HCLSIG BioRDF Subgroup/Meetings/2006-08-14 Conference Call

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Conference Details

  • Date of Call: Monday August 14, 2006
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Participant Access Code: 246733 ("BIORDF")
  • IRC Channel: irc.w3.org port 6665 channel #BioRDF (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1 hour
  • Convener: Susie Stephens
  • Scribe: John Barkley


  • Task update by Matthias Samwald
  • Discuss the F2F Meeting
  • Continue Identifier discussion

Meeting Minutes

Attendees: John Barkley, Kei Chung, Ora Lassila, Joanne Luciano, Sean Martin, Chris Mungall, Alan Ruttenberg, Matthias Samwald, Susie Stephens

Task update by Matthias Samwald

Matthias presented the slides available at:

http://neuroscientific.net/res/semsyn/BioRDF%20task%20update.ppt (Powerpoint format, 180 kb)

Questions/discussion included:

  • Saxon was used as the XQuery processor because of its superior performance.
  • The version of BioPAX used was BioPAX Level 2, 1.0.
  • BioPAX was extended to add KiDB fields and classes to represent subclasses of receptors.
  • Elements of Matthias’ XQuery text for BIND could be reused. Kei mentioned that elements of the SBML to BioPAX could also be reused. Joanne suggested that reusable elements be collected and made available.
  • Elements of Matthias’ XQuery text for generating URIs could probably not be reused since the form of URIs is very application specific.
  • OWL and XQuery files are available at: http://neuroscientific.net/index.php?id=download

F2F Meeting

Susie solicited input on how BioRDF could contribute to the agenda for the F2F in Amsterdam. She sought suggestions on what demos/tutorials could be done to show the progress BioRDF has made since the last F2F. There was agreement that a tutorial on XQuery would be useful. It was also agreed that there should be a discussion on URI Best Practices, and that Taverna would provide a good example of using LSIDs. Susie will email to the list for additional agenda suggestions.

Continued Identifier discussion


Thus far, four areas (Versioning, Metadata, Location Independence, Resolving LSIDs) have been identified in the URI Best Practices discussion. An ad-hoc group of interested parties was formed to continue the discussion in the context of these four areas. This group consists of Kei Chung and Joanne Luciano (who will focus on use cases); and John Barkley, Sean Martin, Alan Ruttenburg, and Matthias Samwald (who will focus on technology).