iHOP Information Hyperlinked over Proteins

Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract iHOP (Information Hyperlinked over Proteins) is an on-line service that provides a ‘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.

Navigating 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 interaction data to facilitate the simultaneous analysis of novel and existing knowledge.

The network presented in iHOP currently contains over 12 million sentences and 80,000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli, etc.

The World Wide Web has changed the way we access information; we prefer to search Google and to follow hyperlinks, instead of reaching for a reference book.

Surfing the internet is possible because the interconnection of related content makes it intuitive and close to the associative organization of human memory.

Until recently, however, navigation of the biomedical literature lagged far behind the possibilities presented by the internet. iHop is one of the first systems that aims to make scientific literature as navigable as the internet.

iHOP is an advanced mimic of biological models and hypotheses with genes and proteins serving as the basic units of information. iHOP provides this 'network of genes and proteins' as a natural way of accessing the more than ten (10) million abstracts in PubMed.

Whereas conventional keyword and related article searches result in long and Not always informative lists of abstracts, navigation along the gene network allows for a stepwise and controlled exploration of the information space.

Each step through the network produces just the information pertaining to one single gene and its interactions.

The exploration of this gene guided information network is intuitive and close to the associative organization of human memory, in which information is retrieved by connecting similar concepts.

The precision of 'gene name' and synonym identification in iHOP ranges between 87% and 99% depending on the organism.

Because researchers can move between sentences taken directly from their source abstracts, however, they always retain control over the reliability and significance of information.

This is an advantage over systems which translate the protein network from the literature into graphical representations, because these representations could give a misleading sense of confidence to the users and cloud the significance of individual associations.

For additional information:

1) Hoffmann, R., Valencia, A. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21(suppl. 2), ii252- ii258 (2005).

2) Hoffmann, R., Valencia, A. A gene network for navigating the literature. Nature Genetics 36, 664 (2004).

System Requirements

Web-based application.

Manufacturer

Manufacturer Web Site iHOP

Price iHOP is a freely available tool from the academic domain. Not a company! Thus, it is necessary to limit server load and to give preference to individual users. See terms of use..

G6G Abstract Number 20225

G6G Manufacturer Number 101762