Ontology meeting 2018-06-25

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Agenda

Editors Discussion

Project Update

Rhea-Reactome_GO alignment--- https://github.com/geneontology/go-ontology/projects/10

Regenerate Imports File

We continue to have issues with imported files. Although we can modify the import files, this isn't really a solution.

Obsoletion plugin for Protege

Please add you Protege versions and the plugin you have here.

Barbara- Protege 5.2.0
David- Protege 5.1.0
Harold- Protege 5.1.0, OBO annotation plugin 0.4.0
Karen- Protege 5.1.0
Kimberly- Protege 5.1.0

  • I have something called OBO annotation editors 0.3.0 - is that the plugin?

Ontology Documentation

Pascale, David and Kimberly have been working on standardizing the ontology documentation to make it align with the documentation work that Kimberly and Pascal have been doing for other areas of GO. Specifically, we have moved the official documentation to the wiki and have arranged the wiki in a way that is similar to the annotation section. We are now going through the documentation to check it for accuracy and to be sure it is up to date.


Ontology Developers' workshop possibility- Geneva in September?

  • David, Pascale and Kimberly will discuss possible dates and make a doodle poll.

GH project link

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

Minutes

  • On call: Barbara, Ben, Chris, David, Eric, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Pascale

Project Update

Rhea-Reactome_GO alignment--- https://github.com/geneontology/go-ontology/projects/10

  • Ben is updating the xrefs between GO terms and Reactome that currently exist in the ontology
    • The vast majority of these are MFs, but it looks like there are a few to BP and CC
  • Chris: will these be in the go-edit file?
  • Reactome 'maintains' these, but are we importing actually importing anything?
  • The onus will be on GO to sanity check these and maintain them
  • Review of logical definitions for molecular function catalytic activity terms
    • Includes reactants, products, and stoichiometry using the official ChEBI nomenclature derived from the Rhea description of the reaction
    • Rhea actually includes the proposed ionization state of reactants and products based on the pH at which the reaction is believed to occur physiologically
  • Note that the logical definition here is direction neutral (no specific L->R)
  • GO will xref to the Rhea master reaction, which has children of L->R, R->L, and the bidirectional reaction
  • One possible offshoot of this work would be a curation tool that allows curators to enter the inputs and outputs of a reaction as described in a paper, and a list of possibly matching GO MF terms for annotation
  • Classification in GO will be based on reactants and products; but ontology editors will need to perform the classification based on reaction mechanism, e.g. oxidoreductase
    • This isn't quite what we originally had in mind for this project, which was to get as much classification from these logical defs as possible
    • In general, we want to select the most generic term possible, although not as generic as the root term
  • Could EC xrefs still help classify wrt mechanism?
  • What should we do with cases where a Rhea ID is more specific than a ChEBI ID?

Regenerate Imports File

  • We continue to have issues with imported files. Although we can modify the import files, this isn't really a solution.
  • None of the editors are quite certain how these files are generated and how to generate them ourselves.
  • Not comfortable with the procedure or something else?
    • If editors have Docker installed, they could run the appropriate commands to generate the imports
  • This should be high priority for the next f2f meeting
  • In the immediate short term, how do we proceed?
  • Berkeley could do one-on-one tutorials for editors and that would help shore up documentation/instructions

Obsoletion plugin for Protege

  • Curators need to check what they have for OBO Annotations Editor
  • A new version of Protege is coming that should have a plug-in for this (being presented at ICBO)

Ontology Documentation

  • Work will resume

Ontology Developers' workshop possibility- Geneva in September?

  • P, D, and K will discuss later this week