Ontology meeting 2014-09-04
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:
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".
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.
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:
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...")