Workshop Bethesda 2007 July summary conclusions

Present:

Gilberto Fragoso, Chris Stoeckert, Richard Scheuerman, Susanna Sansone, Philippe Rocca-Serra, Bill Bug, Liju Fan, Jennifer Fostel, Allyson Lister, Randi Vita, Tina Boussard, Helen Parkinson, James Malone, Kevin Clancy, Alan Ruttenberg, Christian Cocos, Barry Smith, Daniel Rubin (by phone), Mervi Heiskanen, Daniel Schober (by Centra)

Action Items:

Review of San Diego Milestones, outstanding issues

1. Complete assigning credit policy

2. Complete deprecation policy

3. Finalizing meta data annotations and clean up web pages - note we added a new meta data terms and these need to be added to relevant pages

4. Follow up browsing OBI use cases with Bioportal - Bill Bug will outline issues with BIRN

Branch presentations action items

• Each branch provided a summary of progress and problems were discussed

1. Relations branch: submit new relations to OBO via their tracker (Relns branch)

2. DT branch: address naming issues, be more clear on mathematical function vs. method, rename for being in protocol application, or move to plan (DT Branch)

3. DT branch: identify areas of overlap with the SW ontology from Daniel Rubin, which is under development but not yet in use (DT branch)

4. Alan will break out all the meta data properties into a separate OWL file so Bill can use these for BIRNLEX instead of his own (AR/BB)

5. Instrument branch: improve the definition of the platform, 

6. Instrument branch: address reagent part to deal with computational platform where no typical reagents are used and to include being put together for a purpose. Should not include vendor. Will now be included in OWL file to aid editing - AR will do that. 

7. Instrument branch: ProtocolApplication what is the platform used for (Instrument/PA branches)

8. Instrument branch: Resolve issues with artefact and biomaterial overlap in definitions (all)

9. Instrument branch: Remove device and create as a synonym for instrument (Instrument)

10. Digital Entities: Look into overlap with Swan project and the SW ontology (Dig. E)

11. Plan branch: Work on subjects to help classify experiments e.g. offspring, study, twin, (Plan)

12. Plan Branch: Check definitions are Aristotelean. (Plan)

13.  Write up an example for discussion on importing external ontologies esp. relavant for BioMaterial. AR/BB

14. PATO and SO  both have Ploidy as a concept, needs resolving within OBO foundry (BS)

15. Function branch: In Bill's example function and role are mixed. BFO may need to look at whether function and role are appropriate. (BB/BS

16. Protocol Application branch: clinical_diagnosis definition is bad clean up, along with other definitions. (PA)

17. Protocol Applications branch: Syntax needs clean up (PA)

• Following the presentations from the branches we decided to identify common problems e.g. with existing hierarchy and focus on these during the rest of the workshop.

Common Problems Discussion Action Items

18. Artefact object discussion. Two different hierarchies were discussed. No resolution during meeting. These OWL files need to be posted and discussed during a dev call

19. Inferred classes. We worked through an example and identified that exploring existing design pattern work is needed.  Discuss on dev call.

20. Update OBI to BFO1.1

21. Branch editors to identify experiment only qualifiers that will be in OBI and submit to qualities branch (all)

22. All relations in protocol application e.g. to be submitted to the relation ontology (LF/PA branch)

23. Lot and material type - no resolution on this, needs further discussion on dev call

24. Add qualities branch to OWL file (AR)

25. Issue of handling vendor reagents in OBI unresloved - needs more discussion on dev. call

26. Protocol application worked example: find a way to add duration and order to all process 

27. Protocol application worked example: GF to explain to AR about assn of qualities in a class definition e.g. two out put materials have new properties 

28. Interaction with Env ontology to be clarified with Dawn Field (SS)

29. Helper classes for temporary terms. All branches will use branchname_temp (all)

30. SOP workflow needs updating to show reasoning etc. (TW to send code,  Mac user volunteer needed to do it)

31. Competency testing: JM and DS will provide templates for branches to send their use cases

32. Teleconferences are expensive, other options were discussed. SS will look into whether the EBI service has local call rates for international callers

33. Review branches for community views - e.g. OCI has a 'view' on the ontology - need use cases for these prior to deciding on a way of providing these

34. NSF propoal. Letters of support needed AR to provide proposal title for inclusion in letters

35. Volunteers needed to Review a draft of the proposal 

36. Identify a series of check in dates when we assess deadlines will useful for conference calls and will assist in project management. 

37. Add new milestones to the calendar (AL)