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Metabolic Pathways Collection at SRI International the Largest in the World
Date:4/24/2013

MENLO PARK, Calif., April 24, 2013 /PRNewswire/ -- Researchers at SRI International, in collaboration with the Boyce Thompson Institute and the Carnegie Institution, have reached a milestone in their development of MetaCyc, a database and web site (MetaCyc.org) that consolidates much known information about metabolism. MetaCyc now includes 2,000 pathways, each a collection of metabolic reactions and the enzymes that catalyze them, making the database the most comprehensive compilation of metabolic pathway information in the world.

MetaCyc catalogs the universe of metabolism—how organisms biochemically transform one compound to another through intricate networks of synthesis and degradation—by integrating many of the biochemical reactions that have been documented in different forms of life. It includes information about more than 10,900 reactions and more than 10,400 compounds from 35,000 cited publications. More than 2,300 organisms are currently represented, from bacteria, archaea and yeast to plants and animals, including humans.

"As researchers know, there are so many scientific articles available that it can be challenging to synthesize all this information," said Peter Karp , Ph.D., director of the Bioinformatics Research Group at SRI International.  "MetaCyc integrates the fragmented, sometimes inaccessible, data throughout the scientific literature. The synthesis of all these individual publications in MetaCyc provides the big picture."

One example is the MetaCyc compound page for L-glutamate, which contains reactions and pathways from a wide variety of organisms that synthesize and degrade this important compound. MetaCyc can reconcile seemingly disparate pathways that involve the same compounds called by different names by different research teams. 

Another contribution of MetaCyc to the scientific enterprise is to combine the published work of ind
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