HCLSIG BioRDF Subgroup/Meetings/2007-04-02 Conference Call

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Conference Details

  • Date of Call: Monday April 2, 2007
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • 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: Vipul Kashyap
  • Scribe: Olivier Bodenreider

Participants: Susie Stephens, Vipul Kashyap, Olivier Bodenreider, Matthias Samwald, Kei Cheung, John Barkley, Don Doherty, Kerstin Forsberg, Bill Bug, Eric Prud'hommeaux


  • Review action items
  • Progress in data set conversion
  • Presentation content
  • Demo equipment (boxes, network, projector)
  • AOB


Only some of the action items from last call were reviewed, the others involving people not on the call today.

Demo equipment

  • Hardware specifications: powerful laptop (in terms of memory, CPU and disk space), several of them possibly
  • Software specifications: Virtuoso, Oracle RDF store (11g beta), OS: RedHat Entreprise (because of Oracle 11g beta), apache, prefuse and vizster (Using MySQL was discussed as well).
  • Strategy: The demo could be replicated on several laptops, possibly using one machine as server.
  • Network: EricP suggests setting up a local wireless or wired network, rather than going through the Internet.
  • Getting the machines: Vipul contacted HP and was asked to provide details about hardware and software specifications (see above). Susie contacted IBM. Both are optimistic they could get a box from HP and IBM. Bill Bug has contacts at Apple and will coordinate with EricN. Bill also suggested requesting long term machine loans rather than just for the demo at WWW, given the string of upcoming demos (ISMB and Neurosciences meeting).
  • One or two projectors? EricP says one projector is standard at WWW workshops. Using two projectors would be possible if we brought one, but we might not get and extra screen anyway, forcing us to alternate projectors on one screen).

Progress in data set conversion

  • See update on the wiki

Presentation content

  • Bill Bug suggests a scenario in which four sources of information are integrated: gene networks, biochemistry of neurotransmitter metabolism, neuronal compartments and brain regions. We need to show which standard terminologies and ontologies help link concepts from these four sources (Vipul). Meanwhile, Matthias will select only two of them and explore what queries can be developed to illustrate the benefits of integration.

Related discussion regarding the demo

  • User interface: Bill Bug suggests using vizster, an information visualization tool based on the prefuse library, supporting not only visualization of, but also interaction with ("slicing and dicing") the data. Matthias contends that a custom interface might be more appropriate. Both approaches could be used in the demo (Susie). EricP (and Alan Ruttenberg) will coordinate with the information visualization lab at MIT for a possible collaboration.

Next informal F2F meeting

  • on April 10 (afternoon)
  • Susie will send reminders