{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:25Z","timestamp":1740185125224,"version":"3.37.3"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2017,12,18]],"date-time":"2017-12-18T00:00:00Z","timestamp":1513555200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54HG007963"],"award-info":[{"award-number":["U54HG007963"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["OT3 OD025466-01; NHLBI OT3 HL142480-01"],"award-info":[{"award-number":["OT3 OD025466-01; NHLBI OT3 HL142480-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In the era of big data and precision medicine, the number of databases containing clinical, environmental, self-reported and biochemical variables is increasing exponentially. Enabling the experts to focus on their research questions rather than on computational data management, access and analysis is one of the most significant challenges nowadays.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Rcupcake, an R package that contains a variety of functions for leveraging different databases through the BD2K PIC-SURE RESTful API and facilitating its query, analysis and interpretation. The package offers a variety of analysis and visualization tools, including the study of the phenotype co-occurrence and prevalence, according to multiple layers of data, such as phenome, exposome or genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The package is implemented in R and is available under Mozilla v2 license from GitHub (https:\/\/github.com\/hms-dbmi\/Rcupcake). Two reproducible case studies are also available (https:\/\/github.com\/hms-dbmi\/Rcupcake-case-studies\/blob\/master\/SSCcaseStudy_v01.ipynb, https:\/\/github.com\/hms-dbmi\/Rcupcake-case-studies\/blob\/master\/NHANEScaseStudy_v01.ipynb).<\/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\/btx788","type":"journal-article","created":{"date-parts":[[2017,12,16]],"date-time":"2017-12-16T20:08:23Z","timestamp":1513454903000},"page":"1431-1432","source":"Crossref","is-referenced-by-count":3,"title":["Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API"],"prefix":"10.1093","volume":"34","author":[{"given":"Alba","family":"Guti\u00e9rrez-Sacrist\u00e1n","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"},{"name":"Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain"},{"name":"Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Romain","family":"Guedj","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabor","family":"Korodi","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason","family":"Stedman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9383-528X","authenticated-orcid":false,"given":"Laura I","family":"Furlong","sequence":"additional","affiliation":[{"name":"Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain"},{"name":"Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chirag J","family":"Patel","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isaac S","family":"Kohane","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Avillach","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,12,18]]},"reference":[{"key":"2023012713004901700_btx788-B1","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.neuron.2010.10.006","article-title":"The Simons Simplex Collection: a resource for identification of autism genetic risk factors","volume":"68","author":"Fischbach","year":"2010","journal-title":"Neuron"},{"key":"2023012713004901700_btx788-B2","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1136\/amiajnl-2014-002974","article-title":"The National Institutes of Health\u2019s Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data","volume":"21","author":"Margolis","year":"2014","journal-title":"J. Am. Med. Inform. Assoc"},{"volume-title":"Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease","year":"2011","author":"National Research Council","key":"2023012713004901700_btx788-B3"},{"key":"2023012713004901700_btx788-B4","doi-asserted-by":"crossref","first-page":"160096.","DOI":"10.1038\/sdata.2016.96","article-title":"A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey","volume":"3","author":"Patel","year":"2016","journal-title":"Sci. Data"},{"key":"2023012713004901700_btx788-B5","doi-asserted-by":"crossref","first-page":"160018.","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci.Data"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/8\/1431\/48914980\/bioinformatics_34_8_1431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/8\/1431\/48914980\/bioinformatics_34_8_1431.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:50:11Z","timestamp":1674827411000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/8\/1431\/4756095"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,12,18]]},"references-count":5,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2018,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx788","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,4,15]]},"published":{"date-parts":[[2017,12,18]]}}}