 UniProtKB:Q54L90 Petra Fey Q54E64 GO:0005515 PMID:24867644 UniProtKB:C0HLF1 Petra Fey Q54K14 GO:0005515 PMID:24867644 UniProtKB:C0HLF1 Petra Fey Q54KA7 GO:0005515 PMID:24867644 UniProtKB:C0HLF1 Petra Fey Q54NU8 GO:0005515 PMID:24867644 UniProtKB:C0HLF1 Petra Fey Q54TB8 GO:0005515 PMID:24867644 UniProtKB:C0HLF1 Petra Fey Q54YB3 GO:0005515 PMID:24867644 UniProtKB:C0HLF1

alexsign commented 5 years ago

@pfey03 no worries Perta, I'll look in to it. Have a nice holidays!

alexsign commented 5 years ago

Adding George in the loop @ggeorghiou