Add FB Developmental and Anatomy Ontology

[hattrill]

Adding this here (not sure if it is better on Neo tracker?)

Please add two fly ontologies to NEO:

FlyBase Developmental Ontology (FBdv, http://obofoundry.org/ontology/fbdv) Latest version: http://purl.obolibrary.org/obo/fbdv.owl

and

FlyBase Anatomy Ontology (FBbt; http://obofoundry.org/ontology/fbbt) Latest version: http://purl.obolibrary.org/obo/fbbt.owl

[kltm]

@hattrill Just confirming, but this is so that these terms are available in the autocomplete(s), correct?

[hattrill]

@kltm Yes and I assume that you don't want/allow random ontology terms to be dropped into the extension field.

[kltm]

@balhoff I guess the two things to do here are to either just add them separately to the GOlr load (https://github.com/geneontology/pipeline/pull/344) or to add them to go-lego.owl. Any thoughts one way or another?

[balhoff]

I think we should add to go-lego/go-amigo; otherwise we could run into the problems we had before with the reasoner and direct loading into AmiGO.

[kltm]

@balhoff Hm. How many terms are we talking about here? I'd be guessing, looking at the non-GO ontologies we already load (https://amigo.geneontology.org/amigo/search/ontology), that it would be unlikely to make a huge change. If so, could you close the PR out in favor of changes to the ontology build (and link that here)?

[balhoff]

Pull request over here: https://github.com/geneontology/go-ontology/pull/26523.

[kltm]

We don't quite have a state for this, but I would expect this to propagate out by the next release or so.

[vanaukenk]

@kltm @balhoff

Just double-checking about this work before tomorrow's maintenance outage. Will this require a successful snapshot release to percolate to production Noctua?

[balhoff]

Luckily I see FBbt in yesterday's successful snapshot. :-)

[vanaukenk]

Checking this after the 2023-12-14 Noctua maintenance outage, it looks like the FBbt and FBdev terms are now available in Noctua.

@hattrill - if you want to also double-check to make sure everything is working as expected wrt those ontologies, that'd be great, and then we can close this ticket.

Thx.

[hattrill]

All seems good to me wrt ontologies. So I will close this.

@vanaukenk Might need a bit of help with interface, but we can go over this in training after Christmas.

Thanks

[pgaudet]

For extensions in P2GO, we need the following mappings to be present in GO-upper:

[Term] id: FBbt:00007002 is_a: GO:0005623 ! cell

[Term] id: FBbt:10000000 is_a: UBERON:0001062 ! anatomical entity

[Term] id: FBdv:00007012 is_a: UBERON:0000105 ! life cycle stage

PR is here: https://github.com/geneontology/go-ontology/pull/26997

[pgaudet]

Added database: FBdv to dbxref.yaml file

database: FBdv name: Drosophila development rdf_uriprefix: http://purl.obolibrary.org/obo/FBdv generic_urls:

• http://flybase.org/ entity_types:
• type_name: life cycle stage type_id: UBERON:0000105 id_syntax: '[0-9]{8}' url_syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:[example_id] example_id: FBdv:00007012 example_url: http://flybase.org/cgi-bin/fbcvq.html?query=FBdv:00007012

PR is here: https://github.com/geneontology/go-site/pull/2292

[kltm]

Since closing, there have been two more PRs. Is this now completed?