Transformer Biomass Reaction
Task to transform table into Biomass Reaction table
TransformerBiomassReactionTable class
Allows to transform a Table with the right columns names to create a Biomass Reaction Table.
The Biomass Reaction Table is a stoichiometry table describing the composition of a cell (or organism) biomass.
A stoichiometry resource table describing the composition of the biomass.
- The first column is the compound name (offical or user-defined name)
[required] - The next columns are:
- chebi_id: the chebi ids of componds of they are known (each chebi id must be prefixed by the keyword CHEBI:).
[required] - biomass: the biomass reaction data (described like a stoichiometric matrix)
[required] - other colums: these columns describe the reaction of the intermediate biomass constituents (described like a stoichiometric matrix)
[optional]
- chebi_id: the chebi ids of componds of they are known (each chebi id must be prefixed by the keyword CHEBI:).
For example:
| component | chebi_id | biomass | protein |
|---|---|---|---|
| biomass | 1 | ||
| protein | -0.3176 | 1 | |
| DNA | -0.0503 | ||
| RNA | -0.0259 | ||
| Cofactors | -0.0216 | ||
| Cell wall | -0.115 | ||
| Carbohydrates | -0.2021 | ||
| Phospholipids | -0.1542 | ||
| L-alanine zwitterion | CHEBI:57972 | -0.5875 | |
| L-argininium(1+) | CHEBI:32682 | -0.1040 | |
| L-asparagine zwitterion | CHEBI:58048 | -0.4755 | |
| L-aspartate(1-) | CHEBI:29991 | -0.6109 | |
| L-cysteine zwitterion | CHEBI:35235 | -0.4755 |
Input
Initial table
2d excel like table
Output
Table
2d excel like table
Configuration
entity_column
The name of the entity column
stringentitychebi_id_column
The name of the column of ChEBI ID
stringchebi_idbiomass_column
The name of the biomass column
stringbiomass