Lowering barriers topublishing biological data on
the web
Brad Chapman
Department of Molecular BiologyMassachusetts General Hospital
Boston, MA [email protected]
http://friendfeed.com/chapmanb
27 June 2009
Motivation
Motivation
I Web accessible
I Interoperable in standard formats
I Displays for browsing
I Analyses
I Scale
Current state: Reusable libraries
I Parse file formats
I Run programs
I Build analysis pipelines
I Communities
Python examples
I Biopython
I bx-python
I pygr
I PyCogent
Current state: Database schemas
I Represent biological data
I Expand analyses beyond flat files
I Interoperate with standards
BioSQL Chado
Current state: Web applications
Faster and Bigger
Proposal
I ProvideI Reusable presentation componentsI Quickly deployable frameworks
I IntegrateI Bioinformatics librariesI Database schemasI Web development frameworks
Proposal
http://biosqlweb.appspot.com/
Challenges: Design
I ReusableI Components: avoid large frameworkI Multi-language: javascript front end
I AccessibleI Automated data retrieval (REST)I Standard formats (GFF, RDF)
I AvailableI Creative Commons
http://creativecommons.org/about/licenses
I Open Data Commonshttp://www.opendatacommons.org/licenses/
Challenges: Community questions
How do we. . .
I provide plug-in components?
I leverage existing code?
I make reuse easier?
I communicate about these issues?