The search for Ariadne, Barbie, and Superman succeeds with modern bioinformatics tools
Dresden bioinformatics group wins international competition in Madrid
What do Ken and Barbie, Superman, Groucho, and Ariadne have in common?
They are all gene names, which are ambiguous and which are known under different names. Identifying gene names and interactions in text is challenging problem for scientists and the pharmaceutical industry.
A worldwide community of bioinformaticians gathered for the BioCreative meeting on bioinformatics and textmining from 23 to 25 April 2007 in Madrid. They compared their latest solutions to search in the life sciences in a direct competition. The group of Michael Schroeder, Professor for bioinformatics at the BIOTEC of TU Dresden and coordinator of the NoE REWERSE working group on Bioinformatics, participated in the category of gene identification. Jörg Hakenberg, postdoc in the research group, reports entusiastically: "The hard work of the past months has paid off: We have won the gold medal!".
Why is such a search engine as developed by the Schroeder group so important? Some genes, such as Aridne or Barbie have several names, other names refer to several genes. All in all, a terminological jungle.
This problem is further multiplied by the ever growing amount of literature - 2000 articles per day - and the advance of modern experimental methods, which automatically analyse thousands of genes. But the final results still have to be analysed manually. Jörg Heinrich,
chief scientific officer of the Dresden based Resprotect, who work on cancer drugs, calculates: "Thousand interesting candidate genes theoretically lead to millions of interactions between them. Therefore it is paramount to develop novel search technologies, which couple
experimental methods and the exponentially growing literature."
"The medal is indeed golden." confirms Dr. Michael R. Alvers, CEO of Transinsight GmbH, located in BioInnovation Center Dresden. "As part of our collaboration with Professor Schroeder and the TU Dresden we optimise technology transfer of such results into our product GoPubMed, the first knowledge-based search engine worldwide. Our customers and partners such as Unilever and Elsevier are already waiting for the next release of our search engine. Finding genes, proteins, and their relationships in text is hot topic in the pharmaceutical industry."
Founded in 2005, Transinsight is focused on software solutions for the life sciences providing products for knowledge based technologies. The flagship product, GoPubMed, a well established biomedical search engine, is the first knowledge based search engine for the Life Sciences on the Internet. Transinsight is headquartered in one of the leading German biotech incubators, the BioInnovationCenter Dresden BIOZ, where science and business work under one roof. Transinsight works in close collaboration with the Technische Universität Dresden.
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