FlyWeb – Working Across Databases for Drosophila Functional Genomics

by Alistair Miles

Over the last year or so, my main priority has been the FlyWeb Project. Unfortunately, FlyWeb was supported by short-term funding (18 months), and is coming to an end soon. Here are a few belated notes on what we did and why we did it…

The main goal of FlyWeb was to minimize the time required for a researcher in the domain of Drosophila (fruit fly) functional genomics, with no informatics training, to find and compare gene expression data from different databases on a large number of genes. With this in mind, we developed openflydata.org, which hosts the following cross-database gene expression data search applications:

The applications are all pure JavaScript, built using a custom library called FlyUI. They fetch data AJAX-style directly from four SPARQL endpoints, one for each of the four sources of genomic data. On the server side, we use Jena TDB as the underlying RDF storage and query engine, and SPARQLite as the SPARQL protocol server. The whole thing runs on a small EC2 instance.

Further details on our work to convert the four data sources to RDF, in addition to bulk RDF downloads, SPARQL endpoints and more, can be found at the links below:

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