Ontology meeting 2018-09-10: Difference between revisions

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= Agenda =
= Agenda =
== Editors Discussion ==
===Order of Operations for External identifiers===
For CHEBI ids, new ECs, Rhea? Should GO editors or requestors follow up with EC and/or RHEA requests?
For CHEBI ids, new ECs, Rhea? Should GO editors or requestors follow up with EC and/or RHEA requests?


Can we put terms into GO while waiting for ids outside of ontology?
Can we put terms into GO while waiting for ids outside of ontology?


===Project Update===
* RO meeting to take place in Colorado in October


== Editors Discussion ==
===Testing the new version of Protege===
There is a beta version of the new Protege available. We should test it before the official release. What is our plan?
 
===Ticket on another tracker===


===Project Update===
OBI ticket: https://github.com/obi-ontology/obi/issues/963
* RO meeting to take place in Colorado in October


===Ontology Developers' workshop possibility===
===Ontology Developers' workshop===
The meeting will focus on (Depending on who can attend):
The meeting will focus on (Depending on who can attend):
* creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
* creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
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=== Tickets ===
=== Tickets ===
OBI ticket: https://github.com/obi-ontology/obi/issues/963


=== Failures due to use in other ontologies ===
=== Failures due to use in other ontologies ===

Revision as of 10:39, 8 September 2018

Conference Line

Agenda

Editors Discussion

Order of Operations for External identifiers

For CHEBI ids, new ECs, Rhea? Should GO editors or requestors follow up with EC and/or RHEA requests?

Can we put terms into GO while waiting for ids outside of ontology?

Project Update

  • RO meeting to take place in Colorado in October

Testing the new version of Protege

There is a beta version of the new Protege available. We should test it before the official release. What is our plan?

Ticket on another tracker

OBI ticket: https://github.com/obi-ontology/obi/issues/963

Ontology Developers' workshop

The meeting will focus on (Depending on who can attend):

  • creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
    • Filling in missing GO-Rhea xrefs
    • moving from reactions to biochemical pathways
    • implementation of a method to keep in synch with all three resources
    • GO-CAM templates for pathways??
  • potential implementation of Design Patterns and the revival of some type of TermGenie ability
  • GH ticket work and mini-project planning
  • Attendees
    • David H (Can make it)
    • Kimberly (Can make it)
    • Karen
    • Harold (Can make it)
    • Pascale (Can make it)
    • Barbara (Maybe make it)
    • Alan B (Rhea, can make any day)
    • Anne (Rhea, prefers Monday or Tuesday)
    • Chris
    • Peter D?
    • Ben?
    • Jim?

Tickets

Failures due to use in other ontologies

Friday after much discussion, Rachael and I tried to finally obsolete lamina reticularis. When we created the pull request, the Travis check failed due to the use of the term in Uberon. Do we really want this behavior? It will make us dependent on other ontologies to proceed with our work.

https://travis-ci.org/geneontology/go-ontology/builds/425727676?utm_source=github_status&utm_medium=notification https://github.com/geneontology/go-ontology/pull/16345


GH project link

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

Minutes

  • On call:
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