Participants: Andrea, Gary, Ken, Chris, Frank, Jonathan, Alan
These are initially Gary's notes just after the call.
Development status update
BioPAX Release candidate status. We need to move this towards Level 2 completion very soon. The proposed way to do this is to get consensus on decisions over e-mail with interested parties (Gary will lead this during the 3rd week of September). Any consensus will be reported on the list and left to sit for 1 week. If there are no objections during the week, it will be considered decided. Issues remaining are listed here Level 2 Release Candidate Feedback. Alan mentioned that he is looking for an explicit recipe for moving PSI-MI files over or a policy that we can't publish such a policy. Gary is going to make a DIP example and create a mapping document, which will be open for review for 1 week (Alan is committed to being able to review the document during this time)
Administrivia: Authority Of Pages, Committees and Delegation Policy Adopt? Not sure yet for both of these. A number of people have reviewed the documents and all agree that they represent a good step, but more work needs to be done. The pages should be more concise so that people won't be discouraged from reading them (Gary and Jonathan will work on this).
Authority of pages: everyone agrees to endorse pages. Any post-endorsed discussion will take place on an initially blank link called "discussion to endorsed page" Bring up final endorsement at next meeting.
Committees and Delegation Policy - 3 main sections - delegation, who is the group?, tasks This is really just meant to document the existing process, but also provides an opportunity to revisit the process to make it more efficient for community development (allow more people to get involved). Not everyone has digested the material yet. There were no disagreements on the call about the content digested so far. Aim for the next meeting is to have these pages made official. Jonathan will solicit individuals and be the point of contact for page editing/feedback.
BioPAX wiki development - Alan has started a page called 'pathway related data models' to collect data model specifications. He would like to collect some more as a resource to become familiar with the state of the art in pathway knowledge representation. Basic literacy for new groups members. Please add any schema/ontology documents you know of there.
LibBioPAX / conversion status
KEGG - Chris: in short, the KEGG converter is finished (supporting BioPAX Level 1). Coverage reaches 80-90% of KEGG pathways. Certain things could not be converted because they don't fit in BioPAX e.g. generics. We are in contact with KEGG people to validate the conversion + publish on their FTP site (waiting for a response). If people are interested in this, it is
![[WWW]](/wiki/modern/img/moin-www.png)
available for testing purposes. We'd like to try to work with the KEGG group to have all the data on the KEGG site instead of providing the converter publicly (because this makes the KEGG data more accessible and requires less maintenance resources from Chris' group). Full documentation of the mapping is available. WIT - Jeremy and Joanne are helping with this effort, but were not available on the call - Gary will ping Jeremy about this
Reactome - Guanming reports over email "BioPAX exporter has been updated to Ver0.92, the release candidate. However, it is not in the public release until Sept. 26. If people are interesting in testing, they can access it at
http://brie8.cshl.edu, our dev site. Please be aware that the contents in this site are highly volatile." Alan: Are RDF IDs re-used across files? (old issue) He will check with the current pathways.
New tool development supporting BioPAX
- Cytoscape plugin has been updated.
Future meetings
Report on organizing of JapanF2Fmeeting: Nov 2005 - Report from Ken - symposium schedule is almost finalized. Ken created an order of talks - academic/commercial/japan/other standards. Funding decisions are next to work on. Then we need to sort out the technical workshop (face to face) schedule - Alan, Gary, Frank are at least 3 people who are interested in this discussion. Alan wants to know if we can have a field trip to the fish market (very impressive) - the link to it and other Tokyo tourist attractions are available on the Japan meeting page.
Discuss outstanding development/technical issues from Level_2_Release_Candidate_Feedback
-confidence: should we require a publication? Decision: require a publication (min cardinality=1 on xref). -open or closed world? You can close certain things with OWL constructs easily (e.g. max cardinality), but others are hard to close (e.g. min cardinality). Because of this, an OWL validator will not complain if the publication is not there. -CERTAIN/UNCERTAIN should be removed from the sequence position status field, since this is represented as presence/absence in OWL.