Evaluation of a method to identify and categorize section headers in clinical documents

J Am Med Inform Assoc. 2009 Nov-Dec;16(6):806-15. doi: 10.1197/jamia.M3037. Epub 2009 Aug 28.


Objective: Clinical notes, typically written in natural language, often contain substructure that divides them into sections, such as "History of Present Illness" or "Family Medical History." The authors designed and evaluated an algorithm ("SecTag") to identify both labeled and unlabeled (implied) note section headers in "history and physical examination" documents ("H&P notes").

Design: The SecTag algorithm uses a combination of natural language processing techniques, word variant recognition with spelling correction, terminology-based rules, and naive Bayesian scoring methods to identify note section headers. Eleven physicians evaluated SecTag's performance on 319 randomly chosen H&P notes.

Measurements: The primary outcomes were the algorithm's recall and precision in identifying all document sections and a predefined list of twenty-nine major sections. A secondary outcome was to evaluate the algorithm's ability to recognize the correct start and end boundaries of identified sections.

Results: The SecTag algorithm identified 16,036 total sections and 7,858 major sections. Physician evaluators classified 15,329 as true positives and identified 160 sections omitted by SecTag. The recall and precision of the SecTag algorithm were 99.0 and 95.6% for all sections, 98.6 and 96.2% for major sections, and 96.6 and 86.8% for unlabeled sections. The algorithm determined the correct starting and ending text boundaries for 94.8% of labeled sections and 85.9% of unlabeled sections.

Conclusions: The SecTag algorithm accurately identified both labeled and unlabeled sections in history and physical documents. This type of algorithm may assist in natural language processing applications, such as clinical decision support systems or competency assessment for medical trainees.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Electronic Health Records*
  • Humans
  • Information Storage and Retrieval*
  • Natural Language Processing*