Workshop OBI Vancouver 2008 Jan Agenda

=OBI Workshop - Agenda=

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Monday 28/01
8:30 am  - Pickup OBIers lobby Holiday Inn


 * Presentation of use cases.
 * Format: 10 min presentation, 20 min discussion

Morning: 8.45-12
8.45-9.15: Introduction (Ryan)


 * Wireless: BCCRC_Guest
 * Password: welcome2bccrc


 * Coffee shop on first floor


 * Washroom directly outside meeting room (left, female; right, male)


 * Catered lunch (today pizza?) by contribution to kitty (probably ~$10)


 * Dinner @ 6:30


 * Kindly limit multiple ongoing discussions

9.15-9.45: CENTRA CALL (or by teleconference, see remote attendance section for details)


 * What are the objectives of the workshop?
 * Ensure OBI, when complete, can address the requirements of the participating communities
 * Develop list of requirements for OBI/tools to fulfill
 * Ensure branch development (and thus initial release of OBI) can be completed in a timely manner
 * Develop list of issues that need to be resolved for branch development to finish, and where possible propose solutions
 * Develop realistic roadmap for completion with milestones and responsibilities
 * Develop general policies for OBI development to address administrative issues
 * Have fun

9.45-10.15: Roles (Jennifer)

10.15-10.30:break

10.30-11.00: Richard: use case related to infectious disease research

11.00-11.30: Relations (Liju)

11.30-12.00: Protocol application (Bjoern)

Afternoon: 13.15-17
13.15-13.45: Biomaterial (Susanna)

13.45-14.45: Instrument (Melanie) and Data transformation (James) - joint use case describing a flow cytometry experiment

14.45-15.00: break

15.00-15.30: DENRIE (Alan) - data exchange related to a flow cytometry experiment

15.30-16.00: Plan branch (Philippe)

16.00-16.30: Rakhi Bhat (from Lilly) will present her work via teleconference.

16.30-17.00: Outcome: list of requirements for OBI/tools to fulfill

18:30 Tojo's - Reservations for 13 under Ryan. 1133 West Broadway. Walk 6 blocks west or take #9 bus from in front of Holiday Inn running every 5 minutes.

Morning: 9-12
Branch review Each branch will be allocated one hour for discussion. If some time remains at the end of these 2 days we can come back on some of them. Format: 10 min presentation, 50 min discussion

9-10PST: CENTRA CALL


 * Skype available seems to work for free-to-listen - message susanna


 * Moderation - self-moderate your slot. Will cutoff discussion at 59 minutes, leaving time to recognize contribution of others.

OBI Completion Milestones

1) OBI "Working" Release - Have OBI at a stage we are ready to have people use requires: 2) Manuscript requires (1) and: 3) OBO Foundry release
 * Curation_status curation_complete OK (TBD) on all terms - March 1
 * Individual review of OBI
 * Term;problem;solution submitted March 15
 * Problems without suggestions reviewed by group, then advisors
 * Use cases worked out through OBI to demonstrate "it works"
 * Deprecation policy (and other OBO Foundry requirements http://obofoundry.org/crit.shtml)
 * Documentation on how to use
 * Authorship plan
 * Some text


 * Lunch - $10 to kitty - headcount
 * Dinner - banana leaf (Malaysian, across from Holiday Inn; 50% off last night's dinner) - headcount


 * Wednesday - cypress mountain - leave at 4 from BCCRC (bring your gear). Will order take away - headcount (snow 7 food). Reservations for others (Cactus Club?)

10-11: Plan branch (Philippe)

11-12: Qualities (Melanie + all)


 * discussion with PATO
 * term collection

Afternoon: 13-17
13-14: Function (Bill)

14-15: Role (Jennifer)

15-16: Relations (Liju)


 * ambiguity of usage between roles and qualities (RS): maybe grouping roles/relations and function/qualities together for a discussion?


