New tool helps researchers establish links between proteins, genes, drugs and diseases -
Every day, more than 3,000 new summaries are uploaded on PubMed the reference database of the main biomedical literature. Even in the closely defined area of a researcher, it is impossible to stay on top of the bands changing interconnections between these documents. For example, a new gene is described - can it be useful to the specialty of a researcher? It could take many painstaking hours of research to find the answer. Now a new tool developed in Tan alternative laboratory at the University of Colorado Cancer Center and described today in the journal Bioinformatics helps researchers make these connections. The free tool HiPub, is available for download as a plugin for Chrome Web browser.
"HiPub looks through all text and tries to recognize what is called the genes, proteins, drugs, and diseases. It extracts this information and displays in a network. Especially in molecular biology or the biology of cancer, it is helpful to see the links between these things in their biological context, "said Aik Choon Tan, Ph.D., a researcher at the CU cancer Center and associate professor at the CU School of Medicine.
Tan gives the example of a hypothetical researcher who reads a paper exploring the KRAS gene and MEK, known to influence the development of certain cancers. "the researcher wants to know if these genes have any relevance to his specialty, can -being something like p53 [another gene known to influence cancer]. "
queries researchers" p53 "with the new section and HiPub shows how the researcher's interest is connected to the genes of the new paper. If the connections appear convincing, researchers could design experiments to test these linkages.
"The idea of text mining is not new," said Tan. "Computer scientists have done for ten or twenty years. But the real application of text mining in biomedical research is very limited. HiPub is a way to use text mining to simplify the knowledge discovery process. "
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