title: Using natural language processing and machine learning to identify gout flares from electronic clinical notes.
abstract: OBJECTIVE
  Gout flares are not well documented by diagnosis codes, making it difficult to conduct accurate database studies. We implemented a computer-based method to automatically identify gout flares using natural language processing (NLP) and machine learning (ML) from electronic clinical notes.
  
  
  METHODS
  Of 16,519 patients, 1,264 and 1,192 clinical notes from 2 separate sets of 100 patients were selected as the training and evaluation data sets, respectively, which were reviewed by rheumatologists. We created separate NLP searches to capture different aspects of gout flares. For each note, the NLP search outputs became the ML system inputs, which provided the final classification decisions. The note-level classifications were grouped into patient-level gout flares. Our NLP+ML results were validated using a gold standard data set and compared with the claims-based method used by prior literatures.
  
  
  RESULTS
  For 16,519 patients with a diagnosis of gout and a prescription for a urate-lowering therapy, we identified 18,869 clinical notes as gout flare positive (sensitivity 82.1%, specificity 91.5%): 1,402 patients with ≥3 flares (sensitivity 93.5%, specificity 84.6%), 5,954 with 1 or 2 flares, and 9,163 with no flare (sensitivity 98.5%, specificity 96.4%). Our method identified more flare cases (18,869 versus 7,861) and patients with ≥3 flares (1,402 versus 516) when compared to the claims-based method.
  
  
  CONCLUSIONS
  We developed a computer-based method (NLP and ML) to identify gout flares from the clinical notes. Our method was validated as an accurate tool for identifying gout flares with higher sensitivity and specificity compared to previous studies.
authors.affiliation: Kaiser Permanente Southern California, Pasadena.
authors.forename: Chengyi
authors.initials: C
authors.lastname: Zheng
authors.forename: Nazia
authors.initials: N
authors.lastname: Rashid
authors.forename: Yi-Lin
authors.initials: YL
authors.lastname: Wu
authors.forename: River
authors.initials: R
authors.lastname: Koblick
authors.forename: Antony T
authors.initials: AT
authors.lastname: Lin
authors.forename: Gerald D
authors.initials: GD
authors.lastname: Levy
authors.forename: T Craig
authors.initials: TC
authors.lastname: Cheetham
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D003199:Computer Systems; D057286:Electronic Health Records; D006073:Gout / Q000145:classification / Q000175:diagnosis*; D006801:Humans; D009323:Natural Language Processing; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity