{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:47:05Z","timestamp":1778226425674,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.<\/jats:p>\n               <jats:p>Results: rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.<\/jats:p>\n               <jats:p>Availability: rBiopaxParser is an open-source R package and has been submitted to Bioconductor.<\/jats:p>\n               <jats:p>Contact: \u00a0frank.kramer@med.uni-goettingen.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts710","type":"journal-article","created":{"date-parts":[[2012,12,30]],"date-time":"2012-12-30T01:14:02Z","timestamp":1356830042000},"page":"520-522","source":"Crossref","is-referenced-by-count":32,"title":["rBiopaxParser\u2014an R package to parse, modify and visualize BioPAX data"],"prefix":"10.1093","volume":"29","author":[{"given":"Frank","family":"Kramer","sequence":"first","affiliation":[{"name":"1 Department of Medical Statistics, University Medical Center G\u00f6ttingen, Humboldtallee 32 and 2Department of Hematology\/Oncology, University Medical Center G\u00f6ttingen, Robert-Koch-Stra\u00dfe 40, 37073 G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michaela","family":"Bayerlov\u00e1","sequence":"additional","affiliation":[{"name":"1 Department of Medical Statistics, University Medical Center G\u00f6ttingen, Humboldtallee 32 and 2Department of Hematology\/Oncology, University Medical Center G\u00f6ttingen, Robert-Koch-Stra\u00dfe 40, 37073 G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Klemm","sequence":"additional","affiliation":[{"name":"1 Department of Medical Statistics, University Medical Center G\u00f6ttingen, Humboldtallee 32 and 2Department of Hematology\/Oncology, University Medical Center G\u00f6ttingen, Robert-Koch-Stra\u00dfe 40, 37073 G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Annalen","family":"Bleckmann","sequence":"additional","affiliation":[{"name":"1 Department of Medical Statistics, University Medical Center G\u00f6ttingen, Humboldtallee 32 and 2Department of Hematology\/Oncology, University Medical Center G\u00f6ttingen, Robert-Koch-Stra\u00dfe 40, 37073 G\u00f6ttingen, Germany"},{"name":"1 Department of Medical Statistics, University Medical Center G\u00f6ttingen, Humboldtallee 32 and 2Department of Hematology\/Oncology, University Medical Center G\u00f6ttingen, Robert-Koch-Stra\u00dfe 40, 37073 G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim","family":"Bei\u00dfbarth","sequence":"additional","affiliation":[{"name":"1 Department of Medical Statistics, University Medical Center G\u00f6ttingen, Humboldtallee 32 and 2Department of Hematology\/Oncology, University Medical Center G\u00f6ttingen, Robert-Koch-Stra\u00dfe 40, 37073 G\u00f6ttingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,12,28]]},"reference":[{"key":"2023012810252057200_bts710-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":"2023012810252057200_bts710-B2","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/S0076-6879(06)11018-6","article-title":"Interpreting experimental results using gene ontologies","volume":"411","author":"Bei\u00dfbarth","year":"2006","journal-title":"Methods Enzymol."},{"key":"2023012810252057200_bts710-B3","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1186\/1471-2105-12-291","article-title":"Inferring signaling networks from longitudinal data using sampling based approaches in the R-package \u2018ddepn\u2019","volume":"12","author":"Bender","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012810252057200_bts710-B4","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1093\/bioinformatics\/bth458","article-title":"Network structures and algorithms in Bioconductor","volume":"21","author":"Carey","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012810252057200_bts710-B5","doi-asserted-by":"crossref","first-page":"D691","DOI":"10.1093\/nar\/gkq1018","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","author":"Croft","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012810252057200_bts710-B6","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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