title: Natural language processing to ascertain two key variables from operative reports in ophthalmology.
abstract: OBJECTIVE
  Antibiotic prophylaxis is critical to ophthalmology and other surgical specialties. We performed natural language processing (NLP) of 743 838 operative notes recorded for 315 246 surgeries to ascertain two variables needed to study the comparative effectiveness of antibiotic prophylaxis in cataract surgery. The first key variable was an exposure variable, intracameral antibiotic injection. The second was an intraoperative complication, posterior capsular rupture (PCR), which functioned as a potential confounder. To help other researchers use NLP in their settings, we describe our NLP protocol and lessons learned.
  
  
  METHODS
  For each of the two variables, we used SAS Text Miner and other SAS text-processing modules with a training set of 10 000 (1.3%) operative notes to develop a lexicon. The lexica identified misspellings, abbreviations, and negations, and linked words into concepts (e.g. "antibiotic" linked with "injection"). We confirmed the NLP tools by iteratively obtaining random samples of 2000 (0.3%) notes, with replacement.
  
  
  RESULTS
  The NLP tools identified approximately 60 000 intracameral antibiotic injections and 3500 cases of PCR. The positive and negative predictive values for intracameral antibiotic injection exceeded 99%. For the intraoperative complication, they exceeded 94%.
  
  
  CONCLUSIONS
  NLP was a valid and feasible method for obtaining critical variables needed for a research study of surgical safety. These NLP tools were intended for use in the study sample. Use with external datasets or future datasets in our own setting would require further testing. Copyright © 2017 John Wiley & Sons, Ltd.
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
authors.forename: Liyan
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Ophthalmology, Kaiser Permanente Northern California, Oakland, CA, USA.
authors.forename: Neal H
authors.initials: NH
authors.lastname: Shorstein
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
authors.forename: Laura B
authors.initials: LB
authors.lastname: Amsden
authors.affiliation: Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Herrinton
mesh_terms: D000900:Anti-Bacterial Agents / Q000008:administration & dosage; D019072:Antibiotic Prophylaxis / Q000379:methods*; D002387:Cataract Extraction / Q000379:methods*; D057186:Comparative Effectiveness Research / Q000379:methods; D015986:Confounding Factors, Epidemiologic; D005240:Feasibility Studies; D006801:Humans; D056965:Injections, Intraocular; D007431:Intraoperative Complications / Q000453:epidemiology; D009323:Natural Language Processing; D057851:Posterior Capsular Rupture, Ocular / Q000453:epidemiology*; D011237:Predictive Value of Tests; D013530:Surgical Wound Infection / Q000517:prevention & control
chemical_list: D000900:Anti-Bacterial Agents
keywords: comparative effectiveness research; electronic health record; natural language processing; pharmacoepidemiology; practice variation; prophylaxis; surgical-site infection