Lowering barriers to publishing biological data on the web

Lowering barriers topublishing biological data on

the web

Brad Chapman

Department of Molecular BiologyMassachusetts General Hospital

Boston, MA USAchapmanb@50mail.com

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?