{"id":"https://openalex.org/W2899684494","doi":"https://doi.org/10.1093/bioinformatics/bty925","title":"ukbREST: efficient and streamlined data access for reproducible research in large biobanks","display_name":"ukbREST: efficient and streamlined data access for reproducible research in large biobanks","publication_year":2018,"publication_date":"2018-11-03","ids":{"openalex":"https://openalex.org/W2899684494","doi":"https://doi.org/10.1093/bioinformatics/bty925","mag":"2899684494","pmid":"https://pubmed.ncbi.nlm.nih.gov/30395166"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty925","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty925","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1971/28759243/bty925.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1971/28759243/bty925.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019698272","display_name":"Milton Pividori","orcid":"https://orcid.org/0000-0002-3035-4403"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Milton Pividori","raw_affiliation_strings":["Center for Translational Data Science, The University of Chicago, Chicago, IL, USA","Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA"],"raw_orcid":"https://orcid.org/0000-0002-3035-4403","affiliations":[{"raw_affiliation_string":"Center for Translational Data Science, The University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051721434","display_name":"Hae Kyung Im","orcid":"https://orcid.org/0000-0003-0333-5685"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hae Kyung Im","raw_affiliation_strings":["Center for Translational Data Science, The University of Chicago, Chicago, IL, USA","Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA"],"raw_orcid":"https://orcid.org/0000-0003-0333-5685","affiliations":[{"raw_affiliation_string":"Center for Translational Data Science, The University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051721434"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.4136,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.59914996,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"11","first_page":"1971","last_page":"1973"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5091999769210815,"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":0.5091999769210815,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.06800000369548798,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.05400000140070915,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biobank","display_name":"Biobank","score":0.9505915641784668},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.7442613840103149},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7147248983383179},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6236540079116821},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5828690528869629},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5427378416061401},{"id":"https://openalex.org/keywords/software-deployment","display_name":"Software deployment","score":0.5048366189002991},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.4704265594482422},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.4683372974395752},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.41409850120544434},{"id":"https://openalex.org/keywords/data-access","display_name":"Data access","score":0.41280731558799744},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.31910502910614014},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.28706955909729004},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.21044018864631653},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.18354684114456177},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1753755509853363}],"concepts":[{"id":"https://openalex.org/C116567970","wikidata":"https://www.wikidata.org/wiki/Q864217","display_name":"Biobank","level":2,"score":0.9505915641784668},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.7442613840103149},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7147248983383179},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6236540079116821},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5828690528869629},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5427378416061401},{"id":"https://openalex.org/C105339364","wikidata":"https://www.wikidata.org/wiki/Q2297740","display_name":"Software deployment","level":2,"score":0.5048366189002991},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.4704265594482422},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.4683372974395752},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.41409850120544434},{"id":"https://openalex.org/C47487241","wikidata":"https://www.wikidata.org/wiki/Q5227230","display_name":"Data access","level":2,"score":0.41280731558799744},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.31910502910614014},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.28706955909729004},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.21044018864631653},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.18354684114456177},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1753755509853363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018070","descriptor_name":"Biological Specimen Banks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018070","descriptor_name":"Biological Specimen Banks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018070","descriptor_name":"Biological Specimen Banks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018070","descriptor_name":"Biological Specimen Banks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty925","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty925","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1971/28759243/bty925.