HCLSIG BioRDF Subgroup/Meetings/2010/03-22 Conference Call

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Conference Details

  • Date of Call: Monday March 22, 2010
  • Time of Call: 11:00 am 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: 4257 ("HCLS")
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for IRC access.
  • Duration: ~1 hour
  • Frequency: bi-weekly
  • Convener: Kei Cheung
  • Scribe: Kei Cheung


Chris Baker, Kei Cheung, Don Doherty, Satya Sahoo, Matthias Samwald


Rob Frost, Scott Marshall, Michael Miller, Jun Zhao


  • Introduction [Kei]
  • IPhone app demo [Don]
  • Microarray use case -- RDF structure of genelist + experiment + provenance [All]
  • Collaboration with sci. discourse based on the microarray use case [Sudeshna, Jun, Satya, Scott]



Chris Baker joined biordf call for the first time and gave an introduction.

He started sw projects including visual query interface at the Univ. of Concordia in Canada

He worked with Kei on the semantic web/life science book

He moved to Singapore and was involved in text mining projects and lipid ontology

The ontology has axioms and classes for representing lipid molecules

He is now a research chair in Univ. of New Brunswick, Canada

His group develops semantic web services to mark up lipid related abstracts

In addition, semantic assistant framework has been developed

Kei: it may be of interest to the group for Chris to present some of his work

iPhone app

Kei: thank Don for creating the wiki page

Kei: one suggestion -- add a link to allow people to download the iphone app presentation

Kei: iPhone app is a potentially interesting demo of semantic web query federation in the mobile context

Kei: What other sources/services are available for iphone app to potentially incorporate

Don: Gene lists can be incorporated to answer queries such as find disease related information about certain genes that are found differentially expressed in certain conditions.

Kei: we are working on the rdf representation of genelists. Once it’s done, such rdf-formatted genelists can be represented as linked data and loaded into triplestore (e.g., HCLS KB) so the iphone app client can access. We can work with Matthias on this.

Don: agree with the plan

Microarray use case

Kei: will work with Satya and Jun to take the RDF graph (drawn based on a few spreadsheet examples) and the initial RDF version created by Lena to create a more complete version.

Kei: this RDF format (named graph) may be used by the sci. discourse subtask.

Satya: will set up a skype call with Jun and Kei to get it going.

Next BioRDF call will take place in 2 weeks.