Amount of Experimentally validated GOAnnotations dramatically decreased

[yotamfr]

Hello GO team!

I recently updated my local database (MongoDB) of GeneOntology Annotations by downloading goa_uniprot_all.gaf and discovered that the number of Experimentally validated annotations has unexpectedly and dramatically decreased from 829,532 to 67846.

As I hold a copy of the data on a another machine, I know this change has happened somewhere between the dates 23/09/2017 and 04/12/2017.

BEFORE 23/09/2017 : db.goa_uniprot.count({'Evidence': {'$in': ["EXP", "IDA", "IPI", "IMP", "IGI", "IEP"]}, 'DB': 'UniProtKB'}) 829532

AFTER 04/12/2017 : db.goa_uniprot.count({'Evidence': {'$in': ["EXP", "IDA", "IPI", "IMP", "IGI", "IEP"]}, 'DB': 'UniProtKB'}) 67846

Could you please explain to me what happened?

Best, y

[kltm]

@yotamfr Would mind supplying the URLs where downloaded these files from?

[yotamfr]

Yes,

The noiea file I downloaded from: http://geneontology.org/gene-associations/goa_uniprot_all_noiea.gaf.gz

The goa_uniprot_all.gaf I downloaded from: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz

Both contain only 67846 annotations of experimental codes (as for Dec 9 2017).

(*) And, this is the download page where I found the links: http://www.geneontology.org/page/download-annotations

[kltm]

@yotamfr To clarify, you are looking at a drop in the experimental annotations available in the ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz file? If this is the case, it may be best to contact them directly about file changes: https://www.ebi.ac.uk/GOA/contactus .

[yotamfr]

Yes, this is the case. I sent them a message.