Ontology meeting 2017-04-14

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Agenda

Documentation

GOC Meeting, Corvallis, Oregon

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

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