Ontology meeting 2017-04-14

• Bluejeans: https://bluejeans.com/164681006

Agenda

Documentation

• Format for documentation on github: Kimberly and David have been working on the SOP Google document.
  • https://github.com/geneontology/go-ontology/pull/13204
• Need to test this on a new user and transition to github md format

GOC Meeting, Corvallis, Oregon

• GOC Meeting Agenda - Ontology-Related Issues
  • http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
  • What to discuss in Corvallis?
  • Is there time for more ontology editors training in Corvallis or should we try to schedule another workshop over the summer?

Term Genie-type Requests

• We are getting tickets for adding terms that previously would have come in through TermGenie.
• What is the long-term plan for replacing TermGenie?

Ontology Tickets

• Import pipeline
  • Fixing import generation
  • Ontology imports into Protege cause undesirable side effects
  • taxon imports incomplete?
  • Load of go-plus.owl fails while importing uberon_import.owl
  • Automate generation of import modules
  • Taxon constraint for GO:0001944
• Modified protein binding proposal
• What do we need to do for the single step BP?

Editors Rota

• David H away 4/14 - 4/23
• Kimberly away 4/17 - 4/22
• Pascale away 4/14 - ?

Minutes

• On call: Chris, Harold, Karen, Kimberly, Moni, Pascale, Tanya
• github email notifications don't always seem to correspond to the person who actually commented
  • not sure what's going on

Documentation

• Please check Google document and give feedback
• Organization
  • Protege
  • github
  • Ontology editing
• readthedocs - use this

Files for download

• • What files are people loading locally? If older, go-basic.obo, is that still being fully supported?
  • go-basic.obo is behind; Chris will look into this
  • Check this URL: geneontology.org/page/download-ontology

GOC Meeting - Corvallis, Oregon

• Ontology issues
• Single-step biological processes - can/should be deleted or removed?
• Modified protein binding proposal
  • Proposal was emailed from Pascale
  • Please look over and we can talk about in ~two weeks (or sooner)?
• Ontology editing
  • Karen, Harold will not be in attendance, so probably not the best time for a full blown workshop
  • Equivalence axioms - editors would like more guidelines on how to construct these
  • This is why the design patterns are so critical
  • Github ticket is open to remove the design patterns repo into the ontology repo
  • Workshop this summer? Bar Harbor?

TermGenie

• Long-term plans for TermGenie
  • Design patterns will drive TermGenie in the future
  • Will use a table-like editor; work on this is progressing
  • Would be good for editors to familiarize themselves with the design patterns to be ready for the new system

Ontology Tickets

• Import pipeline
  • GO imports other ontologies to be able to make linkages between them or make use of things like NCBITaxon
  • However, some ontologies, like RO, contain subsets of other ontologies, like GO, and they can go stale in one or the other
  • Trying to standardize pipelines for ontology release
  • To fix in GO, Chris changed the import pipeline to filter GO from other, external ontologies
  • Tanya - is there a way to see the taxon constraints outside of Protege?
    • Chris - there is an open AmiGO ticket for this
    • We could also just publish a table for this

Modified Protein Binding Proposal

• Reviewed Pascale and Sylvain's proposal
  • Suggestions:
    • Include the term 'dependent' in the term name to try to make it as clear as possible what the term really means, i.e. the binding is dependent upon the specified modification
    • Plan is to add a subset of protein modifications; others as needed
    • PRO could be used to help make clear what protein form is actually bound
    • What grouping terms are useful here?
  • Will then need to review annotations to make sure term usage is correct