{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T06:28:58Z","timestamp":1778826538209,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Objective To help cancer registrars efficiently and accurately identify reportable cancer cases.<\/jats:p>\n               <jats:p>Material and Methods The Cancer Registry Control Panel (CRCP) was developed to detect mentions of reportable cancer cases using a pipeline built on the Unstructured Information Management Architecture \u2013 Asynchronous Scaleout (UIMA-AS) architecture containing the National Library of Medicine\u2019s UIMA MetaMap annotator as well as a variety of rule-based UIMA annotators that primarily act to filter out concepts referring to nonreportable cancers. CRCP inspects pathology reports nightly to identify pathology records containing relevant cancer concepts and combines this with diagnosis codes from the Clinical Electronic Data Warehouse to identify candidate cancer patients using supervised machine learning. Cancer mentions are highlighted in all candidate clinical notes and then sorted in CRCP\u2019s web interface for faster validation by cancer registrars.<\/jats:p>\n               <jats:p>Results CRCP achieved an accuracy of 0.872 and detected reportable cancer cases with a precision of 0.843 and a recall of 0.848. CRCP increases throughput by 22.6% over a baseline (manual review) pathology report inspection system while achieving a higher precision and recall. Depending on registrar time constraints, CRCP can increase recall to 0.939 at the expense of precision by incorporating a data source information feature.<\/jats:p>\n               <jats:p>Conclusion CRCP demonstrates accurate results when applying natural language processing features to the problem of detecting patients with cases of reportable cancer from clinical notes. We show that implementing only a portion of cancer reporting rules in the form of regular expressions is sufficient to increase the precision, recall, and speed of the detection of reportable cancer cases when combined with off-the-shelf information extraction software and machine learning.<\/jats:p>","DOI":"10.1093\/jamia\/ocw006","type":"journal-article","created":{"date-parts":[[2016,3,30]],"date-time":"2016-03-30T00:18:52Z","timestamp":1459297132000},"page":"1077-1084","source":"Crossref","is-referenced-by-count":47,"title":["Efficient identification of nationally mandated reportable cancer cases using natural language processing and machine learning"],"prefix":"10.1093","volume":"23","author":[{"given":"John D","family":"Osborne","sequence":"first","affiliation":[{"name":"Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama, USA, 35294"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Wyatt","sequence":"additional","affiliation":[{"name":"Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, Alabama, USA, 35294"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew O","family":"Westfall","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA, 35294"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Willig","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA, 35294"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Bethard","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science, University of Alabama at Birmingham, Birmingham, Alabama, USA, 35294"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoff","family":"Gordon","sequence":"additional","affiliation":[{"name":"Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA, 35294"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,3,28]]},"reference":[{"key":"2020110612361927400_ocw006-B1"},{"key":"2020110612361927400_ocw006-B2","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/j.ijmedinf.2014.06.009","article-title":"Text mining of cancer-related information: review of current status and future directions","volume":"83","author":"Spasi\u0107","year":"2014","journal-title":"Int J Med Inf."},{"key":"2020110612361927400_ocw006-B3","article-title":"Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program","volume-title":"Proceedings of the AMIA Symposium","author":"Aronson","year":"2001"},{"key":"2020110612361927400_ocw006-B4","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1136\/jamia.2009.002733","article-title":"An overview of MetaMap: historical perspective and recent advances","volume":"17","author":"Aronson","year":"2010","journal-title":"J Am Med Inform Assoc."},{"key":"2020110612361927400_ocw006-B5","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1016\/j.jbi.2008.12.005","article-title":"Automatically extracting cancer disease characteristics from pathology reports into a disease knowledge representation model","volume":"42","author":"Coden","year":"2009","journal-title":"J Biomed Inform."},{"key":"2020110612361927400_ocw006-B6","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.1007\/s10552-010-9616-4","article-title":"Pattern-based information extraction from pathology reports for cancer registration","volume":"21","author":"Napolitano","year":"2010","journal-title":"Cancer Causes Control."},{"key":"2020110612361927400_ocw006-B7","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1136\/jamia.2010.003707","article-title":"Symbolic rule-based classification of lung cancer stages from free-text pathology reports","volume":"17","author":"Nguyen","year":"2010","journal-title":"J Am Med Inform Assoc."},{"key":"2020110612361927400_ocw006-B8","first-page":"565","article-title":"Facilitating cancer research using natural language processing of pathology reports","volume":"11","author":"Xu","year":"2004","journal-title":"Medinfo."},{"key":"2020110612361927400_ocw006-B9","article-title":"Comparing methods for identifying pancreatic cancer patients using electronic data sources","volume-title":"AMIA Annual Symposium Proceedings","author":"Friedlin","year":"2010"},{"key":"2020110612361927400_ocw006-B10","article-title":"Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases","volume-title":"AMIA Annual Symposium Proceedings","author":"Xu","year":"2011"},{"key":"2020110612361927400_ocw006-B11"},{"key":"2020110612361927400_ocw006-B12","doi-asserted-by":"crossref","first-page":"D267","DOI":"10.1093\/nar\/gkh061","article-title":"The unified medical language system (UMLS): integrating biomedical terminology","volume":"32","author":"Bodenreider","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2020110612361927400_ocw006-B13"},{"key":"2020110612361927400_ocw006-B14"},{"key":"2020110612361927400_ocw006-B15","article-title":"Comparing proportions in overlapping samples","author":"Bland"}],"container-title":["Journal of the American Medical Informatics Association"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/23\/6\/1077\/34147700\/ocw006.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/jamia\/article-pdf\/23\/6\/1077\/34147700\/ocw006.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,6]],"date-time":"2020-11-06T17:43:11Z","timestamp":1604684591000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamia\/article\/23\/6\/1077\/2399248"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3,28]]},"references-count":15,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2016,3,28]]},"published-print":{"date-parts":[[2016,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jamia\/ocw006","relation":{},"ISSN":["1527-974X","1067-5027"],"issn-type":[{"value":"1527-974X","type":"electronic"},{"value":"1067-5027","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,11]]},"published":{"date-parts":[[2016,3,28]]}}}