What is ChloroKB?
ChloroKB is a manually-constructed and curated network of Arabidopsis thaliana metabolism based on a graphical notation system, as proposed in CellDesigner software. Initially focused on chloroplast processes, ChloroKB now includes processes occurring in other subcellular compartments (mitochondrion, peroxisome, cytosol, etc.) to ensure a comprehensive view of Arabidopsis cell metabolism. The cell represented is a generic cell: all the proteins coded by the genome and involved in a given function are represented.
Proteins and metabolites are represented in their context (position(s) in the network, subcellular localization, presence in protein/metabolite complexes and their control by allosteric effectors binding or by post-translational modifications). Highly connected metabolites are represented as “hubs” where all the inputs and outputs are displayed.
The current version of ChloroKB includes 248 biological processes (referred to as maps) and contains information relating to 2051 proteins with a reviewed status which are included in maps,
and 2787 proteins with an unreviewed status which are not yet included in maps.
In addition, 350 unknown proteins, 1268 complexes (protein-metabolite and protein-protein complexes), 1392 simple molecules, 19 ions and 106 chemical inhibitors are represented in maps.
Annotations reported in ChloroKB are supported by 4257 literature citations.
The following main processes are not included in this release of ChloroKB: ions transport (with the exception of ferric and ferrous iron), light reactions and redox processes, cell wall synthesis, flavonoids synthesis, protein import processes, protein folding, DNA/RNA synthesis, transcription and translation machineries. For terpene synthesis, users are redirected to the AtIPD database.
Finally, we consider our database to represent a clickable and modifiable review of Arabidopsis thaliana metabolism, and we will welcome contributions from users (through the contribute to ChloroKB page) to help grow and maintain it.
