User:Jmuhlich/ICSB 2008 SBWiki presentation

{| =SBWiki=
 * [[Image:sbpipeline logo.png]]

A semantic structured wiki for systems biology research
Jeremy Muhlich
 * }

=Current Practice=

raw spreadsheets & SBML hairballs

=New Standards Help...=


 * 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=


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

=Benefits=


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

=Design=


 * 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

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