Difference between revisions of "Ontology meeting 2014-09-04"

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


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

Revision as of 05:35, 4 September 2014

Attendees:

Minutes:

Trello Items

SF jamboree report

Nearly ready. Complete and send.

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

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.

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".

Also see https://www.ebi.ac.uk/panda/jira/browse/GO-307

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/

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 negative regulation of the force of heart contraction (could this have a pos_reg relationship to the above term, tho?)

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...")