Participants: Ranjani R, Vincent L, Alan R, Mike C, Ken F, Gary B, Chris L, Joanne L, Andrea S
Development status update: BioPAX Level 2 Release candidate status -
We are waiting for feedback from Peter Karp about biochemical reactions. We agreed to limit the wait to 2 weeks from now (Wed). If we can't get Peter's final feedback by then, then we agreed to implement a 5 tuple for the affected properties (e.g. KEQ), as Peter has previously suggested. Gary is organizing this.
We agreed to evaluate the OWL changes presented by Matthew Horridge at the Japan F2F meeting for Level 2. The changes are expected not to break backwards compatibility and will not affect existing features. For instance, added restrictions that are desirable for the automated reasoning use case could be added in this way. Joanne and Matthew will lead this + others who want to help - Joanne will send out a note to the list. This is also limited to 2 weeks.
-Gary will copy Alan on communications to Peter
Japan F2F follow-up - administration issues
Posting existing presentations on the wiki - copy the workshop schedule and have a link to each presentation - people can add their own presentations if Ken doesn't have them. (Ken will organize this)
Should we create a survey asking for participant feedback? Start a wiki page with some questions. (Gary will start a page)
How do we report back to the community - current status and where we're at. Who will commit to writing (Alan, Joanne, Chris, Andrea, Mike, Gary). Make a wiki page with an intro. Goal is to communicate to the biopax-discuss list - people who were not at the meeting. This will start out simple. (Alan will organize.)
Photographs - Flickr - create a new one for BioPAX and share the password, then people can post their own pics (Ken will organize)
Discussion of Late 2005 Proposal for BioPAX Development
BioPAX Level 3 workplan
OWL fixes to DX track (isn't this is premature - Alan)
Alan - wants to clarify requirements - right now biological and database requirements are mixed, which makes it hard to reuse the biological requirements. Multiple proposals should be able to reuse/reference the biological requirements.
Ranjani asked Alan to clarify what he meant by database requirements. Some of the requirements related to the data structures used in individual databases. Ranjani raised a concern that to define mappings among DBs in the proposal does not scale. Ranjani agrees with the idea of listing database requirements, but that it is difficult to list all of them. Alan - it's fine for just the individual data providers to list their requirements. Alan raised the database requirement of representing e.g. a homology abstraction and claims that it doesn't really exist in biology, but is really just an idea in bio modeling.
Gary mentioned 4 types of requirements - biological, database modeling, use case of the data, software (non-bio) requirements. Alan just wants people to be clear and list all of these. An example could be software depends on jdom and we follow all the requirements of jdom. E.g. for Cytoscape we expect that a graph of a certain nature is produced.
Chris - maybe starting with a short list of issues that are raised that don't have anything to do with biology could be listed, but it is difficult to ask people to write all of their detailed requirements, since, while considered good practice, it's too much to ask from everyone e.g. a Ph.D. student doing a student project. If requirements are shared, then it will be better handled and will encourage people to add their requirements.
Gary revised his requirements categorization: 1. use case driven bio requirements (what data we want to store and what we want to do with it) 2. database modeling requirement e.g. homology abstraction 3. software requirements e.g. use jdom.
Alan is volunteering to be in the editing role for these requirements.
Alan made a proposal on the 2 tracks - see his wiki page for more details. He is not interested in competition between the two tracks.