Basically, a metabolic network is an assembly of biochemical reactions.
While information about reactions is sufficient for modeling the network, the
more information on associated genes or proteins, the more useful for the
investigation of cellular responses in gene or protein level.
Gene-protein-reaction (GPR) associations can be described in two-layer relations:
“gene and protein” and “protein and reaction”, which are
usually saved in spreadsheet format, the required information and available
models are summarized in http://sb.nhri.org.tw/GEMSiRV/en/Metabolic_Models.
On the other hand, published genome-scale metabolic models are commonly
exchanged in Systems Biology Markup Language (SBML) format, but the protein
information is lost or can not be recovered to the two-layer relation.
Therefore, GEMSiRV provides different schema for
these two types of metabolic reconstructions. If you want to create a project
with clear two-layer relations of GPR associations, please check the checkbox
of Gene-protein-reaction associations are necessary to generate the
three-index schema (gene, protein and reaction indices) for reconstruction.
Otherwise, GEMSiRV will generate the two-index schema
(gene and reaction indices) automatically.
Reconstruction
Click on Reconstruction in the menu bar to open Model databases and Reference databases.
Model importing and
editing
Right click on Model databases to Import
SBML file (.xml) or to Import spreadsheets (.xls),
you can import a metabolic model in SBML/spreadsheet format. Some existing
metabolic models can be found and downloaded from http://sb.nhri.org.tw/GEMSiRV/en/Metabolic_Models
You can directly edit/update the content of the imported model by right
clicking on a cell.
In table of Reaction Index:
In table of Gene Index: