Difference between revisions of "2017 Berkeley GO Editors Workshop II"

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=== Afternoon ===
=== Afternoon ===
Topics: Design Patterns, Tooling
* [https://github.com/geneontology/go-ontology/issues/13692 TermGenie Replacement]
* [https://github.com/geneontology/go-ontology/issues/13692 TermGenie Replacement]

Revision as of 16:40, 10 August 2017

Party! (or at least dinner together)

  • Where: 2 Biehs Court, Oakland, CA 94618
  • When: Wednesday, August 16 (whenever the meeting closes down and you get over there)
  • Ideas for what you'd like to eat? And drink?

Agenda (Draft)

Tuesday 15th



Topics: Design Patterns, Tooling

  • TermGenie Replacement
    • Plan Overview (Chris)
    • yaml design pattern overview (Nicole V, David OS)
    • INCAForm demo (Nicole V)
  • Exercises
    • Add a new term in INCAForm
    • Make a new design pattern
  • Discussion
    • Reusing templates in Noctua
    • Getting stricter about accepting compositional terms

Wednesday 16th



Thursday 17th





  • Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:
    • Equivalent Class, SubClass; Relations: Characteristics, disjoints, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.
  • Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)
  • The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)


  • Design pattern infrastructure
  • Pipelines and how they run, both imports and file output. Starting jobs with ROBOT.
  • Build failures
    • Document the various fail messages and how to correct the issues.
  • Ontology work for GO-CAM
    • QC-checking property chains and relations that will be used for GPAD generation
    • Removing the part_of o regulates chains--- Do we want to instantiate all of the current inferences before removal?
    • How will design patterns be implemented in Noctua?
      • What design patterns should have priority for Noctua?
        • Goals for signaling workshop?


  • Problematic GitHub tickets/mini Projects, backlog
  • Update on status of Molecular Function re-factor
  • Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.
  • Review all documentation of SOPs for ontology editors.



Getting there:

Taxis also available from either MacArthur or Ashby


Visitor parking is available, see:

Meeting Location

Berkeley Lab, Aquatic Park Offices

Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley Physical address: 717 Potter Street, Berkeley, CA 94710

Meeting room: room 181

Travel between hotel and meeting

Aim to be at the lab for 9am


Name Organization Comments
David Hill Jackson Laboratory
Harold Drabkin Jackson Laboratory
Kimberly Van Auken Caltech Arriving SFO Monday, 8/14, 5:03PM
Pascale Gaudet SIB Swiss Institute of Bioinformatics
David Osumi-Sutherland EBI
Karen Christie Jackson Laboratory
Tanya Berardini TAIR/Phoenix
Huaiyu Mi USC
Nicole Vasilevsky OHSU
Matt Horridge Stanford possible


  • Chris Mungall
  • Eric Douglass
  • Monica Munoz-Torres
  • Seth Carbon
  • Suzi Lewis