Ontology meeting 2014-08-14

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Attendees: Harold, DavidH, Chris, Heiko, Tanya, Paola, Nikolai, Judy, DavidOS, Becky

Minutes: Tanya

Presentation about modeling carbohydrate metabolism and its regulation.

Nikolai Renedo (MGI summer student from Tufts) DavidH has edits and files.

Single- vs. multi-organism parentage

Stemming from discussion at the SF jamboree. Becky will join us to clarify some points.

  Example: x signaling pathway in response to virus: is this single organism process (SOP) or multi-organism process (MOP)?
  Determine the perspective: which organism is an agent in the process?
  DavidOS found a bunch of SOP with MOP parts, MOPs with SOP parts are ok
  Evaluate these case by case, some may need to move up to be SOP/MOP-agnostic
  AI: move signal transduction to directly under biological process - will fix the signaling pathway terms
  DavidOS will write up the rules, put where?  Within def of MOP and SOP.  Defs will be improved.

END OF MEETING, PUNT ALL BELOW TO NEXT WEEK

TG internal commit messages & communications with submitters

See email thread "[go-ontology] Fwd: Re: [go-termgenie-help] Your requested term has been obsoleted in the ontology."

New TG templates?

For '[cellular component] binding', e.g. 'exon-exon junction complex binding', 'U2 snRNP binding';

For '[cellular component] organization', now that Chris has added missing logical defs.

Follow-up: TG template uberon metazoan development

Copying over from last week - where are we now?

"Ready for testing, see https://www.ebi.ac.uk/panda/jira/browse/GO-169

Will only infer over is_a, not part_of. Do we really want to add if all the inferences aren't going to be there? Current proposal is to allow it through and then have the gatekeeper add the additional relations based on the anatomy part_of structure. We will need to prepare a standard operating procedure for this (David H and David OS)."

SO (bumped from last week)

Should we use SO and switch later or wait for MSO?

Matt's response:

As for GO's needs, it should be straightforward to use the SO classes for now and automatically replace the 
URIs when the MSO is ready . . .  because the plan is for MSO class IDs to have the same numerical component 
as their SO counterparts, but the leading prefix will be "MSO_" instead of "SO_".  For example, the ID of 
MSO 'gene' will be MSO_0000704 instead of  SO_0000704. Should make swapping them out easy.

See also:

http://wiki.geneontology.org/index.php/XP:biological_process_xp_sequence_molecule


TG Paper

Heiko has shared Google Doc. "The submission final final deadline is end of August."

Review of Jira tickets (bumped from last week)

Last time we got as far as GO-198 included.