2006-03-01 Conference Call Minutes

Minutes recorded by JeremyZucker

Conference Details

Participants

Meeting Minutes (Please add your notes if you have them)

  1. Organizing teleconference scheduling. (proposal - Alan)

    1. 1 week advance notice.

    2. Assign responsibility (rotating?) for convening, posting of agenda, notice to list, facilitation.

    3. Basic agenda initialized with

      • Agenda items not addressed in previous meeting.

      • Review of action items from previous meeting

      • Gary suggested implementing an automated reminder for him

      • Decision: Gary maintains admin role of creating the wiki agenda and sending a reminder e-mail. Will try harder to send 1 week in advance and expects people to say something if this doesn't happen.

  2. Level 2 Release feedback (Emek)

    1. Extra possible constraints

    2. Naming issues

      • Gary summarized Emek's work (Emek not available on this part of the call)

  3. Development status update

    1. DXTrackWorkplan

    2. Proposals ready for review and status of others (Gary/Emek/Alan)

      • Should be easy to read in order to encourage review

    3. How to get going on splitting use cases/implementation proposals.Alan_Ruttenberg/Re-expressing a use case

      • Level 3 should be OWL-compliant

    4. Late 2005 Proposal for BioPAX Development/Working groups proposal (Alan)

    5. PAXerve status update (Emek)

      • Java API for BioPAX

      • Integrated with validator

      • Finished backbone and tests

      • Moving to persistence (Hibernate)

      • BioPAX classes are java final classes

    6. Report on [WWW] debugging the bug E.coli data merge project (Jeremy/Alan) ([WWW] code repository)

      • Published list of errors and bugs to Palsson and SRI groups

      • SRI has responded with some questions. We will answer

      • Code is available on subversion. please check it out and see if it works.

      • When Mapping is an OWL file that merges two data sets.

    7. Namespace conventions (Andrea) (optional, maybe too technical)

      • How to deal with versioning?

      • Manchester group should be consulted before adopting a solution.

    8. Generic KEGG compounds - Policy/Documentation (Alan)

      • Many people use it, leading to semantic errors in data sets.

      • Alan identified these compounds

      • Unit tests should check whether Generics should not be used as unificationXref

      • Should also be part of the Documentation

      • Gary feels that rules can be used as filters

      • Alan proposed generating a list of exceptions from a Perl script

  4. Governance. Gary action item to provide alternative wording for BioPAX Governance

    • Gary has written a document. Hasn't circulated it yet.

    • Will redouble his efforts to get feedback before posting it.

  5. Meeting report on SBGN (Emek)

    • BioPAX will be supported at Level 2 and Level 3

    • CellML will be supporting BioPAX

    • Teranode has a visual demonstration of BioPAX (BioCarta level graphics)

    • Requirement of SBGN for visualization

    • Entity-centric view and state-transition view are almost isomorphic

    • How symbols should be drawn

    • SBGN should focus on Syntax formalization

    • Emek agreed to be liaison and provide examples

  6. Future meetings

    1. BioPAX DXTrack meeting to review beta (Gary)

    2. 2006-04-03_to_07 Informal Workshop on formal semantics for BioPAX at Manchester

    3. Potential workshop with Barry Smith (Alan)

      • Barry Smith works on OBO relationship ontology

      • Barry has funds for setting up meetings and workshops for applying ontology principles to BioPAX

      • Alan will send more information soon.

  7. biopax.org web pages: I propose that either biopaxwiki.org become biopax.org, i.e. that the wiki become the official BioPAX site, or that interested parties work on revamping the biopax.org site so as to remove whatever can't be effectively maintained on the wiki. (Alan)

    • Alan hasn't had a chance to review Gary's edits. Will add comments to wiki page

last edited 2006-03-02 15:12:07 by DanCorwin