Workshop OBI Cambridge 2009

Logistics

• Back to back with 2nd OBO 2nd OBO Foundry workshop.
• Location: IT Training Room, EBI, Cambridge, UK,
• Dates: June 9-12, 2009 (OBO Foundry 7-8)
• Alan notes US East-coast travel ->Dublin then Ryanair to STN may be most cost effective
• Registration closed
• Minutes from meeting

Meeting Bus Timetable and Rooms

Sun 7th June
08:15 – BUS Cambridge Travelodge to EBI
Meeting room: IT Training room (A2-111)(report to EBI security gate to get visitor badges; Philippe/Susanna will pick you up from there)
Refer to 2nd OBO Foundry workshop agenda.
18:30 DRINKS and DINNER on site at the Wellcome Trust Conference Centre Restaurant
21:30 – BUS EBI to Travelodge

Mon 8th June
 08:15 – BUS Cambridge Travelodge to EBI
 Meeting room: IT Training room (A2-111)(go to the room via the EBI reception entrance)
Refer to 2nd OBO Foundry workshop agenda.
18:30 - BUS to sponsored dinner location Cotto Restaurant, Cambridge 
22:00 – BUS from restaurant to Travelodge

Tue 9th June
08:00 – BUS Cambridge Travelodge to EBI
Meeting room: A2-33 (report to EBI reception and wait there from somebody - possibly James- to bring you in the room)
18:30 – BUS EBI to Travelodge
DINNER on your own list of restaurant around the Travelodge, or other restaurants in Cambridge 
(maybe James can help booking a table for everybody in one place).

Wed 10th June
07:50 – BUS Cambridge Travelodge to EBI
Meeting room: A2-33 (report to EBI reception and wait there from somebody - Philippe/Susanna- to bring you in the room)
18:00 – BUS EBI to Travelodge
DINNER on your own list of restaurant around the Travelodge, or other restaurants in Cambridge 
(Philippe/Susanna can help booking a table for everybody in one place).

Thur 11th June
08:00 – BUS Cambridge Travelodge to EBI
Meeting room: Courtyard Room (report to EBI reception and wait there from somebody - Philippe/Susanna- to bring you in the room)
17:30 – BUS EBI to Travelodge
DINNER on your own list of restaurant around the Travelodge, or other restaurants in Cambridge 
(Philippe/Susanna can help booking a table for everybody in one place).

Frid 12th June
08:15 - BUS Cambridge Travelodge to EBI
Meeting room: Courtyard Room (report to EBI reception and wait there from somebody - Philippe/Susanna- to bring you in the room)
Individual or group taxis will be organized to return back to Travelodge, or train station or airports.

Proposed Agenda

The tentative list of possible topics brainstormed has been prioritized during the dev call on 5/27 (where only 6 participants attended) and divided for each day.

Tue 9th June (note that on this day a) OBO Foundry Coord, Philippe and Susanna will not attend; b) Jie only arrives in the afternoon, ref to MGED terms; c) Norman will only attend this day, ref EnvO)

• 9:00-9:30 Sort agenda
• Collaboration with Envo with Norman
• Review of use cases in OBI manucripts
  • Can we complete them all presently, what needs to be done?
• Sample/specimen from Biomaterial

Wed 10th June

• Brief reciprocal update on day 1 and OBO Foundry/Industry discussions
• Continue manuscript work
• BFO discussion (need Barry for this)
• RO discussion (need Chris Mungall for this)
• Parameters (need James, Alan for this)
• Changing URIs due to OBO foundry discussion
• Is OBI ready for release 1.0? If not what is needed. (we believe when manuscript is complete, do all others?)
• Speeding up OBI reasoning, OBO is quicker than OWL... is that a solution Alan ;)
• Evidence Codes

• Development process (5)
  • There is a clear methodology to apply when building ontologies. In brief, this involves stating the 1)Goals - whats the point? 2)The scope, by defining competency question the ontology should ask. 3)This is followed by an evaluation process to determine if we have been able to answer our questions.
    • What is the goal of OBI?
    • What are the OBI competency questions?
    • How are we evaluating that we have answered the competency questions?
  • Only after this process can we determine if OBI is of any benefit and does what it is mean to do. Only after following a process like this can we have confidence in writing a paper and making the statement, OBI is a contribution to science and deserves a publication.

• OBI release process (6)
  • Hasn't happened for a while. How do we address this going forward.
  • Recruit a new member to the release team

• Where are we now and what can we presently do with OBI (specifically what use cases do we now fulfill)? (6)

• Use cases and first release (6)
  • How are we evaluating that a use case is solved?
  • How are we evaluating our competency questions, what are our competency questions? If we have no evaluation process how do we know we have completed a case-study and can present a use-case and the ontology is of scientific importance in order to publish a paper on it?

Thur 11th June

• Jie report on checking that MGED terms are in OBI or other OBO foundry ontologies
• Addressing review from OBO Foundry
• Splitting into smaller focus groups to resolve issues: (6)
  • Addressing the OBI development process, case-study, model case-study, evaluate model, present use-case
  • Addressing the movement of all currently asserted roles and functions to be generic realizable entities
  • Split up into groups to address a specific case-study and work through the development process
• Working through individual use cases (5)
  • Gene Pattern Use Case - close to being able to completely represent this now
  • Neuroscience Use Case - Dirk
  • IEDB use case - Bjoern
  • Vaccine Ontology use case - Oliver
• Status and progress per branch (5)

Frid 12th June

• External ontology coordination. Status, issues, actions (6)
  • review of IEDB OWL export/ IEDB-OBI coordination
  • IAO-OBI coordination (partly possible, later to be confirmed with Alan)
  • Status of Vaccine ontology/OBI coordination
  • Status of Immune Epitope ontology/OBI coordination
• Moving quickterms/quickid into production (5)
• Put redirect from old wiki in place and point to new one
• Funding opportunities (5)
• OBI Organizational structure (5)
  • The current separation into community coordinators and editors may have outlived its usefulness. There should be a ~ 1 hour brainstorming session to discuss a revised organizational structure. This should result in a draft document to be further discussed on the coord list.
• Documenting OBI (4)
• OBI distributions (3)
• Using OWL 2 features in OBI (3)
• Working with MIREOT (3)
• Software demos (0)
  • ISACreator demo

Confirmed attendees

• Susanna Sansone
• Philippe Rocca-Serra
• Alan Ruttenberg
• Bjoern Peters
• Frank Gibson
• Larisa Soldatova
• Yongqunh
• Jie Zheng
• Melanie Courtot
• Dirk Derom
• Phil Lord
• Norman Morrison
• Barry Smith
• Richard Scheuermann