{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T14:05:16Z","timestamp":1791813916599,"version":"4.3.4"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T00:00:00Z","timestamp":1688515200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Marcus Foundation Grant for Precision Medicine"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>Clinical notes are a veritable treasure trove of information on a patient\u2019s disease progression, medical history, and treatment plans, yet are locked in secured databases accessible for research only after extensive ethics review. Removing personally identifying and protected health information (PII\/PHI) from the records can reduce the need for additional Institutional Review Boards (IRB) reviews. In this project, our goals were to: (1) develop a robust and scalable clinical text de-identification pipeline that is compliant with the Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule for de-identification standards and (2) share routinely updated de-identified clinical notes with researchers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Materials and Methods<\/jats:title>\n                  <jats:p>Building on our open-source de-identification software called Philter, we added features to: (1) make the algorithm and the de-identified data HIPAA compliant, which also implies type 2 error-free redaction, as certified via external audit; (2) reduce over-redaction errors; and (3) normalize and shift date PHI. We also established a streamlined de-identification pipeline using MongoDB to automatically extract clinical notes and provide truly de-identified notes to researchers with periodic monthly refreshes at our institution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To the best of our knowledge, the Philter V1.0 pipeline is currently the first and only certified, de-identified redaction pipeline that makes clinical notes available to researchers for nonhuman subjects\u2019 research, without further IRB approval needed. To date, we have made over 130 million certified de-identified clinical notes available to over 600 UCSF researchers. These notes were collected over the past 40 years, and represent data from 2757016 UCSF patients.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jamiaopen\/ooad045","type":"journal-article","created":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T13:15:50Z","timestamp":1688562950000},"source":"Crossref","is-referenced-by-count":58,"title":["A certified de-identification system for all clinical text documents for information extraction at scale"],"prefix":"10.1093","volume":"6","author":[{"given":"Lakshmi","family":"Radhakrishnan","sequence":"first","affiliation":[{"name":"Academic Research Services, Information Technology, University of California, San Francisco , San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1240-9949","authenticated-orcid":false,"given":"Gundolf","family":"Schenk","sequence":"additional","affiliation":[{"name":"Bakar Computational Health Sciences Institute, University of California, San Francisco , San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen","family":"Muenzen","sequence":"additional","affiliation":[{"name":"Bakar Computational Health Sciences Institute, University of California, San Francisco , San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boris","family":"Oskotsky","sequence":"additional","affiliation":[{"name":"Bakar Computational Health Sciences Institute, University of California, San Francisco , San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Habibeh","family":"Ashouri Choshali","sequence":"additional","affiliation":[{"name":"Bakar Computational Health Sciences Institute, University of California, San Francisco , San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Plunkett","sequence":"additional","affiliation":[{"name":"ArcherHall LLC , Sacramento, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharat","family":"Israni","sequence":"additional","affiliation":[{"name":"Bakar Computational Health Sciences Institute, University of California, San Francisco , San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atul J","family":"Butte","sequence":"additional","affiliation":[{"name":"Bakar Computational Health Sciences Institute, University of California, San Francisco , San Francisco, California, USA"},{"name":"Department of Pediatrics, University of California, San Francisco , San Francisco, California, USA"},{"name":"Center for Data-Driven Insights and Innovation, University of California Health , Oakland, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,7,4]]},"reference":[{"issue":"1","key":"2023070505085295700_ooad045-B1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.2337\/dci21-0051","article-title":"Heterogeneity