{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T15:55:16Z","timestamp":1722786916421},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1154,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,15]]},"abstract":"Abstract<\/jats:title>\n Summary: BioPAX is a community-developed standard language for biological pathway data. A key functionality required for efficient BioPAX data exchange is validation\u2014detecting errors and inconsistencies in BioPAX documents. The BioPAX Validator is a command-line tool, Java library and online web service for BioPAX that performs &gt;100 classes of consistency checks.<\/jats:p>\n Availability and implementation: The validator recognizes common syntactic errors and semantic inconsistencies and reports them in a customizable human readable format. It can also automatically fix some errors and normalize BioPAX data. Since its release, the validator has become a critical tool for the pathway informatics community, detecting thousands of errors and helping substantially increase the conformity and uniformity of BioPAX-formatted data. The BioPAX Validator is open source and released under LGPL v3 license. All sources, binaries and documentation can be found at sf.net\/p\/biopax, and the latest stable version of the web application is available at biopax.org\/validator.<\/jats:p>\n Contact: \u00a0igor.rodchenkov@utoronto.ca or gary.bader@utoronto.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt452","type":"journal-article","created":{"date-parts":[[2013,8,6]],"date-time":"2013-08-06T05:30:10Z","timestamp":1375767010000},"page":"2659-2660","source":"Crossref","is-referenced-by-count":9,"title":["The BioPAX Validator"],"prefix":"10.1093","volume":"29","author":[{"given":"Igor","family":"Rodchenkov","sequence":"first","affiliation":[{"name":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"}]},{"given":"Emek","family":"Demir","sequence":"additional","affiliation":[{"name":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"}]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[{"name":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"}]},{"given":"Gary D.","family":"Bader","sequence":"additional","affiliation":[{"name":"1 The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and 2Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,8,5]]},"reference":[{"key":"2023012810464517700_btt452-B1","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":"2023012810464517700_btt452-B2","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/bioinformatics\/btn051","article-title":"LibSBML: an API library for SBML","volume":"24","author":"Bornstein","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012810464517700_btt452-B3","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1093\/bioinformatics\/btq407","article-title":"Editing, validating and translating of SBGN maps","volume":"26","author":"Czauderna","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012810464517700_btt452-B4","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","article-title":"The BioPAX community standard for pathway data sharing","volume":"28","author":"Demir","year":"2010","journal-title":"Nat. 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