{"id":"https://openalex.org/W2774995705","doi":"https://doi.org/10.1093/bioinformatics/btx788","title":"Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API","display_name":"Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API","publication_year":2017,"publication_date":"2017-12-16","ids":{"openalex":"https://openalex.org/W2774995705","doi":"https://doi.org/10.1093/bioinformatics/btx788","mag":"2774995705"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1431/25171224/btx788.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1431/25171224/btx788.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065635969","display_name":"Alba Guti\u00e9rrez\u2010Sacrist\u00e1n","orcid":"https://orcid.org/0000-0002-1245-198X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I4210130874","display_name":"Hospital Del Mar","ror":"https://ror.org/03a8gac78","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210130874"]},{"id":"https://openalex.org/I4210156109","display_name":"Hospital del Mar Research Institute","ror":"https://ror.org/042nkmz09","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210156109","https://openalex.org/I4387153040"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Alba Guti\u00e9rrez-Sacrist\u00e1n","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain","Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain","institution_ids":["https://openalex.org/I4210130874","https://openalex.org/I4210156109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003549846","display_name":"Romain Guedj","orcid":"https://orcid.org/0000-0002-9497-4396"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Romain Guedj","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086422045","display_name":"Gabor Korodi","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabor Korodi","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011229303","display_name":"Jason Stedman","orcid":"https://orcid.org/0000-0002-0718-5648"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Stedman","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028427590","display_name":"Laura I. Furlong","orcid":"https://orcid.org/0000-0002-9383-528X"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I4210130874","display_name":"Hospital Del Mar","ror":"https://ror.org/03a8gac78","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210130874"]},{"id":"https://openalex.org/I4210156109","display_name":"Hospital del Mar Research Institute","ror":"https://ror.org/042nkmz09","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210156109","https://openalex.org/I4387153040"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Laura I Furlong","raw_affiliation_strings":["Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain","Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]},{"raw_affiliation_string":"Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain","institution_ids":["https://openalex.org/I4210130874","https://openalex.org/I4210156109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100638285","display_name":"Chirag J. Patel","orcid":"https://orcid.org/0000-0002-8756-8525"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chirag J Patel","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088509061","display_name":"Isaac S. Kohane","orcid":"https://orcid.org/0000-0003-2192-5160"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Isaac S Kohane","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039453222","display_name":"Paul Avillach","orcid":"https://orcid.org/0000-0002-0235-7543"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Paul Avillach","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5039453222"],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5613,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.67563358,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"34","issue":"8","first_page":"1431","last_page":"1432"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9868000149726868,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9868000149726868,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T14393","display_name":"Health, Environment, Cognitive Aging","score":0.9861000180244446,"subfield":{"id":"https://openalex.org/subfields/2307","display_name":"Health, Toxicology and Mutagenesis"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9837999939918518,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7447175979614258},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6986294984817505},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.447282999753952},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.43532687425613403},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.43411195278167725},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4035142958164215},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3984220027923584},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3515397310256958}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7447175979614258},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6986294984817505},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.447282999753952},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.43532687425613403},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.43411195278167725},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4035142958164215},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3984220027923584},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3515397310256958}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btx788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1431/25171224/btx788.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:repositori.upf.edu:10230/35595","is_oa":true,"landing_page_url":"http://hdl.handle.net/10230/35595","pdf_url":null,"source":{"id":"https://openalex.org/S4306402615","display_name":"Repositori digital de la UPF (Universitat Pompeu Fabra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170486558","host_organization_name":"Universitat Pompeu Fabra","host_organization_lineage":["https://openalex.org/I170486558"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:dash.harvard.edu:1/37068148","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:37068148","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:4837512","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5905576","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5905576","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5905576","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx788","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx788","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1431/25171224/btx788.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3530239307","display_name":null,"funder_award_id":"NHLBI","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4196654959","display_name":null,"funder_award_id":"OT3 OD025466-01; NHLBI OT3 HL142480-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7102145957","display_name":null,"funder_award_id":"U54HG007963","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7192711334","display_name":null,"funder_award_id":"OT3 HL142480-01","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2774995705.pdf","grobid_xml":"https://content.openalex.org/works/W2774995705.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1952553890","https://openalex.org/W2082036307","https://openalex.org/W2302501749","https://openalex.org/W2532137099","https://openalex.org/W2773787581"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044","https://openalex.org/W4387011503"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"In":[2],"the":[3,11,26,46,69,92,95],"era":[4],"of":[5,13,45,62,86,94,104],"big":[6],"data":[7,38,143],"and":[8,19,41,74,79,88,98,113,121],"precision":[9],"medicine,":[10],"number":[12],"databases":[14,67],"containing":[15],"clinical,":[16],"environmental,":[17],"self-reported":[18],"biochemical":[20],"variables":[21],"is":[22,43,117,122],"increasing":[23],"exponentially.":[24],"Enabling":[25],"experts":[27],"to":[28,101],"focus":[29],"on":[30,36],"their":[31],"research":[32],"questions":[33],"rather":[34],"than":[35],"computational":[37],"management,":[39],"access":[40],"analysis":[42,78,87],"one":[44],"most":[47],"significant":[48],"challenges":[49],"nowadays.":[50],"Results":[51],"We":[52],"present":[53],"Rcupcake,":[54],"an":[55],"R":[56,120],"package":[57,82,116],"that":[58],"contains":[59],"a":[60,84],"variety":[61,85],"functions":[63],"for":[64],"leveraging":[65],"different":[66],"through":[68],"BD2K":[70],"PIC-SURE":[71],"RESTful":[72],"API":[73],"facilitating":[75],"its":[76],"query,":[77],"interpretation.":[80],"The":[81,115],"offers":[83],"visualization":[89],"tools,":[90],"including":[91],"study":[93],"phenotype":[96],"co-occurrence":[97],"prevalence,":[99],"according":[100],"multiple":[102],"layers":[103],"data,":[105],"such":[106],"as":[107],"phenome,":[108],"exposome":[109],"or":[110],"genome.":[111],"Availability":[112],"implementation":[114],"implemented":[118],"in":[119],"available":[123,137,145],"under":[124],"Mozilla":[125],"v2":[126],"license":[127],"from":[128],"GitHub":[129],"(https://github.com/hms-dbmi/Rcupcake).":[130],"Two":[131],"reproducible":[132],"case":[133],"studies":[134],"are":[135,144],"also":[136],"(https://github.com/hms-dbmi/Rcupcake-case-studies/blob/master/SSCcaseStudy_v01.ipynb,":[138],"https://github.com/hms-dbmi/Rcupcake-case-studies/blob/master/NHANEScaseStudy_v01.ipynb).":[139],"Supplementary":[140,142],"information":[141],"at":[146],"Bioinformatics":[147],"online.":[148]},"counts_by_year":[{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2017-12-22T00:00:00"}
