Ontology meeting 2014-09-04

Attendees:

Minutes:

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

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

We 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.