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geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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incomplete file filtered_goa_uniprot_all_noiea.gpad.gz #365

Open francoiscoste opened 5 months ago

francoiscoste commented 5 months ago

I wanted to download the file filtered_goa_uniprot_all_noiea.gpad.gz from http://release.geneontology.org/2024-01-17/annotations/index.html but it is almost empty...

Indeed the (compressed) gaf file is 6MB while the gpad one is only 11KB while they should be of comparable size. On the site, we see: filtered_goa_uniprot_all.gaf.gz 17 GB filtered_goa_uniprot_all_noiea.gaf.gz 6 MB filtered_goa_uniprot_all_noiea.gpad.gz 11 KB

Could you fix this or tell me where I could download the complete filtered_goa_uniprot_all_noiea.gpad.gz file? Thanks in advance, François Coste

suzialeksander commented 4 months ago

Hi @francoiscoste, we're looking into the contents but the file sizes seem to be consistent with the last few releases, so it's possible if there is an issue it's an upstream problem. We're currently still investigating, thanks for bringing this to our attention.

suzialeksander commented 4 months ago

Hi @francoiscoste, it seems this file has been quite small for several years. We recommend obtaining this file from the source: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

Note that GOA is not the same as GO; GOA is a curation group at EMBL-EBI and we simply provide their file. For more information, see https://www.ebi.ac.uk/GOA/downloads

kltm commented 3 months ago

@sierra-moxon My guess here is that this is an anomaly caused by our previously not-so-great GPAD emitter; I would expect this to be working after your code is merged. Does that sound like a reasonable assumption? (We'll revisit either way.)

pgaudet commented 2 months ago

This is not yet fixed; on snapshot, the GAF has 290,956 lines but the GPAD only exactly 1000 lines of annotations, as if there was a limit (like you might do when debugging? )

@sierra-moxon @kltm thanks for looking into this

kltm commented 2 months ago

@pgaudet The expectation would be that this would work after https://github.com/geneontology/go-site/issues/2286 has been completed and merged.