Ontology meeting 2017-10-27

Conference Line

• Zoom: https://stanford.zoom.us/j/828418143

Agenda

Compound Functions and Multiple Parentage

https://github.com/geneontology/go-ontology/issues/14161

GH project link

https://github.com/geneontology/go-ontology/projects/1

Discussion

• 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
    • property_value: creation_date 2017-05-16T17:48:35Z xsd:dateTime
    • property_value: http://purl.org/dc/elements/1.1/creator "tanyaberardini" xsd:string
    • id: GO:0090740
    • id: GO:0090741

• Imports still have relationships
  • Will re-visit this issue when we have Chris on the call

• 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