HCLSIG/SWANSIOC/Meetings/2009-01-16 Conference Call

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Conference Details

  • Date of Call: Friday January 16, 2009
  • 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: 4257 ("HCLS")
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC)
  • Duration: ~1 hour
  • Convener: Tim Clark
  • Scribe:

Agenda

  • Progress Report
  • - SWAN-SIOC IG Note status: Paolo Ciccarese and Alex Passant
  • - SWAN-SIOC-myExperiment status: Tim Clark, Susie Stephens and David Newman Lilly Experiment Ontology
  • Presentation on SAAGE: Sudeshna Das, Harvard University
  • - Semantic Annotation and Analysis of Genomic Experiments
  • Action items and next meeting schedule

Minutes

<Susie> Attendees: Sudeshna, David, Paolo, Tim, Susie, Scott, EricP

<Susie> Agenda: http://esw.w3.org/topic/HCLSIG/SWANSIOC/Meetings/2009-01-16_Conference_Call

<Susie> SWAN-SIOC IG Note status

<Susie> Paolo: 3 documents needed: 1. SIOC, 2. SWANSIOC integration 3. Index

<Susie> Paolo: think it's good to have an overview document

<Susie> Paolo: Next steps are setting up the accounts for Paolo and Alex

<Susie> Paolo: Will use existing IG notes as a model.

<Susie> ACTION: Paolo to get EricP to set up directory accounts

<ericP> paolo_ciccarese, should i set up the directory structure described in http://www.w3.org/mid/20090109194128.GB6042@w3.org ?

<ericP> i wasn't sure you were convinced of that dir structure

<paolo_ciccarese> ericP, it is fine to me to have four folders

<Susie> SWAN-SIOC-myExperiment status

<Susie> Tim: David Newman has posted material

<Susie> Tim: Susie shared the Lilly experiment ontology

<Susie> Tim: I've scheduled a call with the main developer of the ontology

<Susie> Tim: Paolo and David will join the call too

<Susie> David: Been working on the modularized ontology

<Susie> Paolo: Not too time consuming to modularize SWAN, as it was somewhat designed that way

<Susie> David: Modularizing myExperiment took time due to changing the RDF namespaces

<Susie> Action: Tim will send out a doodle proposal for coordinating times with Maurice (Lilly)

<Susie> Paolo: Is there a document that describes the Lilly experiment ontology?

<Susie> Susie: I'm not aware that there is one

<Susie> Action: Tim will ask Maurice is there is a more current version of the ontology and documentation

<Susie> Presentation on SAAGE

<Susie> Sudeshna: 5 laboratories involved

<Susie> Sudeshna: cross institute collaboration

<Susie> Sudeshna: Funding from the Harvard Stem Cell Institute

<Susie> Sudeshna: Can we pull together information on genomic experiments across the 5 organizations

<Susie> Sudeshna: Start with microarray experiments (there are about 100 of them)

<Susie> Sudeshna: Build a repository of this data, allow scientists to access and analyze the data

<Susie> Sudeshna: Although MAGE exists, there aren't nice tools to allow end users to analyze the data

<Susie> Sudeshna: Want to know what stage a cell was at

<Susie> Sudeshna: MAGE doesn't support that

<Susie> Sudeshna: Want to start by stating the stage of development of the cell

<Susie> Sudeshna: The cell type

<Susie> Sudeshna: The cell type is an evolving tree

<Susie> Sudeshna: Need to use ontologies to define the disease states, if chemicals used to treat sample, genetic modifications

<Susie> Sudeshna: Still at the requirements gathering stage

<Susie> Sudeshna: Interface allow you to select cells of interest and perform meta-analysis

<Susie> Sudeshna: With time also repositories for proteomics, and siRNA screening that could link to the gene expression data

<Susie> Tim: The repository will be in Drupal, MySQL, php with semantic metadata

<Susie> Tim: Use semantics to categorize experiments

<Susie> Tim: keeping data in relational and having metadata in a triple store is like the Lilly approach

<Susie> Tim: Might be possible to use Taverna for the analysis, which makes it compatible with myExperiment

<Susie> Susie: Lilly is collaborating with Manchester on adding provenance to LSG

<Susie> Susie: LSG is Lilly's discovery IT framework that is available in SourceForge

<Susie> Tim: Next call in 2 weeks on Jan. 30

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