{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T01:12:48Z","timestamp":1774660368034,"version":"3.50.1"},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T00:00:00Z","timestamp":1638316800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T00:00:00Z","timestamp":1639958400000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"miracum","award":["01ZZ1801F"],"award-info":[{"award-number":["01ZZ1801F"]}]},{"name":"miracum","award":["01ZZ1801A"],"award-info":[{"award-number":["01ZZ1801A"]}]},{"DOI":"10.13039\/501100014584","name":"Universit\u00e4tsmedizin der Johannes Gutenberg-Universit\u00e4t Mainz","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100014584","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Med Inform Decis Mak"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years. The integration of genomic and clinical data is increasingly used to select personalized therapies in dedicated tumor boards (Molecular Tumor Boards) or to identify patients for basket studies. Genomic alterations and clinical information can be stored, integrated and visualized in the open-access resource cBioPortal for Cancer Genomics. cBioPortal can be run as a local instance enabling storage and analysis of patient data in single institutions, in the respect of data privacy. However, uploading clinical input data and genetic aberrations requires the elaboration of multiple data files and specific data formats, which makes it difficult to integrate this system into clinical practice. To solve this problem, we developed cbpManager.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>cbpManager is an R package providing a web-based interactive graphical user interface intended to facilitate the maintenance of mutations data and clinical data, including patient and sample information, as well as timeline data. cbpManager enables a large spectrum of researchers and physicians, regardless of their informatics skills to intuitively create data files ready for upload in cBioPortal for Cancer Genomics on a daily basis or in batch. Due to its modular structure based on R Shiny, further data formats such as copy number and fusion data can be covered in future versions. Further, we provide cbpManager as a containerized solution, enabling a straightforward large-scale deployment in clinical systems and secure access in combination with ShinyProxy. cbpManager is freely available via the Bioconductor project at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/bioconductor.org\/packages\/cbpManager\/\">https:\/\/bioconductor.org\/packages\/cbpManager\/<\/jats:ext-link> under the AGPL-3 license. It is already used at six University Hospitals in Germany (Mainz, Gie\u00dfen, L\u00fcbeck, Halle, Freiburg, and Marburg).\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>In summary, our package cbpManager is currently a unique software solution in the workflow with cBioPortal for Cancer Genomics, to assist the user in the interactive generation and management of study files suited for the later upload in cBioPortal.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12911-021-01719-z","type":"journal-article","created":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T12:02:48Z","timestamp":1640001768000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1014-4521","authenticated-orcid":false,"given":"Arsenij","family":"Ustjanzew","sequence":"first","affiliation":[]},{"given":"Alexander","family":"Desuki","sequence":"additional","affiliation":[]},{"given":"Christoph","family":"Ritzel","sequence":"additional","affiliation":[]},{"given":"Alina Corinna","family":"Dolezilek","sequence":"additional","affiliation":[]},{"given":"Daniel-Christoph","family":"Wagner","sequence":"additional","affiliation":[]},{"given":"Jan","family":"Christoph","sequence":"additional","affiliation":[]},{"given":"Philipp","family":"Unberath","sequence":"additional","affiliation":[]},{"given":"Thomas","family":"Kindler","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg","family":"Faber","sequence":"additional","affiliation":[]},{"given":"Federico","family":"Marini","sequence":"additional","affiliation":[]},{"given":"Torsten","family":"Panholzer","sequence":"additional","affiliation":[]},{"given":"Claudia","family":"Paret","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,12,20]]},"reference":[{"issue":"5","key":"1719_CR1","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1158\/2159-8290","volume":"2","author":"E