Last week, SRI International completed an agreement with Double- Twist to make the EcoCyc and MetaCyc metabolic pathway databases, as well as new databases for eight organisms, available through a website hosted by SRI, ecocyc.org.
Peter Karp, director of the bioinformatics research group at SRI that originally developed EcoCyc and MetaCyc, praised DoubleTwist for its “generosity” in making the resources freely available through SRI’s site.
The arrangement brings the database full circle. SRI first developed EcoCyc, a collection of all known metabolic pathways for Escherichia coli, in 1997 and licensed it exclusively to Pangea Systems, which relaunched itself as DoubleTwist in 1999. Karp, who joined Pangea at the time EcoCyc was licensed, returned to SRI shortly before the launch of DoubleTwist.
DoubleTwist will continue to provide access to EcoCyc and MetaCyc, which describes pathways, reactions, and enzymes of a variety of organisms, through ecocyc.doubletwist.com, and will continue to sell licenses to the databases for on-site installation, said DoubleTwist spokeswoman Nicole Litchfield.
Under DoubleTwist, EcoCyc and MetaCyc were freely available to academics and available to commercial users with a license. “SRI now hosts the servers and we have granted them the rights to providing their own channel to these resources on the Web,” said Litchfield.
Now, in addition to free availability for both academic and commercial users, Karp said the SRI website offers eight new pathway databases built with the PathoLogic pathway prediction software originally developed to expand the utility of EcoCyc and MetaCyc. The new organisms are the yeast Saccharomyces cerevisiae, the spirochete Trepanema pallidum, and the bacteria Bacillus subtilis, Mycobacterium pneumoniae, Mycobacterium tuberculosis, Chlamydia trachomatis, Haemophilus influenza, and Helicobacter pylori.
The June 15 release of EcoCyc 5.6 contains over 100 new E. coli transcription units and 10 new pathways, while MetaCyc 5.6 contains 80 new pathways.
While EcoCyc and MetaCyc were compiled using experimental data from the biomedical literature, the eight new databases were built using PathoLogic only. Karp has submitted a paper comparing the predictions with experimental data that reports “reasonable” results for the program’s accuracy. Karp said several academic groups have already offered to add curated data to the M. tuberculosis and B. subtilis databases.
The SRI group is currently seeking an NIH grant to support further development of the software and is working with collaborators, including the Carnegie Institute of Washington and the Institute for Genomic Research, to expand the capability of the software and apply it to new organisms.