Ontology meeting 2016-08-25

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Attendees: Paola, David H, David OS, Harold, Judy, Tanya, Chris, Jim, Melanie


Minutes: Paola

xref error

These keep coming in at commit:

ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from
ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of
Chris: solution: svn update the whole ontology directory and they should be gone forever (or possibly appear just once again).

TG freeform

Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:

"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."

Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?

We opened a ticket on the TG tracker for Chris to see how easy it is to turn TGFF off (https://github.com/geneontology/termgenie/issues/94).
AI: Paola to email go-consortium reminding not to use TGFF, and stating that we may close it down soon (refer to the ticket above). DONE

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)

Protein complexes


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?
  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'
  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?
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

  • 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.
+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)

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.