HCLSIG/SWANSIOC/Meetings/2010-11-29 Conference Call

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  • Use cases for other biomedical repositories (Kees van Bochove)
  • ISA-tab to RDF conversion (Philippe Rocca-Serra)

Data+Experiment Task Page


SciDisc Minutes 11.29.10

In attendance:

  • Gully Burnes
  • Paolo Ciccarese
  • Tim Clark
  • Sudeshna Das
  • Joanne Luciano
  • Scott Marshall
  • Philippe Rocca-Serra
  • Kees van Bochove

Scribe: Scott Marshall

Kees presented the summary of the 2010 Symposium on Metadata Capture held on Nov 10, 2010 at Utrecht, The Netherlands. Slides here

  • Survey of biomedical repositories:
    • Molgenis (Morris Swertz) provides dynamic data and processing infrastructure
    • SysMO, java application (Katy Wolstencroft) generates an eXcel file.
    • GCSF (Barend Mons) Provides Generic Study Capture Framework that makes use of Bioportal to enrich the interface with ontology autocompletion in the interface
    • BioRDF (Scott Marshall) use case for microarray provenance
  • The added value of Semantic Web would be to be able to have your own private datastore. Uploading all your experiments to EBI is a problem, especially when things still have to be published
  • "How do I get the biologists to phrase a SPARQL query?

Philippe presented the ISA-tab format and RDF representation. Slides here

  • Motivation and origins of ISAtab: microarray, mass spec data from projects, needed support for various formats
  • Researchers can declare variables and base them on ontologies from Bioportal
  • Goal is to focus on representing experimental design with details such as sample sizes (this complements work in BioRDF on molecular aspects)
  • Reused existing ontologies such as OBI but for scientific discourse probably an overview is sufficient