Major changes 2023-09-25

[pgaudet]

• NCBITaxon:9823|Sus scrofa 12962 / 222290 5.83%
• NCBITaxon:9615|Canis lupus familiaris -6745 / 216295 -3.12%
• NCBITaxon:9913|Bos taurus -22347 / 198471 -11.26%
• NCBITaxon:4896|Schizosaccharomyces pombe | -3593 / 51306 | -7.00% (se https://github.com/geneontology/go-releases/issues/50)
• NCBITaxon:36329|Plasmodium falciparum 3D7 -3722 / 18739 -19.86%

[pgaudet]

Emailed Alex about S scofa, Canis, B taurus as most changes for these organisms are due to changes in Ensembl annotations

His reply:

I've notice it as well. The EnsEMBL team seems to update their production pipeline and made changes to many genomes lately as well. I'm ignoring this usually, unless difference is really significant. I believe next year the EnsEMBL data will be more stable.

[pgaudet]

Plasmodium falciparum 3D7: Drop is because IEAs are > 2 year old

Emailed Uli

I am QC’ing the data for the next GO release, and there is an issue with the Plasmodium falciparum 3D7 IEA annotations, that are now more than 2 year old, so according to our practices, these annotations will be filtered out from the GO products, including AmiGO. This affects about 3,500 annotations, ie an overall drop of 20% in the Plasmodium falciparum annotations. My question is, how does your pipeline work; can the scripts to run IEAs be made more frequent? Thanks, Pascale

Uli:

Thanks for your e-mail and for letting me know about the IEA annotations. Unfortunately, we currently only run those predictions when the genome is being updated. We’ve been discussing to run this more frequently for all genomes. It is currently not clear though when this can be implemented. Thanks, Uli

Pascale:

Thanks for the quick response. I’ll see if we can let the annotations through for now. We may be able to get the IEAs directly from UniProt/GOA, this way they would be up to date, since they run them monthly.