Curation in Metabolic Databases: Implementing Tools and Rules Across the Universal Metabolic Database MetaCyc to Species-Specific Plant/Genome Databases

MetaCyc (http://metacyc.org) is a multi-species database providing non-redundant metabolic data from over 2400 species, particularly plants and microorganisms. The ongoing effort to improve, complement and expand the existing scope of curated pathways is crucial for the importance of the database as a significant reference and research tool for scientists studying plant metabolism. The primary goal of metabolic databases to capture the universe of primary and specialized (secondary) metabolism has been extended towards the presentation of plasticity and interconnectivity of biochemical networks.  MetaCyc has been the principal matrix for many Pathway/Genome Database’s (PGDB’s) which have been predicted based on their sequenced genomes. The value of the database is defined by the accuracy, consistency and currentness of released data. Manual curation comprises the extraction, validation and presentation of structural and functional data from the body of scientific literature associated to pathways, compounds, enzymes, and genes. High data quality is assured by furnishing pathways and enzymes with evidence and citations linking back to the original source of research. Pathway tools represents the comprehensive software platform that allows curators to generate reactions, construct pathways and annotate enzymes and genes. We will present the scope of Pathway tools, explore the content of MetaCyc and explain how to access and query the database to retrieve information on pathways, enzymes and genes. We will also provide an overview of SolCyc (http://solcyc.solgenomics.net/) a collection of species-specific databases of primarily Solanacea (tomato, pepper, eggplant, petunia) and close relatives such as coffee and how to compare species across available PGDB’s.