Edge Lists

Download Edge List

The Download Edge List feature allows you to export the reconstructed model as different types of edge lists: Reaction–Metabolite, Metabolite–Metabolite, or Reaction–Reaction.

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Reaction–Metabolite

In this format, edges connect reactions to their associated metabolites.

Example:

graph LR 
    A --> R1 
    B --> R1 
    R1 --> C 
    R1 --> D 

    %% Define styles
    classDef reaction fill:#4a90e2,stroke:#2c3e50,stroke-width:2px,rx:5px,ry:5px,color:#fff;
    classDef metabolite fill:#27ae60,stroke:#145a32,stroke-width:1.5px,color:#fff,stroke-dasharray:0;

    %% Assign classes
    class R1,R2,R3 reaction;
    class A,B,C,D,E,F,G metabolite;

Source	Target	Type
A	R1	Substrate → Rxn
B	R1	Substrate → Rxn
R1	C	Rxn → Product
R1	D	Rxn → Product

where

• A, B: Substrates
• R1: Reaction
• C, D: Products

Note: Directionality is preserved.

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Metabolite–Metabolite

In this format, edges connect substrates to products through the reactions that consume/produce them.

Example:

graph LR 
    A --> R1 
    B --> R1 
    R1 --> C 
    R1 --> D 

    %% Define styles
    classDef reaction fill:#4a90e2,stroke:#2c3e50,stroke-width:2px,rx:5px,ry:5px,color:#fff;
    classDef metabolite fill:#27ae60,stroke:#145a32,stroke-width:1.5px,color:#fff,stroke-dasharray:0;

    %% Assign classes
    class R1,R2,R3 reaction;
    class A,B,C,D,E,F,G metabolite;

Source	Target	Type
A	C	Substrate → Product
A	D	Substrate → Product
B	C	Substrate → Product
B	D	Substrate → Product

where

• A, B: Substrates
• C, D: Products

Note: Directionality is preserved.

---

Reaction–Reaction

In this format, edges connect reactions via shared metabolites

Example:

graph LR
    %% Reaction 1: A + B → C
    A --> R1
    B --> R1
    R1 --> C

    %% Reaction 2: C → D + E
    C --> R2
    R2 --> D
    R2 --> E

    %% Reaction 3: D + F → G
    D --> R3
    F --> R3
    R3 --> G

    %% Define styles
    classDef reaction fill:#4a90e2,stroke:#2c3e50,stroke-width:2px,rx:5px,ry:5px,color:#fff;
    classDef metabolite fill:#27ae60,stroke:#145a32,stroke-width:1.5px,color:#fff,stroke-dasharray:0;

    %% Assign classes
    class R1,R2,R3 reaction;
    class A,B,C,D,E,F,G metabolite;

Source	Target	Shared Metabolite(s)
R1	R2	C
R2	R3	D

where

• R1 produces C
• R2 consumes C
• R2 produces D
• R3 consumes D