Ontology meeting 2016-10-20

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Attendees:DavidH, DavidOS, Moni, HJD, Tanya, Paola, Jim, Chris

Minutes: David H

Regrets:Melanie

GoToMeeting invite: https://global.gotomeeting.com/join/859015101

Protein complex discussion at GOC LA meeting

At the managers call on Oct 19th, the agenda for the upcoming GOC LA meeting was discussed. This point in particular: (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Protein_Complexes) "Action item [from the 2015-09 Washington, D.C. meeting]: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included."

The question was raised of who could/should present a proposal at the GOC LA meeting to use to reach a resolution (rather than simply having another long discussion). Suzi asked: could David OS work with Peter to come up with a proposal to present? (Chris won't have the chance.)

Here are the minutes from Geneva:

https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.wwwbdoeygi1h

DOS: Outcome of this agreement  = PILOT PROJECT TO INFER ANNOTATIONS IS CANCELLED.  Work on inferred classifications needs to shift back to the ontology.  We still have no means for specifying species independent complexes by composition, apart, perhaps, from complexes made up oligomerised members of the same protein family (e.g. see smads).  In cases where we have documentation of conservation, we can at least enumerate examples.


DOS: We need a consistent PI decision on this before any proposals can be made.

Merging GO calls

This will be discussed at the GOC LA meeting (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Conference_Calls_and_Communication). The EBI office raised some concerns about merging the ontology call with others. David OS, could you please relay these comments in LA?

Chris, Paola and DavidOS wish to continue this call. DOS will report on why this is necessary.


Adding items to the agenda for the GOC LA meeting

This is being finalised, so if any of us would like to add anything, please do so ASAP (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda).

DOS: I've provisionally added  a section on GAF/GPAD inference from LEGO models
* Introduction to inferring annotations from LEGO:  Extended Gene Product to GO term relations; Reasoning across causal chains.
* Jim Balhoff:  Inference using Blazegraph
* DOS: Templates, design patterns and inference.

equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ?

From last week's discussion:

https://github.com/geneontology/go-ontology/issues/12721

gene_ontology_write.obo imports cheb_import.owl. This lacks the equivalence axioms (GCIs). But we have a file called bio_chebi.owl which has them. bio_chebi.owl was last updated 19 months ago: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/bio-chebi.owl?view=log

 During the move to using ChEBI, a few issues wrt distinctions were introduced for the purpose of reasoning in OWL for GO. We mapped equivalent axioms; some terms were conflated. In BioCHEBI, the equivalences are made, but we don’t know the downstream pipeline. 
 
 These equivalent axioms are not imported when you load gene_ontology_write.obo - they were at some point - but it needs an import statement to BioChEBI. It is in chebi_import.owl, but  nothing shows that they’re being used.
 
 We need to fix BioChEBI input, or come up with an alternate strategy.
 
 Tanya: these are being used in TermGenie. So some process is updating that file at least for TermGenie.
 Heiko once said: “ontology uses BioCHEBI”, but it is not using it now. 
 Relevant discussion has moved to this ticket: https://github.com/geneontology/go-ontology/issues/12735
 
 *ACTION*: Chris is working on it.

Follow-up: SOP for merging terms in OBO-Edit

For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#SOP_when_merging_terms.

Paola tested and drafted an SOP, and added documentation here: http://wiki.geneontology.org/index.php/Editor_Guide#SOP_for_merging_terms_in_OBO-Edit

Everyone will take a look at the documentation and comment if necessary.

Jenkins github new tickets reports

From Melanie: Birgit mentioned that "For the last few weeks my daily Jenkins updates have no new notifications and very occasionally updates." I usually check the tracker directly and delete those, can someone have a look?

[Paola] I confirm I haven't seen those reports at all lately - and there HAVE been new GH ontology tickets, as well as updates.

Chris will look into this. Tanya has sent him an example of the weekly emails she has been receiving. Adding the issue to the ticket on the go-site tracker.

Follow-up: GitHub projects

See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects

Plan is to look at https://github.com/geneontology/go-ontology/projects/1 and see how this works for us.

Beginning with: https://github.com/geneontology/go-ontology/issues/12723

GH12753

PURL for GO basic seems to be pointing to an old file. Chris will look into the ticket.