HCLSIG/SWANSIOC/Meetings/2009-01-09 Conference Call

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Conference Details

  • Date of Call: Friday January 9, 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
  • Linkage to MyExperiment
  • IG Note
  • Action items and next meeting schedule

Minutes

Attendees: Tim, David, Scott, Paolo, Matthias

<Susie> Tim: I've updated the primary objectives

<Susie> -> http://esw.w3.org/topic/HCLSIG/SWANSIOC

<Susie> 1. Integrate SWAN and SIOC ontologies.

<Susie> 2. Implement "Community-of-communities" Use Case

<Susie> 3. Integrate SWAN and myExperiment ontologies

<Susie> 4. Implement DiscourseAndExperiment Use Case

<Susie> 5. Guide the semantic enhancement of Drupal

<Susie> David: Look good

<Susie> Susie: Objectives look good

<Susie> Tim: Gap between SWANSIOC and MyExperiment in that there isn't a description of a physical experiment

<Susie> Tim: Looked at OBI

<Susie> Tim: It's a huge project, but couldn't find 'experiment' in there anywhere

<Susie> Tim: Could do depth first or a beadth first approach

<Susie> Susie: Lilly's Experiment Ontology might be useful

<Susie> Susie: Lilly Ontology is at http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Experiment_Ontology

<Susie> Tim: Sudeshna and I are doing a funded project with the Harvard Stem Cell Institute

<Susie> Tim: Look at how the stem cells differentiate through OMIC experiments

<Susie> Tim: Building repository for the results of these experiments, and it will become part of SCF

<Susie> Tim: There will be semantic characterization of the data

<Susie> Tim: We'll develop analytic methods for these OMIC experiments

<Susie> Tim: None of that is work for this group

<Susie> Tim: Could use Taverna for the workflow definer

<Susie> Tim: Useful in repository of experimental data to have an RDF description of an experiment

<Susie> Tim: Because capturing provenance is important

<Susie> Tim: MyExperiment states this is the workflow used, analysis, etc,

<Susie> David: Most work done with cloud services provided by MyExperiment

<Susie> Tim: That would be OK too

<Susie> Scott: Many types of provenance. MyExperiment primarily has execution provenance

<Susie> Scott: Tim more interested in provenance related to data, e.g. machine readable metadata about microarray experiments

<Susie> Tim: That's correct

<Susie> Tim: Also interested who ran the experiment, where it's written up in a lab notebook, what the hypothesis is, etc.

<Susie> Tim: SWAN could be used to capture the hypothesis information

<Susie> Tim: Focus on experiments that lots of people do, where lots of automation and Excel files

<Susie> Tim: Have money to do this work for a couple of years

<Susie> Tim: Could do the work as part of the task

<Susie> Scott: Many people would find it valuable, as long as most people don't have to do the work themselves

<Susie> Scott: Used to work in a microarray lab

<Susie> Tim: So you'll have thoughts you can contribute

<Susie> Scott: Yesterday Tim mentioned that MyExperiment is more focused on computer analysis, want to add that MyExperiment can treat computational work as an experiment

<Susie> Tim: Should have a class called 'experiment' with subclasses of 'computational' and 'lab'

<Susie> Scott: Most biologists dismiss computational experimentation

<Susie> David: Initially computational experiments is what we are doing, but no reason not to expand it

<Susie> David: Integrating in vitro experiment models

<Susie> David: microarray flows are already in MyExperiment

<Susie> Tim: Another driving project could be brain imaging

<Susie> Tim: There are groups of people interested in the ontology of brain imaging

<Susie> Tim: We could help other peoples work

<Susie> David: Trying to split up MyExperiment ontology, so people could just integrate the bit they are interested in

<david_newman> http://rdf.myexperiment.org/new_class_hierarchy

<Susie> ACTION: David Newman to ask Dave de Roure to get him signed up as a HCLS participant

<Susie> Susie: Should be able to get a wiki account even before a member of HCLS

<Susie> Tim: Semantic Annotation Analysis Genomic Experiment (SAAGE) - Tim will distribute more information about this

<Susie> ACTION: Tim distribute information about SAAGE

<Susie> ACTION: Dave post URLs on Wiki about MyExperiment

<Susie> Tim: This will take some work, but we could get on a roll

<Susie> Tim: Harvard can be the lab for the group

<Susie> Tim: Susie - is there someone at Lilly who could serve as an advisor in this?

<Susie> Susie: Maurice Manning would be the best person

<Susie> ACTION: Susie to see if Maurice would like to participate

<Susie> ACTION: Paolo to look at the modularization of MyExperiment

<Susie> Scott: Is this the work that will be written up in an IG note

<Susie> Tim: We've been talking about writing up objectives 1 & 2 in an IG note

<Susie> Tim: Could do one for 1& 2 now if we don't include an implementation

<Susie> Tim: Need to see how long the implementation will take

<Susie> Scott: Could you start writing in parallel?

<Susie> Tim: A lot has already been written up, and is already at the editing point

<Susie> Tim: The other objectives would be in another document

<Susie> ACTION: Tim to confirm that Alex and Paolo want to be editors

<Susie> Tim: Then we'll decide the format for writing up the note

<Susie> Tim: Next call on January 16

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