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Transformer Biomass Reaction

TASK
Typing name :  TASK.gws_gena.TransformerBiomassReactionTable Brick :  gws_gena

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]

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
Table

Output

Table
2d excel like table
Table

Configuration

entity_column

Optional

The name of the entity column

Type : stringDefault value : entity

chebi_id_column

Optional

The name of the column of ChEBI ID

Type : stringDefault value : chebi_id

biomass_column

Optional

The name of the biomass column

Type : stringDefault value : biomass