title: Mining peripheral arterial disease cases from narrative clinical notes using natural language processing.
abstract: Lower extremity peripheral arterial disease (PAD) is highly prevalent and affects millions of individuals worldwide. We developed a natural language processing (NLP) system for automated ascertainment of PAD cases from clinical narrative notes and compared the performance of the NLP algorithm with billing code algorithms, using ankle-brachial index test results as the gold standard.
  
  
  
  We compared the performance of the NLP algorithm to (1) results of gold standard ankle-brachial index; (2) previously validated algorithms based on relevant International Classification of Diseases, Ninth Revision diagnostic codes (simple model); and (3) a combination of International Classification of Diseases, Ninth Revision codes with procedural codes (full model). A dataset of 1569 patients with PAD and controls was randomly divided into training (n = 935) and testing (n = 634) subsets.
  
  
  
  We iteratively refined the NLP algorithm in the training set including narrative note sections, note types, and service types, to maximize its accuracy. In the testing dataset, when compared with both simple and full models, the NLP algorithm had better accuracy (NLP, 91.8%; full model, 81.8%; simple model, 83%; P < .001), positive predictive value (NLP, 92.9%; full model, 74.3%; simple model, 79.9%; P < .001), and specificity (NLP, 92.5%; full model, 64.2%; simple model, 75.9%; P < .001).
  
  
  
  A knowledge-driven NLP algorithm for automatic ascertainment of PAD cases from clinical notes had greater accuracy than billing code algorithms. Our findings highlight the potential of NLP tools for rapid and efficient ascertainment of PAD cases from electronic health records to facilitate clinical investigation and eventually improve care by clinical decision support.
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minn.
authors.forename: Naveed
authors.initials: N
authors.lastname: Afzal
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minn.
authors.forename: Sunghwan
authors.initials: S
authors.lastname: Sohn
authors.affiliation: Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minn.
authors.forename: Sara
authors.initials: S
authors.lastname: Abram
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minn.
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Scott
authors.affiliation: Division of Primary Care Medicine, Knowledge Delivery Center and Center for Innovation, Mayo Clinic, Rochester, Minn.
authors.forename: Rajeev
authors.initials: R
authors.lastname: Chaudhry
authors.affiliation: Department of Health Sciences Research, Mayo Clinic, Rochester, Minn.
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minn.
authors.forename: Iftikhar J
authors.initials: IJ
authors.lastname: Kullo
authors.affiliation: Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minn. Electronic address: olson.adelaide@mayo.edu.
authors.forename: Adelaide M
authors.initials: AM
authors.lastname: Arruda-Olson
mesh_terms: D000067575:Administrative Claims, Healthcare; D000465:Algorithms; D055109:Ankle Brachial Index; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D057286:Electronic Health Records; D006801:Humans; D038801:International Classification of Diseases; D035002:Lower Extremity / Q000098:blood supply*; D008910:Minnesota; D015233:Models, Statistical; D009323:Natural Language Processing; D058729:Peripheral Arterial Disease / Q000145:classification / Q000175:diagnosis*; D012189:Retrospective Studies