2006-01-11 Conference Call Minutes

Dan C, Joanne L, Jonathan R, Emek D, Gary B, Frank S, Ken F, Geeta JT, Vincent L, Ranjani R, Andrea S

Initial notes by Gary B.

Short items:

1. Development status update

   1. Official release of BioPAX Level 2 v1.0 (Gary)

      • Location of release package, for sanity check

      • Documentation changes proposed by Alan

      • Gary will work offline with Alan to deal with last changes to documentation and then create the release (OWL file + zip file). Alan will do a sanity check on the zip file.

2. Grant status (Gary)

   • Looks like we will get the NIH conference grant (not finalized, but program officer gave us a positive message). It will be for US workshops with limited funding for about 1 meeting per year.

3. F2F Survey (Alan)

   • Survey monkey for post-f2f survey is available (ask Alan for the password if you want to access it and review it). Everyone seems to be ok with it, so Alan will send it out.

4. HCLS BioPAX Talk (Joanne,Alan)

   • Health care for life sciences special interest group for W3C - BioPAX will be discussed. The first meeting may be open, Alan and Joanne will check and send a message to the list. Alan has applied for invited expert status to the W3C - his goal is to connect with other experts. Joanne is a member through Manchester.

5. Quick Poll: Move to biweekly teleconferences? (Alan)

   • There is not overwhelming desire to hold biweekly calls. Maybe we could have them as needed. Gary mentioned that in the past biweekly was too much and people stopped attending completely, thus we moved to monthly.

Discussions:

1. Workplan/proposed way forward (Emek and Alan)

   1. BioPAX 2.5/3.0 workgroup proposal as alternative to DX/SW. See here

• Emek: ideas are still a bit more tangled than he would like - too much interference between the two groups and would rather have them a bit more separated - if the requirements concern both groups, it is not clear how this process would work. Alan will remove it. Also, 2.5,3.0 instead of 3/4. Alan mentions 3 reasons for this. 1) The timeline for the 2.5 release is more consistent with a point release than a full release 2) There was strong agreement in Japan that Matthew's OWL fixes should be dealt with in the next release. The 2.5 proposal is a compromise in the sense that those who have short-term needs gain a release without having to address them (other than those they want to address), and the others gain a visible goal to address them in a timely manner. I think it will be harder to call the short-term effort level 3 unless much more of Matthew's observations are fixed, and I think that will interfere with the short term goals 3) There is already stuff in 2.0 that some, including me, find uncomfortable. In this proposal it gets to stay as is, enabling progress in the short term. Correspondingly, in return for agreeing to this, we get some bound on when these issues will be addressed.

• Reasoner would be a requirement for accessing the data of post 2.5/3.0

• Gary feels that the 2.5 name is confusing it should be 3.0 and possibly Level 4. The reason is that it is inconsistent with expectations of original roadmap (mentioned in abstract, publications), thus is confusing to users. Also timeline is not a factor in deciding what to name a release, it's mostly about feature set and marketing. (otherwise the workplan proposal is fine)

• Ken feels it should be 3.0 and BioPAX SW - a new name that will appeal to the public (otherwise the workplan proposal is nice)

• Frank's first notion is that Ken is probably right

• Dan C - 2.5 sticking with OWL is asking for trouble because it is not respecting OWL semantics - he would like to just have 2.5 declared in e.g. UML, RDF (Emek says this would add unnecessary cost)

• Alan is sympathetic to Dan's criticism - use OWL, but make it clear.

• Alan will move discussion about the workplan to the discuss list

  1. Alan Ruttenberg/Re-expressing a use case

  2. Manchester: At the Japan F2F it was proposed that that a group of BioPAX members interested in learning OWL and bringing BioPAX into conformance with OWL semantics visit the computer science group at Manchester, where there is significant expertise in OWL modeling and description logics. Alan Rector has expressed a willingness to conduct such a session in Q1. A number of working group members have expressed interest in participating. We need to start planning for such a trip, and in particular, start to arrange funding.

1. Motion to endorse BioPAX Governance. Discussion here

• A large change to the document was recently made, so anyone who is interested should read this document and get comments to Alan ASAP.

1. biopax.org web pages (Alan): The biopax.org web site increasingly becomes stale, as more and more activity happens on the wiki. In addition, as there is wider involvment on the wiki, that site becomes more evidently an expression of public face that the MSKCC group want to put on the BioPAX efforts, as it's content is entirely determined by that group. Accordingly I propose that biopax.org be redirected to biopaxwiki.org and that if the MSKCC group wishes to retain this forum that they move it to http://cbio.mskcc.org/biopax/ and edit the site to reflect this change.

Other things:

• First International Workshop on the Systems Biology Graphical Notation

  • Feb. 11 - 12, 2006 @ Tokyo, Japan

    • BioPAX-SBGN Mapping