Spanish Scientists Develop Powerful New Tool For Exploration And Integration Of Biological Information

Robert Hoffmann and Alfonso Valencia of the Spanish National Centre 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, 01 Jul 2004), the two scientists describe how iHOP, which was developed as part of the EU-funded ORIEL and TEMBLOR projects, 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.

Technology

The technology behind iHOP is a combination of state-of-the-art components and novel in-house developments. Key features are the organisation 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. Production of state data is based entirely on XML technology and avoidance of complex front-end database queries means response times are extremely fast.

Connecting biomedical concepts

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 involving on average only four steps.

Hoffmann and Valencia expect this highly connected network to trigger a revolution in new text-mining tools that will bring biomedicine within closer reach of both the scientific community and the wider public.

Media Contact

Les Grivell alfa

Further information:

http://www.embo.org

All news from this category: Life Sciences

Articles and reports from the Life Sciences area deal with applied and basic research into modern biology, chemistry and human medicine.

Valuable information can be found on a range of life sciences fields including bacteriology, biochemistry, bionics, bioinformatics, biophysics, biotechnology, genetics, geobotany, human biology, marine biology, microbiology, molecular biology, cellular biology, zoology, bioinorganic chemistry, microchemistry and environmental chemistry.

Back to the Homepage

Comments (0)

Write comment

Latest posts

Researchers confront optics and data-transfer challenges with 3D-printed lens

Researchers have developed new 3D-printed microlenses with adjustable refractive indices – a property that gives them highly specialized light-focusing abilities. This advancement is poised to improve imaging, computing and communications…

Research leads to better modeling of hypersonic flow

Hypersonic flight is conventionally referred to as the ability to fly at speeds significantly faster than the speed of sound and presents an extraordinary set of technical challenges. As an…

Researchers create ingredients to produce food by 3D printing

Food engineers in Brazil and France developed gels based on modified starch for use as “ink” to make foods and novel materials by additive manufacturing. It is already possible to…

By continuing to use the site, you agree to the use of cookies. more information

The cookie settings on this website are set to "allow cookies" to give you the best browsing experience possible. If you continue to use this website without changing your cookie settings or you click "Accept" below then you are consenting to this.

Close