Bio-SODA – Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data (SNSF)
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.
Key data
Projectlead
Project team
Dr. Manuel Gil, Erich Zbinden, Ana-Claudia Sima, Prof. Dr. Maria Anisimova, Prof. Dr. Marc Robinson-Rechavi (Uni Lausanne) (Université de Lausanne), Prof. Dr. Christophe Dessimoz (Uni Lausanne) (Université de Lausanne), Tarcisio Mendes de Farias (Uni Lausanne) (Swiss Institute of Bioinformatics SIB), Dr. Heinz Stockinger (SIB) (Swiss Institute of Bioinformatics SIB)
Project partners
Université de Lausanne; Swiss Institute of Bioinformatics SIB
Project status
completed, 04/2017 - 03/2021
Institute/Centre
Institute of Computer Science (InIT); Institute of Computational Life Sciences (ICLS)
Funding partner
NFP 75 «Big Data»
Further documents and links
Publications
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Bio-SODA UX : enabling natural language question answering over knowledge graphs with user disambiguation
2022 Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt
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Bio-SODA : enabling natural language question answering over knowledge graphs without training data
2021 Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt
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Querying knowledge graphs in natural language
2021 Liang, Shiqi; Stockinger, Kurt; de Farias, Tarcisio Mendes; Anisimova, Maria; Gil, Manuel
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A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL
2020 Sima, Ana-Claudia; Dessimoz, Christophe; Stockinger, Kurt; Zahn-Zabal, Monique; Mendes de Farias, Tarcisio
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Semantic integration and enrichment of heterogeneous biological databases
2019 Sima, Ana-Claudia; Stockinger, Kurt; de Farias, Tarcisio Mendes; Gil, Manuel
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Enabling semantic queries across federated bioinformatics databases
2019 Sima, Ana-Claudia; Mendes de Farias, Tarcisio; Zbinden, Erich; Anisimova, Maria; Gil, Manuel; Stockinger, Heinz; Stockinger, Kurt; Robinson-Rechavi, Marc; Dessimoz, Christophe
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VoIDext : vocabulary and patterns for enhancing interoperable datasets with virtual links
2019 Mendes de Farias, Tarcisio; Stockinger, Kurt; Dessimoz, Christophe
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