Bio-SODA – Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data (SNSF NRP 75 "Big Data")
At a glance
- Project leader : Prof. Dr. Kurt Stockinger
- Project team : Dr. Maria Anisimova, Prof. Dr. Christophe Dessimoz (Uni Lausanne), Dr. Manuel Gil, Tarcisio Mendes de Farias (Uni Lausanne), Prof. Dr. Marc Robinson-Rechavi (Uni Lausanne), Ana-Claudia Sima, Dr. Heinz Stockinger (SIB), Erich Zbinden
- Project status : completed
- Funding partner : SNSF (NFP 75 «Big Data» / Projekt Nr. 167149)
- Project partner : Université de Lausanne, Swiss Institute of Bioinformatics SIB
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.
Distributed and Parallel Databases.
40(2), pp. 409-440.
Available from: https://doi.org/10.1007/s10619-022-07414-w
Proceedings of the 33rd SSDBM.
International Conference on Scientific and Statistical Database Management (SSDBM), Online, 6-7 July 2021.
Available from: https://doi.org/10.1145/3468791.3469119
Journal of Big Data.
Available from: https://doi.org/10.1186/s40537-020-00383-w
Sima, Ana-Claudia; Dessimoz, Christophe; Stockinger, Kurt; Zahn-Zabal, Monique; Mendes de Farias, Tarcisio,
8, pp. 1822.
Available from: https://doi.org/10.12688/f1000research.21027.2
Database: The Journal of Biological Databases and Curation.
Available from: https://doi.org/10.1093/database/baz106
Anisimova, Maria, ed.,
Evolutionary genomics : statistical and computational methods.
Methods in Molecular Biology ; 1910.
Available from: https://doi.org/10.1007/978-1-4939-9074-0_22
Mendes de Farias, Tarcisio; Stockinger, Kurt; Dessimoz, Christophe,
OTM 2019 Conference Proceedings.
On the Move to Meaningful Internet Systems: OTM 2019 Conferences, Rhodes, Greece, 21 - 25 October 2019.
Lecture Notes in Computer Science ; 11877.
Available from: https://doi.org/10.1007/978-3-030-33246-4_38