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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i340-i349
© 2003 Oxford University Press

Extracting synonymous gene and protein terms from biological literature

Hong Yu * and Eugene Agichtein

Department of Computer Science, Columbia University, New York, NY, USA

Received on January 6, 2003 ; accepted on February 20, 2003

Motivation: Genes and proteins are often associated with multiple names. More names are added as new functional or structural information is discovered. Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance.

Results: We have explored four complementary approaches for extracting gene and protein synonyms from text, namely the unsupervised, partially supervised, and supervised machine-learning techniques, as well as the manual knowledge-based approach. We report results of a large scale evaluation of these alternatives over an archive of biological journal articles. Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database.

Data Availability: The extracted gene and protein synonyms are available at http://synonyms.cs.columbia.edu/

Contact: hongyu,eugene{at}cs.columbia.edu

* To whom correspondence should be addressed.


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