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


Proposal:
'''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   
 
* 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’”
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins,  
* Classification of complex by function: switch genus to 'macromolecular complex'  (for example of why this is necessary, see: https://github.com/geneontology/go-ontology/issues/12620#issuecomment-247048464)
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'  (for example of why this is necessary, see: https://github.com/geneontology/go-ontology/issues/12620#issuecomment-247048464)


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

Revision as of 07:03, 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
  • 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' (for example of why this is necessary, see: https://github.com/geneontology/go-ontology/issues/12620#issuecomment-247048464)

These edits have now been completed (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.

Implement a system for keeping partonomies in sync (Uberon & CC -> BP)

https://github.com/geneontology/go-ontology/issues/12658

We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.

We can solve the problem by using GCIs to infer partonomy

  • These GCIs can be incorporated into Design patterns, TermGenie etc.
  • GCIs are visible in Protege 5 under terms used in them
  • We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.

I propose we test this out on the organization branch.