Information Hyperlinked over Proteins

IHOP ( information Hyperlinked Over Proteins) is a freely accessible literature search engine that used in abstracts of PubMed articles occurring gene and protein names as hyperlinks, thus facilitating the search for thematically related to each other life science articles. Above all, a simple and fast search for interaction partners of gene products or for items that describe relevant interactions is possible. Furthermore, there is a carefully researched list of synonyms of gene names.

Background

Operation

Gene designations are imported ( from databases such as UniProt and Entrez Gene ) as well as abstracts of PubMed articles once a month. The abstracts will be machined after Gensynonymen and MeSH terms ( Medical Subject Headings) to search ( dictionary -based search). For each gene and each abstract a source page is created that contains structured sentences in the original text, with Gensynonyme, MeSH terms and associated verbs are highlighted. Genseiten contain additional information (such as homologous genes). When users request the corresponding source pages are presented as HTML pages.

Result

In the search for a gene or gene product ( ie protein; between gene and protein is not distinguished) those taken from abstracts sets are hits, in the name of the desired gene in conjunction with a MeSH term or with another Genbezeichnung occurs (which is an interaction of the two gene products suggests ). An important feature are the numerous gathered from different databases synonym names for a gene. The corresponding MeSH term can be used for a google or PubMed search. That are discussed in connection with the first gene second gene leads the other hand, as a hyperlink to a separate page, so in turn is collected on which the information for this gene ( the link to the corresponding MeSH terms or other genes, by promoting interactions with the gene over which one has come to the page, led in the first place ). This ability to use gene designations as hyperlinks, the original idea and the real strength of iHOP; thus, it provides a quick overview of interrelated gene products. The respective extracts from abstracts can be saved and the connection between the gene products are displayed graphically.

Swell

• Hoffmann, R., Valencia, A.: A Gene Network for Navigating the Literature. Nature Genetics 36, 664 ( 2004).
• Hoffmann, R., Valencia, A.: Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 ( suppl. 2), ii252 - ii258 ( 2005).