HCLSIG BioRDF Subgroup/Meetings/2006-12-11 Conference Call

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Conference Details

  • Date of Call: Monday December 11, 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: Elizabeth Wu


  • Task Review - Matthias Samwald
  • Discuss scientific queries from SWAN - Elizabeth Wu
  • Use case that includes gene and spatial information - Scott Marshall


Attendees: Susie Stephens, Joanne Luciano, Elizabeth Wu, June Kinoshita, Alan Ruttenberg, Kei Cheung, Scott Marshall, Matthias Samwald, Don Doherty, John Barkley, Gwen Wong.

SS: Congratulations to Kei Cheung for having his book published.

SS: asked people if they like the idea of having a schedule for scribing, so that everyone shared the load evenly.

SS: We talked about which conferences it would make sense for the group to show the demo at. One option was the BioOntologies SIG at ISMB. JL was to follow up with Robert Stevens to see if this would be an option.

JL: Talked with Robert Stevens, and he recommended that we submit a proposal. Call for industry track proposal has a deadline of March 4, 2007. Application deadline April 23, 2007. This is more like a workshop proposal.

SS: Asked if JL had managed to get in touch with Siderean about sharing the bioinformatics demo.

JL: Said that she had pinged Siderean, but was still waiting for feedback.

SS: Asked Scott Marshall if he had been able to get in touch with the people in The Netherlands who have an open source faceted browsing application to see if they would give us a demo.

SM: Said that he had been in touch with the group in The Netherlands. They are interested in exploring the use of OWL with their software, so that the OWL classes can become the facets. They are also interested in showing us a demo, but would prefer to wait until they have been able to build a demo that used life sciences data.

SS: Could they use some of the data that BioRDF has already generated?

SM: They should be able to use some of our data, but they will also need to decide upon the facets, and that will take time. He agreed to provide feedback on faceted browsing with ontologies and bio data by Jan. 22

SS: Is not on the call today, so we will follow up on his action items next time.

MS: Provided a task update. He said that he has primarily been focused on debugging the BIND data set that he has in OWL. He said that this should be finished by the end of January, so should be able to give an update during the call on February 5, 2007.

MS: Said that he is also working to convert some pathway data sets, e.g. Reactome and Biocyc from the BioPAX representation to BioZen. Not all data will be available within BioZen, as some will have been lost in the initial conversion to BioPAX. However, the goal of the OWL to OWL conversion, is to make the pathway data more accessible to higher level ontologies.

SM: He provided his thoughts on extending the scientific queries. Using current PD use case, would be a really nice addition to link query into a visualization tool, asked Bill Bug for ready off the shelf tool from BIRN. Appeal to people working in image data, expression data mapped to brain Atlas, e.g. Mouse BIRN. Bill Bug recommends the Mouse Brain Atlas tool.

SS: If dealing with treatment data? Does it make sense to link to other species?

AR: Yes, would be more interesting to map MRI data in human brain. For demo, not sure how to make this mapping readily meaningful.

DD: Getting human data raised another level of concern. As long as animal has dopamine or relevant structures, those animal data should be ‘fair game’. OK to include mouse data in demo.

KC: agreed, most models are animal models.

SS: what additional dataset needed to be in RDF to extend to visualization?

KC: does image come with structured annotation?

SM: brain atlas, mapping is taking care of (for free), not sure how ontology is involved. Ontology is ‘data-mediator’, will need to integrate with rest of BIRN tool. Will continue to learn from Bill what is available, not yet identify the source we need to RDF.

JK: described a Alzheimer use case to the group (http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Dec/0038.html)

SS: How many datasets already in RDF?

JK: SWAN, Antibodies, BrainPharm, KEGG, could convert AlzGene, Love to look at gene expression maps in Mouse Brain.

Action Item – by January 8, identify a list of databases needed in RDF for this use case

AR: Hard part is the literature searches and obtaining patient data in immunization studies.

AR: want to follow up with June to discuss the use case further.

SS: Next call on 8th January 2007. Keep communication on emails.


  • JL will see if Siderean will make their software available as a demo.
  • BB to send out the URL for the use cases again.
  • BB will identify some of the best use cases, and will go over them during the next BioRDF call.
  • BD will post a workflow of the clinical trial process on the wiki.
  • All ISMB industry track assess (looks like papers to me)
  • SS set up a scribe list
  • SM feedback on faceted browsing with ontologies and bio data by Jan. 22
  • MS update on improving quality of the BIND ontology by Feb 5.
  • MS conversion of pathways from BioPAX source to BioZen by ?
  • EW/JK provide list of data sources for Alzheimers demo by Jan 8.