Exploring Metabolic Networks: Metacyc and SolCyc as Examples for High-Level Data Curation, Depository and Management Across and within Species

The multi-species database MetaCyc (http://metacyc.org) and species-specific databases such as SolCyc (http://solcyc.solgenomics.net/) represent data repositories which provide access to non-redundant metabolic data in the context of relevant pathways ideally furnished with detailed information about affiliated compounds, genes and enzymes. The curation process is tapping widescale resources which allow integrating genomics, proteomics and metabolomics data into one information hub, e.g. MetaCyc. The most recent version of MetaCyc (release 18.1) contains 2203 pathways and close to 12.000 enzymatic reactions associated with about 10.000 enzymes and genes. The pathways are experimentally elucidated and supported by 41.532 citations. The ongoing effort to improve, complement and expand the existing scope of curated pathways is crucial for the importance of metabolic databases to serve as significant reference and research tools for plant metabolism researchers. 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. Using MetaCyc as reference database, SolCyc, a collection of single-species databases of primarily Solanacea (tomato, pepper, eggplant, petunia) and close relatives such as coffee has been created which comprises and displays the fraction of metabolism applicable for the respective individual organism. The cellular overview permits overlaying large-scale functional genome data such as gene expression, proteomic, and metabolite profiling data onto the metabolic map to illustrate the results in a broad metabolic context.