Ontology meeting 2017-05-19

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GOC Meeting, Corvallis, Oregon

Annotation Documentation

Add the 'curator note' property to selected classes: improving curator documentation centered around particular terms in the ontology, by embedding it directly in the ontology. See GitHub issue at https://github.com/geneontology/go-ontology/issues/13384

Ontology Editing (Protege/GitHub) Documentation

  • What's up with this? Final version somewhere?
    • Moni is working on porting the Ontology Editors Guide to GitHub (from Google Doc), so it can be more easily displayed and browsed. You can see examples of files already ported over to GH (proof of concept) here: https://github.com/geneontology/go-ontology/tree/master/docs For example, this is the file with information for initial set up.
    • The Ontology Editors Guide in Google Docs still has some commentary from Pascale, which requires attention. We could either 1) resolve those comments early next week, or, 2) freeze the document as is and transport it to be finalized on Github.
    • Moni and Chris will connect GitHub & ReadTheDocs (to display documentation). An example of what this documentation will look like can be seen in this other project.

  • Where to find the documentation for obsoleting terms?

Inference e-mails are Back


David has checked the file and has noted the strange ones in the ticket.

  • The response ones are pretty easy. They don't have necessary and sufficient logical defs.
  • The dentin transport one is a weird result of the reasoning.
  • The protein ones are technically correct but misleading. I am pretty sure it is due to the equivalence between PRO and ChEBI. I suspect Pascale might have these in her sights for clean up.

Ontology Developer Training

Follow up on idea of doing an advanced Ontology Developer Training workshop this summer

  • Who will participate ?
    • People who are currently active in editing the ontology.
  • Where will it be?
    • The Bay area.
  • When will it be?
    • The week of August 14th is best, but we won't have Seth.
  • Potential Topics
    • Equivalence axioms - editors would like more guidelines on how to construct these.
    • OWL GCIs- Where do they live and how do they work?
    • Advanced Querying?
    • Pipelines and how they run. Starting jobs with ROBOT.
    • Build failures
      • Document the various fail messages and how to correct the issues.
    • Problematic GitHub tickets/mini Projects

Github Ticket Discussion



Present: David H, Harold, Karen, Pascale, David OS, Chris M, Moni, Eric, Jim, Paul T, Tanya