HCLSIG BioRDF Subgroup/Meetings/2007-01-08 Conference Call

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Conference Details

  • Date of Call: Monday January 8, 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: Matthias Samwald


  • Review Action Items.
  • Kei Cheung will provide a status update regarding the BMC Bioinformatics paper.
  • Daniel Rubin highlights the use of images within scientific queries.
  • Bill Bug to highlight some of the most appropriate use cases from BIRN
  • Finalize decisions regarding the best venue for the demo.
  • AOB


BioRDF Telcon, 8. January 2007

Attendees: Trish Whetzel, Alan Ruttenberg, Scott Marshall, John Barkley, Don Doherty, Kerstin Forsberg, Susie Stephens, Daniel Rubin, Helen Chen, Vipal Kashyap, Matthias Samwald, Tim Clark, Elizabeth Wu, June Kinoshita, Ewan, Marco, Kei Cheung, Bill Bug, Olivier Bodenreider

Susie Stephens: There have been many different proposals for demos recently. In the next weeks we need to decide on what we will build for the demo. Ideally some of the proposed use cases will overlap, so that we can select more than one.

Kei Cheung: Thanked everyone for contributions to the HCLS paper.

Daniel Rubin: Gave overview of his thoughts on incorporating images into the use case.

Bill Bug: Pressing need for image data. Simple annotation of images would be easier than 'atlasing'. Mouse Brain Atlasing Tool (MBAT) is lacking semantic annotation. However, on the imaging side these systems are very advanced. The BIRN brain atlas and MBAT are also interoperable. The 'query atlas' (another atlasing system) is integrated in BIRN. In mouse-BIRN, the Atlasing functions are already working. However, the tools are very complex. Up to 75% of the functions in these systems is in fact identical. What is important to users of these applications is primarily geometric objects, not necessarily something that can be linked directly to an ontology of brain structures.

Scott Marshall: Adding visualisation to data browsing / query results could also be useful.

(Tim?): We have to distinguish the "textbook perspective" (already solidified, well-founded information) from the "research perspective".

June Kinoshita: Possible use case with existing data: IgG signalling in neurodegeneration, maybe of importance for Abeta vaccine. Information about co-location does not necessarily need to be accompanied by an image, but having images is a very powerful tool. It can lead researchers to look at brain regions they would not have looked at otherwise.

Bill Bug: Overlap of affected brain regions in different conditions and timepoints is of special importance for brain imaging.

Susie Stephens: There seems to be a lot of overlap in interest between the imaging in the BIRN project and the work of SWAN. Two venues to show the demo: ISMB and the World Wide Web conference. The demo needs to be completed by may or june.

Bill Bug: Writes a whitepaper, asks authors if it is OK to include the Alzheimer's use case.

Susie Stephens: BIRN and SWAN will arrange possible collaboration on the integration of images. Don is also working on imaging data for Parkinson's.

June Kinoshita: Overlap between AD and PD use case could be Mouse brain (alpha-synuclein) images.

Don Doherty: Tim mentioned Lewy bodies as another option?

June Kinoshita: Researchers are targeting a-synuclein for immunotherapy. This might be an interesting thing for a connection between Alzheimer's and Parkinson's.