Extracting synonymous gene and protein terms from biological literature.
BACKGROUND
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.
Yu
Hong
H
Department of Computer Science, Columbia University, New York, NY, USA. hongu@cs.columbia.edu
Agichtein
Eugene
E
D000043:Abstracting and Indexing / Q000379:methods* / Q000592:standards; D000082:Acetaminophen; D000465:Algorithms; D001695:Biology / Q000379:methods / Q000592:standards; D019295:Computational Biology / Q000379:methods / Q000592:standards; D003628:Database Management Systems; D016206:Databases, Bibliographic; D004282:Documentation; D005796:Genes; D016247:Information Storage and Retrieval / Q000379:methods / Q000592:standards; D009323:Natural Language Processing; D010506:Periodicals as Topic; D011506:Proteins; D009626:Terminology as Topic; D018875:Vocabulary, Controlled
D011506:Proteins; D000082:Acetaminophen