Ontology meeting 2014-10-02

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Attendees: Paola, Heiko, David H, Harold, Chris, Paul T, Tanya, Jane, David OS

Minutes: Paola


GOC meeting in Barcelona

AI: All look at agenda. If your name is next to a topic, write down an approximate time needed for discussion.

Dealing with SF

Just a reminder that we wrote on the report:

"We will continue using the 'mini-project' category to mark ontology requests that can’t be dealt with in a short amount of time. We will revisit such pending requests globally and periodically, and evaluate the need to hold similar meetings again. We might try to do such a review before the next GOC meeting (to be held in Barcelona in mid-October 2014) so that, if necessary, the team might set aside some time for discussion during said meeting."

We are back to a backlog of ~350 open tickets. Though this time it may be more a matter of all of us taking time for SF rather than needing to discuss many tickets with the other editors - or not? There are 20 open 'mini-projects', and 7 open 'jamboree' tickets. How do we feel about resources - how realistically will we manage to keep the numbers down? Or shall we (and the submitters) have to live with backlog and waits? Do we wish/need to plan for another jamboree soon, and if yes, would a bit of travel money be available for that?

Maybe take at least an hour to discuss strategies in Barcelona. Put it in the agenda?

David H discussed with Judy. The current way we're doing it is unsustainable, so it's already on the agenda for Barcelona.

Hermit issues in Jenkins

We'll switch back to Elk while we wait for David OS to discuss these with others at OWLED.

Follow-up on 'transport'

See action items here - where are we? http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-11#Transport_terms_.28carried_over_from_last_week.29

Tanya and Heiko put in new ordering in TG. AI: all look at and comment. It's in the treeview, not in the list.

Follow-up on accumulation of inferred links

At the previous call we agreed to try this:

"We will run it manually the first couple of times just to make sure that everyone is happy with it. Then it will become part of the pipeline. A is_a B, B, is_a C, A is_a C, where A is_a C isInferred, then remove A is_a C"

Further email discussion followed and we ended up with

"We should only remove redundant links A is_a Z where there is a path A is_a B is_a C … is_a Z of length at least two links. This is guaranteed safe."

Are we all good with this, or do we still have doubts? Shall we go ahead and try a dry run?

DOS: My understanding is that we agreed to only strip redundant classifications (is_a) when they are flagged as inferred.

redundant = two or more is_a links. we'll do a dry run, and check what comes out.

Follow-up on inferences & Jenkins

From the last call:

"See email thread [go-ontology] build-go-assert-inferences - Build # 92 - Failure!

It is possible to to manually trigger the assert inferences job. Chris showed how to look at the report in Jenkins. Action item: All of us get permission to trigger the build and then to look at the report if we are doing a lot of work. This way we can preemptively check for errors before the next Tuesday."

Do we all have permission to trigger the build now, and how do we do it?

 There are now two options:

* Preview report via e-mail on Thursday evening/Friday morning, see here for the corresponding Jenkins job:
  http://build.berkeleybop.org/job/build-go-assert-inferences-preview/
* General preview triggered after each build:
  http://build.berkeleybop.org/job/build-go-assert-inferences-report/

With this pipeline implemented, we won't need to all have permission, but David OS might use it. You'd need to have an account on Jenkins. AI: email Heiko our Jenkins login names if we wish.

Follow-up on negatively_regulates o part_of/positively_regulates o part_of

(Need them for SF 11166)

Chris made a correction. The new diff is attached to his email with subject 'reasoner diff before and after' and dated Sept. 25th. The list is quite long - did anyone get a chance to review it?

We also need to think of this in the context of the call on monday. See: http://go-genkisugi.rhcloud.com/seed/model/gomodel:542732ad0000005 Would NOS inhibitor activity classify under the negative regulation term here? Because that is implied by the classic GAF annotation

AI: Let's give it another week and look at at least sections of it... we will all look at random sections of it and comment/decide at next week's call. If we haven't had time, we'll go ahead all the same.

Discussion on direct/indirect regulation. AI: Some of us will look at examples and figure out suggestions. David H will submit Nikolai's work as an RO ticket, and will check his presentation/slides into svn.

MF refactoring follow-up

Comments at the end of this doc: https://docs.google.com/document/d/1y-6to0vwEJHc3i3wdPnJoCAq910auPQp5jBvafpJvL0/edit#heading=h.x7xjmjjghqb5

We'll discuss this in Barcelona as a smaller group.

TG template for 'cell migration'

What is the most appropriate relation to use? See email thread '[go-ontology] cell migration templates'

Bump to TOP of agenda for next week.

GO into NCIt

Bump to second item for next week.

Monthly review of Jira tickets

Bump to first meeting after Barcelona.