Tool for Biological Information
Madrid - Robert Hoffmann and Alfonso Valencia of the Spanish National Center of Biotechnology (CNB/CSIC) in Madrid have developed a new web-based tool called iHOP (Information Hyperlinked over Proteins) to help researchers explore scientific literature and integrate information in a more controlled and targeted manner.
Reporting in the Nature Genetics journal (Nature Genetics 36, 664, July 1, 2004), the two scientists describe how iHOP converts the 14 million abstracts in the PubMed (National Library of Medicine) bibliographic database into a network of interlinked references to genes, proteins, mutations, diseases and (bio)chemical compounds. By using genes and proteins as hyperlinks between sentences and articles, iHOP makes the information stored in PubMed accessible as one navigable resource.
Key features of iHOP are the organization of textual and genomic information in a relational database and the use of the latest text-mining technology for the detection of biomedical entities in natural text.
While conventional keyword searches result in long and not always informative lists of abstracts, navigation along this gene-guided network allows for a stepwise and controlled exploration of the information space. The iHOP system shows that distant medical and biological concepts can be related by surprisingly few intermediate genes; the shortest path between any two genes involves on average only four steps.
iHOP is available at: www.pdg.cnb.uam.es/UniPub/iHOP/.