2006-05-03 Conference Call Minutes

Participants: Ranjani, Alan, Emek, Gary, Dan, Ken

1. Development status update

   1. DXTrackWorkplan status update (Emek/Gary) - Emek and Gary have been working to sort out open issues and will post them to the proposals soon. Alan: Weekly status reports sent to the list would be good from people working on BioPAX, like Emek and Gary.

• Dan also asked about feedback on Dan's proposals. Alan suggested Dan could talk about this at the CSHL meeting. Gary can chat with Dan offline about them or write some comments on the wiki.

http://biopaxwiki.org/cgi-bin/moin.cgi/Late_2005_Proposal_for_BioPAX_Development/Discuss

1. Late 2005 Proposal for BioPAX Development/Working groups proposal status update (Alan) - will be discussed at the workshop

• -action item Emek for use case separation page - no major comments, but it is a little verbose

  1. BioPAX Validator / PAXerve interoperability (Ranjani)

-emek has posted code on CVS (interfaces and basic implementation of the class) - Ranjani is reviewing the code. Ken Fukuda expressed interest in working with the paxserv API as well. Emek is writing a parser using the code. Ethan Cerami would like to integrate this into cPath and is providing feedback on requirements.

1. debugging the bug E.coli data merge project (Jeremy/Alan) ( code repository) status update

-since last month - more work on merging reactions. group did some processing to find a list of ~150 reactions that needed to be manually mapped. This was split into 3 groups. Jeremy/Alan have been doing this and have been finding bugs in their mapping. 1. left/right assymetry - some reactions only matched when the left/right were swapped. will prepare a proposal to discuss this - how can people write their reactions so they can be recognized to be the same. 2. generic reactions weren't being matched - a class based system would help with that. This still depends on a feature of OWL 1.1 (qualified cardinality restriction) - not sure if these features will be ready by the June meeting. There will be an XML schema version of OWL as well.

1. Governance. Gary action item to provide alternative wording for BioPAX Governance (action item from 2 calls ago)

• - gary is sorry we was not able to get to it by this call, but will be doing is soon.

1. Meeting report on 2006-04-03_to_07 Informal Workshop on formal semantics for BioPAX at Manchester (item from last call)

• - class based representation is much more powerful, but the details need to be worked out. Some details have been worked out e.g. phosphorylation reactions - compounds as classes. Some issues in OWL may still come up. Next steps: take up proposals at the use case level for existing biopax and see what happens with the class based representation - basically do more worked examples as we have time. Alan, Jeremy, Chris Lemer, Olivier will be working on it. More was learned about how to use instances and what they are good for. There is an instance and query based solution for workflows (which are like pathways). The main thing you can do with instances is to make cycles - you can't make a class of benzene rings in OWL where you describe the ring (can't for a loop in classes because you need a variable). You can define this with instances. Emek asks if this would happen with reactions as classes for most pathways. Alan is not sure - more work needs to be done e.g. two pathways that have the same reactions and differ by their topology and one topology is a cycle.

-emek asked if Alan had time to reply to Matthias' issues he raised in his paper. Alan is still reviewing them in detail. -Alan is working with the HyBrow people to see if he can owl-ize their ontology - they are interested in the context issue. Where is the boundary between context and the major event? It doesn't exist. Gary: What about differentiating experimental vs. biological model context? Wouldn't genomics and proteomic technologies solve this problem before we can solve it computationally. Alan: at least there should be a window for this problem. Maybe this could be a dinner discussion at the CSHL meeting. Dan: be more explicit which data is a model in BioPAX. Alan: This is a question of scope.

1. Presentations from Japan meeting (Ken) - Sorry about the delay. Ken just uploaded all presentation files that he had on this disk - only the f2f meeting slides, not the symposium slides. Action item: Emek will update the page to see who is missing from the page and then follow up with those people to eventually make a complete page of presentations from

2. Future meetings

   1. Cold Spring Harbor meeting organization report (Emek) - finalizing the participants list. Around 20 people are interested. We are coming up with a budget and started sending e-mails to people to get confirmation of attendance, and will be sending more today. We will not be able to fund everyone, so people will confirm their participation.

   2. Potential workshop with Barry Smith (Alan) (action item from 2 calls ago) - alan is still holding off on asking him to not be overcommitted. Push to next meeting.

3. Feedback on biopax.org (Alan) (action item from 2 calls ago) - alan hasn't had time, push to the next meeting.