Ontology meeting 2014-08-21

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Attendees: Paola, David, Harold, Tanya, Heiko, Chris, Judy

Minutes: Paola

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."

AI: Heiko will make the commit message visible in the commit email that submitters receive upon acceptance/obsoletion of TG terms.

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.

AI: Heiko will make templates for these two. Paola will open Jira tickets and assign to Heiko.

For extrinsic/integral/intrinsic components of membrane? https://sourceforge.net/p/geneontology/ontology-requests/11084/ and email thread "[go-ontology] Template/pattern for membrane part terms". Chris suggests discussing this again today: https://www.ebi.ac.uk/panda/jira/browse/GO-307

AI: Punt this to 2 weeks from now when David OS is here. In the meantime, Paola will add Marc's terms by hand (cloning sibling terms in OE).

(Related) Transport terms

Where are we with this? As discussed at SF jamboree: 1) display existing transport templates in a more user-friendly way (Tanya will show Heiko the outline we were thinking about); 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.

AI: Tanya will discuss with Heiko on Monday. For the additional templates, punt to 2 weeks from now when David OS is back.

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)."

AI: Let's go ahead and use the template. TG gatekeepers may add the part_of links manually for the time being, if desired; this will be fixed eventually. Paola will advertise the template.

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

AI: Chris will add the RNA subtypes to the ontology for use with metabolism, catabolism, binding terms. UPDATE: Chris writes: SO logical defs now in ontology. Imports etc should be all set up. Needs work in that SO and CHEBI don't 'join up', but this can wait til SMO

TG paper

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

AI: Heiko needs more feedback, so all of us please look at it again asap.

Review of Jira tickets (bumped from last week)

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

Now got as far as GO-247 included.

AI: David OS and Jane may want to take a look at their tickets comprised between GO-198 and GO-247.

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