of diabetes: \u03b2-cells, phenotypes, and precision medicine: Proceedings of an International Symposium of the Canadian Institutes of Health Research\u2019s Institute of Nutrition, Metabolism and Diabetes and the U.S. National Institutes of Health\u2019s","volume":"45","author":"Cefalu","year":"2022","journal-title":"Diabetes Care"},{"key":"2023070505085295700_ooad045-B2","first-page":"180219","article-title":"Enabling precision medicine in neonatology, an integrated repository for preterm birth research","volume":"5","author":"Sirota","year":"2018"},{"issue":"7","key":"2023070505085295700_ooad045-B3","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1097\/ACM.0b013e318065be1e","article-title":"Medical education research and IRB review: an analysis and comparison of the IRB review process at six institutions","volume":"82","author":"Dyrbye","year":"2007","journal-title":"Acad Med"},{"key":"2023070505085295700_ooad045-B4","first-page":"37","article-title":"Reducing the time for IRB reviews: a case study","volume":"48","author":"Liberale","year":"2017","journal-title":"J Res Admin"},{"key":"2023070505085295700_ooad045-B5","first-page":"57","article-title":"Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes","volume":"3","author":"Norgeot","year":"2020"},{"issue":"23","key":"2023070505085295700_ooad045-B6","first-page":"E215","article-title":"PhysioBank, PhysioToolkit, and PhysioNet: components of a new research resource for complex physiologic signals","volume":"101","author":"Goldberger","year":"2000"},{"key":"2023070505085295700_ooad045-B7","first-page":"112","article-title":"Improved de-identification of physician notes through integrative modeling of both public and private medical text","volume":"13","author":"McMurry","year":"2013"},{"key":"2023070505085295700_ooad045-B8","author":"UCSF. UCSF DeID CDW","year":"2022"},{"key":"2023070505085295700_ooad045-B9","first-page":"941","article-title":"EMERSE: the electronic medical record search engine","volume":"2006","author":"Hanauer","year":"2006","journal-title":"AMIA Annu Symp Proc"},{"issue":"12","key":"2023070505085295700_ooad045-B10","first-page":"849","article-title":"The MITRE Identification Scrubber Toolkit: design, training, and assessment","volume":"79","author":"Aberdeen","year":"2010"},{"key":"2023070505085295700_ooad045-B11","first-page":"252","author":"Toutanova"},{"key":"2023070505085295700_ooad045-B12","author":"Schenk","year":"2022"},{"issue":"1","key":"2023070505085295700_ooad045-B13","doi-asserted-by":"crossref","first-page":"S420","DOI":"10.14309\/01.ajg.0000705320.33817.a5","article-title":"Accurate machine classification of ulcerative colitis Mayo subscores from electronic health record procedure reports","volume":"115","author":"Rudrapatna","year":"2020","journal-title":"Am J Gastroenterol"},{"issue":"10","key":"2023070505085295700_ooad045-B14","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1038\/s41591-021-01506-3","article-title":"Federated learning for predicting clinical outcomes in patients with COVID-19","volume":"27","author":"Dayan","year":"2021","journal-title":"Nat Med"},{"key":"2023070505085295700_ooad045-B15","author":"Farrand","journal-title":"2022"},{"issue":"5","key":"2023070505085295700_ooad045-B16","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1136\/jamia.2009.001560","article-title":"Mayo clinical text analysis and knowledge extraction system (cTAKES): architecture, component evaluation and applications","volume":"17","author":"Savova","year":"2010","journal-title":"J Am Med Inform Assoc"},{"key":"2023070505085295700_ooad045-B17","author":"Abramowitsch","year":"2020.","journal-title":"Apache cTAKES High Throughput Orchestration [Conference Presentation]"}],"container-title":["JAMIA Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jamiaopen\/article-pdf\/6\/3\/ooad045\/50801018\/ooad045.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jamiaopen\/article-pdf\/6\/3\/ooad045\/50801018\/ooad045.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T13:16:05Z","timestamp":1688562965000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamiaopen\/article\/doi\/10.1093\/jamiaopen\/ooad045\/7219298"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,4]]},"references-count":17,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,7,4]]}},"URL":"https:\/\/doi.org\/10.1093\/jamiaopen\/ooad045","relation":{},"ISSN":["2574-2531"],"issn-type":[{"value":"2574-2531","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,10,1]]},"published":{"date-parts":[[2023,7,4]]},"article-number":"ooad045"}}