HCLSIG BioRDF Subgroup/Meetings/2007-10-15 Conference Call

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Conference Details

  • Date of Call: Monday October 15, 2007
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: +33.4.89.06.34.99 (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
  • Scribe: Olivier Bodenreider

Agenda

  • SfN Poster Update - Don
  • F2F / Meeting Updates (F2F, ISWC, WWW, Bio-IT World) - Susie
  • URI note - Jonathan
  • Knowledgebase extensions - Alan
  • Documentation of SenseLab conversion - Kei
  • Clinical data set assessment (SEER, ADNI, GIS, IARC) - Matthew, Kei, Susie
  • Demo of Prova - Adrian
  • AOB

Attendees

Susie Stephens, Olivier Bodenreider, Kei Cheung, EricP, Alan Ruttenberg, Don Doherty, Jonathan Rees, Adrian Paschke

Minutes

Meeting Updates

  • F2F: possible time change for the BioRDF session to make sure the CDISC folks can attend the session (Vipul will coordinate with Tanya and EricN)
  • ISWC - BOF: 4 people signed up already; proposals need to be sent before Oct. 19 (for details, see: http://esw.w3.org/topic/HCLS/ISWC2007/BOF)
  • WWW: Alan and Susie are working with Lee Feigenbaum on a tutorial proposal for WWW.
  • BioIT World: Send one paragraph to Susie by Oct. 24 if you want to present there.

URI note

  • DavidBooth suggested making Jonathan's analysis shorter (around 2 pages), so that more people would get engaged and provide feedback; additional explanations could be put on the side to provide background if necessary.
  • Jonathan is finalizing the notes, has already shared drafts with selected people, and is expected to release them next month.

Knowledge base extensions

  • AlanRuttenberg is working on RDF for citations. He mentioned that two recent hires at Science Commons will also contribute to various aspects of the BioRDF project, including conversion of additional databases (e.g., radiology images, caBIG sources)

HCLS demo

  • A mirror for the demo has been set up at DERI. Oracle is also interested in installing the demo.
  • JonathanRees volunteers to write a readme file. Some issues including academic attribution and interactions with PubMed still need to be worked out. Jonathan points out that the preferred mode for redistributing the demo would be to distribute the code and let the potential hosts deal with content issues, if any.

SfN Poster Update

  • DonDoherty has posted a rough draft of the poster, showing the PubMeSH data flow diagram, the SPARQL query (with a step-by-step walk through), and a portion of the corresponding graph.
  • A screenshot of the Allen Brain Atlas could be added, possibly showing 4 panes as in BIRN.
  • Subsequent drafts will be released in PDF format.

Documentation of SenseLab conversion

  • KeiCheung is working with the architect if SenseLab to create a dump of the database that could be shared with the HCLS community. This involves removing private data (e.g., user profile) from the current database. Kei requested feedback as to what information should the community would like to find in the dump. AlanRuttenberg offered to provide feedback.

Clinical data set assessment

  • Sources under investigation include SEER, ADNI, GIS, and IARC
  • KeiCheung provided a short description of GIS, a suite of geospatial tools used for cancer research at the National Cancer institute (NCI). GIS includes 4 major components: a database of geographical information, tools for spatial data analysis, visualization tools, and statistical information sources. One possible application is to create mashups of geographical and epidemiological cancer information.

Demo of Prova