Workshop OBI 2009 Feb

Venue
British Columbia Cancer Research Center (BCCRC) 675 West 10th Avenue Vancouver, BC V5Z 1L3, Canada

For conference calling, call the number 6047074539, using password 777888#.

Agenda

 * Deliverables list:
 * plan for the manuscript in place, and all sections assigned
 * all core Representational Units (RUs) identified, and related issues either resolved or documented, including those involving outside ontologies
 * Quick Terms proposal documented, and working first example
 * Roles for dependent continuants / conferred qualities


 * Vancouver workshop agenda

1. Monday 2nd - 9am to 12am and 1pm to 5pm


 * Policies
 * Namespace (e.g. MSI) - PRS and SAS
 * OBI/Feb 2 - Policy accepted as proposed by PRS&SAS
 * PRS/Feb 2 - Submit slides to OBI documentation in docs folder under svn DONE
 * AR/Feb 9 - Will come up with a way to say “original definition”, change note includes original definition. Dated/editorwill be submitted to OBI Foundry through proposal for IAO metadata
 * AR&PRS/Feb 9 - Will fix the way we do dbxref
 * MC/Feb 9 - Make and edit to Policy document that editors will add date of edit, add imported definition goes in the note when adding new definitions
 * Defined classes: Refine and agree on obi policy regarding prohibited assertions under defined classes: https://wiki.cbil.upenn.edu/obiwiki/index.php/DefinedClasses
 * MC/Feb 9 - Edit to OBI policy page: Nothing is asserted under defined class in released OBI. For development class can do this, but cannot be tagged as “ready for release”. Summary: Nothing that is tagged “ready for release” can be asserted under a defined class.
 * MC/Feb 9 - Add sentence to wiki Things with necessary and sufficient conditions blah blah blah


 * Quick ID - FG and AR (Note this is really ongoing work and not in a suitable state for comment or discussion as yet, rather this is just a heads-up that is exists http://obi-ontology.org/page/Quick_id)
 * FG/TBD - Will condense QuickID doc to a summary page to make appealing once policy is finished
 * Quick term - BP and PRS
 * PRS/Feb 2 - Share slides onto OBI documentation resource in svn under docs folder DONE
 * OBI/Feb 2 - Adopt PRS proposal for a template for analyte measuring assay
 * PRS&PL/March 2 - Data entry form mechanism - Will make spreadsheet or Protege plugin or MediaWiki or GoogleDocs or emailing text file or Protege ppl. Assay is priority for end users & as showcase for manuscript
 * PRS&PL/March 2 - Will write script to process templates
 * ?/? - Need new relation for proxy_for


 * Use cases
 * James Malone (Melanie Courtot)
 * JM/Feb 3 - Share GenePattern use case slides in svn under docs folder
 * JM/Feb 9 - Planned_specification -> Workflow_Specification -> GenePattern_Workflow_Specification (includes specific file formats required for GenePattern) as a defined class
 * Bjoern Peters
 * BP/Feb 3 - Share slides through svn in docs folder DONE
 * Jennifer Fostel
 * JP/Feb 3 - Share slides through svn in docs folder DONE
 * Arrays and Designs - PRS/SAS
 * PRS/Feb 3 - Share slides through svn in docs folder DONE

2. Tuesday 3rd - 9am to 12am and 1pm to 5pm
 * Variables discussion
 * BP/Feb 6 - Add in results of the variables discussion to OBI. DONE (by someone else, in IAO).
 * [lunch] Send tasty selections to rbrinkman@bccrc.ca
 * Eric Deutsch - 30 minutes presentation/discussion: addition of terms from the proteomics/mass spectrometry community
 * ED/Feb4 share slides on OBI svn in docs folder
 * FG&ED&PRS/Feb 4 Do quick term binning - Done: discussed with Eric how to proceed by binning MS terms under basic BFO hierarchy


 * Core RU (branch discussion for branches that don't have core representational units)
 * Role - JF
 * Relations - FG
 * FG/Feb 4 Upload slides with notes taken during workshop to svn/docs - Done
 * DT - JM
 * JM/Feb 4 Upload slides with notes taken during workshop to svn/docs
 * DENRIE - CS
 * AR&BP/Feb 9 - IAO Cage fight


