Abbreviation definition identification based on automatic precision estimates

Sunghwan Sohn, Donald C. Comeau, Won Kim, John W. Wilbur

Research output: Contribution to journalArticlepeer-review

47 Scopus citations


Background: The rapid growth of biomedical literature presents challenges for automatic text processing, and one of the challenges is abbreviation identification. The presence of unrecognized abbreviations in text hinders indexing algorithms and adversely affects information retrieval and extraction. Automatic abbreviation definition identification can help resolve these issues. However, abbreviations and their definitions identified by an automatic process are of uncertain validity. Due to the size of databases such as MEDLINE only a small fraction of abbreviation-definition pairs can be examined manually. An automatic way to estimate the accuracy of abbreviation-definition pairs extracted from text is needed. In this paper we propose an abbreviation definition identification algorithm that employs a variety of strategies to identify the most probable abbreviation definition. In addition our algorithm produces an accuracy estimate, pseudo-precision, for each strategy without using a human-judged gold standard. The pseudo-precisions determine the order in which the algorithm applies the strategies in seeking to identify the definition of an abbreviation. Results: On the Medstract corpus our algorithm produced 97% precision and 85% recall which is higher than previously reported results. We also annotated 1250 randomly selected MEDLINE records as a gold standard. On this set we achieved 96.5% precision and 83.2% recall. This compares favourably with the well known Schwartz and Hearst algorithm. Conclusion: We developed an algorithm for abbreviation identification that uses a variety of strategies to identify the most probable definition for an abbreviation and also produces an estimated accuracy of the result. This process is purely automatic.

Original languageEnglish (US)
Article number402
JournalBMC bioinformatics
StatePublished - Sep 25 2008

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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