HCLSIG BioRDF Subgroup/Meetings/2006-02-20 Conference Call

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Conference Details

  • Date of Call: Monday February 20, 2006
  • Time of Call: 11:00am Eastern Time/16:00 UTC
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Participant Access Code: 246733 ("BIORDF")
  • Duration: ~1 hour
  • Convener: Susie Stephens
  • Scribe: Davide Zaccagnini


During the call we plan to primarily focus on the next steps required to help us to reach the 3 month goals:

  1. Identify the initial data sources to be used in the demo.
  2. Explore additional data sources that would be required for the demo to span ‘bench to bedside’.
  3. Learn about GRDDL, SPARQL, OWL, etc.
  4. Increase knowledge of neuroscience.
  5. Set up a Wiki for communication.

Meeting Minutes

Attendees: Davide Zaccagnini, Roger Cutler, John Berkeley, Eric Neumann, Kei Cheung, Vipul Kashyap, Scott Marshall, Alan Ruttenberg, Robin McEntire, Susie Stephens

Communication and interactions: Weekly calls will be held in the initial period to guarantee quick and effective tasks definition and assignments, later on the schedule may be relaxed. Call’s time and day are confirmed for Monday 11AM EST. This will be shared with other potential participants, not present in this call, for feedback and eventual modification. As for now the conference will not be combined with the Ontology Group’s conf call. Alan Ruttenberg has set up a BioRDF Wiki site (http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup). Susie and Alan will convene a call with the other sub-groups to identify touch points, but the core goal of the BioRDF group will be to make data available as RDF.

Goals: The group’s goal is to make data available as RDF rapidly. The group will focus on practical experiences and use cases. In addition, relevant examples highlighting the benefit provided by semantic web standards over traditional technologies will be identified and presented in the final demo. Lower economic costs and flexibility are possibly among potential benefits. Vipul pointed out the possible need to address human intervention for adding semantics to unstructured data. The group would rather focus on technical aspect of the transformation and human intervention will therefore be tackled as an interaction point with the Ontology working group.

Identification of data sources: Olivier volunteered to catalogue the NCBI data resources. He said that he should be able to provide a short description by the end of the month. Susie will see if he could get this done in time for next week’s call, so that people can select data sources to start converting into RDF. Olivier has also volunteered to share and coordinate a more detailed catalogue that would include information relating to the kind of data represented and how the data are represented, but this would take longer to prepare.

John Wilbanks has kindly agreed to give the group a primer to neuroscience during a call in March. This would give us the opportunity to learn more about the clinical requirements. It may make sense to invite members from the SWANS and Synapse projects to participate in the call too.

Descriptions of NCBI data resources will be circulated within the group to provide a basis for scoping out a clinical use case. Davide volunteered to work on the use case definition. Vipul volunteered to ask clinicians from Partners for medical issues to be addressed by use cases.

Eric pointed out that the identification of a specific clinical case should not hold the group from moving forward on other tasks since most of insights and solutions for transforming unstructured data into RDF will be generalizable to different clinical domains.

Alan proposed a tool in LISP that he developed for transforming Excel sheets into OWL, running Pellet on OWL and querying it with SPARQL, the tool can be made available for interested members.

Technology: Susie has invited Eric Prud’hommeaux to give the group a primer on SPARQL and GRDDL.