Cerami","year":"2012","unstructured":"Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. AACR. 2012;2(5):401\u20134. https:\/\/doi.org\/10.1158\/2159-8290.","journal-title":"AACR"},{"key":"1719_CR2","doi-asserted-by":"publisher","unstructured":"Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling. 2013; 6(269):l1. https:\/\/doi.org\/10.1126\/scisignal.2004088.","DOI":"10.1126\/scisignal.2004088"},{"issue":"9","key":"1719_CR3","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1038\/nrd892","volume":"1","author":"AL Hopkins","year":"2002","unstructured":"Hopkins AL, Groom CR. The druggable genome. Nat Rev Drug Discov. 2002;1(9):727\u201330. https:\/\/doi.org\/10.1038\/nrd892.","journal-title":"Nat Rev Drug Discov"},{"issue":"12","key":"1719_CR4","doi-asserted-by":"publisher","first-page":"3070","DOI":"10.1093\/annonc\/mdx528","volume":"28","author":"D Van der Velden","year":"2017","unstructured":"Van der Velden D, Van Herpen C, Van Laarhoven H, Smit E, Groen H, Willems SM, et al. Molecular tumor boards: current practice and future needs. Ann Oncol. 2017;28(12):3070\u20135. https:\/\/doi.org\/10.1093\/annonc\/mdx528.","journal-title":"Ann Oncol"},{"key":"1719_CR5","unstructured":"Chang W, Cheng J, Allaire J, Sievert C, Schloerke B, Xie Y, et al. shiny: Web Application Framework for R. R package version 1.6.0. 2021. https:\/\/CRAN.R-project.org\/package=shiny. Accessed 30 Jun 2021."},{"key":"1719_CR6","unstructured":"cBioPortal\u2014Using the metaImport Script. https:\/\/docs.cbioportal.org\/5.1-data-loading\/data-loading\/using-the-metaimport-script. Accessed 30 Jun 2021."},{"key":"1719_CR7","unstructured":"Xie Y, Cheng J, Tan X. DT: A Wrapper of the JavaScript Library 'DataTables'. R package version 0.18. 2021. https:\/\/CRAN.R-project.org\/package=DT. Accessed 30 Jun 2021."},{"key":"1719_CR8","unstructured":"Ushey K, Allaire J, Tang Y. reticulate: Interface to 'Python'. R package version 1.20. 2021. https:\/\/CRAN.R-project.org\/package=reticulate. Accessed 30 Jun 2021."},{"key":"1719_CR9","unstructured":"Lun A. basilisk: Freezing Python Dependencies Inside Bioconductor Packages. R package version 1.4.0. 2021. https:\/\/bioconductor.org\/packages\/basilisk\/. Accessed 30 Jun 2021."},{"key":"1719_CR10","unstructured":"Wickham H, Hesselberth J. pkgdown: Make Static HTML Documentation for a Package. R package version 1.6.1. 2020. https:\/\/CRAN.R-project.org\/package=pkgdown. Accessed 30 Jun 2021."},{"key":"1719_CR11","unstructured":"Bailey E. shinyBS: Twitter Bootstrap Components for Shiny. R package version 0.61. 2015. https:\/\/CRAN.R-project.org\/package=shinyBS. Accessed 30 Jun 2021."},{"key":"1719_CR12","doi-asserted-by":"publisher","unstructured":"Ganz C. rintrojs: A Wrapper for the Intro.js Library. Journal of Open Source Software 2016;1(6), 63.https:\/\/doi.org\/10.21105\/joss.00063.","DOI":"10.21105\/joss.00063"},{"key":"1719_CR13","unstructured":"Ustjanzew A, Marini F. cbpManager: Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. R package version 1.1.0. 2021. https:\/\/bioconductor.org\/packages\/cbpManager\/. Accessed 30 Jun 2021."},{"key":"1719_CR14","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1200\/CCI.20.00108","volume":"5","author":"R Kundra","year":"2021","unstructured":"Kundra R, Zhang H, Sheridan R, Sirintrapun SJ, Wang A, Ochoa A, et al. OncoTree: a cancer classification system for precision oncology. JCO Clin Cancer Inf. 2021;5:221\u201330. https:\/\/doi.org\/10.1200\/CCI.20.00108.","journal-title":"JCO Clin Cancer Inf"},{"key":"1719_CR15","unstructured":"cBioPortal\u2014File Formats\u2014Mutation Data. https:\/\/docs.cbioportal.org\/5.1-data-loading\/data-loading\/file-formats#mutation-data. Accessed 30 Jun 2021."},{"issue":"1","key":"1719_CR16","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1186\/s13073-020-00791-w","volume":"12","author":"DC Koboldt","year":"2020","unstructured":"Koboldt DC. Best practices for variant calling in clinical sequencing. Genome Med. 2020;12(1):91. https:\/\/doi.org\/10.1186\/s13073-020-00791-w.","journal-title":"Genome Med"},{"key":"1719_CR17","doi-asserted-by":"publisher","unstructured":"Kandoth C. mskcc\/vcf2maf: vcf2maf. v1.6.19. 