User:Jmuhlich/ICSB 2008 SBWiki presentation

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A semantic structured wiki for systems biology research

Jeremy Muhlich

Current Practice

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raw spreadsheets & SBML hairballs

New Standards Help...

MAGE (BioAssay) BioPax
  • MI (Minimum Information) efforts such as MIAME/MAGE are good for published data, but too rigid for daily use and generally require a curator/enforcer
  • Ontologies like BioPax and SBO are sound computer science theory, but to biologists this is just mapping one hairball onto another

SB-Wiki: Practical Documentation

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  • Annotate early, during research not after
  • Use concepts from existing standards
  • Rigorously apply "80/20" rule


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  • Group consensus documentation
    • "Opinionated" views
  • Collaborative editing
  • Easy sharing
  • Change tracking, history preservation


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  • High-level structure based on MIBBI (Minimum Information for Biological and Biomedical Investigations)
    • There is a richer underlying ontology, but the user doesn't need to know about that
  • A unique form for each type of "thing" with a few important fields
    • No required fields! Just enter what you have and get on with your life
  • Alignment with existing ontologies and standards (e.g. SBML/MIRIAM) eases transition to those formats upon publication


  • Closer integration with DataRail
  • Smart model re-import
  • Model "export" with MIRIAM annotations added
  • Expand ontology to support different areas of systems biology research

Personal tools