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. 2025 Feb 4;41(2):btaf048.
doi: 10.1093/bioinformatics/btaf048.

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

Victor Paton  1 , Denes Türei  1 , Olga Ivanova  1 , Sophia Müller-Dott  1 , Pablo Rodriguez-Mier  1 , Veronica Venafra  2   3 , Livia Perfetto  2 , Martin Garrido-Rodriguez  1   4   5 , Julio Saez-Rodriguez  1   5
Affiliations

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

Victor Paton et al. Bioinformatics. .

Abstract

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.

Availability and implementation: 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.

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Figures

Figure 1.
Figure 1.
Overview of NetworkCommons. The package connects four different areas: data, prior knowledge, contextualization methods, and evaluation.
See this image and copyright information in PMC

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