Workshop OBI 2009 Feb

Contents

The Winter 2009 workshop will be February 2-6, 2009, in Vancouver

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


    • Variables discussion
      • BP/Feb 6 - Add in results of the variables discussion to OBI. DONE (by someone else, in IAO).

2. Tuesday 3rd - 9am to 12am and 1pm to 5pm

  • [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)
  • 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

(1)OBI:Core (don't touch under pain of chastisement unless approved by OBI CC)

(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)
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