{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T13:30:15Z","timestamp":1754487015037,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,26]],"date-time":"2017-10-26T00:00:00Z","timestamp":1508976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","award":["FKZ01ZX1508 and FKZ031L0024A"],"award-info":[{"award-number":["FKZ01ZX1508 and FKZ031L0024A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Seamless exchange of biological network data enables bioinformatic algorithms to integrate networks as prior knowledge input as well as to document resulting network output. However, the interoperability between pathway databases and various methods and platforms for analysis is currently lacking. The Network Data Exchange (NDEx) is an open-source data commons that facilitates the user-centered sharing and publication of networks of many types and formats.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present a software package that allows users to programmatically connect to and interface with NDEx servers from within R. The network repository can be searched and networks can be retrieved and converted into igraph-compatible objects. These networks can be modified and extended within R and uploaded back to the NDEx servers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ndexr is a free and open-source R package, available via GitHub (https:\/\/github.com\/frankkramer-lab\/ndexr) and Bioconductor (http:\/\/bioconductor.org\/packages\/ndexr\/).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx683","type":"journal-article","created":{"date-parts":[[2017,10,26]],"date-time":"2017-10-26T03:13:31Z","timestamp":1508987611000},"page":"716-717","source":"Crossref","is-referenced-by-count":13,"title":["ndexr\u2014an R package to interface with the network data exchange"],"prefix":"10.1093","volume":"34","author":[{"given":"Florian","family":"Auer","sequence":"first","affiliation":[{"name":"Department of Medical Statistics, University Medical Center G\u00f6ttingen, G\u00f6ttingen, Germany"}]},{"given":"Zaynab","family":"Hammoud","sequence":"additional","affiliation":[{"name":"Department of Medical Statistics, University Medical Center G\u00f6ttingen, G\u00f6ttingen, Germany"}]},{"given":"Alexandr","family":"Ishkin","sequence":"additional","affiliation":[{"name":"Discovery Science, Clarivate Analytics, Boston, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1471-9513","authenticated-orcid":false,"given":"Dexter","family":"Pratt","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego, La Jolla, CA, USA"}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California San Diego, La Jolla, CA, USA"},{"name":"Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2857-7122","authenticated-orcid":false,"given":"Frank","family":"Kramer","sequence":"additional","affiliation":[{"name":"Department of Medical Statistics, University Medical Center G\u00f6ttingen, G\u00f6ttingen, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,10,26]]},"reference":[{"key":"2023012712404525800_btx683-B1","first-page":"1695","article-title":"The igraph software package for complex network research","author":"Csardi","year":"2006","journal-title":"InterJournal Complex Systems"},{"key":"2023012712404525800_btx683-B2","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The reactome pathway knowledgebase","volume":"44","author":"Fabregat","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712404525800_btx683-B3","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1145\/514183.514185","article-title":"Principled design of the modern web architecture","volume":"2","author":"Fielding","year":"2002","journal-title":"ACM Trans. Internet Technol"},{"key":"2023012712404525800_btx683-B4","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012712404525800_btx683-B5","doi-asserted-by":"crossref","first-page":"2703","DOI":"10.1091\/mbc.10.8.2703","article-title":"Molecular interaction map of the mammalian cell cycle control and DNA repair systems","volume":"10","author":"Kohn","year":"1999","journal-title":"Mol. Biol. 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