2006-02-08 Conference Call Minutes

Participants: Gary, Emek, Joanne, Jonathan, Chris L, Ranjani, Carl, Ken, Alan, Dan, Geeta, Andrea, Elgar, Jeremy

  1. Development status update

    1. Quick update: BioPAX Level 2 Release (Gary) - the release is out.

    2. Quick update: [WWW] Survey results (Alan)

    3. Quick question: Spam on biopax-dev google group - should we prevent people sending meeting announcements to biopax-dev? (Gary) - not a problem, if it is a problem, we can deal with it.

    4. Future development plan discussion (Emek)

      1. DXTrackWorkplan (Emek) - States and generics proposal process has been started for people who registered on the DX workplan page. This is only in the context of the DX track. Requirements and domain analysis is split out. Alan is interested in states and in the portion that is common to both tracks. So it needs to be more organized, we can deal with it offline.

      2. Late 2005 Proposal for BioPAX Development/Working groups proposal (Alan) - last remaining point is about version number. No resolution, proposed to postpone the labeling issue. No one should say that the next level is anything specific. DX versus SW labels considered harmful. Consider changing DX -> "ShortTerm" so as to avoid misunderstanding. We all have same goal.

    5. Gene Regulation Proposal status update (Gary) - Update to the gene regulation proposal. Alan and Gary will work offline to make sure requirements from this document are modular/ separate requirements from implementation.

    6. Report on debugging the bug project merge work (Jeremy/Alan) - collaboration between 4 groups initiated at ICSB - Peter Karp, Adam Feist (Pallson) to merge e.coli databases. There are a lot of issues with merging. Want to understand how to use OWL + reasoner to automate some of this.

      1. Problems with unificationXrefs of small molecules: bugs, isomers, charge state.

      • Initial reasoner found inconsistencies in EcoCyc. 3 issues: 1 bug with CAS IDs, 2. CAS doesn't deal with isomers well - this is a bug in CAS, but the validator will flag the error. There should be a best practice on how to deal with these. 3. charge states - CAS or SMILES doesn't make a distinction between these. Maybe states will solve some of this.

      1. What to do when a molecule doesn't fit into one of our categories. [WWW] Examples from Ecocyc.

      • Alan will be posting a wiki page on this.

  2. Future meetings

    1. [WWW] SBGN meeting report (Emek) - Ken is an organizer and Emek will be attending and will represent BioPAX. SBGN is a graphical notation for pathway. Emek will try to make sure that SBGN will be compatible with BioPAX in the future. There is no presentation scheduled for BioPAX. Let Emek know if you have any issues and Emek will write a report. If BioPAX decides to do a presentation, Alan is willing to review.

  3. Motion to endorse BioPAX Governance. Discussion [WWW] here (Jonathan/Alan)

    • Emek - the document doesn't match well with the current funding mechanism, which is academic-focused (NIH), which means there is a PI. PI responsible for funds inconsistent with group make decisions.

    • Ken - can't see a way to include funding issues - the governance document is based on trust. He doesn't think there can be a clear modification that can solve the funding issues, because funding has their own restrictions.

    • Jonathan - we just need transparency.

    • Alan - Distinction between requesting funding on behalf of BioPAX versus funding to participate in BioPAX. Former is a group process (possibly delegated) latter anyone can do.

    • Joanne thinks that anyone can propose a workshop. Her proposal is that BioPAX can form a consortium and apply for funding. Funding so far has been academic - won't stay that way.

    • Joanne - Trust hasn't worked well for her - issue of consulting fees due her from previous grant.

    • Jonathan: "how about biopax can't take funding at all? Or make a corporation, or steering committee? risk: people will take advantage of biopax to do their own stuff.e.g. Jonathan gets a grant to develop biopax; then takes the money and runs on some random track that differs from what the group wants.

    • Alan worries that unless there is coordination, multiple groups might apply for funding for similar "BioPAX" confusing/turning off funders.

    • Ken suggests that Sander group comes up with a proposal. He will also contribute from his own experience.

    • Take it offline on the dev list. Ken, Emek, Gary, Joanne, Jonathan, Alan, Jeremy. Some proposed wording in the next two weeks.

We ran out of time to cover the following points - they can be automatically put on the agenda next month if still open.

  1. Future meetings

    1. Manchester planning - call for OWL implementors. (Joanne/Alan)

    2. Potential workshop with Barry Smith (Alan)

  2. 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)

last edited 2006-02-08 18:34:03 by AlanRuttenberg