Ontology meeting 2012-01-11

Brief communications

In preparation for the Protege workshop in Hinxton

• Do we need to have a call with all participants before then? We already have a call planned for Thu. Jan. 19th to discuss Paul T's proposal. Otherwise, we can all refer to the Protege workshop wiki for the list of tools we need to have up and running on our laptops.

New TG

• We agreed that the GO Editors could take turns in acting as gatekeepers for the new Termgenie, to check terms submitted by curators and by other editors.

Here's a proposal for a rota, that tries to take into account SF triage and GO-help rotas as well as traveling to the Hinxton workshop. Feel free to edit if you're not happy with the schedule:

Week beginning Jan. 9th: Becky

Week beginning Jan. 16th: David

Week beginning Jan. 23rd: Paola

Week beginning Jan. 30th: Jane

Week beginning Feb. 6th: Tanya

• FYI, we've submitted a request in the TG tracker for a template to create chemical-binding terms.

http://code.google.com/p/termgenie/issues/detail?id=16&q=label%3AType-Defect

• New TG template for regulation of MF & BP:

A minor point: synonyms for "positive regulation" include "up regulation", but not "up-regulation" nor "upregulation". Same for negative regulation, where the new TG provides only "down regulation" but not "down-regulation" nor "downregulation". This should be fine, because if a user searched GO with "upregulation/up-regulation of ..." he/she should still be able to find the relevant term, and there would be less clutter in the ontology, but just to double-check.

Discussion notes

Discussion notes I: regulation_of by regulation_of terms

• It seems that we still need a long-term solution for terms such as the following:

https://mailman.stanford.edu/pipermail/go-ontology/2011-December/002052.html

This also relates to many SF requests we have, e.g. "negative regulation of cellular hyperosmotic salinity response by negative regulation of transcription from RNA Polymerase II promoter". These unresolved requests may be retrieved by the following link (which also includes "in response to" terms that are in the agenda for the following call):

https://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=440764&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=diannafisk&keyword=&artifact_id=&submit=Filter&mass_category=&mass_priority=&mass_resolution=&mass_assignee=&mass_artgroup=&mass_status=&mass_cannedresponse=&_visit_cookie=6bc221a73edb707c2244b67272dcc757

We also have this type of request:

https://sourceforge.net/tracker/?func=detail&aid=3206709&group_id=36855&atid=440764

We need to agree on a strategy to deal with these. Then, we'd need the relevant templates in the new TG please.

Proposed Solution (Chris)

It's imperative that we capture the essential asymmetry of these terms. An intersection of two regulation terms doesn't work (see the recent problem re phos/kinase activity)

Solution 1 : introduce a sub-relation of regulates to mark out one partner

Solution 2 : make the definition of the form

"regulation of X via Y" EquivalentTo Y and 'has part' some "regulation of X"

(same for neg/pos)

If we also include axioms

has_part o regulates -> regulates has_part o negatively_regulates -> negatively_regulates has_part o positively_regulates -> positively_regulates

Then we end up with the desired(?) inferences, i.e.

"regulation of X via Y" SubClassOf "regulation of X" "regulation of X via Y" SubClassOf Y

This requires "regulation of X" to be pre-composed (TG doesn't yet handle nested expression but it will in the future)

 regulation of X by Y
 ==>
 regulation and (regulates some X) and (regulates some Y)

Discussion notes II: "involved_in" versus "during"

• Stemming from this SF discussion:

https://sourceforge.net/tracker/?func=detail&aid=3390682&group_id=36855&atid=440764

We also have this request:

https://sourceforge.net/tracker/?func=detail&aid=3386148&group_id=36855&atid=440764