Data format

Model data format

Metabolic model consists of an Excel file defining the metabolic network, metabolic_model.xlsx, a label.json file defining labeling information, and an image file of the metabolic map, metabolic_pathway.tiff. Each file is described below.

Metabolic model Excel file

The metabolic model Excel file consists of these sheets, info, model, MS, atom, biomass, and position.

Sheet name Description
info General information about the model
model Definition of reactions in the metabolic model
MS Observed mass fragments for metabolites
atom The number of atoms for each element in the metabolites
biomass The biomass coefficients for the biomass equation
position Positions of reactions in the metabolic map image

info sheet

The info sheet contains general information about the model, such as the model name, author, date, and description.

info_sheet

model sheet

The model sheet defines the reactions in the metabolic model. Each row represents a reaction, with columns for reaction ID, reaction, and atom mapping information. Each reaction is represented in the format “A + B –> C + D”, where A, B, C, and D are metabolite IDs.

Reaction format

Symbol Meaning
(space) Separates each metabolite and symbol.
+ Indicates multiple metabolites.
--> Indicates the irreversible reaction.
<=> Indicates the reversible reaction.
Metabolite name Meaning
A Indicates metabolite A.
Subs_A Indicates substrate A and this metabolite will become efflux reaction in the model.
Sym_A Indicates symbiotic metabolite A such as a succinate.
Column name Description
ID Reaction ID, that must be unique in the model.
Reaction Reaction formula as described above.
Transition Atom mapping information for the reaction. The number of parts must match that of the reaction. Each part describes the mapping from substrate to product.
Independent Boolean value indicating whether the reaction sets as independent (TRUE) or dependent (FALSE) in the model. If TRUE, the reaction flux will be enforced to be independent variable.

model_sheet

MS sheet

The MS sheet lists the observed mass fragments for metabolites. Each row corresponds to a metabolite, with columns for metabolite ID, name, and the mass fragments observed in the experiment.

Column name Description
ID Metabolite ID, that must not be duplicated in the model (including model shhet).
Reaction Reaction formula for producing the metabolite to be measured.
Transition Atom mapping information for the reaction. The number of parts must match that of the reaction. Each part describes the mapping from substrate to product.
Used Boolean value indicating whether the mass fragment is used (TRUE) or not (FALSE) in the model fitting.

ms_sheet

biomass sheet

The biomass sheet defines the biomass coefficients for the biomass equation. Each row represents a metabolite and its coefficient in the biomass equation.

Column name Description
Precursor Metabolite name in the biomass equation (must match the metabolite name in the model).
Biomass Coefficient of the metabolite in the biomass equation in mmol gDCW^-1.

biomass_sheet

position sheet

The position sheet specifies the positions of reactions in the metabolic map image.

Column name Description
ID Reaction ID, that must match the reaction ID in the model sheet.
x X-coordinate of the reaction position in the metabolic map image (in pixels).
y Y-coordinate of the reaction position in the metabolic map image (in pixels).

position_sheet

label.json file

The label.json file defines the tracer labeling information for each substrate metabolite. In general, the file is automatically generated when the user inputs tracer information through the GUI. Each metabolite is represented as a JSON object, with the following structure:

{
    "x_1_Glc": {
        "name": "[1]Glc",
        "num": 6,
        "label": [
            "#100000",
            "#000000"
        ],
        "ratio": [
            0.99,
            0.01
        ]
    },
    "x_12_Glc": {
        "name": "[12]Glc",
        "num": 6,
        "label": [
            "#110000",
            "#100000",
            "#010000",
            "#000000"
        ],
        "ratio": [
            0.98,
            0.01,
            0.01,
            0
        ]
    },
    ...
}
Key Description
Tracer key Tracer key generated from a tracer name automatically (e.g., x_1_Glc). Edited manually is not recommended.
name Tracer name (e.g., [1]Glc for glucose labeled at carbon 1). name was defined by the user.
num Number of labeled atoms in the metabolite (e.g., 6 for glucose).
label List of labeling patterns represented as binary strings (e.g., #100000 for glucose labeled at carbon 1).
ratio List of fractions corresponding to each labeling pattern. The sum of the ratios must be 1.

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