title: Using BLAST for identifying gene and protein names in journal articles.
abstract: We describe a system which automatically identifies gene and protein names in journal articles, an important and non-trivial first step in knowledge extraction of protein and gene actions. Our system uses a database of gene and protein names and is based on BLAST [Altschul et al., Nucleic Acids Res. 25 (1997) 3389-3402], a popular tool for DNA and protein sequence comparison. We describe a method that consists of mapping sequences of text characters into sequences of nucleotides that can be processed by BLAST. We demonstrate that this approach is feasible: the system matches gene and protein names with a recall of 78.8% and a precision of 71.7%, which includes names that are not part of the system database. An analysis of the results suggests techniques that can be used to improve performance further.
authors.affiliation: Department of Medical Informatics, Columbia University, New York, NY, USA. mk651@columbia.edu
authors.forename: M
authors.initials: M
authors.lastname: Krauthammer
authors.forename: A
authors.initials: A
authors.lastname: Rzhetsky
authors.forename: P
authors.initials: P
authors.lastname: Morozov
authors.forename: C
authors.initials: C
authors.lastname: Friedman
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019992:Databases as Topic; D005796:Genes; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D011506:Proteins; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D011506:Proteins