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A network of gene -> compound that is extracted from the KGML metabolic reaction data.
Each KGML <reaction> element connects a set of metabolites (substrates and products) and is linked to a gene entry (type="gene") by sharing the same id value. This model expands the reaction network into a long-table form: every (gene_id, compound_id) pair produces one row, so that it is friendly for CSV export and downstream network analysis.
01 Syntax
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| ExtractNetwork | 1 | Extract the gene-compound metabolic reaction network from a loaded KGML pathway object. |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| gene_id | 1 | The gene identifier(s) of the enzyme entry that catalyzes the reaction. |
| ko_id | 1 | The KO identifier (e.g. |
| compound_id | 1 | The metabolite identifier (e.g. |
| reaction_id | 1 | The reaction identifier, kept in its full KEGG form (e.g. |
| pathway_id | 1 | The pathway identifier (e.g. |
| pathway_title | 1 | The pathway title / name. |
| role | 1 | The role of the metabolite in the reaction: substrate or product. |
| compound_name | 1 |
04 Members
Boolean)Extract the gene-compound metabolic reaction network from a loaded KGML pathway object.
| Name | Type | Description |
|---|---|---|
kgml | pathway | The pathway object loaded by pathway.LoadMap(). |
combineGenes | Boolean | When |
A long-table enumeration, one row per (gene_id, compound_id) pair, with the reaction direction recorded in GeneMetaboliteNetwork.role.
The gene identifier(s) of the enzyme entry that catalyzes the reaction. In the original KGML entry this is the name attribute of a type="gene" entry, kept in its full KEGG form (e.g. taes:123057580).
The KO identifier (e.g. ko:K20039) resolved from the ortholog entry that shares the same reaction id, or an empty string when no ortholog mapping is available in the species-specific pathway map.
The metabolite identifier (e.g. C00082) referenced by a substrate or product node.
The reaction identifier, kept in its full KEGG form (e.g. rn:R00737). A reaction may reference several rn ids separated by spaces.
The pathway identifier (e.g. path:taes00940).
The pathway title / name.
The role of the metabolite in the reaction: substrate or product.