 * Core RU (branch discussion for branches that don't have core terms )
 * Variable/Parameters
 * Biomaterial - MC
 * Instrument -FG
 * FG/Feb 4 Upload slides with notes taken during workshop to svn/docs Done
 * PAPP - Function - BP and PRS
 * AR/Feb 4 Fix action specification
 * BP&JF&MC/Feb 7 - Protocol application goes away and all other suggested changes DONE
 * BP/Feb 4 Upload slides with notes taken during workshop to svn/docs DONE

3. Wednesday 4th - 9am to 4pm (Cypress trip)


 * We are not in Kansas anymore - Room change to Jon Jambor room BCCA (across the street turn right go down long hall and leave breadcrumbs)


 * Core RU continued


 * 11am: phone conference with Barry
 * news on BFO (Barry)
 * Treatment of relations, defined classes, and defined qualities. (Barry/Alan)
 * Roles and qualities of dependent continuants (Barry/Alan)

4. Thursday 5th - 9am to 12am and 1pm to 5pm


 * Manuscript discussion (Bjoern)

(1)OBI:Core (don't touch under pain of chastisement unless approved by OBI CC)
 * Tools and Projects - 30 minutes max for presentation (20 minutes presentation - 10 minutes discussion)
 * NCBO presentation (Trish)
 * Neurocommons hacking / reasoning with OBI session (Alan)
 * OBI release - how to access it and where (MC-AR and discussion with all)
 * How to let people flexibly use OBI -> multiple releases

(2)OBI:Full Everything tagged: ready for release (3)OBI_devel (OBI:Crap) – what is in subversion doesn't get released. Use at your own peril. (4)OBI:Custom - Users can edit #imports and roll their own OBI terms
 * ?/? - Need to avoid all asserted classes making it into release version (from PRS template for Assay proposal
 * VO and OBI (Oliver)
 * Automated Investigations (Larisa)
 * Collaboratice Protege (James)
 * time permitting: protege experimental writer (Alan), OCRe - http://rctbank.ucsf.edu/home/ocre.html

Other possible Agenda items
Please add proposed agenda items below. If you have any specific time constraint please use the dated slots below and add why the constraint.


 * What happens next? The longer term plan for continuing OBI development.
 * OBI classes into IAO and BFO
 * Making the old wiki read-only and moving over to the new wiki
 * define a standard procedure for communities to submit new terms to OBI (I believe this is related to the QuickTerms and QuickID sub-project)
 * What should the community do to facilitate the process?
 * How will OBI incorporate? Who will be responsible?
 * Do we need different processes for asserted vs defined classes?

Participants

 * Ryan Brinkman
 * Melanie Courtot
 * Richard Scheuermann
 * Alan Ruttenberg
 * Bjoern Peters
 * Helen Parkinson
 * James Malone
 * Jennifer Fostel
 * Chris Stoeckert
 * Eric Deutsch
 * Trish Whetzel (2/4 - 2/6)
 * Susanna Sansone
 * Philippe Rocca-Serra
 * Frank Gibson
 * Larisa Soldatova
 * Oliver He
 * Philip Lord

Schedule
A trip to Cypress will be organized on the Wednesday evening, directly after the meeting.

A whole day trip to Whistler (for non skiers another) is planned on the Friday.

Whistler transportation

[Greyhound is the best way to go] You want to travel from Vancouver to Whistler village (or Creekside) You probably want the 6:30 am ride up to get there for when the mountain opens at 8:30 The mountain closes at 3:30, so the 4;30 gets you back downtown at 7

Things to organize

 * Power bars
 * Hotel discount code
 * Cars to Cypress
 * Whistler transportation
 * Dinner reservations (Banana Leaf Malaysian / Cactus Club upper scale pub/ Plaza 500 west coast/ Indian Buffet / All u can eat sushi on Broadway / Memphis Blues BBQ)
 * Lunch catering (kitty? Tracy's food book & delivery)