{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:03Z","timestamp":1740185103666,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2018,9,26]],"date-time":"2018-09-26T00:00:00Z","timestamp":1537920000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009706","name":"EU","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009706","id-type":"DOI","asserted-by":"publisher"}]},{"name":"EFPIA Innovative Medicines Initiative Joint Undertaking eTRIKS","award":["115446"],"award-info":[{"award-number":["115446"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Standardization and semantic alignment have been considered one of the major challenges for data integration in clinical research. The inclusion of the CDISC SDTM clinical data standard into the tranSMART i2b2 via a guiding master ontology tree positively impacts and supports the efficacy of data sharing, visualization and exploration across datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present here a schema for the organization of SDTM variables into the tranSMART i2b2 tree along with a script and test dataset to exemplify the mapping strategy. The eTRIKS master tree concept is demonstrated by making use of fictitious data generated for four patients, including 16 SDTM clinical domains. We describe how the usage of correct visit names and data labels can help to integrate multiple readouts per patient and avoid ETL crashes when running a tranSMART loading routine.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The eTRIKS Master Tree package and test datasets are publicly available at https:\/\/doi.org\/10.5281\/zenodo.1009098 and a functional demo installation at https:\/\/public.etriks.org\/transmart\/datasetExplorer\/ under eTRIKS\u2014Master Tree branch, where the discussed examples can be visualized.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty809","type":"journal-article","created":{"date-parts":[[2018,9,25]],"date-time":"2018-09-25T19:11:43Z","timestamp":1537902703000},"page":"1562-1565","source":"Crossref","is-referenced-by-count":0,"title":["Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART"],"prefix":"10.1093","volume":"35","author":[{"given":"Adriano","family":"Barbosa-Silva","sequence":"first","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"},{"name":"Department of Clinical Pharmacology, Centre for Translational Bioinformatics, William Harvey Research, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M6BQ, UK"}]},{"given":"Dorina","family":"Bratfalean","sequence":"additional","affiliation":[{"name":"CDISC, Clinical Data Interchange Standards Consortium and CDISC EU Foundation, Saint-Louis, Alsace, France"}]},{"given":"Wei","family":"Gu","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"}]},{"given":"Venkata","family":"Satagopam","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"}]},{"given":"Paul","family":"Houston","sequence":"additional","affiliation":[{"name":"CDISC, Clinical Data Interchange Standards Consortium and CDISC EU Foundation, Saint-Louis, Alsace, France"}]},{"given":"Lauren B","family":"Becnel","sequence":"additional","affiliation":[{"name":"CDISC, Clinical Data Interchange Standards Consortium and CDISC EU Foundation, Saint-Louis, Alsace, France"}]},{"given":"Serge","family":"Eifes","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"},{"name":"Information Technology for Translational Medicine (ITTM) S.A, Esch\/Belval, Luxembourg"}]},{"given":"Fabien","family":"Richard","sequence":"additional","affiliation":[{"name":"Centre National de la Recherche Scientifique (CNRS), Lyon, Auvergne-Rh\u00f4ne-Alpes, France"}]},{"given":"Andreas","family":"Tielmann","sequence":"additional","affiliation":[{"name":"Department of Research and Bioinformatics, Merck KGaA, Darmstadt, Germany"}]},{"given":"Sascha","family":"Herzinger","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"}]},{"given":"Kavita","family":"Rege","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"}]},{"given":"Rudi","family":"Balling","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"}]},{"given":"Paul","family":"Peeters","sequence":"additional","affiliation":[{"name":"BioSci Consulting, Maasmechelen, Belgium"}]},{"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[{"name":"University of Luxembourg, Luxembourg Centre for Systems Biomedicine, L-4371 Belvaux, Luxembourg"}]}],"member":"286","published-online":{"date-parts":[[2018,9,26]]},"reference":[{"key":"2023012806492648000_bty809-B1","first-page":"1","article-title":"Integrating clinical data into the i2b2 repository","volume":"2009","author":"Abend","year":"2009","journal-title":"Summit Transl. 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