Bio-SODA: Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data

At a glance

Project leader: Prof. Dr. Kurt Stockinger

Project team: Christophe Dessimoz (Uni Lausanne), Marc Robinson-Rechavi (Uni Lausanne), Heinz Stockinger (SIB), Dr. Maria Anisimova

Financing: SNF

Project start date: 01-03-2017

Project partner(s): SIB Swiss Institute of Bioinformatics, University of Lausanne

Short description

One of the major promises of Big Data lies in the simultaneous mining of multiple sources of data. This is particularly important in life sciences, where different and complementary data are scattered across multiple resources. To overcome this issue, the use of RDF/semantic web technology is emerging, but querying these systems often proves to be too complex for most users—thereby hampering wide development and adoption of these technologies.

This project aims at enabling sophisticated semantic queries across large, decentralized and heterogeneous databases via an intuitive interface. The system will enable scientists, without prior training, to perform powerful joint queries across resources in ways that cannot be anticipated and therefore goes far and above the query functionality of specialized knowledge bases.

The project represents an interdisciplinary collaboration between information systems and bioinformatics—directly building upon the team’s prior experience in integrating databases at a major Swiss bank, in developing world-leading bioinformatics databases, in combining biological ontologies for data analysis, and in maintaining the highly accessed bioinformatics resource portal ExPASy.