Ontology meeting 2015-09-17

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Attendees: Chris, Paola, Harold, David x2, Tanya, Heiko

Minutes: Melanie

Progress report

All: send ontology items to DavidH for progress report All (managers) check google doc

Follow-up: creating TermGenie templates with UBERON

(For reference: https://www.ebi.ac.uk/panda/jira/browse/GO-168 and sub-tasks)

Becky asked recently about the morphogenesis template. Chris/Heiko, could you please update us on where we are wrt the partonomy issue.

Minutes: Templates not released yet. AI: Right now, decision to go ahead and release them even though they're incomplete (e.g. part_of inference). Editors will add relations manually (part of for anatomy) Next step: Use of EMR to materialise GCIs (EMR = entity materialising reasoners which adds part of axioms for ex. It is its own github project but also part of OwlTools) -> editors wouldn't need to add missing relations manually. This needs to be implemented, tested etc.

http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/experimental/part-inference/ https://github.com/owlcollab/expression-materializing-reasoner

SOP for adding curators' initials

Up until now, when a new curator joined the GOC and needed his/her initials added, we'd add them in the GO.curator_dbxref file (e.g. GOC:pr). At the GOC meeting, Chris told us about the new users file in GitHub. Should we start editing that file instead? (And where does it live again please?)

Update - discussed here: http://jira.geneontology.org/browse/GO-952. Summary:

Protocol 1 [for editors]:

go to https://github.com/geneontology/go-site/blob/master/metadata/users.yaml

click the edit button which takes you to https://github.com/geneontology/go-site/edit/master/metadata/users.yaml

Make edits. Commit. You may be asked to make a branch. Then click the green button to make a pull request (this is the same protocol for making edits to obo foundry metadata, there is better docs for this here, see http://obofoundry.github.io/faq/how-do-i-edit-metadata.html it's essentially the same idea for GO)

Protocol 2 [for non-editors]:

File a ticket here for someone to do this for you https://github.com/geneontology/go-site/issues

QUESTION FOR CHRIS: Should we stop editing the GO.curator_dbxref file then?

Minutes: YES - this is now officially deprecated


Should we all start using it? Comments on testing?

Minutes: Protege 4: breaks imports over https (i.e, github). Strong reason to switch to Protege 5. Some P5 feedback: press escape to escape the search window. Speed = slow at least for some.Seems faster if you turn out the reasoner and re run it manually. David OS does everything in P5. DavidH finds it slower and uses P4. Chris M uses P5. Tanya has P5 but edits in OBO edit. P5 doesn't do conversion to OBO yet.

AI: all to comment on ticket at https://github.com/protegeproject/protege/issues/151#issuecomment-129502781 to draw attention to it. AI: all to stop using P4 and switch to P5

JBMS ontology issue

Work we could submit?

Minutes: DavidOS: creating slims (roche, ask) Paola: Giardia project: added 40 terms to describe sub cellular components, though no annotation effort. Maybe paper general update on cellular component branch, including vesicle bit. Or keep vesicle separated and try to do annotation (though not for this paper). Paola waiting to hear back from collaborators on Giardia as to whether they will have annotation resource.

Review of Jira tickets

Minutes: DavidH: should we move things under github? ChrisM: yes, plan was to close JIRA. https://github.com/grena/jira-to-github

AI: DavidH will bring this up at managers call. Proposal is for everybody to summarise their tickets and move to github.

Please go through JIRA issues in advance of meeting. We will aim to devote about 20' of the call to discuss Jira tickets.