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30395166","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30395166","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5537185","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6546122","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty925","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty925","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/11/1971/28759243/bty925.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G1228430442","display_name":null,"funder_award_id":"R01 MH107666","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G1524478970","display_name":null,"funder_award_id":"P30 DK020595","funder_id":"https://openalex.org/F4320309626","funder_display_name":"University of Chicago"},{"id":"https://openalex.org/G18062229","display_name":null,"funder_award_id":"P30DK020595","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G3760333202","display_name":null,"funder_award_id":"DK020595","funder_id":"https://openalex.org/F4320309626","funder_display_name":"University of Chicago"},{"id":"https://openalex.org/G5850737185","display_name":null,"funder_award_id":"MC_PC_17228","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G74223059","display_name":null,"funder_award_id":"P30 DK020595","funder_id":"https://openalex.org/F4320332577","funder_display_name":"Diabetes Research and Training Center"},{"id":"https://openalex.org/G92855890","display_name":"Diabetes Research and Training Center","funder_award_id":"3p30dk020595-46s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309626","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332577","display_name":"Diabetes Research and Training Center","ror":"https://ror.org/024mw5h28"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2899684494.pdf","grobid_xml":"https://content.openalex.org/works/W2899684494.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1840403001","https://openalex.org/W1911952697","https://openalex.org/W2062207606","https://openalex.org/W2082704080","https://openalex.org/W2122425433","https://openalex.org/W2895486342"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4392173297","https://openalex.org/W4311683883","https://openalex.org/W4212902261","https://openalex.org/W4400311305","https://openalex.org/W4221030787","https://openalex.org/W2790811106","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4287775886"],"abstract_inverted_index":{"SUMMARY:":[0],"Large":[1],"biobanks,":[2],"such":[3],"as":[4],"UK":[5,40,99],"Biobank":[6,41,100],"with":[7,71,146,203],"half":[8],"a":[9,92,120,129,139,174,206],"million":[10],"participants,":[11],"are":[12],"changing":[13],"the":[14,30,39,64,82,98,135,165,172,188,192,198],"scale":[15],"and":[16,20,34,53,75,77,115,131,168,194,205,217],"availability":[17],"of":[18,32,38,81,171,177],"genotypic":[19],"phenotypic":[21,114],"data":[22,42,66,83,125,136,160],"for":[23,97,191,211],"researchers":[24],"to":[25,58,62,68,84,104,111,156,164],"ask":[26],"fundamental":[27],"questions":[28],"about":[29],"biology":[31],"health":[33],"disease.":[35],"The":[36,214],"breadth":[37],"is":[43,183,196,209,219],"enabling":[44],"discoveries":[45],"at":[46],"an":[47,153],"unprecedented":[48],"pace.":[49],"However,":[50],"this":[51],"size":[52],"complexity":[54],"pose":[55],"new":[56],"challenges":[57],"investigators":[59],"who":[60],"need":[61],"keep":[63],"accruing":[65],"up":[67],"date,":[69],"comply":[70],"potential":[72],"consent":[73],"changes,":[74],"efficiently":[76,112],"reproducibly":[78],"extract":[79],"subsets":[80],"answer":[85],"specific":[86],"scientific":[87],"questions.":[88],"Here":[89],"we":[90],"propose":[91],"tool":[93,155],"called":[94],"ukbREST":[95,152],"designed":[96],"study":[101],"(easily":[102],"extensible":[103],"other":[105,147],"biobanks),":[106],"which":[107],"allows":[108],"authorized":[109],"users":[110],"retrieve":[113],"genetic":[116],"data.":[117],"It":[118,182,201],"exposes":[119],"REST":[121],"API":[122],"that":[123],"makes":[124],"highly":[126],"accessible":[127,163],"inside":[128],"private":[130],"secure":[132],"network,":[133],"allowing":[134],"specification":[137],"in":[138,185,221],"human":[140],"readable":[141],"text":[142],"format":[143],"easily":[144],"shareable":[145],"researchers.":[148],"These":[149],"characteristics":[150],"make":[151,157],"important":[154],"biobank's":[158],"valuable":[159],"more":[161],"readily":[162],"research":[166],"community":[167],"facilitate":[169],"reproducibility":[170],"analysis,":[173],"key":[175],"aspect":[176],"science.":[178],"AVAILABILITY":[179],"AND":[180],"IMPLEMENTATION:":[181],"implemented":[184],"Python":[186],"using":[187],"Flask-RESTful":[189],"framework":[190],"API,":[193],"it":[195],"under":[197],"MIT":[199],"license.":[200],"works":[202],"PostgreSQL":[204],"Docker":[207],"image":[208],"available":[210,220],"easy":[212],"deployment.":[213],"source":[215],"code":[216],"documentation":[218],"Github:":[222],"https://github.com/hakyimlab/ukbrest.":[223]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
