Introduction to the Plant Metabolic Network: 18 Databases and Omics-Level Tools for Analysis and Discovery

The Plant Metabolic Network (PMN, www.plantcyc.org) houses a growing set of publicly available plant metabolic pathway databases. In 2013, new versions of the core resources PlantCyc (version 8.0) and AraCyc (version 11.5) were joined by six new databases for monocots:  OryzaCyc, SorghumBicolorCyc, BrachypodiumCyc, SetariaCyc, BarleyCyc, and SwitchgrassCyc, plus one for a eudicot: ChineseCabbageCyc. Nine other databases available at the PMN include economically important  and phylogenetically diverse species (CornCyc, PoplarCyc, GrapeCyc, SoyCyc, CassavaCyc, MossCyc, SelaginellaCyc, PapayaCyc, and ChlamyCyc) and more databases are sceheduled for release in 2014. PlantCyc, a multi-species database with over 900 metabolic pathways, as well as the 17 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 also discuss how users can submit new information to help us improve the depth and coverage of all our databases.