Large-scale regulatory and signaling network assembly through linked open data

Huge efforts are currently underway to address the organization of biological knowledge through linked open databases. These databases can be automatically queried to reconstruct regulatory and signaling networks. However, assembling networks implies manual operations due to source-specific identifi...

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Bibliographic Details
Published in:Database : the journal of biological databases and curation 2021-01, Vol.2021
Main Authors: Lefebvre, M, Gaignard, A, Folschette, M, Bourdon, J, Guziolowski, C
Format: Article
Language:English
Subjects:
Bioinformatics
Computer Science
Life Sciences
Modeling and Simulation
Original
Quantitative Methods
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Summary:Huge efforts are currently underway to address the organization of biological knowledge through linked open databases. These databases can be automatically queried to reconstruct regulatory and signaling networks. However, assembling networks implies manual operations due to source-specific identification of biological entities and relationships, multiple life-science databases with redundant information and the difficulty of recovering logical flows in biological pathways. We propose a framework based on Semantic Web technologies to automate the reconstruction of large-scale regulatory and signaling networks in the context of tumor cells modeling and drug screening. The proposed tool is pyBRAvo (python Biological netwoRk Assembly), and here we have applied it to a dataset of 910 gene expression measurements issued from liver cancer patients. The tool is publicly available at https://github.com/pyBRAvo/pyBRAvo.
ISSN:1758-0463
1758-0463
DOI:10.1093/database/baaa113