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Bioinformatics Vol. 17 no. 90001 2001
Pages S97-S106
© 2001 Oxford University Press

Disambiguating proteins, genes, and RNA in text: a machine learning approach

Vasileios Hatzivassiloglou 1, Pablo A. Duboué 1 and Andrey Rzhetsky 2

1 Department of Computer Science, Columbia University, 1214 Amsterdam Avenue, New York, NY, 10027, USA
2 Genome Center and Department of Medical Informatics, Columbia University, 1150 St. Nicholas Avenue, New York, NY, 10032, USA

Received on February 6, 2001 ; revised on April 3, 2001 ; accepted on April 3, 2001

We present an automated system for assigning protein, gene, or mRNA class labels to biological terms in free text. Three machine learning algorithms and several extended ways for defining contextual features for disambiguation are examined, and a fully unsupervised manner for obtaining training examples is proposed. We train and evaluate our system over a collection of 9 million words of molecular biology journal articles, obtaining accuracy rates up to 85%.

Contact: vh{at}cs.columbia.edu


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