Ontology meeting 2016-04-07

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Attendees: Paola, Chris, Tanya, Heiko, Harold, Melanie, Karen (part of call)

Minutes: Melanie


Computed annotation to 'do not annotate terms'

Karen noticed that we have some annotations to 'sperm part' coming from the GOC pipeline. It looks as if they are coming from an annotation that has an annotation extension part_of sperm. The pipelines shouldn't make annotations to terms marked 'do not annotate directly to this term". I have moved this to the top of the agenda because Karen would like to take part in the discussion. 

 DOS: In this case I think they should.  If terms annotated with the extension "'part of' sperm" 
 were added to the ontology instead of being post-composed as extensions, then they would 
 end up under 'sperm part'.  The inferred annotations are there in lieu of mechanisms for 
 grouping/enrichment to these terms based on the contents of annotation extensions.

 MC: checked with Tony and is not in GOA (our GOC pipeline does not add annotations to 'do not (manually) annotate terms'). Hypothesis is it may be coming from the AE-based inference pipeline from Heiko?

Minutes: Heiko confirmed this is coming from their pipeline. Karen created a ticket in the annotation tracker and Heiko was assigned.

Follow-up: vesicular transport

Revise for consensus:

https://github.com/geneontology/go-ontology/issues/12317

Minutes: wait for DOS in 2 weeks. No editors call next week (Biocuration and travel to GO meeting)

Review slides for GOC meeting

Plan is to give flash updates of ontology stats and ontology focused projects.

Minutes: Heiko and Melanie provided stats. Paola asked David H and Chris if anything to bring up. (David H not attending call today) Paola: ontology keeps growing at same pace than 2015, same true for ontology requests. We expect as much work in the ontology development area going forward as currently. Rate at which ontology requests are coming is unsustainable - tickets come in at a faster pace than we can process them - so there is a backlog, and it increases. Chris: this should be brought up at meeting.

(Old) terms in TermGenie review queue

7/16/15 meiotic APC-fizzy-related complex 

 MC:based on http://wiki.geneontology.org/index.php/Ontology_meeting_2016-01-28, Tanya is following up on this. She had said: GH11977 and GH11757 are related, need to take to annotation call

Minutes: Tanya: we will talk about this at the next annotation call after biocuration (multiple tickets)

2/12/16 short-term synaptic potentiation 

 MC: this one came during my shift. There is a corresponding GitHub ticket at https://github.com/geneontology/go-ontology/issues/12299. I asked Sylvain last week if he had anything else to add to the ticket (which is pending resolution) and he said no.

Not sure who the 'reviewers' were when these terms came in. Should the terms be obsoleted and GH tickets opened?

Minutes: GH tickets are opened. Tanya will email DOS as he is involved in both.

More 'response to non-physiological chemical stimulus' terms coming in via TG

This week we had: response/cellular response to ouabain and response/cellular response to Dizocilpine

https://en.wikipedia.org/wiki/Ouabain

https://en.wikipedia.org/wiki/Dizocilpine

I'm going to reject the term requests on the same grounds as previously, but am starting to suspect we have a communication problem here.

Minutes: Paola on rota this week. 4 requests for responses to plant poison injected in rat brain (reject)) and similar. Chris suggests we invite Stan to attend the call in 2 weeks time for discussion and to look for viable alternatives to RGD needs. Paola will send him an email, and obsolete the terms. Update: Stan won't be available on Thu April 21st, but we could try for a following date.

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