PATHDB: A METABOLIC DATABASE WITH SOPHISTICATED SEARCH AND VISUALIZATION TOOLS

National Center for Genome Research, 1800A Old Pecos Trail, Santa Fe, NM, 87505. USA.

PathDB is a publicly available database of plant metabolism developed and housed at the National Center for Genome Resources. PathDB has been designed to store a wide range of data in very great detail, including kinetic information; locations ranging from sub-cellular to whole organism level; taxonomic information; compound structures and chemical properties; and thermodynamic properties of reactions. PathDB is a relational database with a non-redundant, hierarchical design. Compounds are the basic building block of reactions, which can be linked to specific catalysts. Reactions are also used to construct pathways. Transport steps, catalyzed and uncatalyzed reactions are represented in PathDB. This, together with detailed location data, provides a rather complete framework for representing known metabolism. The software to query and visualize data was written in Java and thus runs on Windows, Macintosh and Unix architectures. A Query Tool allows construction of complex queries and a Pathway Viewer (described elsewhere in this meeting) generates pathway diagrams automatically. Version 1.0 of the Query Tool and Pathway Viewer are available from NCGR's Web site at http://www.ncgr.org/.