2006-09-06 Conference Call Minutes

Conference Details

• Date of Call: Wednesday, 6 September 2006 (2006-09-06)

• Time of Call: 12:00:00 EDT = 16:00:00 UTC

• Dial-In #: 1-641-297-5600 (Iowa) (confirmed by Alan)

• Participant Access Code: 33281

• Duration: ~1 hour

• Skype Transcript

• Moderator: Gary Bader

• Scribe : Jeremy Zucker

• Convener: Alan Ruttenberg

Draft Agenda

1. Choose date, nominate convener, moderator, scribe for next meeting.

   1. Date: Wednesday, September 27, 2006. Noon EST.

   2. Convener: Joanne Luciano with help from Alan

   3. Moderator: Gary

   4. Scribe: Jonathan (volunteered in absentia)

2. Development status

   1. Validator (Alan/Ranjani)

      1. Alan put the non-OWL constraints into AnnotationProperties, and validate with SPARQL queries

      2. Emek: SPARQL is a pain, you can't encode all constraints into SPARQL, so the validator should just be in a fully Turing-comlete programming language.

      3. Alan: Which programming language?

   2. Paxerve (Emek)

      1. Available on Sourceforge CVS

      2. Reads Jena model and generates a Paxerve in-memory model.

      3. SPARQL queries will still require the Jena model.

   3. Proposal status update

      1. Genetic Interaction (Gary)

         1. PATO Phenotype ontology solves a lot of problems.

         2. It is in OBO format

      2. States/Generics (Emek)

         1. Will provide update at next meeting

      3. URI/CV (Alan)

         1. Will provide update at next meeting

      4. Gene Regulation (Gary)

         1. GeneExpression is not a Conversion interaction

         2. Matthias/Jeremy: Make a separate Transcription and Translation class (and a combination of the two called expression)

         3. Stakeholders: Cancer CellMap and INOH.

         4. More updates at next meeting

   4. Debugging the bug - progress report (Jeremy)

      1. total nr. of reactions: 2366

      2. (:METACYC 64)

      3. (:EXPANDED-RXN-MATCH 113)

      4. ((LEFT REMOVE PROTON) 164)

      5. ((RIGHT REMOVE PROTON) 299)

      6. ((LEFT SUBSTITUTE AMMONIA AMMONIUM) 5)

      7. ((RIGHT SUBSTITUTE AMMONIA AMMONIUM) 33)

      8. (:UNMAPPED-CPDS 294)

      9. (:DIFFUSION 269)

      10. (:EXCHANGE 300)

      • And there are now still 452 reactions not being mapped for unknown reasons, which certainly improved a bit.

   5. INOH BioPAX release update (Ken)

      • Ready soon.

   6. Matthias: working on SPARQL/PHP converter to Bio-Zen

3. Barry Smith workshop late November/mid December? (20-21 Nov., 28-29 Nov., 29-30 Nov., or 11-12 Dec.) (Alan)

   1. Jeremy: any time

   2. Elgar late november/early december

   3. Joanne: will provide accommodations. Shouldn't this adjoin the F2F meeting?

   4. Gary will check with Chris

   5. Emek will check with Chris

   6. Ranjani will need to check

   7. Ken prefer 20-21 Nov.

4. SBGN meeting update (Emek)

   1. Requests permission to represent BioPAX at SBGN. approved.

5. Administrative: Delegations.

   1. Postponed to September 27 meeting