 * definition of a role: currently processes can't be bearer of roles. A role is not context dependent as pointed out by Alan, it is more related to "socially sanctioned". The general notion of role has to be clarified, for a lot of people function is something inherent to the object you consider (e.g. heart is pumping blood) whereas a role is something context dependent (e.g. protein plays a reagent role in this experiment). This should be explained by Barry and Alan in more details.


 * instrument: what is the function and what is the role


 * redundancy between relation and roles?

16-17: Protocol application (Bjoern)


 * protocol_application: natural process: how to represent, how to link to GO. Induction of natural process - a protocol application in which some natural process (usually defined by GO) is set off.

Outcome: summary of issues / status

Morning: 8:30-12
Continue branch reviews

8:30-10PST: CENTRA CALL

Barry Smith takes the floor...

10-11: Instrument (Melanie)

11-12: Protocol application (Bjoern)

Afternoon: 12-16
13-14: DENRIE (Alan)


 * biomaterial: states: in vivo, in vitro, pre and post mortem....currently "states" are under "to_be_fixed"


 * biomaterial as a branch name: how do we define it, how do we differentiate between biomaterial and artefact object


 * instrument and biomaterial: how to deal with commercial terms

14-15: Biomaterial (Melanie)

15-16: End of the day: discussion about remaining issues (e.g. update from EnvO: what goes there? See slides from Norman Morrison)

Outcome: issues solved and identification of remaining issues


 * End of meeting at 4pm, then snow trip to Cypress mountain: https://wiki.cbil.upenn.edu/obiwiki/index.php/January2008Workshop#Snow

Thursday 31/01
Parallel or Plenary sessions (to be determined by group vote)

Morning: 9-12
9-10PST: CENTRA CALL

Depending on progress during the previous days, we'll choose to have a plenary session or not on Tuesday morning.

Session 1 - General policies - Dorothy Lam Boardroom, ground floor.

How do we resolve difficult development decisions (e.g. long discussion on analyte) How do we keep track of these decisions?

Engineering methodology, from the motivations (why are we here what is the problem(s) we are trying to address).

Discussion on where there are multiple branch implications e.g. algorithms and their application. Where to build, how to ensure consistency

Other concerns raised by members: - formalize "why do we try and avoid multiple inheritance?"

- Some methods are using the hierarchy in an ontology to compute annotation-based similarity measures. What happens for these if we choose to use roles, which tends to "flatten" the hierarchy?

- discussion on analyte, stimulus

- From Daniel Schober: proposal to prefix helper classes with underscore

Session 2 - OWL technicalities - 14th floor conference meeting room

Ontology mapping: how do we import other ontologies in OBI cf https://wiki.cbil.upenn.edu/obiwiki/index.php/OntologyImports

Representing mappings to other ontologies in OBI. DT will map to MO terms by the workshop and they want discuss representation of that in OBI

How do we deal with time?

Discussion of polysemy and ways to solve that, DT have examples

Afternoon: 12-16

 * Road map to release: branch dissolution? -> Single OBI file? -> Evaluation? -> Iterate?
 * Deprecation policy and other implications if public release.

Outcome: issues solved, with a practical example when applicable - roadmap for release process

Morning: 9-12
9-10PST: CENTRA CALL -

Grants opportunities discussion

OBI implementations

=List of attendees=

"physical" attendees

 * Ryan Brinkman
 * William Bug
 * Melanie Courtot
 * Liju Fan
 * Jason Greenbaum
 * James Malone
 * Helen Parkinson
 * Bjoern Peters
 * Philippe Rocca-Serra
 * Alan Ruttenberg
 * Susanna Sansone
 * Richard Scheuermann
 * Barry Smith

"remote" attendees

 * Tina Boussard
 * Jennifer Fostel
 * Gilberto Fragoso
 * Allyson Lister
 * Monnie McGee
 * Elisabetta Manduchi
 * Daniel Rubin
 * Daniel Schober
 * Chris Stoeckert

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