HCLSIG BioRDF Subgroup/Meetings/2006-11-13 Conference Call

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Conference Details

  • Date of Call: Monday November 13, 2006
  • 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
  • Participants: Matthias Samwald, Scott Marshall, Kerstin Forsberg, Marja Koivunen, Eric Neumann, John Barkley, Joanne Luciano, Bill Bug, Tim Clark, Elizabeth Wu, June Kinoshita, Susie Stephens


  • ISWC overview.
  • Housekeeping.
  • Make progress on demo.
  • Identify further scientific questions.

Susie Stephens: Overview of Workshop in ISWC 25 different, short presentations from many areas (bio-, cheminformatics, healthcare, different technologies used). Link to workshop can be found from main BioRDF page (http://esw.w3.org/topic/HCLS/ISWC/Workshop/Abstracts) Some topics of keynote speeches: How can Semantic Web people gain awareness. What can be achieved through 'collective intelligence'. Workshop on OWL 1.1 - a working group might be formed.

Joanne Luciano: Did not agree with some proposed enhancements to OWL by BioPAX developers at the conference.

Bill Bug: BioPAX does not make good use of reasoning engines.

Joanne Luciano: However, OWL 1.1 extensions ARE very reasonable and will be well-accepted. Already implemented in Protégé 4 (complete rewrite of Protégé, includes Pellet) and Reasoners. The new Protégé is a pleasure to work with.

Thanks for Susie for her work at organising the workshop!

When should the paper for BMC bioinformatics be released to the mailing list?

Bill Bug: There is a need to point out how what we are doing relates to the NCBO and the OBO Foundry. People are recognizing differences between the creation of small, isolated ontologies and the creation of broader, bigger Semantic Web ontologies. Building large ontologies leads to different needs and practices. We need a public announcement of the role of HCLSIG to connect to other groups.

Eric Neumann: Eric discussed BMC paper with Kei. The paper is too large. The key is in writing the conclusion. Two alternatives: 1) Describe what the group is doing with Semantic Web Technologies and its uses 2) Do not talk about the HCLSIG, but make a paper about the VISIONS (this would require squeezing the descriptions of the work done on half a page).

Susie Stephens: The task forces are working quite independently, so its hard to write a paper purely as described in alternative 1. We need to convey some vision. Half a page would be enough to describe the task forces.

Tim Clark: Important: Integrating scientific discourse with ontologized facts and data. The thing that is done in SWAN. New things are discovered and discussed - this needs to be covered!

Bill Bug: Gene Ontology / evidence codes: Tying ontologies to data needs to have well-ontologized evidence for making that connection.

Tim Clark: This should also be in the paper.

Matthias Samwald: The BMC paper is on Google - Docs. If you want to join and collaborate, send an e-mail to me, samwald@gmx.at

Susie Stephens: People should make the data they converted to RDF available through the WIKI. We now have links on the BioRDF home page for people to use for their data and documents.

Susie Stephens: The demo -- we need to have MANY queries that can be answered with our demo, not just one. In order to stick to timelines, maybe we should identify a conference where we want to demonstrate what we have, as deadline. Focus on neuroscience: only about Parkinson's and Huntington's, why not other things? Is it OK to include Alzheimer's?

[Several people agree]

Scott Marshall: Huntington's is a good example, because it has a clear phenotype.

June Kinoshita: Alzheimer's research has a large online-community (e.g. AlzForum), which is a big advantage.

Bill Bug: We should make clear what we want to accomplish. AlzForum and other groups provide good and varied use-cases.

Bill Bug: An article states "Many clinical misdiagnoses could be avoided when doctors would just use Google" (!).

Susie Stephens: Which conference should we choose as a deadline? May would be a nice timeframe.

[Different people made several suggestions (e.g. ISMB, AMIA, World Wide Web conference), please send them to the mailing list or write them down in the WIKI] [The question will also be sent to the mailing list]

Susie Stephens: Will check deadlines for the conferences.

Bill Bug: ISMB 2007 Vienna - deadlines - demo - 5/11/2007; papers 2/2/2007; highlight-papers track 3/4/2007; posters 3/23/2007; SIGs 12/15/2006; special sessions 10/29/2006 (http://www.iscb.org/ismbeccb2007/deadlines/)

Susie Stephens: How should we find scientific questions driving our developments?

June Kinoshita: Will identify scientific questions for Alzheimers.

Bill Bug: Many use cases / questions can be derived from BIRN. Will send a link to the mailing list.