Ontology meeting 2017-10-27

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Conference Line


Should we pick a different time for this meeting?

Feedback from Barbara

Compound Functions and Multiple Parentage


GH project link



  • On call: Barbara, Eric, Harold, Karen, Kimberly, Pascale, Tanya
  • Brief discussion about the status of the TermGenie replacement tool

New Meeting Time

  • Mondays, 9am PST
  • November 13th we'll switch
  • Paul T. confirm?

In Progress Label

  • Still happening, but maybe not a big deal?

Feedback from Barbara

  • Protege 5.2 bug
    • 'property_value:' precedes Created_by and Creation_date
    • this means that Barbara has to remove these two fields for each term she makes
    • Tanya is also using Protege 5.2 and has the same format, but it doesn't seem to be breaking anything
  • Other feedback from Barbara on documentation
    • Some already addressed; others to be discussed with David before updating docs
    • We discussed deleting branches on your local machine - this may just be personal preference
    • github tip: 'git checkout -- filename' will remove all changes to that file

Compound Functions

  • The ticket re. DNA clamp unloader activity is now closed.
  • We will re-visit, though, the issue of modeling in the ontology regulation of one function when a gene product has multiple functions.

Transporter Activities

  • Uptake transmembrane transporter activity
  • Inorganic anion transmembrane transporter
    • Placement of cyanide transporter
  • Where possible, will try to fix asserted parentage if it is not correct
  • Let the reasoner and ChEBI classification, via logical defs, assert the proper parentage