REACTO, AN ONTOLOGY OF THE REACTIONS INVOLVED IN GLYCAN METABOLISM

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The biosynthesis, remodeling and turnover of glycans in living cells are extremely complex processes. Glycan structure is the result of metabolic processes that include generation of energy-rich precursors such as nucleotide sugars, transfer of individual sugar residues to growing glycan chains, and trimming of the resulting glycan structures. Each of these processes corresponds to a collection of biochemical reactions that are catalyzed by specific enzymes. Thus, an understanding of glycan metabolism requires knowledge of the structures of the relevant glycans, the cellular machinery involved in transforming one structure into another, and the chemical reactions corresponding to these transformations. We designed the ReactO ontology to embody knowledge regarding specific biochemical reactions involved in glycan metabolism, although its general design can be used to describe a broad range of enzyme-catalyzed reactions. That is, ReactO is not designed to embody explicit knowledge of glycan or enzyme structure. Thus, a major challenge that we face in developing ReactO is its full integration with other knowledge repositories that embody this structural knowledge. We are developing ReactO not only as a highly desirable tool for representing and accessing knowledge about glycan metabolism, but as a prototype for integrating several related but highly focused ontologies.