Essie: a concept-based search engine for structured biomedical text

J Am Med Inform Assoc. 2007 May-Jun;14(3):253-63. doi: 10.1197/jamia.M2233. Epub 2007 Feb 28.


This article describes the algorithms implemented in the Essie search engine that is currently serving several Web sites at the National Library of Medicine. Essie is a phrase-based search engine with term and concept query expansion and probabilistic relevancy ranking. Essie's design is motivated by an observation that query terms are often conceptually related to terms in a document, without actually occurring in the document text. Essie's performance was evaluated using data and standard evaluation methods from the 2003 and 2006 Text REtrieval Conference (TREC) Genomics track. Essie was the best-performing search engine in the 2003 TREC Genomics track and achieved results comparable to those of the highest-ranking systems on the 2006 TREC Genomics track task. Essie shows that a judicious combination of exploiting document structure, phrase searching, and concept based query expansion is a useful approach for information retrieval in the biomedical domain.

Publication types

  • Evaluation Study

MeSH terms

  • Abstracting and Indexing*
  • Algorithms*
  • Genomics
  • Information Storage and Retrieval / methods*
  • National Library of Medicine (U.S.)
  • Software
  • Unified Medical Language System
  • United States
  • User-Computer Interface*