Knowledge integration and management for computational biology

Biomedical research is an increasingly knowledge-intensive discipline. Researchers need effective and easy-to-use tools to integrate knowledge from different and heterogeneous sources, to correlate their observations with preexisting knowledge, and to convert the results of their experiments into easily managed datasets. All this needs to be performed quickly, in an automated fashion, and without requiring the user to be familiar with the structure and organization of the multiple databases involved in the analysis and annotation process.

We are developing Genephony, a web-based tool for the creation and manipulation of sets of genomic information. Genephony allows the user to create datasets by parsing uploaded files, by deriving them from existing datasets, or by combining existing datasets. Datasets can then be browsed, filtered, and exported in a variety of common formats. Genephony is optimized to handle large quantities of data, such as those resulting from high-throughput experiments, and can therefore be used not just as a browser for genomic knowledge, but also as a large-scale annotation tool. A pre-release is currently available here for testing purposes only.