{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T12:38:39Z","timestamp":1779107919616,"version":"3.51.4"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,30]],"date-time":"2019-12-30T00:00:00Z","timestamp":1577664000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Joint Research Center for Computational Biomedicine"},{"DOI":"10.13039\/100004326","name":"Bayer AG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004326","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The OmniPath App has been developed for Cytoscape 3 in the Java programing language. The latest source code and the plugin can be found at: https:\/\/github.com\/saezlab\/Omnipath_Cytoscape and http:\/\/apps.cytoscape.org\/apps\/omnipath, respectively.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz968","type":"journal-article","created":{"date-parts":[[2019,12,28]],"date-time":"2019-12-28T12:09:13Z","timestamp":1577534953000},"page":"2632-2633","source":"Crossref","is-referenced-by-count":38,"title":["Bringing data from curated pathway resources to Cytoscape with OmniPath"],"prefix":"10.1093","volume":"36","author":[{"given":"Francesco","family":"Ceccarelli","sequence":"first","affiliation":[{"name":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany"},{"name":"Computer Laboratory, University of Cambridge , CB3 0FD, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denes","family":"Turei","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany"},{"name":"European Molecular Biology Laboratory (EMBL)"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Attila","family":"Gabor","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany"},{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Bioquant, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julio","family":"Saez-Rodriguez","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University , Aachen 52074, Germany"},{"name":"Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine , Bioquant, Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,12,30]]},"reference":[{"key":"2023013110250263000_btz968-B1","doi-asserted-by":"crossref","first-page":"D685","DOI":"10.1093\/nar\/gkq1039","article-title":"Pathway commons, a web resource for biological pathway data","volume":"39","author":"Cerami","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2023013110250263000_btz968-B2","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1101\/gr.240663.118","article-title":"Benchmark and integration of resources for the estimation of human transcription factor activities","volume":"29","author":"Garcia-Alonso","year":"2019","journal-title":"Genome Res"},{"key":"2023013110250263000_btz968-B3","doi-asserted-by":"crossref","first-page":"152","DOI":"10.12688\/f1000research.4254.2","article-title":"WikiPathways App for Cytoscape: making biological pathways amenable to network analysis and visualization","volume":"3","author":"Kutmon","year":"2014","journal-title":"F1000Res"},{"key":"2023013110250263000_btz968-B4","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/nrg3885","article-title":"Quantitative and logic modelling of molecular and gene networks","volume":"16","author":"Le Novere","year":"2015","journal-title":"Nat. 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