The Plant Metabolic Network - from Arabidopsis thaliana to Zea mays: 11 Metabolic Pathway Databases Power Research in Plant Metabolism

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 to provide new resources and analysis tools to the Zea mays, Vitis vinifera, Glycine max, Manihot esculenta, Physcomitrella patens, Selaginella moellendorffii, Carica papaya, Chlamydomonas reinhardtii, Arabidopsis thaliana, and Populus trichocarpa communities. 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. These freely-available on-line resources provide information about more than 2500 plant enzymes with experimental evidence. A suite of tools allows these curated resources to be explored and exploited by researchers and educators. PMN users can also analyze their own transcriptomic, proteomic, or metabolomic data using the Metabolic (Cellular) Overview. Free downloadable versions of the PMN databases can be analyzed and modified using a locally-installed copy of the Pathway Tools program (developed by SRI International). Based on the continuing development and refinement of a new computational pipeline to annotate enzyme function, we plan to release databases for several new plant species semi-annually, including for Orzya sativa and Sorghum bicolor in 2013. We hope to provide valuable tools and data resources to PMN visitors and encourage user submissions of new information to help us improve the depth and coverage of all our databases.