{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,27]],"date-time":"2026-07-27T23:38:53Z","timestamp":1785195533188,"version":"3.55.0"},"reference-count":23,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2022,5,24]],"date-time":"2022-05-24T00:00:00Z","timestamp":1653350400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"the National Research Foundation (NRF) of Korea","doi-asserted-by":"publisher","award":["2019R1F1A1061665"],"award-info":[{"award-number":["2019R1F1A1061665"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"the National Research Foundation (NRF) of Korea","doi-asserted-by":"publisher","award":["2020R1F1A1068423"],"award-info":[{"award-number":["2020R1F1A1068423"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"the Korean government (MSIT)","doi-asserted-by":"publisher","award":["2019R1F1A1061665"],"award-info":[{"award-number":["2019R1F1A1061665"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"the Korean government (MSIT)","doi-asserted-by":"publisher","award":["2020R1F1A1068423"],"award-info":[{"award-number":["2020R1F1A1068423"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JCM"],"abstract":"<jats:p>Background and Aims: The utility of clinical information from esophagogastroduodenoscopy (EGD) reports has been limited because of its unstructured narrative format. We developed a natural language processing (NLP) pipeline that automatically extracts information about gastric diseases from unstructured EGD reports and demonstrated its applicability in clinical research. Methods: An NLP pipeline was developed using 2000 EGD and associated pathology reports that were retrieved from a single healthcare center. The pipeline extracted clinical information, including the presence, location, and size, for 10 gastric diseases from the EGD reports. It was validated with 1000 EGD reports by evaluating sensitivity, positive predictive value (PPV), accuracy, and F1 score. The pipeline was applied to 248,966 EGD reports from 2010\u20132019 to identify patient demographics and clinical information for 10 gastric diseases. Results: For gastritis information extraction, we achieved an overall sensitivity, PPV, accuracy, and F1 score of 0.966, 0.972, 0.996, and 0.967, respectively. Other gastric diseases, such as ulcers, and neoplastic diseases achieved an overall sensitivity, PPV, accuracy, and F1 score of 0.975, 0.982, 0.999, and 0.978, respectively. The study of EGD data of over 10 years revealed the demographics of patients with gastric diseases by sex and age. In addition, the study identified the extent and locations of gastritis and other gastric diseases, respectively. Conclusions: We demonstrated the feasibility of the NLP pipeline providing an automated extraction of gastric disease information from EGD reports. Incorporating the pipeline can facilitate large-scale clinical research to better understand gastric diseases.<\/jats:p>","DOI":"10.3390\/jcm11112967","type":"journal-article","created":{"date-parts":[[2022,5,24]],"date-time":"2022-05-24T22:04:06Z","timestamp":1653429846000},"page":"2967","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Natural Language Processing for Information Extraction of Gastric Diseases and Its Application in Large-Scale Clinical Research"],"prefix":"10.3390","volume":"11","author":[{"given":"Gyuseon","family":"Song","sequence":"first","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Su Jin","family":"Chung","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, 39FL Gangnam Finance Center 152, Teheran-ro, Gangnam-gu, Seoul 06236, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3692-8807","authenticated-orcid":false,"given":"Ji Yeon","family":"Seo","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, 39FL Gangnam Finance Center 152, Teheran-ro, Gangnam-gu, Seoul 06236, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sun Young","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, 39FL Gangnam Finance Center 152, Teheran-ro, Gangnam-gu, Seoul 06236, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eun Hyo","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, 39FL Gangnam Finance Center 152, Teheran-ro, Gangnam-gu, Seoul 06236, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goh Eun","family":"Chung","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, 39FL Gangnam Finance Center 152, Teheran-ro, Gangnam-gu, Seoul 06236, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4143-7383","authenticated-orcid":false,"given":"Sung Ryul","family":"Shim","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Department of Health and Medical Informatics, Kyungnam University College of Health Sciences, Changwon 51767, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5736-8813","authenticated-orcid":false,"given":"Soonok","family":"Sa","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moongi Simon","family":"Hong","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kang Hyun","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunchan","family":"Jang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chae Won","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7669-1213","authenticated-orcid":false,"given":"Jung Ho","family":"Bae","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Korea"},{"name":"Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National 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