Ontology meeting 2016-09-08

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Attendees: DavidOS, DavidH, Chris, Melanie, Harold, Tanya

Regrets: Paola

Minutes: Tanya/Chris


MF Overhaul

Where do we stand with this? I thought David had put in the high-level terms that were required, but was there more that needed to be done? 

 https://github.com/geneontology/molecular_function_refactoring/issues/

 need someone to review mapping on https://github.com/geneontology/molecular_function_refactoring/issues/5#issuecomment-  
 165838078
 Need axiomatization to support refactoring

 AI: DOS will tag tickets with requires-axiomatization and assign to chris

 TF renaming is side-issue (tagged this low-priority)

 We agree that TF activity means DNA binding to most biologists

 AI David OS will take 1/2 a day and complete this

 AI Chris will implement. Retain original as SYSTEMATIC synonyms

Github Action Plan

Is everyone able to keep up to date with tickets? [Paola: number of requests has increased lately. Total number of open tickets is relatively stable around 370, but it's taking more effort and time to keep it like that.] We should try to make an end of the year push to close as many tickets as possible. 

 Growing number of tickets - cannot

 AI: stay the course. We will have a dedicated week in december.

 AI: David Hill will put on next managers call.

 AI: Chris to make sure that TG free form is not open for business.

 DOS: move to pattern-based

 DOS and CJM will work on DPizing membrane branch

Closing EBI GO Jira instance

We'll remove the EBI GO Jira instance on Sept 30th.

Chris, David H + David OS, please address open tickets/close them/move them as appropriate. (Chris, could you please look into Heiko's items too.)

We did address some of them at an editors' call some time ago. If you feel that any particular issue still needs group discussion, please note it here.

Link to Jira: https://www.ebi.ac.uk/panda/jira/browse/GO/?selectedTab=com.atlassian.jira.jira-projects-plugin:issues-panel 

 Some tickets reviewed.  Plan is to move those worthy of moving to github and leave the others behind, to be 'closed' when that
 JIRA instance goes away.

Daily report of terms and stats DID NOT REACH THIS

See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats

Chris, is there a quick fix to reinstate this please, or should a ticket be filed? 

Ticket: https://github.com/geneontology/go-site/issues/217

Metadata update DID NOT REACH THIS

Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.

Modified proteins DID NOT REACH THIS

There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC. [[1]] [[2]] [[3]] 

Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.
Preliminary plan:
   1. Merge all the terms for modified protein binding  (e.g. gylcosylated protein binding) into 'protein binding'
   2. Add comment to 'protein binding':   Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein).   In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)

Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit

Protein complexes DID NOT REACH THIS

https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346

Val says 

 "many people use the "protein complex" term, and would expect that to retrieve complexes 
  like the ribosome and the spliceosome and telomerase (I suspect) Is it possible to define a 
  protein complex as a complex which has only proteins, or protein and RNA components?

 so 
  protein complex
   --ribonucleoprotein complex

  Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, 
  then it moves down...

 This way people will retrieve all protein complexes with the protein complex term.
 Similarly  protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" 
 search. I doubt there are any biologists who would not describe the telosome as a 'protein complex'
 https://en.wikipedia.org/wiki/Shelterin

  but you would not currently retrieve it with a protein complex search.."

 Harold: I just think it's wrong. Don't think most biologists would agree that 
 these complexes with other components are protein complexes
 DOS: Agree.  Don't like the loss of expressiveness either.
 
 Discussion of compromise proposals - renaming or synonyms on protein complex?

Proposal:

macromolecular complex: update definition to say it contains at least one protein; 
make ‘protein-containing complex’ a synonym of this term 
and suggest to Val to consider tweaking the search tool at PomBase? 

protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, 
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”

FAO update DID NOT REACH THIS

  • FAO now has a home on github
  • We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain
  • See Inferences Changes Report for: 2016-08-24 - e.g.
[Term]
+id: GO:0075251 ! uredospore formation
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process

New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism) DID NOT REACH THIS

Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)

NTR: population of unicellular-organism process terms [[4]] 

Discussion is ongoing and recorded in the GH ticket above.
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