Workshop OBI 2008 July

OBI workshop - July 7th-11th, EBI, Cambridge, UK
This OBI workshop is hosted by the European Bioinformatics Institute (EBI) and set to bring together the Coordinators and the Core Developers.

This workshop is held back-to-back with the OBO Foundry workshop.

Organizers:
 * Philippe Rocca-Serra
 * Susanna-Assunta Sansone

Logistics
EBI meeting rooms:
 * Wednesday: room C209/10 (Sanger building)
 * Thursday, room A2-33 (EBI building)
 * Friday: room C209/10 (Sanger building)

Travel directions to EBI and (partly) sponsored accommodation:
 * Refer to the OBO Foundry workshop page for information.

Sponsored transportation:
 * The EBI is approximately 20 minutes from central Cambridge by car. Public transport is infrequent and unreliable which is why we shall be providing transportation from/to the accommodation at Homerton College (right outside the entrance, in visitor parking area) and EBI for the entire duration of the OBI workshop. Please, refer to the workshop agenda for the organized transportation times

Sponsored Food:
 * Note that only lunch vouchers will be provided and can be redeemed to the onsite restaurant facilities (Murray's or Dina).

Agenda
 Few topics to be discussed, but do not have place in the agenda
 * Information Artifact Ontology presentation by Alan
 * Vaccine investigation community
 * They have decided to postpone their NIH R01 grant resubmission to Nov 5th. So if the OBI coord group agrees to provide a Letter of Support for our Vaccine Ontology development, they can wait until Oct 08


 * how do we deal with time (e.g. time series analysis) -> Note that the issue might have been addressed during the OBO meeting /BFO session (another BFO related discussion is Can role be born by dependent continuants?
 * Tools to visualize toplevel classes connected through relation (OwlViz, Jambalaya, External tools?, ...): Get a holistic network based view on main OBI-upper level structure: Show how branches 'hub-nodes' protocol, protocol application, device, (function), data transformation, role, biomaterial are related to each other.

Wednesday, July 9th, 2008
8.15 Transport from Homerton College to EBI
 * NOTE: Since on that morning a parallel ChEBI meeting (EBI Hall View Room), attended by ChEBI group plus Michael, Suzi, Alan, Barry and Chris M is taking place, we propose to start the OBI meeting with the following topic

 9.00 - 10.30 Session 1:

' Report/Update on OBO Foundry Meeting: 30 minutes -> cover BFO related discussion relevant to OBI work '

' How to enhance and promote cross-branch work '
 * E.g.:
 * Function/Instrument case study
 * Process & Biomaterial & Instrument & Quality
 * Potentially: Data Transformation & Denrie & Quality

 10.30 - 11.00 Break - get your own coffee/tea at the bar

 11.00 - 12.00 Session 2: Review of milestones and actions

12.00 - 13.00 Lunch at canteen on the Campus - sponsored vouchers

13.00 - 14.00 Session 3: Summary of ChEBI discussion and outcomes of session 1

14.00 - 16.00 Session 4: Problem/Issues reported by OBI-Branches

' Independent Continuant Axis '
 * Biomaterial: Coverage (e.g. what do we import from other ontologies?), navigation/link to other resources, complex biomaterial entities (e.g. how do we deal with chemical mixtures, complex/composed materials)
 * Instrument: Need resolution of Function + Distinguish between device and instrument

'Occurent Axis'
 * ProtocolApplication: Needs resolution of Objective + Refinement of Plan definition. issues with Algorithm
 * DataTransformation: Needs resolution of 'Objective' discussion + resolution on 'Feature' in BFO space (in order for instance to specify log base for a log transformation).

'Dependent Continuant Axis'
 * Role: Quality/Historical Role ->related to timeline and time issue
 * Denrie:
 * Is specification a realizable entity or not: current view is that these are realizable
 * Proposal for Objective and Conclusion
 * Function: Need Resolution on Modeling issue -> go over use cases and options

'Relation:'
 * Need to discuss submission from DENRIE (information "about" something (and "encodes" relation)) and from Quality/PA (quality results_from process with reverse relation process confers quality)

 16.00 - 16.30 Break - get your own coffee/tea at the bar

16.30 - 17.45 Session 4 (continued): Problem/Issues as reported by OBI-Branches

17.45 Transport from EBI to Homerton College

Thursday, July 10th, 2008
8.15 Transport from Homerton College to EBI

 9.00 - 10.30 Session 6: Planning the evaluation phase
 * Who plans to test/use OBI v1.0 release in the next 6 months and how?
 * E.g. use of OBI in Symba database by Allyson
 * How can we use these applications for the evaluation phase?
 * Or do we need coordinate or even design evaluations projects for each use case identified?


 * Recrute External people: Ted Leftfield (GenePattern, already interacting with DT-branch), Possibly others.


 * Involve Publishers/Journal Editors: 'Nature Ontologies?'

 10.30 - 11.00 Break - get your own coffee/tea at the bar

 11.00 - 12.00 Session 7: Extending OBI and plans for other releases
 * Possible strategies to discuss
 * New rounds of term collection
 * Review OBO foundry ontologies to collect Instruments, protocol application, data transformations...
 * Involve Vendor and provide guidelines for OBIfication of catalogues (starting with instruments/devices)
 * Evaluate term enrichment techniques

12.00 - 13.00 Lunch at canteen on the Campus - sponsored vouchers

13.00 - 15.30 Session 8: Plan for manuscript(s)
 * Publication planning - framework and assignment of writing
 * What are the required criteria to decide that we are ready for release 1.0/publication
 * Should we have one main piece and several technical papers?
 * These can be both the technical (working practice) documents - authored by the relevant OBI contributors- and application project done by individual partecipants only
 * These could potentially be put together as a special issue

 15.30 - 16.00 Break - get your own coffee/tea at the bar

16.00 - 17.45 Session 9: Fundings + Preparing for the Next OBI Meeting
 * proposed location for the winter meeting 2009: MIT, Boston, date: End of January/Early February
 * proposed location for the summer meeting 2009: EBI, Cambridge, date: Early July

17.45 Transport from EBI to Homerton College

Friday, July 11th, 2008
8.15 Transport from Homerton College to EBI

 9.00 - 10.30 Session 10a: Tools 
 * Current practices
 * Protege good practices: get everyone up to speed
 * Use of SVN branches for evaluation: dropping OBI auto id plugins; automatic creation of definition for a number of qualities/historical roles
 * Protégé +SVN vs Collaborative Protégé:
 * Daniel review and Alan's comment

 10.30 - 11.00 Break - get your own coffee/tea at the bar

 11.00 - 12.00 Session 10b: Tools 
 * Feature requests
 * batch loader for quick terms ?
 * batch loader for defined classes ?
 * batch loader capable of setting all restrictions ?
 * automatic release- report creation –notification/reminder
 * term tracking/submission tracking

12.00 - 13.00 Lunch at canteen on the Campus - sponsored vouchers

Who is still here????

17.45 Transport from EBI to Homerton College

Confirmed delegates
1. Tina	       Boussard

2. Melanie	Courtot

3. Frank	Gibson

4. Suzanna	Lewis

5. Allyson	Lister

6. James	Malone

7. Luisa       Montecchi

8. Norman	Morrison

9. Helen	Parkinson

10. Bjoern	Peters

11. Philippe   Rocca-Serra

12. Alan	Ruttenberg

13. Susanna-Assunta	Sansone

14. Richard H. Scheuermann

15. Daniel	Schober

16. Barry	Smith

17. Christian Stoeckert