GO extension config - Githubissues

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GO extension config #922

Closed ValWood closed 6 years ago

ValWood commented 6 years ago

SO:0000655 should be available under GO:0008173

ValWood commented 6 years ago

~add 25S to curs/5598c8bdf6555b06~

ValWood commented 6 years ago

This text might be a bit confusing:

These extension types are available for rRNA base methylation (GO:0070475): qualifier ... column 17 (PR:nnn ID for gene product form) ... processes ...

perhaps we shoud say "modifies" here. This could mean "biological processes this modification is involved in" because it is a "function" really.....

ValWood commented 6 years ago

I'm doing this in Artemis. I had already done

/GO="aspect=F; term=rRNA (adenine) methyltransferase activity; qualifier=heterologous_system; GOid=GO:0016433; evidence=IGI; db_xref=PMID:30093689; with=SGD:S000002490; has_direct_input=SO:0001002; date=20180816"

but my extension wasn't picked up (will check logs)

ValWood commented 6 years ago

fixed to annotation_extension=has_direct_input(SO:0001002); check tomorrow (rrp8)

ValWood commented 6 years ago

hmph didn't work...

ValWood commented 6 years ago

this is weird, I think this term is in Canto no?

mRNA SPAC56F8.09.1: unknown term name "rRNA (adenine-N1-)-methyltransferase activity" and unknown GO ID "GO:0106142": failed to load qualifier 'aspect=F; term=rRNA (adenine-N1-)-methyltransferase activity; qualifier=heterologous_system; GOid=GO:0106142; evidence=IGI; db_xref=PMID:30093689; with=SGD:S000002490; annotation_extension=has_direct_input(SO:0001002); date=20180816' from SPAC56F8.09.1:

maybe not, checking (I did this in artemis, but I thought I copied name from canto...)

ValWood commented 6 years ago

well the term def exists in canto....

exists

I curated in artemis as it was "complementation"

term rejected in logs @kimrutherford any ideas?

kimrutherford commented 6 years ago

term rejected in logs @kimrutherford any ideas?

It's missing from Chado because the go-basic.obo file in SVN is a few weeks old. Sometimes the GO pipeline doesn't work. I've just changed the load script to use the PURL URL to get go-basic.obo. Chris recommended that ages ago but I never got around to it. Canto gets the GO OBO file via a PURL URL already.

The go-basic.obo via the PURL has the missing term so it should be OK tomorrow.

kimrutherford commented 6 years ago

The warning has gone from the logs and the annotation is now on the main site: https://www.pombase.org/term/GO:0106142

There is a new warning in the gaf-check log because the term isn't in GO SVN yet.

ValWood commented 6 years ago

It's on the web page so closing...