New online search tool to explore genes in medical literature
14 December 2006
A new version of iHOP, a free online tool for exploring genes and proteins
in scientific literature, has been launched. The iHOP service provides fast,
accurate, comprehensive, and up-to-date summary information on more than
80,000 biological molecules by automatically extracting key sentences from
millions of PubMed documents when a search is requested.
PubMed is a service of the US National Library of Medicine that includes
more than 16 million citations from life science journals for biomedical
(information hyperlinked over proteins) has been available at no cost to the
public since 2004 and has become one of the most used resources for
biomedical research, accessed by up to 200,000 different users per month.
The new version provides current information on even more genes and chemical
compounds, covering all organisms — ranging from human and chimpanzee to
yeast and HIV — making iHOP useful to tens of thousands of biomedical
iHOP allows researchers to explore a network of gene
interactions by directly navigating the pool of published scientific
literature. Rather than providing long lists of entire abstracts upon
keyword searches, iHOP selectively retrieves information that is specific to
genes and proteins and summarizes their interactions and functions. The
system adds value by filtering and ranking extracted sentences according to
significance, impact factor, date of publication, and syntax.
genes and proteins as hyperlink sources between sentences and abstracts,
iHOP converts the information in PubMed into a navigable information
network, exploiting the power of the Internet for scientific literature
investigation,” said Sloan-Kettering Institute postdoctoral fellow Robert
Hoffmann, who started the iHOP project when he worked at the Protein Design
Group in Madrid, Spain.
The most recent work of the Computational Biology Center at Memorial Sloan
Kettering Cancer Center (MSKCC), headed by Chris Sander, Chairman of the
Sloan-Kettering Institute's Computational Biology Program, has taken iHOP to
the next level in terms of speed, accuracy, relevance, and coverage.
is a next-generation search tool that allows scientists to extract
comprehensive information regarding the function of genes in signaling
pathways, interaction networks, and biological processes,” said Dr. Sander.
“We are now able to provide daily updates, processing about 2000 new
publications per day, which makes iHOP the most comprehensive and up-to-date
resource for literature-derived gene information on the Web.”
complexity of the information stored in scientific databases and journals
and the growing number of scientific publications gave rise to the need for
text-mining systems to help researchers navigate through these interrelated
information resources. Openly accessible text-mining systems, such as iHOP,
facilitate the integration of database and text information and support
researchers in the formulation of novel hypotheses.
“We plan to extend the
iHOP concept to full text sources and the algorithmic exploration of gene
networks,” added Dr. Hoffmann.
Access to iHOP is freely available at
More information about computational biology research is at