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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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf048","type":"journal-article","created":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T15:25:24Z","timestamp":1738337124000},"source":"Crossref","is-referenced-by-count":4,"title":["NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6074-6897","authenticated-orcid":false,"given":"Victor","family":"Paton","sequence":"first","affiliation":[{"name":"Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University , Heidelberg, 69120,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7249-9379","authenticated-orcid":false,"given":"Denes","family":"T\u00fcrei","sequence":"additional","affiliation":[{"name":"Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University , Heidelberg, 69120,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9111-4593","authenticated-orcid":false,"given":"Olga","family":"Ivanova","sequence":"additional","affiliation":[{"name":"Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University , Heidelberg, 69120,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9710-1865","authenticated-orcid":false,"given":"Sophia","family":"M\u00fcller-Dott","sequence":"additional","affiliation":[{"name":"Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University , Heidelberg, 69120,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4938-4418","authenticated-orcid":false,"given":"Pablo","family":"Rodriguez-Mier","sequence":"additional","affiliation":[{"name":"Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University , Heidelberg, 69120,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3830-618X","authenticated-orcid":false,"given":"Veronica","family":"Venafra","sequence":"additional","affiliation":[{"name":"Department of Biology and Biotechnologies \u201cC. Darwin\u201d, University of Rome La Sapienza , 00185 Rome,","place":["Italy"]},{"name":"Ph.D. Program in Cellular and Molecular Biology, Department of Biology, University of Rome \u2018Tor Vergata\u2019 , 00133 Rome,","place":["Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4392-8725","authenticated-orcid":false,"given":"Livia","family":"Perfetto","sequence":"additional","affiliation":[{"name":"Department of Biology and Biotechnologies \u201cC. 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