HCLSIG BioRDF Subgroup/Meetings/2007-02-12 Conference Call

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Conference Details

  • Date of Call: Monday February 12, 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: Susie Stephens, Vipul Kashyap
  • Scribe: John Barkley


  • Review Action Items - Susie
  • Demo audience - all
  • Progress with the demo script - Alan
  • Use case progress - Bill, Don, Elizabeth, June, Tim, et al.
  • Progress report on UI tools - Scott
  • Information Flow Diagram - Vipul, Susie
  • Time lines for demo - Joanne
  • AOB


Participants: John Barkley, Bill Bug, Helen Chen, Kei Cheung, Don Doherty, Vipul Kashyap, June Kinoshita, Joanne Luciano, Alan Ruttenberg, Susie Stephens, Gwen Wong

Susie suggested that we depart from the agenda and review why we are doing the demo and the steps involved with producing the demo.

Susie: We want to show the demo at the WWW Conference, where the audience will be primarily IT people, and ISMB, where the audience will be scientists. We want the demo to be visually appealing and show the benefits of Semantic Web technology.

We should try to combine the Parkinson’s and Alzheimer’s use cases. We don’t need to implement the entire use case. We may only implement subelements of the use case. Tasks involved in the demo’s production include:

  • generation of a use case script for both Parkinson’s and Alzheimer’s.
  • selection of datasets.
  • integrating datasets.
  • user interface
  • presentation script

By next week, John will write something describing the benefits of Semantic Web technology. This will provide input into the selection of use case subelements to be implemented.

Kei: The description of the benefits should include the ease of linking datasets with Semantic Web.

Joanne: I have created a new wiki page for the demo: http://esw.w3.org/topic/HCLS/HCLSIG_DemoHomePage_HCLSIG_Demo

Gwen: [Reporting on progress with the use case script] I have assembled PubChem references that can be loaded into BrainPharm.

Don: I’ve also been working on the use case, working with Bill on the possible inclusion of PATO.

June: We’re hoping Alan can flesh out the use case with more detail leading to a demo scenario.

Joanne: We need to identify benefits so that we can determine what we want the demo to highlight.

Kei: I am including Gwen’s PubChem references into BrainPharm. I believe the BrainPharm ontology can be used to link the Parkinson’s and Alzheimer’s use cases.

Scott: I have been brainstorming with some food informatics people about how to make use cases more specific. [To Alan] Have any queries been identified? The UI is dependent on the demo script.

Alan: I have been having technical problems.

Susie: Perhaps we can get a script next week.

Alan: Not sure.

Susie: Perhaps June and Gwen can focus on the use case so that it can be completed next week.

Alan: The science aspect of the use case is going well. I spent time looking at the Parkinson’s use case.

We need to identify resources and what’s in them.

Susie: Once the use case is finalized, we can determine how to integrate datasets. Perhaps, we can have F2F meetings among those converting datasets to help this process go smoothly.

Alan: F2F’s would be a plus. Answering a question from Scott about Alan’s efforts with Helen regarding their collaboration on ACPP, Alan said that he was able to encode ACPP’s inclusion/exclusion rules in OWL. However, ACPP’s ontology was probably not applicable to the demo.

Helen: For the demo, we could include some rules following the OWL encoding.

Bill: We should include both OWL DL and rules, noting the existence of SWRL.

Susie: I will check with Eric and Tonya about a F2F in the March time frame.

Alan: We should meet earlier and more often.

Vipul: We could meet before the Semantic Web gathering in the Boston area.

Susie: Alan’s F2F meeting schedule suggestion is a good idea. We should also arrange for call in. I think that we should have the demo run on a laptop in case there is no Internet. It would also be possible to have a video. The demo should last no longer than 10-15 minutes.

Alan: A good user interface toolkit is available at http://www.prefuse.org/. Being able to do the demo on a laptop is a good idea. I volunteer to present the demo.

Susie: We need to figure out who will do it, both for the WWW Conference and ISMB.

Joanne: We should be flexible about who gives the demo.

John: If the demo is going to be on a laptop, I presume that it will run in real time. This implies that queries will have to take less than around 10 seconds.

Susie: We should leave that question until next week.

We should make the demo generic so that it could be presented in different forums. The overall presentation should be tailored to the audience.

More on all this next week.