HCLSIG/SWANSIOC/Meetings/2010-11-29 Conference Call
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Zakim RRS Agent Magic (for meeting scribes) /invite Zakim #BioRDF /invite RRSAgent #BioRDF RRSAgent, please draft minutes RRSAgent, please make log world-visible
Agenda
- Use cases for other biomedical repositories (Kees van Bochove)
- ISA-tab to RDF conversion (Philippe Rocca-Serra)
Minutes
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