{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:10Z","timestamp":1740185110305,"version":"3.37.3"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,10,2]],"date-time":"2021-10-02T00:00:00Z","timestamp":1633132800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003329","name":"MINECO","doi-asserted-by":"publisher","award":["PCIN2017-076"],"award-info":[{"award-number":["PCIN2017-076"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERA-Net Cofund on Intestinal Microbiomics","award":["AC19 00096","AC19 00111"],"award-info":[{"award-number":["AC19 00096","AC19 00111"]}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003741","name":"ICREA","doi-asserted-by":"publisher","award":["2017SGR1546"],"award-info":[{"award-number":["2017SGR1546"]}],"id":[{"id":"10.13039\/501100003741","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Generalitat de Catalunya\u2019s Agency AGAUR"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The FOBI ontology can be of great help in nutrimetabolomic studies due to its wide variety of applications, including the possibility of performing different enrichment analyses. However, the programming skills required to query and explore it may limit its use by the scientific community.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present the fobitools framework, comprised of an R\/Bioconductor package and its complementary web interface. These two tools allow researchers to interact and explore the FOBI ontology in a highly user-friendly way. The fobitools framework is focused on the novel concept of food enrichment analysis in nutrimetabolomic studies. However, other useful features, such as the network interactive visualization of FOBI and the automatic annotation of dietary free-text data are also presented.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Both the fobitools R\/Bioconductor package and the fobitoolsGUI web-based application, together with their installation instructions and examples, are freely available at https:\/\/github.com\/nutrimetabolomics\/fobitools and https:\/\/github.com\/nutrimetabolomics\/fobitoolsGUI, respectively.<\/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\/btab626","type":"journal-article","created":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T20:54:33Z","timestamp":1633035273000},"page":"3969-3971","source":"Crossref","is-referenced-by-count":0,"title":["The fobitools framework: the first steps towards food enrichment analysis"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6466-877X","authenticated-orcid":false,"given":"Pol","family":"Castellano-Escuder","sequence":"first","affiliation":[{"name":"Biomarkers and Nutritional & Food Metabolomics Research Group, Department of Nutrition, Food Science and Gastronomy, Food Innovation Network (XIA), University of Barcelona , Barcelona, Spain"},{"name":"Statistics and Bioinformatics Research Group, Department of Genetics, Microbiology and Statistics, University of Barcelona , Barcelona, Spain"},{"name":"CIBERFES, Instituto de Salud Carlos III , Madrid, Spain"}]},{"given":"Cristina","family":"Andr\u00e9s-Lacueva","sequence":"additional","affiliation":[{"name":"Biomarkers and Nutritional & Food Metabolomics Research Group, Department of Nutrition, Food Science and Gastronomy, Food Innovation Network (XIA), University of Barcelona , Barcelona, Spain"},{"name":"CIBERFES, Instituto de Salud Carlos III , Madrid, Spain"}]},{"given":"Alex","family":"S\u00e1nchez-Pla","sequence":"additional","affiliation":[{"name":"Statistics and Bioinformatics Research Group, Department of Genetics, Microbiology and Statistics, University of Barcelona , Barcelona, Spain"},{"name":"CIBERFES, Instituto de Salud Carlos III , Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2021,10,2]]},"reference":[{"key":"2023051607353640400_btab626-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023051607353640400_btab626-B2","doi-asserted-by":"crossref","first-page":"baaa033","DOI":"10.1093\/databa\/baaa033","article-title":"FOBI: an ontology to represent food intake data and associate it with metabolomic data","volume":"2020","author":"Castellano-Escuder","year":"2020","journal-title":"Database"},{"key":"2023051607353640400_btab626-B3","doi-asserted-by":"crossref","first-page":"W486","DOI":"10.1093\/nar\/gky310","article-title":"MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis","volume":"46","author":"Chong","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023051607353640400_btab626-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12859-017-2006-0","article-title":"Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data","volume":"19","author":"Marco-Ramell","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023051607353640400_btab626-B5","doi-asserted-by":"crossref","first-page":"W71","DOI":"10.1093\/nar\/gkq329","article-title":"MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data","volume":"38","author":"Xia","year":"2010","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab626\/40522259\/btab626.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/21\/3969\/50337614\/btab626.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/21\/3969\/50337614\/btab626.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T08:06:21Z","timestamp":1684224381000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/21\/3969\/6380553"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,10,2]]},"references-count":5,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2021,11,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab626","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,11,1]]},"published":{"date-parts":[[2021,10,2]]}}}