Ontology meeting 2016-09-15: Difference between revisions

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


Val says
Proposal:
  "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;  
  macromolecular complex: update definition to say it contains at least one protein;  
  make ‘protein-containing complex’ a synonym of this term  
  make ‘protein-containing complex’ a synonym of this term  
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  protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins,  
  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’”
  if you are looking for a more general term please consider using the parent ‘macromolecular complex’”
Classification of complex by function: switch genus to 'macromolecular complex':
These edits have now been done (DOS branch), but have not yet been committed.  Are editors' happy to commit ASAP?


===FAO update===
===FAO update===

Revision as of 06:42, 15 September 2016

Attendees:

Regrets:

Minutes:


Daily report of terms and stats

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

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

Modified proteins

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

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

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’”

Classification of complex by function: switch genus to 'macromolecular complex':

These edits have now been done (DOS branch), but have not yet been committed. Are editors' happy to commit ASAP?

FAO update

  • 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)

Take to GO annotation call or GO meeting?

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

Discussion is ongoing and recorded in the GH ticket above.
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