term name sometimes does not appear

[ValWood]

see
http://amigo.geneontology.org/amigo/gene_product/PomBase:SPCC162.08c

GO:0005487

maybe it is obsolete? but in that case it isn't very clear when you click on it....
http://amigo.geneontology.org/amigo/term/GO:0005487

[pgaudet]

It is the secondary ID of GO:0017056.
The mapping should happen automatically...?

[kltm]

It looks like it was replaced by GO:0017056; this smacks of an upstream data problem--I had thought that there was automatic replacement in the pipeline in these cases. @dougli1sqrd , do you know if this actually occurs, or is it just in my head?

[pgaudet]

@kltm @cmungall @dougli1sqrd

if it occurs- where would that be documented ?
According to this, the rule exists:
https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000020.md

but it says it's a 'soft check'; is this correct ? shouldn't it be a 'replace' script?

TO DO: It would be nice if each rule page pointed to the error report.

Thanks, Pascale

[kltm]

@dougli1sqrd Can you confirm this one way or another, so we know where the upstream issue is and can move this out of the AmiGO tracker?

@pgaudet if you have a TODO, it should be opened in the proper tracker.

[pgaudet]

@kltm Thanks ! moved my todo here: geneontology/go-annotation#1928

[kltm]

At least in this case, this has been cleared. This is/was likely an upstream data issue.

[kltm]

Found another instance with:
http://amigo.geneontology.org/amigo/search/annotation?q=GO:0001105&sfq=document_category:%22annotation%22

[pgaudet]

AFAIK this is the case for many merged terms.

[kltm]

@dougli1sqrd Is there currently not an upgrade step running in the GAF processing pipeline?

[pgaudet]

Fixed, thanks !!!!!!