Ontology meeting 2012-06-13

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Minutes: Paola

30-minute call

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

Update on Caltech meeting

Devoted mostly to the development of a common annotation tool. A crucial issue for this is the specification of the LEGO model. At one of the next editors' call, Chris will talk about it in more detail. In summary, we're going to chain together individual functions in the context of specific pathways. What was missing previously was a way to interconnect these. The new model will be based on a nested series of logical definitions. Individual terms can be the building blocks, and annotators can fill in the gaps.

Cardiac conduction

Touching base: Becky is taking care of the signaling part; as for Ruth's questions on SF about terms related to heart rate, at the content meeting we decided not to put those in as linked to cardiac conduction, but rather to keep them as a separate aspect.

Cell cycle ontology review

Val is organizing a meeting with an expert, possibly in July or August. AI: We'll check with Jane about possible dates and if we need to bring David or other people in, and if so where is the funding coming from. Prior to that meeting, we'll need to review pending SF items about cell cycle.

Chebi paper

Chris will report on that next week.

TermGenie paper

Heiko is working on that.

TermGenie synonyms problem with "regulation of" terms

Heiko will fix this. DONE.

OBO-Edit dictionary warnings and SVN

We have 2 options: 1) we share the user.dict file in SVN 2) we bulk-add in advance every possible chemical term in the user-dict Chris suggests we go with 1) for now. Let's start with one user-dict for GO rather than merge all our dicts. AI: Heiko will check with Nomi about dicts. We'll start with loading Becky's or Paola's user.dict file in SVN. Strategy 1) doesn't preclude 2), but let's see how 1) works first AI: Put that on the agenda for the next OE call (that's Tuesday June 19th) [can we follow David OS's suggestions?]

Transcription work

David is and will be in touch with Karen about the open/pending transcription-related SF items.

Apoptosis GO project

Paola will attend an Abcam conference on Apoptosis and Cancer [1].