2020. https:\/\/github.com\/mskcc\/vcf2maf. Accessed 30 Jun 2021; https:\/\/doi.org\/10.5281\/zenodo.593251.","DOI":"10.5281\/zenodo.593251"},{"issue":"1","key":"1719_CR18","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","volume":"17","author":"W McLaren","year":"2016","unstructured":"McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122. https:\/\/doi.org\/10.1186\/s13059-016-0974-4.","journal-title":"Genome Biol"},{"issue":"16","key":"1719_CR19","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq603","volume":"38","author":"K Wang","year":"2010","unstructured":"Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16): e164. https:\/\/doi.org\/10.1093\/nar\/gkq603.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"1719_CR20","doi-asserted-by":"publisher","first-page":"1747","DOI":"10.1101\/gr.239244.118","volume":"28","author":"A Mayakonda","year":"2018","unstructured":"Mayakonda A, Lin D-C, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28(11):1747\u201356. https:\/\/doi.org\/10.1101\/gr.239244.118.","journal-title":"Genome Res"},{"issue":"5","key":"1719_CR21","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491\u20138. https:\/\/doi.org\/10.1038\/ng.806.","journal-title":"Nat Genet"},{"key":"1719_CR22","unstructured":"cBioPortal Staging Application Usage Guide. https:\/\/github.com\/thehyve\/cbioportal-staging. Accessed 30 Jun 2021."},{"key":"1719_CR23","doi-asserted-by":"publisher","unstructured":"Prokosch HU, Acker T, Bernarding J, Binder H, Boeker M, Boerries M, et al. MIRACUM: medical informatics in research and care in University Medicine. Methods Inf Med. 2018 Jul;57(S 01):e82\u2013e91. https:\/\/doi.org\/10.3414\/ME17-02-0025.","DOI":"10.3414\/ME17-02-0025"},{"issue":"2","key":"1719_CR24","doi-asserted-by":"publisher","first-page":"93","DOI":"10.3390\/diagnostics10020093","volume":"10","author":"P Buechner","year":"2020","unstructured":"Buechner P, Hinderer M, Unberath P, Metzger P, Boeker M, Acker T, et al. Requirements analysis and specification for a molecular tumor board platform based on cBioPortal. Diagnostics. 2020;10(2):93. https:\/\/doi.org\/10.3390\/diagnostics10020093.","journal-title":"Diagnostics"},{"key":"1719_CR25","doi-asserted-by":"publisher","unstructured":"Winter A, St\u00e4ubert S, Ammon D, et al. Smart Medical Information Technology for Healthcare (SMITH). Methods Inf Med. 2018;57(S 01):e92\u2013e105. https:\/\/doi.org\/10.3414\/ME18-02-0004.","DOI":"10.3414\/ME18-02-0004"},{"key":"1719_CR26","doi-asserted-by":"publisher","unstructured":"Haarbrandt B, Schreiweis B, Rey S, et al. HiGHmed\u2014an open platform approach to enhance care and research across institutional boundaries. Methods Inf Med. 2018 Jul;57(S 01):e66\u2013e81. https:\/\/doi.org\/10.3414\/ME18-02-0002.","DOI":"10.3414\/ME18-02-0002"},{"key":"1719_CR27","doi-asserted-by":"publisher","unstructured":"Prasser F, Kohlbacher O, Mansmann U, Bauer B, Kuhn KA. Data Integration for Future Medicine (DIFUTURE). Methods Inf Med. 2018;57(S 01):e57\u2013e65. https:\/\/doi.org\/10.3414\/ME17-02-0022.","DOI":"10.3414\/ME17-02-0022"}],"container-title":["BMC Medical Informatics and Decision Making"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12911-021-01719-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12911-021-01719-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12911-021-01719-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T12:09:49Z","timestamp":1640002189000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcmedinformdecismak.biomedcentral.com\/articles\/10.1186\/s12911-021-01719-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["1719"],"URL":"https:\/\/doi.org\/10.1186\/s12911-021-01719-z","relation":{},"ISSN":["1472-6947"],"issn-type":[{"value":"1472-6947","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12]]},"assertion":[{"value":"27 July 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 December 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 December 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"358"}}