Bio-SODA – Enabling Complex, Semantic Queries to Bioinformatics Databases through Intuitive Searching over Data (SNSF NRP 75 "Big Data")

Auf einen Blick

Projektleiter/in : Prof. Dr. Kurt Stockinger
Projektteam : 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
Projektstatus : abgeschlossen
Drittmittelgeber : SNF (NFP 75 «Big Data» / Projekt Nr. 167149)
Projektpartner : Université de Lausanne, Swiss Institute of Bioinformatics SIB

Beschreibung

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.

Weiterführende Informationen

https://bigdata-dialog.ch/completed-project-biosoda-an-intuitive-search-function-for-bioinformatics-databases/

Publikationen

Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt,

2022.

Bio-SODA UX : enabling natural language question answering over knowledge graphs with user disambiguation.

Distributed and Parallel Databases.

40(2), S. 409-440.

Verfügbar unter: https://doi.org/10.1007/s10619-022-07414-w
Sima, Ana Claudia; Mendes de Farias, Tarcisio; Anisimova, Maria; Dessimoz, Christophe; Robinson-Rechavi, Marc; Zbinden, Erich; Stockinger, Kurt,

2021.

Bio-SODA : enabling natural language question answering over knowledge graphs without training data [Paper].

In:

Proceedings of the 33rd SSDBM.

International Conference on Scientific and Statistical Database Management (SSDBM), Online, 6-7 July 2021.

ACM.

S. 61-72.

Verfügbar unter: https://doi.org/10.1145/3468791.3469119
Liang, Shiqi; Stockinger, Kurt; de Farias, Tarcisio Mendes; Anisimova, Maria; Gil, Manuel,

2021.

Querying knowledge graphs in natural language.

Journal of Big Data.

8(3).

Verfügbar unter: https://doi.org/10.1186/s40537-020-00383-w
Sima, Ana-Claudia; Dessimoz, Christophe; Stockinger, Kurt; Zahn-Zabal, Monique; Mendes de Farias, Tarcisio,

2020.

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL.

F1000Research.

8, S. 1822.

Verfügbar unter: https://doi.org/10.12688/f1000research.21027.2
Sima, Ana-Claudia; Mendes de Farias, Tarcisio; Zbinden, Erich; Anisimova, Maria; Gil, Manuel; Stockinger, Heinz; Stockinger, Kurt; Robinson-Rechavi, Marc; Dessimoz, Christophe,

2019.

Enabling semantic queries across federated bioinformatics databases.

Database: The Journal of Biological Databases and Curation.

2019(baz106).

Verfügbar unter: https://doi.org/10.1093/database/baz106
Sima, Ana-Claudia; Stockinger, Kurt; de Farias, Tarcisio Mendes; Gil, Manuel,

2019.

Semantic integration and enrichment of heterogeneous biological databases

.

In:

Anisimova, Maria, Hrsg.,

Evolutionary genomics : statistical and computational methods.

New York:

Springer.

S. 655-690.

Methods in Molecular Biology ; 1910.

Verfügbar unter: https://doi.org/10.1007/978-1-4939-9074-0_22
Mendes de Farias, Tarcisio; Stockinger, Kurt; Dessimoz, Christophe,

2019.

VoIDext : vocabulary and patterns for enhancing interoperable datasets with virtual links [Paper].

In:

OTM 2019 Conference Proceedings.

On the Move to Meaningful Internet Systems: OTM 2019 Conferences, Rhodes, Greece, 21 - 25 October 2019.

Cham:

Springer.

S. 607-625.

Lecture Notes in Computer Science ; 11877.

Verfügbar unter: https://doi.org/10.1007/978-3-030-33246-4_38

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