Natural language processing of clinical notes for identification of critical limb ischemia

Naveed Afzal, Vishnu Priya Mallipeddi, Sunghwan Sohn, Hongfang Liu, Rajeev Chaudhry, Christopher G. Scott, Iftikhar J. Kullo, Adelaide M. Arruda-Olson

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Background Critical limb ischemia (CLI) is a complication of advanced peripheral artery disease (PAD) with diagnosis based on the presence of clinical signs and symptoms. However, automated identification of cases from electronic health records (EHRs) is challenging due to absence of a single definitive International Classification of Diseases (ICD-9 or ICD-10) code for CLI. Methods and results In this study, we extend a previously validated natural language processing (NLP) algorithm for PAD identification to develop and validate a subphenotyping NLP algorithm (CLI-NLP) for identification of CLI cases from clinical notes. We compared performance of the CLI-NLP algorithm with CLI-related ICD-9 billing codes. The gold standard for validation was human abstraction of clinical notes from EHRs. Compared to billing codes the CLI-NLP algorithm had higher positive predictive value (PPV) (CLI-NLP 96%, billing codes 67%, p < 0.001), specificity (CLI-NLP 98%, billing codes 74%, p < 0.001) and F1-score (CLI-NLP 90%, billing codes 76%, p < 0.001). The sensitivity of these two methods was similar (CLI-NLP 84%; billing codes 88%; p < 0.12). Conclusions The CLI-NLP algorithm for identification of CLI from narrative clinical notes in an EHR had excellent PPV and has potential for translation to patient care as it will enable automated identification of CLI cases for quality projects, clinical decision support tools and support a learning healthcare system.

Original languageEnglish (US)
Pages (from-to)83-89
Number of pages7
JournalInternational Journal of Medical Informatics
StatePublished - Mar 2018


  • Critical limb ischemia
  • Electronic health records
  • Natural language processing
  • Peripheral artery disease
  • Subphenotyping

ASJC Scopus subject areas

  • Health Informatics


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