FlyWeb: Linking Laboratory Image Data with Public Databases and Publication Repositories
Overview
The FlyWeb Project is implementing a proof-of-concept data web to integrate research data resulting from gene expression experiments in the fruit fly Drosophila melanogaster with related life science data and publications.
For scientists in many domains, the difficulty of finding and 'joining up' data scattered across many heterogeneous sources remains a significant blocker to hypothesis generation and discovery. New web standards such as RDF, OWL and SPARQL offer hope, providing an opportunity to create data webs where research data and metadata from databases and repositories are published and linked together via the Web, serving research needs within and across domains. The FlyWeb project is putting these ideas to the test within the domain of Drosophila functional genomics.
Aims and objectives
The project is developing a data web linking a number of sources of genomic data relating to the fruit fly Drosophila melanogaster. This data web is being provided as a service to software developers and bioinformaticians. To demonstrate the potential of this data web, the project is also building on-line data search and mashup tools on top of the data web that help scientists to be more productive and generate insights, through quick and easy location, comparison and analysis of data from different sources.
Project methodology
The team is taking an agile approach, working closely with domain researchers to identify gaps in current online services for the Drosophila research community, then targeting both data web and user interface development accordingly. To construct the data web, the team is converting a number of important sources of Drosophila data and metadata to RDF/OWL, and publishing these via Web services using the SPARQL protocol. To construct user tools, the team is developing a library of Web 2-style user interface components that query and visualise data from the data web and can be easily combined to create new data mashups. These tools are deployed in a public Web site openflydata.org.
Anticipated outputs and outcomes
- a data web for Drosophila functional genomics
- on-line data search tools and data mashups
- improvements to the robustness, performance and scalability of current open-source data web technologies
- data web know-how transferable to other domains
Technology / Standards used
RDF, OWL, SPARQL, Jena, Java, Tomcat, Apache, Javascript, YUI
Lead Institution
University of Oxford
Project partners
University of Cardiff
Project Staff
Project Manager
Project Team