Open ValWood opened 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
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
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.
I've updated the C. elegans annotation.
I'll use QuickGO as the reference here but I won't make a spreadsheet (there are not many annotations)
@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 .
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.
uniprot done. I'll paste in the table below
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UniProtKB:Q8MQ03 | zen-4 | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:11782313 | 6239 Caenorhabditis elegans | ComplexPortal -- | -- | -- | -- | -- | -- | -- | -- UniProtKB:Q9XUS9 | cyk-4 | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:11782313 | 6239 Caenorhabditis elegans | ComplexPortal ComplexPortal:CPX-3463 | spind_caeel | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:11782313 | 6239 Caenorhabditis elegans | ComplexPortal UniProtKB:O16048 | pav | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:15958489 | 7227 Drosophila melanogaster | FlyBase UniProtKB:O62528 | pav | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:15958489 | 7227 Drosophila melanogaster | FlyBase UniProtKB:Q8SXT9 | pav | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:15958489 | 7227 Drosophila melanogaster | FlyBase UniProtKB:Q9VZF5 | pav | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:15958489 | 7227 Drosophila melanogaster | FlyBase UniProtKB:Q9HDY1 | ase1 | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000315 IMP | PMID:15647375 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | PomBase UniProtKB:Q9HDY1 | ase1 | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000314 IDA | PMID:17254972 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | PomBase 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 UniProtKB:G5ED58 | spd-1 | involved_in | GO:1903562 microtubule bundle formation involved in mitotic spindle midzone assembly | ECO:0000314 IDA | PMID:26088160 | 6239 Caenorhabditis elegans | WB
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.