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Bioinformatics (Oxford, England) Pub Date : 2025-02-05 DOI:10.1093/bioinformatics/btaf048

Victor Paton, Denes Türei, Olga Ivanova, Sophia Müller-Dott, Pablo Rodriguez-Mier, Veron I Ca Venafra, Livia Perfetto, Martin Garrido-Rodriguez, Julio Saez-Rodriguez

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引用次数: 0

摘要

摘要：我们介绍的 NetworkCommons 是一个整合先验知识、omics 数据和网络推断方法的平台，可促进这些方法的使用和评估。NetworkCommons 的目标是成为网络生物学社区的基础设施，通过增强互操作性和集成性，支持开发更好的方法和基准：NetworkCommons 使用 Python 实现，可通过编程访问多个 omics 数据集、网络推理方法和基准设置。它是一款免费软件，可从 https://github.com/saezlab/networkcommons 获取，并存放在 Zenodo 中，网址为 https://doi.org/10.5281/zenodo.14719118 。补充数据：有关数据、知识、方法、评估策略及其实施的投稿指南、附加图表和说明可在补充数据和 NetworkCommons 文档（https://networkcommons.readthedocs.io/）中查阅。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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

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 .

Supplementary data: Contribution guidelines, additional figures, and descriptions for data, knowledge, methods, evaluation strategies and their implementation are available in the Supplementary Data and in the NetworkCommons documentation at https://networkcommons.readthedocs.io/.

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来源期刊

Bioinformatics (Oxford, England)

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