Text Analysis

iHOP – Information Hyperlinked over Proteins

A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. iHOP uses this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.

iHOP currently contains information on 2,700 organisms, 110,000 genes, and 28.4 million PubMed sentences.

Screenshot of iHOP for the gene C11orf30 / EMSY.

Hoffmann R, Valencia A. A gene network for navigating the literature., Nat Genet. 2004 Jul. [Full Text].

Hoffmann R., Using the iHOP information resource to mine the biomedical literature on genes, proteins, and chemical compounds. Curr Protoc Bioinformatics. 2007 Dec.

Fernández JM, Hoffmann R, Valencia A., iHOP web services., Nucleic Acids Res. 2007 Jul (Web Server issue). [Abstract].

Hoffmann R, Valencia A., Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics. 2005 Sep. [Abstract].

Hoffmann R, Krallinger M, Andres E, Tamames J, Blaschke C, Valencia A., Text mining for metabolic pathways, signaling cascades, and protein networks. Sci STKE. 2005 May. [Abstract].