A gene network for navigating the literature

A network of genes and proteins extends through the scientific literature, touching on phenotypes, pathologies and gene function. We report the development of an information system that provides this network as a natural way of accessing the more than ten million abstracts in PubMed. By using genes and proteins as hyperlinks between sentences and abstracts, we convert the information in PubMed into one navigable resource and bring all the advantages of the internet to scientific literature investigation.
Moreover, this literature network can be superimposed on experimental interaction data (e.g. yeast two-hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network, called Information Hyperlinked over Proteins (iHOP), contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.
The iHOP server is publicly accessible here.

Hoffmann, R., Valencia, A. A gene network for navigating the literature. Nature Genetics 36, 664 (2004).
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Click here for the technical implementation of the iHOP concept.