{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T08:52:52Z","timestamp":1775897572473,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"vor","delay-in-days":85,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"GE Healthcare and Vanderbilt University Medical Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Objective<\/jats:title><jats:p>Automatically identifying patients at risk of immune checkpoint inhibitor (ICI)-induced colitis allows physicians to improve patientcare. However, predictive models require training data curated from electronic health records (EHR). Our objective is to automatically identify notes documenting ICI-colitis cases to accelerate data curation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Materials and Methods<\/jats:title><jats:p>We present a data pipeline to automatically identify ICI-colitis from EHR notes, accelerating chart review. The pipeline relies on BERT, a state-of-the-art natural language processing (NLP) model. The first stage of the pipeline segments long notes using keywords identified through a logistic classifier and applies BERT to identify ICI-colitis notes. The next stage uses a second BERT model tuned to identify false positive notes and remove notes that were likely positive for mentioning colitis as a side-effect. The final stage further accelerates curation by highlighting the colitis-relevant portions of notes. Specifically, we use BERT\u2019s attention scores to find high-density regions describing colitis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The overall pipeline identified colitis notes with 84% precision and reduced the curator note review load by 75%. The segment BERT classifier had a high recall of 0.98, which is crucial to identify the low incidence (&amp;lt;10%) of colitis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Curation from EHR notes is a burdensome task, especially when the curation topic is complicated. Methods described in this work are not only useful for ICI colitis but can also be adapted for other domains.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our extraction pipeline reduces manual note review load and makes EHR data more accessible for research.<\/jats:p><\/jats:sec>","DOI":"10.1093\/jamiaopen\/ooad017","type":"journal-article","created":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T21:31:15Z","timestamp":1680384675000},"source":"Crossref","is-referenced-by-count":6,"title":["Accelerated curation of checkpoint inhibitor-induced colitis cases from electronic health records"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0000-8558","authenticated-orcid":false,"given":"Protiva","family":"Rahman","sequence":"first","affiliation":[{"name":"Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Ye","sequence":"additional","affiliation":[{"name":"Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathleen F","family":"Mittendorf","sequence":"additional","affiliation":[{"name":"Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michele","family":"Lenoue-Newton","sequence":"additional","affiliation":[{"name":"Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7744-9039","authenticated-orcid":false,"given":"Christine","family":"Micheel","sequence":"additional","affiliation":[{"name":"Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jan","family":"Wolber","sequence":"additional","affiliation":[{"name":"Pharmaceutical Diagnostics, GE Healthcare , Chalfont St Giles, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Travis","family":"Osterman","sequence":"additional","affiliation":[{"name":"Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Fabbri","sequence":"additional","affiliation":[{"name":"Biomedical Informatics, Vanderbilt University Medical Center , Nashville, Tennessee, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,1]]},"reference":[{"issue":"8","key":"2023040121310831700_","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1136\/jclinpath-2018-205143","article-title":"Immune checkpoint inhibitor-induced gastrointestinal and hepatic injury: pathologists\u2019 perspective","volume":"71","author":"Karamchandani","year":"2018","journal-title":"J Clin Pathol"},{"key":"2023040121310831700_","first-page":"258","author":"Martineau","year":"2009"},{"key":"2023040121310831700_","first-page":"269","author":"Ratner","year":"2017"},{"key":"2023040121310831700_","first-page":"4171","author":"Devlin"},{"key":"2023040121310831700_","first-page":"233","author":"Davis","year":"2006"},{"key":"2023040121310831700_","author":"Michel","year":"2019"},{"key":"2023040121310831700_","author":"Li","year":"2021"},{"key":"2023040121310831700_","first-page":"276","author":"Clark"},{"key":"2023040121310831700_","first-page":"85","author":"Bolotova","year":"2020"},{"issue":"11","key":"2023040121310831700_","doi-asserted-by":"crossref","first-page":"e19612","DOI":"10.2196\/19612","article-title":"Amplifying domain expertise in clinical data pipelines","volume":"8","author":"Rahman","year":"2020","journal-title":"JMIR Med Inform"}],"container-title":["JAMIA 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