Major changes 2024-04-09 snapshot

geneontology / go-releases

Tasks and notes for monthly GO releases

0 stars 0 forks source link

Major changes 2024-04-09 snapshot #80

Closed pgaudet closed 2 weeks ago

pgaudet commented 5 months ago

NCBITaxon:10090|Mus musculus | + 72676 annotations
NCBITaxon:3702|Arabidopsis thaliana | -49620 annotations
NCBITaxon:44689|Dictyostelium discoideum | -21736 annotations
MGI | -138963 / 179277 | -77.51%

@kltm @dustine32

this seems like a lot ?

pgaudet commented 5 months ago

@LiNiMGI confirms that this change for MGI is OK with the new MGI pipeline.

kltm commented 5 months ago

@pgaudet Okay, I'm feeling like there might be something wrong with the stats, or at least we need to drill down a little more to see what's going on. Compare ZFIN for: (recent try; 249782) https://amigo-staging.geneontology.io/amigo/search/annotation?q=*:*&fq=taxon_subset_closure_label:%22Danio%20rerio%22&sfq=document_category:%22annotation%22 (release; 249768) https://amigo.geneontology.org/amigo/search/annotation?q=*:*&fq=taxon_subset_closure_label:%22Danio%20rerio%22&sfq=document_category:%22annotation%22

Taking a look at the still-functioning filters, things seem similar. I'm wondering if the issue is that the last release is "damaged", making the comparison algorithm wonky.

pgaudet commented 5 months ago

OK, but the stats do not report major changes for ZFIN.

What am I supposed to conclude?

For example for Dicty = loss of 19259 annotations in staging compared to AmiGO

Also in AmiGO, Dicty has 73621 proteins, but only 54362 on staging

Arabidopsis = loss of 34067 annotations

pgaudet commented 5 months ago

Emailed Alex about Dicty annotations, I found examples of manual exp annotations that exist in P2GO but that are not in the GAF file on the GOA ftp (one is: DDB_G0271980 rabR acts_upstream_of_or_within GO:0006909 PMID:18559084)

pgaudet commented 5 months ago

Reply from Alex WRT Dicty:

I talked to UniProt production and it looks like it was 50% deep in number of dictyBase cross references last release. This is back to normal this release and data will be fixed at the end of May.

pgaudet commented 5 months ago

TAIR is regenerating a new file; should be available next week or so (May 1st 2024 or so).