Ontology meeting 2017-04-21

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

Agenda

Action point from last meeting

Documentation

Rediscuss next week Moni and Tanya: Please review the documentation at https://github.com/geneontology/go-ontology/pull/13204

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

Curator documentation

• Chris suggests to use a new tag in protege;
• Pascale suggests also creating a 'Curator beginners' guide'
  • Suzi suggests using information from the GO handbook

ACTION POINT Review existing documentation:

• https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit
• http://geneontology.org/page/go-annotation-conventions
• http://geneontology.org/page/go-annotation-standard-operating-procedures#paper
• A guide to best practices for Gene Ontology (GO) manual annotation.
• Look at GO handbook
• Create soft rule for Golgi + secretory pathway

GOC Meeting, Corvallis, Oregon

• GOC Meeting Agenda - Ontology-Related Issues
  • http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
  • Add discussion point as needed

• • Moni mentions someone (who?) asked for a general introduction about GO/Noctua prior to the Noctua WS

Moving design patterns to the GO repository

Chris updating ticket

Ontology Tickets

• How to handle missing taxa? see [1]
  • Chris gave a short tutorial (Pascale: tried to capture some of it, but this is by no means accurate)

Go to the directory in terminal:

• • src/ontology
  • git pull
  • ncbitaxon
  • edit to add needed taxon
  • git (etc) -import
  • downloads the entire NCBI taxonomy, and adds the new term

• Transport questions [2]
  • David OS agrees that it's better to avoid 'import/export instead of transmembrane transport

• Taxon import incomplete see [3]

• Removal of redundant class assertions [4]: Pascale would like to know how that impacts the assertions that we should make when creating/modifying terms
• Chris will generate a GO inference report

Jenkin reports

Tanya is asking whether she needs to look at the Jenkin reports [go-ontology] Build failed in Jenkins: go-termgenie-check #1885[go-ontology] Build failed in Jenkins: sync-go-editors-from-github #9345 -> No

Minutes

• On call:

Pascale, Chris, Eric, Harold, Jim, Karen, Moni, Suzi, Paul, David OS, Tanya

Editors Rota

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