Abstract
SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species.Database URL https://solgenomics.net/tools/solcyc/
Highlights
The post genomic era has seen the rise of new technologies and intensified research focusing on function and regulation of genes and their encoded proteins in the cell and within complex metabolic networks [1]
All SolCyc databases at the Sol Genomics Network (SGN) have been created using the Pathway Tools software component Pathologic, which predicts the metabolic networks in those organisms based on MetaCyc as reference database [43]
Other tools were used for these databases to transform GFF (Generic Feature Format) annotation files to the files that Pathway Tools parse
Summary
The post genomic era has seen the rise of new technologies and intensified research focusing on function and regulation of genes and their encoded proteins in the cell and within complex metabolic networks [1]. The transition of traditional biology into an information-based science is marked by the need to efficiently store and manage data and to extract meaningful biological insights. This requires the development of annotation common standards, as well as methods for exchanging data across a broad range of organisms [7, 8]. Species-specific metabolic databases, called Pathway/Genome Databases (PGDBs) for short, can be built automatically by matching annotated genes for a given species against a reference database of pathways. These derivative databases are ranked, according to the level of expert annotation they received, into three tiers. Tier 3 databases are generated purely computationally and are not curated in any way, tier 2 databases are partially curated and the highest level, tier 1, represents continually updated and intensively manually curated databases [18]
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