HCLSIG BioRDF Subgroup/Meetings/2007-06-18 Conference Call

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Conference Details

  • Date of Call: Monday June 18, 2007
  • Time of Call: 11:00am Eastern Time
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (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: Kei Cheung


  • Select additional data sets for incorporation into the demo - all
  • Discussion of next steps and focus for URI note - Jonathan
  • Further review of demo ontology - Matthias, Alan, etc.
  • AOB


BioRDF teleconference call (6/18/07)

Scribe: Kei Cheung Participants: John Barkely, Helen Chen, Kei Cheung, Don Doherty, Scott Marshall, Jonathan Rees, Alan Ruttenberg, Matthias Samwald, Susie Stephens

Susie: Agenda items: demo & poster, URI, Review of the Banff demo ontologies, other

Alan: update on the current ontologies used for the Banff demo. URI resolution is one of the next important things to do. Some sort of semantic web map may be created. For example, class diagram of nerondb.

Alan: for the poster, we might want to talk about the process. What the audience may be think?

Kei: What type of audience? Are they ontologists and/or biologists?

Alan: probably, the target should be ontologists.

Susie: based on some previous experience (e.g., ISMB 2005 in Detroit), out reach to other types of audience.

Matthias: a map may be used.

Alan: a map seems to make sense to indicate inference, circles (datasets), sidebar for highlighting issues, etc.

Susie: should an abstract be included in the poster? It might mention HCLS, AD, infrastructure, number of triples, etc.

Matthias: the poster presentation should be coordinated with the demo presentation.

Susie: Eric Neumann will present the demo

Scott: What about text mining?

Alan: In neurocommons, some text mining work has been done in the context of Huntington Disease. Evaluation of HCLS interest in text mining is needed.

Matthias: neurocommons can play a role in bridging the text mining world and the database world.

Susie: the map that Matthias is working should be shown to the mailing list for people to look at and give feedback.

Matthias: it shouldn’t be a problem.

Susie: next topic HP server – temporary site for neurocommons.

Alan: it’s ready.

Susie: how long will be transition.

Alan: still waiting.

Susie: more datasets.

Alan: will work with John on the name space issue.

Kei: SenseLab’s neurondb, modeldb, and brainpharm ontologies are essentially done. However, there is an ongoing need to update the ontologies as the databases evolve. It’s not a trivial process. Intensive manual work is needed.

Alan: documentation is needed.

Kei: a paper is being written. A small group face-to-face meeting (at Yale) may help to understand the process involved in continued evolution and maintenance of SenseLab ontologies.

Alan: the idea to have a face-to-face meeting at Yale is good.

Susie: Alzgene?

Alan: will work with Elizabeth Wu.

Susie: mesh to pubmed.

Jonathan: working on notes.

Susie: end of September?

Susie: Pubmed to Entrez gene has similar status to mesh to pubmed.

Susie: ABA?

Alan: working on it. GENSAT if needed.

Kei: GENSAT might be useful for microarray projects. Will look into it.

Susie: CCDB?

Matthias: working with CCDB group on SAO. The goal is to try to align it with BFO.

Susie: Antibody?

Alan: sitting and waiting. More work needs to be done.

Susie: SWAN?

Alan: needs to follow up.

Susie: Pubmed? Follow up with Eric Neumann.

Susie: Cell type?

Matthias: PDSPK database

Susie: URI?

Jonathan: the central person coordinating it. Collecting information/materials from different groups.

Kei: What about Banff Manisfesto?

Jonathan: it seems to be proposed only by one or two persons.

Susie: we should think and talk more about this web architecture.