Introduction to the Plant Metabolic Network: Data and Tools for Analysis, Discovery, and Teaching

The Plant Metabolic Network (PMN, www.plantcyc.org) houses a growing set of plant metabolic pathway databases. In 2012, new versions of the core resources, PlantCyc (version 7.0), AraCyc (10.0), and PoplarCyc (5.0) were joined by CornCyc, GrapeCyc, SoyCyc, CassavaCyc, MossCyc, SelaginellaCyc, PapayaCyc, and ChlamyCyc with many more species on their way in 2013 and beyond.  PlantCyc, a multi-species database with over 900 metabolic pathways, as well as the 10 single-species databases all house information about metabolic genes, enzymes, compounds, reactions, and pathways.  We will introduce these data resources and highlight some of the tools that can be used to explore and exploit them, including the Metabolic (Cellular) Overview that enables users to analyze their own transcriptomic, proteomic, and metabolomic data in a metabolic pathway context. We will demonstrate the recently introduced Groups feature that makes it easier than ever to build customized datasets and share them online with co-workers, students, and collaborators. We will also show some of the special features, such as custom pathway creation, available to people who use a locally-installed copy of the Pathway Tools program (developed by SRI International) to work with freely downloadable versions of the PMN databases. We will briefly describe the development and refinement of our own PMN computational pipeline for annotating enzyme function and we will discuss how users can submit new information to help us improve the depth and coverage of all our databases.