J Am Med Inform Assoc 8:598-609 doi:10.1136/jamia.2001.0080598
  • Original Investigation
  • Research Paper

Use of General-purpose Negation Detection to Augment Concept Indexing of Medical Documents

A Quantitative Study Using the UMLS

  1. Pradeep G Mutalik,
  2. Aniruddha Deshpande,
  3. Prakash M Nadkarni
  1. Affiliation of the authors: Yale University School of Medicine, New Haven, Connecticut
  1. Correspondence and reprints: Pradeep G. Mutalik, MD, Department of Diagnostic Radiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510; e-mail: 〈Pradeep.Mutalik{at}
  • Received 22 December 2000
  • Accepted 15 May 2001


Objectives To test the hypothesis that most instances of negated concepts in dictated medical documents can be detected by a strategy that relies on tools developed for the parsing of formal (computer) languages—specifically, a lexical scanner (“lexer”) that uses regular expressions to generate a finite state machine, and a parser that relies on a restricted subset of context-free grammars, known as LALR(1) grammars.

Methods A diverse training set of 40 medical documents from a variety of specialties was manually inspected and used to develop a program (Negfinder) that contained rules to recognize a large set of negated patterns occurring in the text. Negfinder's lexer and parser were developed using tools normally used to generate programming language compilers. The input to Negfinder consisted of medical narrative that was preprocessed to recognize UMLS concepts: the text of a recognized concept had been replaced with a coded representation that included its UMLS concept ID. The program generated an index with one entry per instance of a concept in the document, where the presence or absence of negation of that concept was recorded. This information was used to mark up the text of each document by color-coding it to make it easier to inspect. The parser was then evaluated in two ways: 1) a test set of 60 documents (30 discharge summaries, 30 surgical notes) marked-up by Negfinder was inspected visually to quantify false-positive and false-negative results; and 2) a different test set of 10 documents was independently examined for negatives by a human observer and by Negfinder, and the results were compared.

Results In the first evaluation using marked-up documents, 8,358 instances of UMLS concepts were detected in the 60 documents, of which 544 were negations detected by the program and verified by human observation (true-positive results, or TPs). Thirteen instances were wrongly flagged as negated (false-positive results, or FPs), and the program missed 27 instances of negation (false-negative results, or FNs), yielding a sensitivity of 95.3 percent and a specificity of 97.7 percent. In the second evaluation using independent negation detection, 1,869 concepts were detected in 10 documents, with 135 TPs, 12 FPs, and 6 FNs, yielding a sensitivity of 95.7 percent and a specificity of 91.8 percent. One of the words “no,” “denies/denied,” “not,” or “without” was present in 92.5 percent of all negations.

Conclusions Negation of most concepts in medical narrative can be reliably detected by a simple strategy. The reliability of detection depends on several factors, the most important being the accuracy of concept matching.


  • This work was supported by National Institutes of Health grant R01 LM06843-01 from the National Library of Medicine.

  • * More details are available online, at, as appendixes to this article.

  • The observers were the three authors. The first and third authors (PGM and PMN) were the developers of Negfinder, while the second author (AD) was the primary reviewer. The final tally of the results was done only after all three observers conferred and discussed their findings, which were then re-examined by the primary reviewer, taking into account types of errors found or missed by all the observers. Although the reliability of the observers was not measured, this iterative process was found to considerably increase the reliability of the error detection.

  • The lexer/parser specification can be downloaded from Evaluation of the lexer/parser requires Visual Parse++, a free time-limited evaluation copy of which can be downloaded from The Visual Basic code uses a SQL server database, the schema of which can be requested from the third author(PMN)

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