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Knowledge-based Gene Symbol Disambiguation
Linköping University, Department of Computer and Information Science, Database and information techniques. Linköping University, The Institute of Technology.
2008 (English)In: Second International Workshop on Data and Text Mining in Bioinformatics,2008, New York: ACM , 2008, 73-76 p.Conference paper (Refereed)
Abstract [en]

Since there is no standard naming convention for genes and gene products, gene symbol disambiguation (GSD) has become a big challenge when mining biomedical literature. Several GSD methods have been proposed based on Medline references to genes. However, nowadays gene databases, e.g. Entrez Gene, provide plenty of information about genes, and many biomedical ontologies, e.g. UMLS Metathesaurus and Semantic Network, have been developed. These knowledge sources could be used for disambiguation, in this paper we propose a method which relies on information about gene candidates from gene databases, contexts of gene symbols and biomedical ontologies. We implement our method, and evaluate the performance of the implementation using BioCreAtIvE II data sets.

Place, publisher, year, edition, pages
New York: ACM , 2008. 73-76 p.
National Category
Computer Science
URN: urn:nbn:se:liu:diva-42969DOI: 10.1145/1458449.1458466Local ID: 70300ISBN: 978-1-60558-251-1OAI: diva2:263826
Second International Workshop on Data and Text Mining in Bioinformatics,2008
Available from: 2009-10-10 Created: 2009-10-10 Last updated: 2014-07-01

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Tan, He
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Database and information techniquesThe Institute of Technology
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