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geneontology / go-releases

Tasks and notes for monthly GO releases
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+7.27% IEAs =>> 122636 / 1686504 #40

Closed pgaudet closed 1 year ago

pgaudet commented 1 year ago

Ensembl: +23.71%

pgaudet commented 1 year ago
TaxID | Species | Change -- | -- | -- NCBITaxon:9615\|Canis lupus familiaris | 13351 / 33677 | 39.64% NCBITaxon:8364\|Xenopus tropicalis | 7965 / 29828 | 26.70% NCBITaxon:8355\|Xenopus laevis | 2201 / 18347 | 12.00% NCBITaxon:3218\|Physcomitrium patens | 10729 / 10729 | 100.00% NCBITaxon:44689\|Dictyostelium discoideum | -3547 / 5590 | -63.45% NCBITaxon:242507\|Pyricularia oryzae 70-15 | 6283 / 6283 | 100.00% NCBITaxon:243230\|Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 | 1093 / 1093 | 100.00% NCBITaxon:2697049\|Severe acute respiratory syndrome coronavirus 2 | 15 / 15 | 100.00%
pgaudet commented 1 year ago

corresponding to the increse in the number of annotated entities:

pgaudet commented 1 year ago

Emailed Malcolm

Hi Malcolm,

I hope you are doing well. I am QC’ing the upcoming GO release, and I noticed both species of Xenopus have large increases in number of entities

• NCBITaxon:8364|Xenopus tropicalis | 7965 / 29828 + 26% • NCBITaxon:8355|Xenopus laevis | 2201 / 18347 | + 12%

https://github.com/geneontology/go-releases/issues/40#issuecomment-1647594612

Is this expected?

Thanks, Pascale

pgaudet commented 1 year ago

Reply from Malcolm:

Thanks for getting in touch. We have been going through an intensive period of genome annotation review and reconciliation between the Xenopus genes on the NCBI and UniProt sites. As a result we have made additional linkages for many existing gene pages and created 1000's of new gene pages for previously poorly characterized genes, so the increases you see are in line with what we would expect.

Thanks,

Malcolm

pgaudet commented 1 year ago

Dicty drop was due to problem with GOA pipeline, see https://github.com/geneontology/go-releases/issues/39