Review annotations to GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly

ValWood commented 1 month ago

Dear all,

The proposal has been made to obsolete GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly

see https://github.com/geneontology/go-ontology/issues/24046

Impacted groups: PomBase 2 (done) WB 1 (done) FlyBase 4 @hattrill, these all appear to be the same annotation in QuickGO; there is only a single annotation in AmiGO. UniProt 2 @Antonialock ComplexPortal 3 @sandraorchard

Thanks.

ValWood commented 1 month ago

Weirdly, the script gives me only 2 annotations but QuickGO has 12 https://www.ebi.ac.uk/QuickGO/annotations?goUsage=descendants&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:1903562&evidenceCode=ECO:0000269&evidenceCodeUsage=descendants

check this has not been actioned in another ticket

pgaudet commented 1 month ago

Yeah sometimes I wonder if AmiGO has everything, but I haven't been able to find a way to troubleshoot this systematically.

In this case it does look like AmiGO is missing some annotations.

Can you make sure that the pombase annotations that we see in QuickGO are in the Pombase GAF file ? We should open a ticket in go-site to ask @kltm

ValWood commented 1 month ago

The PomBase annotations are already removed. The Fly and worm annotation is reported (there are 4 identical Fly annotations in QuickGO).

The missing annotations are Uniprot

UniProtKB:P17119	KAR3	involved_in	GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly	ECO:0000314 IDA	PMID:25313961		559292 Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	UniProt
UniProtKB:Q01649	CIK1	involved_in	GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly	ECO:0000315 IMP	PMID:25313961		559292 Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	UniProt

I checked QuickGO and Protein2GO and was unable to see any 'date added', so I'm not sure whether they should be in the GO database are not. The Complex Portal annotations are also absent which aligns with missing data from EBI.

vanaukenk commented 1 month ago

I've updated the C. elegans annotation.

ValWood commented 1 month ago

I'll use QuickGO as the reference here but I won't make a spreadsheet (there are not many annotations)

kltm commented 1 month ago

@pgaudet AmiGO should have pretty much exactly what is in the final local qc'ed GAFs, as supplied by the pipeline and listed in the build here https://github.com/geneontology/pipeline/blob/snapshot-post-fail/Jenkinsfile#L107-L131 .

vanaukenk commented 1 month ago

I'll check about the C. elegans annotations from ComplexPortal. I know we can't pass the protein-containing complex annotations through WB, but we should be able to get the gene-centric annotations from ComplexPortal.

Antonialock commented 1 month ago

uniprot done. I'll paste in the table below

hattrill commented 1 month ago

FB done

sandraorchard commented 2 days ago

Removed from the C.elegans complex in Complex Portal

geneontology / go-annotation

Review annotations to GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly #5346