Ontology meeting 2014-05-29

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Attendees: Paola, DavidH, Harold, Heiko, PaulT, DavidOS, Becky, Chris

Minutes: Tanya

MF overhaul - how to proceed?

  • Is Paul's doc sufficient prioritisation or do we need more?
  Top priority: implement the new/revised classes and subclasses: function regulator, molecular transducer, and molecular sensor.
  • David proposed that we use WebProtege to work on this as a collaborative work
 Use WebProtege to create alpha version that everyone can comment on and edit and at the end of the day produce a version.
 Chris worried about intertwining WebProtege testing and MF overhaul.
 OK, do as a test. DavidOS will start this.

- Change tracking and comment functions could be very useful - Gives us experience of web Protege, helping us judge what might be needed to move to using it as part of the GO pipeline.

Bumped from last week

http://wiki.geneontology.org/index.php/Ontology_meeting_2014-05-22

CHEBI

  Bumped to next week again as Jane is away.

(Stemming from the 'secondary metabolite' merge issue) Jane to report from the CHEBI workshop.

Monthly review of Jira tickets

  https://www.ebi.ac.uk/panda/jira/browse/GO-232
  We need to think about SF items focused on transport, localization, and targeting.
  Establishment of localization does not necessarily involve transport.  This is already in the ontology.
  DavidH: How do targeting terms relate to localization/location? Different parts of the ontology have 
  DavidH will read through definitions of higher level terms and evaluate distinction between targeting, transport, localization, location.
  Chris: Is_a hierarchy rather than partonomy?
  DavidOS: Yes.
  DavidOS: Agent discussion.  Agency clause in definitions {via the action of some agent}.  Is it necessary?
  Chris: Isn't the gene product annotated with this term the agent?
  DavidH: agent is in there to differentiate it from free diffusion.  transport = active AND passive transport, not just active transport, 
  also transport along actin cytoskeleton and axon exist.
  ACTION:  go with conservative approach, document problems, property hierarchy reflects current structure, gives us a simple way to 
  formalize this branch
  2007 Transporters Meeting Docs collects meeting minutes and notes from the series of Transporter/Transport related meetings
  that took place Feb-Oct 2007.

Making multi-organism annotation a reality

https://www.ebi.ac.uk/panda/jira/browse/GO-300

  Separate meeting with DavidOS, Chris, and Paul will handle some of this.  
  Discussion on rest tabled.

Recording work on SF tickets

A proposal is to standardize svn commit messages using SF tickets headers plus edits done, e.g. (hypothetical)

  For closing SF items, this is the suggested standard:
  SF10883 demethylase binding - closed
  For other SF related work:
  SF10883 demethylase binding - work in progress, (+ very brief edit description)

Where's a good place to record this (or other proposal) as doc?

  Tanya will add to Editors Guide.
  Brief discussion on moving away from SF and to something else (github?) followed.  Some pros and cons discussed.  No action.

Viewing explanations in Protege

Do a run-through if needed - not needed

  Paola still has tiny issue with getting no diff with Protégé saved file.
  DavidOS will try to help Harold with his Protégé problems.

Prefixing 'obsolete' to all obsolete classes

Done?

  Not discussed.

Protein metabolic process (PMP)

What should go under it and what shouldn't

  DavidH: PMP has subclass = protein modification, PMP is too broad
  PMP definition – does protein include bound cofactors, if not included then link has to go
  DavidH will tweak definition of PMP for review next week.
  More discussion on Paul’s point next week – more specific and detailed grouping terms for metabolism.
  Metabolism = union of biosynthesis and catabolism as the future.

Change relation for metabolism terms

https://sourceforge.net/p/geneontology/ontology-requests/10881/

  Not discussed.

Links to annotation guidance

  Not discussed.

For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2014-05-08#Links_to_annotation_guidance

Chris added 'curator guidance link' RO_0002484.

To discuss today:

- how should we record the propagation rule (I,P,R) - axiom annotation

- using axioms rather than regexps

- consistent location of docs: go wiki, drupal, or go nuts?