{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T22:35:34Z","timestamp":1768516534489,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T00:00:00Z","timestamp":1524528000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Spanish Ministry of Economy and Competitiveness","award":["MTM2015-68140-R"],"award-info":[{"award-number":["MTM2015-68140-R"]}]},{"name":"European Commission FP7","award":["GA#308333"],"award-info":[{"award-number":["GA#308333"]}]},{"DOI":"10.13039\/100000025","name":"National Institutes of Mental Health","doi-asserted-by":"crossref","award":["NIMH R01MH107205"],"award-info":[{"award-number":["NIMH R01MH107205"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R\/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. However, there is a need to perform similar analyses at the chemicals-genes or chemicals-diseases levels to provide complementary knowledge of the causal path between chemicals and diseases. While the Comparative Toxicogenomics DatabaseTM (CTD) provides information about these relationships, there is no software for integrating it into R\/Bioconductor analysis pipelines. CTDquerier helps users to easily download CTD data and integrate it in the R\/Bioconductor framework. The package also contains functions for visualizing CTD data and performing enrichment analyses. We illustrate how to use the package with a real data analysis of asthma-related genes. CTDquerier is a flexible and easy-to-use Bioconductor package that provides novel hypothesis about the relationships between chemicals and diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CTDquerier R package is available through Bioconductor and its development version at https:\/\/github.com\/isglobal-brge\/CTDquerier.<\/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\/bty326","type":"journal-article","created":{"date-parts":[[2018,4,23]],"date-time":"2018-04-23T06:41:15Z","timestamp":1524465675000},"page":"3235-3237","source":"Crossref","is-referenced-by-count":9,"title":["<tt>CTDquerier<\/tt>: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies"],"prefix":"10.1093","volume":"34","author":[{"given":"Carles","family":"Hernandez-Ferrer","sequence":"first","affiliation":[{"name":"Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), Barcelona, Spain"},{"name":"CIBER Epidemiolog\u00eda y Salud P\u00fablica (CIBERESP), Madrid, Spain"},{"name":"Computational Health Informatics Program, Boston Children\u2019s Hospital, Boston, USA"}]},{"given":"Juan R","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain"},{"name":"Universitat Pompeu Fabra (UPF), Barcelona, Spain"},{"name":"CIBER Epidemiolog\u00eda y Salud P\u00fablica (CIBERESP), Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2018,4,24]]},"reference":[{"key":"2023012704180414700_bty326-B1","doi-asserted-by":"crossref","first-page":"D914","DOI":"10.1093\/nar\/gku935","article-title":"The Comparative Toxicogenomics Database\u2019s 10th year anniversary: update 2015","volume":"43","author":"Davis","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012704180414700_bty326-B2","doi-asserted-by":"crossref","first-page":"D972","DOI":"10.1093\/nar\/gkw838","article-title":"The comparative toxicogenomics database: update 2017","volume":"45","author":"Davis","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012704180414700_bty326-B3","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1007\/s10995-010-0599-2","article-title":"The association between second hand smoke and low birth weight and preterm delivery","volume":"15","author":"Khader","year":"2011","journal-title":"Matern. Child Health J"},{"key":"2023012704180414700_bty326-B4","doi-asserted-by":"crossref","first-page":"e46524.","DOI":"10.1371\/journal.pone.0046524","article-title":"Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database","volume":"7","author":"King","year":"2012","journal-title":"PLoS One"},{"key":"2023012704180414700_bty326-B5","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1007\/s10654-013-9828-5","article-title":"Traffic, asthma and genetics: combining international birth cohort data to examine genetics as a mediator of traffic-related air pollution\u2019s impact on childhood asthma","volume":"28","author":"MacIntyre","year":"2013","journal-title":"Eur. J. Epidemiol"},{"key":"2023012704180414700_bty326-B6","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1289\/ehp.6028","article-title":"The Comparative Toxicogenomics Database (CTD)","volume":"111","author":"Mattingly","year":"2003","journal-title":"Environ. Health Perspect"},{"key":"2023012704180414700_bty326-B7","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.jaci.2012.02.040","article-title":"Case-control admixture mapping in latino populations enriches for known asthma-associated genes","volume":"130","author":"Torgerson","year":"2012","journal-title":"J. Allergy Clin. Immunol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3235\/48919190\/bioinformatics_34_18_3235.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3235\/48919190\/bioinformatics_34_18_3235.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T04:39:19Z","timestamp":1674794359000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/18\/3235\/4983065"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,24]]},"references-count":7,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2018,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty326","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,15]]},"published":{"date-parts":[[2018,4,24]]}}}