{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T16:21:08Z","timestamp":1774282868321,"version":"3.50.1"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,3,5]],"date-time":"2021-03-05T00:00:00Z","timestamp":1614902400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"L\u2019Oreal Research and Innovation chair in Digital Biology and Natural Sciences and Engineering Research Council of Canada [NSERC","award":["CG118883"],"award-info":[{"award-number":["CG118883"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The growing production of massive heterogeneous biological data offers opportunities for new discoveries. However, performing multi-omics data analysis is challenging, and researchers are forced to handle the ever-increasing complexity of both data management and evolution of our biological understanding. Substantial efforts have been made to unify biological datasets into integrated systems. Unfortunately, they are not easily scalable, deployable and searchable, locally or globally.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This publication presents two tools with a simple structure that can help any data provider, organization or researcher, requiring a reliable data search and analysis base. The first tool is\u00a0Kibio, a scalable and adaptable data storage based on Elasticsearch search engine. The second tool is\u00a0KibioR, a R package to pull, push and search\u00a0Kibio\u00a0datasets or any accessible Elasticsearch-based databases. These tools apply a uniform data exchange model and minimize the burden of data management by organizing data into a decentralized, versatile, searchable and shareable structure. Several case studies are presented using multiple databases, from drug characterization to miRNAs and pathways identification, emphasizing the ease of use and versatility of the Kibio\/KibioR framework.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>Both KibioR and Elasticsearch are open source. KibioR package source is available at https:\/\/github.com\/regisoc\/kibior and the library on CRAN at https:\/\/cran.r-project.org\/package=kibior.<\/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\/btab157","type":"journal-article","created":{"date-parts":[[2021,3,2]],"date-time":"2021-03-02T20:12:06Z","timestamp":1614715926000},"page":"2706-2713","source":"Crossref","is-referenced-by-count":3,"title":["KibioR &amp; Kibio: a new architecture for next-generation data querying and sharing in big biology"],"prefix":"10.1093","volume":"37","author":[{"given":"R\u00e9gis","family":"Ongaro-Carcy","sequence":"first","affiliation":[{"name":"Centre de Recherche du CHU de Qu\u00e9bec\u2014Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 4G2, Canada"},{"name":"D\u00e9partement de M\u00e9decine Mol\u00e9culaire, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Pier","family":"Scott-Boyer","sequence":"additional","affiliation":[{"name":"Centre de Recherche du CHU de Qu\u00e9bec\u2014Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 4G2, Canada"},{"name":"D\u00e9partement de M\u00e9decine Mol\u00e9culaire, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrien","family":"Dessemond","sequence":"additional","affiliation":[{"name":"Centre de Recherche du CHU de Qu\u00e9bec\u2014Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 4G2, Canada"},{"name":"D\u00e9partement de M\u00e9decine Mol\u00e9culaire, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fran\u00e7ois","family":"Belleau","sequence":"additional","affiliation":[{"name":"Centre de Recherche du CHU de Qu\u00e9bec\u2014Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 4G2, Canada"},{"name":"D\u00e9partement de M\u00e9decine Mol\u00e9culaire, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mickael","family":"Leclercq","sequence":"additional","affiliation":[{"name":"Centre de Recherche du CHU de Qu\u00e9bec\u2014Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 4G2, Canada"},{"name":"D\u00e9partement de M\u00e9decine Mol\u00e9culaire, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"P\u00e9rin","sequence":"additional","affiliation":[{"name":"L\u2019Or\u00e9al Research and Innovation , Advanced Research, Aulnay-Sous-Bois, Paris 93 600, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7922-790X","authenticated-orcid":false,"given":"Arnaud","family":"Droit","sequence":"additional","affiliation":[{"name":"Centre de Recherche du CHU de Qu\u00e9bec\u2014Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 4G2, Canada"},{"name":"D\u00e9partement de M\u00e9decine Mol\u00e9culaire, Universit\u00e9 Laval , Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,3,5]]},"reference":[{"key":"2023051609202765600_btab157-B1","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1038\/494416a","article-title":"Big biology: the \u2019omes puzzle","volume":"494","author":"Baker","year":"2013","journal-title":"Nat. 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