HCLSIG BioRDF Subgroup/Meetings/2007-01-22 Conference Call

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Conference Details

  • Date of Call: Monday January 22, 2007
  • 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: Kei Cheung


  • Review Action Items.
  • Progress report on URI document - Alan, Jonathan
  • Update on hosting the demo - Helen
  • Progress report on faceted browsing tool - Scott
  • Discuss extension to AD use case for images - Bill, Elizabeth, June, Tim, et al.
  • Discuss intersection points with the PD use case - Don, Bill, June, et al.
  • Require data sets for the integrated demo - Elizabeth
  • Time lines for completing the demo - Susie
  • AOB


Participants: Scott Marshall, Daniel Rubin, Olivier Bodenreider, Matthias Samwald, Kei Cheung, Vipul Kashyap, Elizabeth Wu, Tim Clark, June Kinoshita, John Barkley, Helen Chen, Bill Bug, Alan Ruttenberg, Joanne Luciano, Jonathan Rees, Don Doherty, Susie Stephens

  • Susie gave an outline of the agenda
  • Joanne gave an update on Siderean's Seamark Navigator. It didn’t seem to be a viable tool for our group.
  • Bill talked about use case from BIRN incorporating images and working with Tim and June with a focus on BIRN and spatial querying
  • Susie would post the clinical workflow with the minutes (Bill Dyer)
  • Bill: ACPP, clinical trials, medical records …
  • Susie: venue for the demo. For example, ISMB industrial track (workshop?)
  • Bill said that the group should also explore other opportunities to showcase. He would look into such opportunities.
  • Matthias mentioned other opportunities at ISMB.
  • Joanne said that it might be possible to do the demo at the BioPAX consortium.
  • Jonathan gave an update on the URI doc (notes). A draft is being worked on. More context needs to be added. A completed draft would be available by the end of next week.
  • Susie said that it would be better if such documents exist as W3C notes which are linked from the BioRDF wiki.
  • Helen reported on where to the host the demo. There are a number of possibilities: 1) NCBO, 2) NLM, 3) University of Tennessee, 4) W3C.
  • Joanne mentioned the possibility of hosting the demo via BioPAX
  • Daniel said that BioPortal would provide URI service. Feedback and comments are welcome. Community needs should be identified.
  • Olivier pointed out that although these are not being considered by NLM at the moment, it doesn’t mean that they won’t be considered in the future.
  • Bill said that some extended discussion were provided on existing data and knowledge sources relating to Alzheimer’s Disease, for example. BIRN project (e.g., BIRNex) as well as BioPortal provide distilled knowledge sources.
  • Scott: keeping the longevity (including backup and maintenance) of an oracle RDF server is an issue. If needed, it can be done at CWI?
  • Susie: there are many good options to host the demo, although BioPortal is one good option.
  • Scott talked about a browsing tool (http://e-culture.multimedian.nl/demo/search). It uses RDF only (no OWL support). It supports SPARQL queries. It is possible to extend the tool to support OWL in the future.
  • Scott asked whether datasets are available over the web.
  • Susie said that there are links to some of the datasets. What is the role of the demo? Tool and interface? OWL support? BioOnt?
  • Bill pointed out that there are querying tools provided by BIRN. BIRN also provides the so-called “brain graph” querying capability.
  • Susie asked what interface would make sense. Maybe we need multiple tools welding together. For example, Fresnel?, Haystack, BioDash.
  • Scott said that the demo should involve different types of data (e.g., diseases, binding sites, neuronal compartments, cell types, etc).
  • Joanne said that literature databases might also be included.
  • Alan said that we might need to go backward focusing on demo and technology.
  • Susie suggested that they could be done in parallel with a focus on AD use case.
  • Bill said it might be possible to combine the AD and HD use cases. How to interrelate them. Also, how to interrelate BioRDF and BioOnt.
  • Joanne said that Bill did a good job summarizing it with examples of scientific questions.
  • Susie agreed that solid use cases should be driven by scientific questions. These use cases should be written up.
  • Vipul also agreed that the demo should show the good use and value of SW technologies.
  • Susie asked how to coordinate the effort between BioRDF and BioOnt. There are overlap in terms of TC’s and use cases. The two groups should collaborate on the common use cases.
  • Bill said that BioRDF and BioOnt help identify distilled knowledge resources of the datasets. Mapping between these resources could be established.
  • Susie said that data should be assigned to use case and mapping between the datasets.