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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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Typo in the mgi-prediction file? #276

Closed ukemi closed 2 years ago

ukemi commented 2 years ago

While importing the annotations from the mgi-prediction file, we are having the following annotation kicked out: MGI MGI:3642276 Rnf212b GO:0016925 PMID:21873635 IBA PANTHER:PTN001099470|SGD:S000004386 P RING finger protein 212B UniProtKB:D3Z423|PTN001862305 protein taxon:10090 20170228GOC

It looks like it is derived from a PAINT annotation and somewhere in the pipeline a change had not been propagated correctly. At MGI: MGI:3642276 Gm10332 MGI:5589964 Rnf212b

Gm10332 is a withdrawn marker and should not have annotations associated with it. So either this annotation should be removed of switched to MGI:5589964 if that is the object that is annotated in the source annotation from PAINT.

kltm commented 2 years ago

@balhoff @dustine32 @ukemi I just noticed this and wanted to see if it was still active? Within that, is this an issue on the PAINT side of things, or within the pipeline on this side. If on this side, it would be produced then from owltools with the --gaf-prediction-file flag.

ukemi commented 2 years ago

@hdrabkin, is this still getting kicked out?

hdrabkin commented 2 years ago

I do not see this annotation in any of our QCs for the load, but also the annotation does not appear in the MGI db. We assume it was removed from PAINT so is no longer in the PAINT gaf we load.

ukemi commented 2 years ago

Will close then.