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NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks

We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrastructure for the network biology community that supports the development of better methods and benchmarks, by...

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Bibliographic Details
Main Authors: Paton, Victor (Author) , Türei, Dénes (Author) , Ivanova, Olga A. (Author) , Müller-Dott, Sophia (Author) , Rodriguez Mier, Pablo (Author) , Venafra, Veronica (Author) , Perfetto, Livia (Author) , Garrido-Rodriguez, Martin (Author) , Sáez Rodríguez, Julio (Author)
Format: Article (Journal)
Language:English
Published: February 2025
In: Bioinformatics
Year: 2025, Volume: 41, Issue: 2, Pages: 1-4
ISSN:1367-4811
DOI:10.1093/bioinformatics/btaf048
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.1093/bioinformatics/btaf048
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Author Notes:Victor Paton, Denes Türei, Olga Ivanova, Sophia Müller-Dott, Pablo Rodriguez-Mier, Veronica Venafra, Livia Perfetto, Martin Garrido-Rodriguez, Julio Saez-Rodriguez
Description
Summary:We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrastructure for the network biology community that supports the development of better methods and benchmarks, by enhancing interoperability and integration.NetworkCommons is implemented in Python and offers programmatic access to multiple omics datasets, network inference methods, and benchmarking setups. It is a free software, available at https://github.com/saezlab/networkcommons, and deposited in Zenodo at https://doi.org/10.5281/zenodo.14719118.
Item Description:Online veröffentlicht am 5. Februar 2025
Gesehen am 13.10.2025
Physical Description:Online Resource
ISSN:1367-4811
DOI:10.1093/bioinformatics/btaf048

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