From: Toward the automated generation of genome-scale metabolic networks in the SEED
Steps | Purpose of Tools | Implementation in the SEED | Database Contributions |
---|---|---|---|
ANNOTATION | Â | The SEED already provides tools for annotation, based on similarity searching and context-based methods | The SEED already provides a database of high-quality genome annotations organized into subsystems (see [11]) |
SUB-ASSEMBLY AND SUB-NETWORK VERIFICATION | Curating associations between functional roles and reactions in a particular metabolic context | Reverse-engineering of published genome-scale metabolic models; analysis of gene-reaction associations in the KEGG database; integrated display of KEGG pathway maps in subsystems, highlighting functional roles and associated reactions | Associations between functional roles and KEGG reactions in subsystems |
 | Assembling and verifying the coherence of reaction subnetworks in subsystems | Petri net representation of KEGG reactions; encoded scenarios in subsystems; finding paths through reaction subnetworks from scenario inputs to scenario outputs | Reuseable coherent reaction subnetworks in subsystems |
 | Assembling and verifying the coherence of connected reaction subnetworks across subsystems | Connections between scenarios in different subsystems; finding paths through connected scenarios, from overall inputs to overall outputs | List of curated subsystems with coherent reaction subnetworks for functional variants that interconnect to cover central and intermediary metabolic pathways |
ASSEMBLY AND NETWORK VERIFICATION | Assembling and verifying the coherence and completeness of an organism-specific reaction network | Identifying gaps in the reaction network, by cross-checking inputs and outputs for all paths through implemented scenarios, and checking for paths from minimal substrates to biomass compounds; creating files for FluxAnalyzer [36] | Organism-specific complete and coherent reaction networks for central and intermediary metabolism |