HCLSIG BioRDF Subgroup/Meetings/2007-02-05 Conference Call

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Conference Details

  • Date of Call: Monday February 5, 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, Vipul Kashyap
  • Scribe: Scott Marshall


  • Review Action Items
  • Participation at ISMB - Bill, Matthias, Joanne
  • Progress report on UI tools - Scott
  • Use case progress (images & AD - PD intersection) - Bill, Don, Elizabeth, June, Tim, et al.
  • AOB



Participants: Scott_Marshall, Susie_Stephens, Vipul_Kashyap, Joanne_Luciano, Don_Doherty, Eric_Neumann, Bill_Bug, [IPcaller], Kei_Cheung, John_Barkley, Kerstin_Forsberg, Alan Ruttenberg, Matthias Samwald

  • Vipul discusses aligning use case strongly with demo
  • Bill suggests starting with AD use case
  • June: points to wiki page for ADPD use case, we tried to relate AD to Parkinson's
  • RS - short for Research Statement
  • June: reverse engineer data sources such as BrainPharm
  • Bill: Looking at SenseLab data that is related to the use case
  • Kei: When we've done further data conversion in BrainPharm, we should have more ways to capture neurological
  • Vipul: ACTION ITEM: Someone help populate ontology
  • June: If you search for alpha-synuclein in BioCyc you find a large number of citations
  • Eric: You could hack in the hypotheses to point to the article that they were derived from.
  • Vipul: Action Item: Don will send PD research statements to incorporate into SWAN
  • Helen: How will the process of entry into SWAN work?
  • Alan: I'm trying to understand how we fit the hypothesis together with the rest of the text, questions on the wiki?
  • Eric: You need to set up a script/scenario that explains who's doing what with the data, to explain the flow
  • ACTION ITEM: Alan will define a demo script.
  • Joanne: tentative timeline?
  • Alan: Will know more tomorrow.
  • Vipul: Some of us need to take ownership of particular RDF data
  • Alan: Expects to see a process of query refinement
  • Bill: Current pages point result from existing work
     Might want to look at the original documents that led to the current (which doesn't communicate everything)
  • Bill: Two different ways of acting out a use case
  • Vipul: Moving on to other points:
  • Vipul: How do we identify the concepts of ontological importance?
  • Vipul: Someone want to take the lead on the information flow diagram?
  • Alan: It's too early for that.
  • Vipul: For BIONT tomorrow: info flow diagram, distilled knowledge sources
  • Alan: Would like RDF dumps of SWAN and BrainPharm to work with.
  • Vipul: There are now 6 action items.
  • Alan: People should be familiar with how to pose a question using SPARQL.
  • Bill: Don't think that we'll have enough resources to integrate BIRN tools for the demo.


  • ACTION: Populate Brain Pharm with PD Use Case Data [1]
  • ACTION: Don will send research statements to SWAN Team [2]
  • ACTION: To create the information flow diagram - Susie, Vipul owners [3]
  • ACTION: Alan R to do the demo script and look at BIll Bug's pointers [4]
  • ACTION: Get the RDF dumps from BrainPharm and SWAN - Kei and Tim
  • ACTION: Use the RDF dumps to analyze references for Knowledge Artifacts - BIONT
  • ACTION: Familiar with using one RDF Time --- ALL