BioSODA - Biological Search Over DAtabases

"Complex bioinformatics databases hold enormous amounts of knowledge that can only be retrieved with technical know-how. The goal of this project is to develop an intuitive, Google-like search function designed to help identify new correlations in the stored data." NFP75 Big Data

Web tools / interfaces

QALD4 (biomedical task)
Bgee and OMA (bioinformatics)
CORDIS (EU-funded projects)
federation server - SPARQL frontend
BioQuery - dynamic search interface with query catalog
BioSodaUX - NLP search interface

Resources / code

Bio-SODA search engine and API (github)
BioQuery web frontend (github)


Semantic Integration and Enrichment of Heterogeneous Biological Databases

(Evolutionary Genomics pp 655-690, July 2019)

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

(online, October 2019)

Enabling Semantic Queries Across Federated Bioinformatics Databases

(Database, Volume 2019, November 2019, baz106)

Enabling Complex Semantic Queries to Bioinformatics Databases through Intuitive Search Over Data

(Thesis, University of Lausanne, October 2020)

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data

(33rd International Conference on Scientific and Statistical Database Management (SSDBM 2021), April 2021)

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

(Distributed and Parallel Databases 40.2-3 (2022))


NRP75 Big Data National Research Programme

Follow up project

INODE Intelligent Open Data Exploration - EU Horizon 2020