BIOINFORMATICS Text Mining.pdfVIP

BIOINFORMATICS Vol. 21Suppl. 2 2005, pages ii252–ii258 doi:10.1093/bioinformatics/bti1142 Text Mining Implementing the iHOP concept for navigation of biomedical literature Robert Hoffmann?,? and Alfonso Valencia National Center of Biotechnology, CNB-CSIC. Campus de la UAM. Madrid E-28049, Spain ABSTRACT Motivation: The World Wide Web has profoundly changed the way in which we access information. Searching the internet is easy and fast, but more importantly, the interconnection of related contents makes it intuitive and closer to the associative organization of human memory. However, the information retrieval tools currently available to research- ers in biology and medicine lag far behind the possibilities that the layman has come to expect from the internet. Results: By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be conver- ted into one navigable resource. iHOP (Information Hyperlinked over Proteins) is an online service that provides this gene-guided network as a natural way of accessing millions of PubMed abstracts and brings all the advantages of the internet to scientific literature research. Nav- igating across interrelated sentences within this network is closer to human intuition than the use of conventional keyword searches and allows for stepwise and controlled acquisition of information. Moreover, this literature network can be superimposed upon experimental inter- action data to facilitate the simultaneous analysis of novel and existing knowledge. The network presented in iHOP currently contains 5 million sentences and 40 000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. Availability: iHOP is freely accessible at b. uam.es/UniPub/iHOP/ Contact: hoffmann@ Supplementary Information: Supplementary data are available at Bioinformatics online. 1 INTRODUCTION The internet has funda