Mining metabolites: extracting the yeast metabolome from the literature.

ABSTRACT: Text mining methods have added considerably to our capacity to extract biological knowledge from the literature. Recently the field of systems biology has begun to model and simulate metabolic networks, requiring knowledge of the set of molecules involved. While genomics and proteomics technologies are able to supply the macromolecular parts list, the metabolites are less easily assembled. Most metabolites are known and reported through the scientific literature, rather than through large-scale experimental surveys. Thus it is important to recover them from the literature. Here we present a novel tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome. With ten-fold cross validation on a manually an

SUBMITTER: Nobata C 

PROVIDER: S-EPMC3111869 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature