{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:47:03Z","timestamp":1778226423630,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":299,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Purpose: PaxtoolsR package enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons webservice for users of the R language to aid in advanced pathway analyses. Features include the extraction, merging and validation of pathway data represented in the BioPAX format. This package also provides novel pathway datasets and advanced querying features for R users through the Pathway Commons webservice allowing users to query, extract and retrieve data and integrate these data with local BioPAX datasets.<\/jats:p>\n                  <jats:p>Availability and implementation: The PaxtoolsR package is compatible with versions of R 3.1.1 (and higher) on Windows, Mac OS X and Linux using Bioconductor 3.0 and is available through the Bioconductor R package repository along with source code and a tutorial vignette describing common tasks, such as data visualization and gene set enrichment analysis. Source code and documentation are at http:\/\/www.bioconductor.org\/packages\/paxtoolsr. This plugin is free, open-source and licensed under the LGPL-3.<\/jats:p>\n                  <jats:p>Contact: \u00a0paxtools@cbio.mskcc.org or lunaa@cbio.mskcc.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv733","type":"journal-article","created":{"date-parts":[[2015,12,18]],"date-time":"2015-12-18T23:10:02Z","timestamp":1450480202000},"page":"1262-1264","source":"Crossref","is-referenced-by-count":30,"title":["PaxtoolsR: pathway analysis in R using Pathway Commons"],"prefix":"10.1093","volume":"32","author":[{"given":"Augustin","family":"Luna","sequence":"first","affiliation":[{"name":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00d6zg\u00fcn","family":"Babur","sequence":"additional","affiliation":[{"name":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B\u00fclent Arman","family":"Aksoy","sequence":"additional","affiliation":[{"name":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emek","family":"Demir","sequence":"additional","affiliation":[{"name":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[{"name":"Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,12,18]]},"reference":[{"key":"2023020112212272700_btv733-B1","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btt539","article-title":"Pattern search in BioPAX models","volume":"30","author":"Babur","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020112212272700_btv733-B2","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":"2023020112212272700_btv733-B3","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJ. Complex Syst"},{"key":"2023020112212272700_btv733-B4","author":"Demir","year":"2013"},{"key":"2023020112212272700_btv733-B5","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. Biotechnol"},{"key":"2023020112212272700_btv733-B6","doi-asserted-by":"crossref","first-page":"e1003194","DOI":"10.1371\/journal.pcbi.1003194","article-title":"Using biological pathway data with paxtools","volume":"9","author":"Demir","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023020112212272700_btv733-B7","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1093\/bioinformatics\/bts710","article-title":"rBiopaxParser\u2014an R package to parse, modify and visualize BioPAX data","volume":"29","author":"Kramer","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020112212272700_btv733-B8","doi-asserted-by":"crossref","first-page":"85","DOI":"10.3390\/biology3010085","article-title":"R-Based software for the integration of pathway data into bioinformatic algorithms","volume":"3","author":"Kramer","year":"2014","journal-title":"Biology"},{"key":"2023020112212272700_btv733-B9","doi-asserted-by":"crossref","first-page":"2659","DOI":"10.1093\/bioinformatics\/btt452","article-title":"The BioPAX Validator","volume":"29","author":"Rodchenkov","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020112212272700_btv733-B10","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1186\/1471-2105-14-217","article-title":"Rcytoscape: tools for exploratory network analysis","volume":"14","author":"Shannon","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023020112212272700_btv733-B11","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/8\/1262\/49018739\/bioinformatics_32_8_1262.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/8\/1262\/49018739\/bioinformatics_32_8_1262.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T17:27:16Z","timestamp":1675272436000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/8\/1262\/1744516"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,18]]},"references-count":11,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2016,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv733","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/021105","asserted-by":"object"}]},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,4,15]]},"published":{"date-parts":[[2015,12,18]]}}}