Effective use of latent semantic indexing and computational linguistics in biological and biomedical applications

Hongyu Chen, Bronwen Martin, Caitlin M. Daimon, Stuart Maudsley
2013 Frontiers in Physiology  
Text mining is rapidly becoming an essential technique for the annotation and analysis of large biological data sets. Biomedical literature currently increases at a rate of several thousand papers per week, making automated information retrieval methods the only feasible method of managing this expanding corpus. With the increasing prevalence of open-access journals and constant growth of publicly-available repositories of biomedical literature, literature mining has become much more effective
more » ... ith respect to the extraction of biomedically-relevant data. In recent years, text mining of popular databases such as MEDLINE has evolved from basic term-searches to more sophisticated natural language processing techniques, indexing and retrieval methods, structural analysis and integration of literature with associated metadata. In this review, we will focus on Latent Semantic Indexing (LSI), a computational linguistics technique increasingly used for a variety of biological purposes. It is noted for its ability to consistently outperform benchmark Boolean text searches and co-occurrence models at information retrieval and its power to extract indirect relationships within a data set. LSI has been used successfully to formulate new hypotheses, generate novel connections from existing data, and validate empirical data. Keywords: latent semantic indexing, data mining, computational linguistics, molecular interactions, drug discovery www.frontiersin.org
doi:10.3389/fphys.2013.00008 pmid:23386833 pmcid:PMC3558626 fatcat:476phl67nngrvkp6naon4qx2qa