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geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
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Untraceable annotation for ZDB-GENE-060818-1 #626

Closed pgaudet closed 2 years ago

pgaudet commented 2 years ago

Hello, Working with @thomaspd - In AmiGO we see this ZFIN annotation:

ZDB-GENE-060818-1  | bmp1a | bone morphogenetic protein 1a |   | protein phosphopantetheinylation |   | GOC | Danio rerio | IDA |   | dorsal-ventral patterning protein tolloid-related-related pthr45645 | protein_coding_gene |   | PMID:16824737 ZFIN:ZDB-PUB-060719-5 | 20060822

However it's not in P2GO. We cannot tell where it's coming from. I thought GOC annotations were the 'predictions' but I dont find it in http://release.geneontology.org/2021-09-01/products/annotations/zfin-prediction.gaf We dont see this in Noctua either.

@kltm @dustine32 Any idea what's going on ?

kltm commented 2 years ago

While we are between runs and no longer have the history (easily available) from the last release, it can currently be found in zfin-src.gaf.gz, so that's the zfin upstream file.

pgaudet commented 2 years ago

Can someone from ZFIN look into this ? @sramachand maybe

kltm commented 2 years ago

@pgaudet Can you explain the problem a little more, as this seems unlikely to be an AmiGO issue?

sramachand commented 2 years ago

I took a look at the annotation. There is an IMP annotation for dorsal/ventral pattern formation but does not have any data in the "with" field. There is also an IGI annotation for the same but with morpholinos curated.

pgaudet commented 2 years ago

Thanks @sramachand Any idea why this is attributed to GOC???

For QuickGO/P2GO : I think this is not showing up in QuickGO/P2GO because it is failing a QC check @alexsign?

Thanks, Pascale

ValWood commented 2 years ago

Probably GOC annotation is because there is an F-P link between GO:0008897 holo-[acyl-carrier-protein] synthase activity and protein phosphopantetheinylation .

This is why it would be good to remove the F-P links between MFs and the corresponding BP terms that represent MFs, it will really help to evaluate the remaining annotations.

pgaudet commented 2 years ago

Discussing with @kltm The is likely an issue with the F-P link, as @ValWood wrote. This should be dealt with separately, we probably have other tickets about this.