{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:32:32Z","timestamp":1773275552373,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large pathway datasets requires software that can combine data mapping, querying and visualization as well as providing access to diverse data resources on the Internet. ChiBE is an open source software application that features user-friendly multi-view display, navigation and manipulation of pathway models in BioPAX format. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art visualization methods, including compound or nested structures for visualizing cellular compartments and molecular complexes. Users can easily query and visualize pathways through an integrated Pathway Commons query tool and analyze molecular profiles in pathway context.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.bilkent.edu.tr\/%7Ebcbi\/chibe.html<\/jats:p>\n               <jats:p>Contact: \u00a0ugur@cs.bilkent.edu.tr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp665","type":"journal-article","created":{"date-parts":[[2009,12,10]],"date-time":"2009-12-10T01:46:35Z","timestamp":1260409595000},"page":"429-431","source":"Crossref","is-referenced-by-count":45,"title":["ChiBE: interactive visualization and manipulation of BioPAX pathway models"],"prefix":"10.1093","volume":"26","author":[{"given":"Ozgun","family":"Babur","sequence":"first","affiliation":[{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"},{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"},{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"}]},{"given":"Ugur","family":"Dogrusoz","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"},{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"}]},{"given":"Emek","family":"Demir","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"}]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[{"name":"1 Center for Bioinformatics, 2 Computer Engineering Dept., Bilkent University, Ankara, Turkey and 3 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,12,9]]},"reference":[{"key":"2023012511003415500_B1","doi-asserted-by":"crossref","first-page":"2196","DOI":"10.1002\/pmic.200700769","article-title":"PATIKAmad: putting microarray data into pathway context","volume":"8","author":"Babur","year":"2008","journal-title":"Proteomics"},{"key":"2023012511003415500_B2","doi-asserted-by":"crossref","first-page":"D504","DOI":"10.1093\/nar\/gkj126","article-title":"Pathguide: a pathway resource list","volume":"34","author":"Bader","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012511003415500_B3","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1093\/bioinformatics\/17.5.461","article-title":"A graph layout algorithm for drawing metabolic pathways","volume":"17","author":"Becker","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012511003415500_B4","doi-asserted-by":"crossref","first-page":"D623","DOI":"10.1093\/nar\/gkm900","article-title":"The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases","volume":"36","author":"Caspi","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012511003415500_B5","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1093\/bioinformatics\/btg416","article-title":"An ontology for collaborative construction and analysis of cellular pathways","volume":"20","author":"Demir","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012511003415500_B6","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1093\/bioinformatics\/btn459","article-title":"PathCase: pathways database system","volume":"24","author":"Elliott","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012511003415500_B7","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1093\/bioinformatics\/17.9.829","article-title":"Knowledge representation of signal transduction pathways","volume":"17","author":"Fukuda","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012511003415500_B8","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","article-title":"CellDesigner 3.5: a versatile modeling tool for biochemical networks","volume":"96","author":"Funahashi","year":"2008","journal-title":"Proc. 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