title: Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases.
abstract: Identification of a cohort of patients with specific diseases is an important step for clinical research that is based on electronic health records (EHRs). Informatics approaches combining structured EHR data, such as billing records, with narrative text data have demonstrated utility for such tasks. This paper describes an algorithm combining machine learning and natural language processing to detect patients with colorectal cancer (CRC) from entire EHRs at Vanderbilt University Hospital. We developed a general case detection method that consists of two steps: 1) extraction of positive CRC concepts from all clinical notes (document-level concept identification); and 2) determination of CRC cases using aggregated information from both clinical narratives and structured billing data (patient-level case determination). For each step, we compared performance of rule-based and machine-learning-based approaches. Using a manually reviewed data set containing 300 possible CRC patients (150 for training and 150 for testing), we showed that our method achieved F-measures of 0.996 for document level concept identification, and 0.93 for patient level case detection.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University, School of Medicine, Nashville, TN, USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Xu
authors.forename: Zhenming
authors.initials: Z
authors.lastname: Fu
authors.forename: Anushi
authors.initials: A
authors.lastname: Shah
authors.forename: Yukun
authors.initials: Y
authors.lastname: Chen
authors.forename: Neeraja B
authors.initials: NB
authors.lastname: Peterson
authors.forename: Qingxia
authors.initials: Q
authors.lastname: Chen
authors.forename: Subramani
authors.initials: S
authors.lastname: Mani
authors.forename: Mia A
authors.initials: MA
authors.lastname: Levy
authors.forename: Qi
authors.initials: Q
authors.lastname: Dai
authors.forename: Josh C
authors.initials: JC
authors.lastname: Denny
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D015179:Colorectal Neoplasms / Q000175:diagnosis*; D057225:Data Mining / Q000379:methods*; D057286:Electronic Health Records; D006801:Humans; D009323:Natural Language Processing