Ontology meeting 2014-09-04

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Attendees:

Minutes:

Trello Items

(The upper level priorities that not all of us can see)

  Worked on aligning these priorities with what we are actually doing.
 1. Agree that we need a meeting to work on implementing AE extensions in noctua
  TODO: DOS to send Doodle poll to set up date for this.
 2. Molecular Function refactoring - Everyone please go through Paul's draft on WebProtege and add comments.
 We will then devote a section of a meeting to going through and prioritising.

SF jamboree report

Paola sent round the final report. Please let her know if any change is needed, then forward.

 DOS still to contribute. Will do so ASAP.

Follow-ups to previous calls

Editors who were on leave during the past couple of weeks, please review the minutes and take note of action items if any:

http://wiki.geneontology.org/index.php/Ontology_meeting_2014-08-21

http://wiki.geneontology.org/index.php/Ontology_meeting_2014-08-28

 Not discussed.  Jane and DOS should look through to find any items that should be added to future editor's meeting agendas for further discussion.

Relations files

Can Chris clarify the content/import structure of the various relations files for us (i.e. RO, gorel, go_annotation_extensions) - there is some confusion about what to consume and edit.

  gorel_edit.owl to become master
  Plan is to import (some slice of?) RO
  -  but will this cause problems for structure unless we can sufficiently restrict how much of RO is imported.
  Hold off on telling Tony to switch until we have tested this

New TG templates for extrinsic/integral/intrinsic components of membrane

For requests like this one: https://sourceforge.net/p/geneontology/ontology-requests/11084/

Discussed in email thread "[go-ontology] Template/pattern for membrane part terms".

 We may be able to automate some classification using new part relations - subProperties of part_of.  
 DOS to build some test patterns to see if we can get all the inference we need.
 All patterns should be written up using Dead simple OWL design patterns: 
 https://github.com/dosumis/dead_simple_owl_design_patterns
 TODO: DOS to make JIRA ticket linking all these together.  Add to this ticket that we will need code to map up to part_of 
 as users will expect to see these part relationships.

Transport terms

As discussed at SF jamboree, we will:

1) display existing transport templates in a more user-friendly way;

2) add more templates, e.g. for 'transmembrane import' and 'transmembrane export'; David OS will specify more templates if needed.

We'll then email the GOC to alert curators that they may request new terms, use specific terms rather than generic ones, and move their existing annotations if they wish/can.

Should 'protein localization to CC membrane' is_a 'protein localization to CC'?

And if yes (+1 from Paola and David H so far), how can we populate the missing links automatically.

See https://sourceforge.net/p/geneontology/ontology-requests/11090/

TODO: DOS to add property chains to RO so that this, and similar, can be inferred.

Regulation of Regulation terms

Revisiting these terms: we (David OS and Becky) tried to model this in Noctua, but kept hitting errors. The paper is PMID:17242280, and the summary is here:

[[1]]

Question: How to best create the 'regulation of regulation' terms: PMCA4 regulates cardiac contractility through modulation of nNOS activity and thereby attenuation of the beta-adrenergic response. One option is:

adrenergic receptor signaling pathway involved in positive regulation of the force of heart contraction
negative regulation of adrenergic receptor signaling pathway involved in negative regulation of the force of heart contraction (could this have a neg_reg relationship to the above term, tho?)
positive regulation of adrenergic receptor signaling pathway involved in positive regulation of the force of heart contraction (could this have a pos_reg relationship to the above term, tho?)
 Discussed but no conclusion reached.

Agenda items for GOC meeting in Barcelona

We should present a brief update on TG. It seems that some curators may not be aware of, or remember, the full array of templates. (As my Latin teacher said: "Repetita iuvant...")