{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:39:47Z","timestamp":1772138387363,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,1,19]],"date-time":"2018-01-19T00:00:00Z","timestamp":1516320000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_PC_14089"],"award-info":[{"award-number":["MC_PC_14089"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/L014815\/1"],"award-info":[{"award-number":["MR\/L014815\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000341","name":"Arthritis Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000274","name":"British Heart Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000274","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000589","name":"Chief Scientist Office","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000589","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000269","name":"Economic and Social Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009250","name":"National Institute for Social Care and Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009250","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>Unlocking the data contained within both structured and unstructured components of electronic health records (EHRs) has the potential to provide a step change in data available for secondary research use, generation of actionable medical insights, hospital management, and trial recruitment. To achieve this, we implemented SemEHR, an open source semantic search and analytics tool for EHRs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>SemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualized mentions of a wide range of biomedical concepts within EHRs. Natural language processing annotations are further assembled at the patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data are serviced via ontology-based search and analytics interfaces.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>SemEHR has been deployed at a number of UK hospitals, including the Clinical Record Interactive Search, an anonymized replica of the EHR of the UK South London and Maudsley National Health Service Foundation Trust, one of Europe\u2019s largest providers of mental health services. In 2 Clinical Record Interactive Search\u2013based studies, SemEHR achieved 93% (hepatitis C) and 99% (HIV) F-measure results in identifying true positive patients. At King\u2019s College Hospital in London, as part of the CogStack program (github.com\/cogstack), SemEHR is being used to recruit patients into the UK Department of Health 100\u2009000 Genomes Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast at searching phenotypes; time for recruitment criteria checking was reduced from days to minutes. Validated on open intensive care EHR data, Medical Information Mart for Intensive Care III, the vital signs extracted by SemEHR can achieve around 97% accuracy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Results from the multiple case studies demonstrate SemEHR\u2019s efficiency: weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of patients, bringing in more and unexpected insight compared to study-oriented bespoke IE systems. SemEHR is open source, available at https:\/\/github.com\/CogStack\/SemEHR.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jamia\/ocx160","type":"journal-article","created":{"date-parts":[[2018,1,8]],"date-time":"2018-01-08T16:16:21Z","timestamp":1515428181000},"page":"530-537","source":"Crossref","is-referenced-by-count":101,"title":["SemEHR: A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research*"],"prefix":"10.1093","volume":"25","author":[{"given":"Honghan","family":"Wu","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"},{"name":"School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing, China"}]},{"given":"Giulia","family":"Toti","sequence":"additional","affiliation":[{"name":"National Addiction Centre, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"}]},{"given":"Katherine I","family":"Morley","sequence":"additional","affiliation":[{"name":"National Addiction Centre, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"},{"name":"Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Australia"}]},{"given":"Zina M","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"},{"name":"Farr Institute of Health Informatics Research, University College London, London, UK"}]},{"given":"Amos","family":"Folarin","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"},{"name":"Farr Institute of Health Informatics Research, University College London, London, UK"}]},{"given":"Richard","family":"Jackson","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"}]},{"given":"Ismail","family":"Kartoglu","sequence":"additional","affiliation":[{"name":"InterDigital Europe, London, UK"}]},{"given":"Asha","family":"Agrawal","sequence":"additional","affiliation":[{"name":"King\u2019s College Hospital NHS Foundation Trust, London, UK"}]},{"given":"Clive","family":"Stringer","sequence":"additional","affiliation":[{"name":"King\u2019s College Hospital NHS Foundation Trust, London, UK"}]},{"given":"Darren","family":"Gale","sequence":"additional","affiliation":[{"name":"King\u2019s College Hospital NHS Foundation Trust, London, UK"}]},{"given":"Genevieve","family":"Gorrell","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Sheffield, Sheffield, UK"}]},{"given":"Angus","family":"Roberts","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Sheffield, Sheffield, UK"}]},{"given":"Matthew","family":"Broadbent","sequence":"additional","affiliation":[{"name":"South London and Maudsley NHS Foundation Trust, London, UK"}]},{"given":"Robert","family":"Stewart","sequence":"additional","affiliation":[{"name":"South London and Maudsley NHS Foundation Trust, London, UK"},{"name":"Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, UK"}]},{"given":"Richard JB","family":"Dobson","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King\u2019s College London, London, 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