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Introduction Version

Transformer Phenotype Table

TASK
Typing name :  TASK.gws_gena.TransformerPhenotypeTable Brick :  gws_gena v

Task to transform table into Phenotype table

TransformerPhenotypeTable class

Allows to transform a Table with the right columns names to create a Phenotype Table. The Phenotype Table is a generic table of entity IDs (CheBI IDs, Rhea IDs, EC Numbers, User-defined IDs, ...).

The phenotype table is similar to the flux table but the fluxes are related to entities (metabolite, biomass) instead of reactions. Qualitative observations are described by upper and lower bound only.

  • The first column is the list of entity ids. They uniquely identify each reaction of a network.
  • The next columns are:
    • target: the value of the flux measured experimentally (e.g. mol/L/h) [required]
    • upper_bound: the upper bound of the flux (e.g. mol/L/h) [required]
    • lower_bound: the lower bound of the flux (e.g. mol/L/h) [required]
    • confidence_score: the confidence score of the flux [required]
    • ... : other optional columns

For example:

id target lower_bound upper_bound confidence_score chebi_id
biomass 0 1000 1.0 biomass
2-oxoglutarate 0 1000 1.0 CHEBI:16810
glutamine 1.23 0 2.0 1.0 CHEBI:18050

This Task manages multiple simulations. So if you have different values of target,lower_bound,upper_bound; set them as a list like this: id,target,lower_bound,upper_bound,confidence_score,chebi_id id1,"[0.04, 0.045, 0.035]","[0.01, 0.008, -0.02]","[0.03, -0.003, 0.001]","[1, 1, 1]",CHEBI

Input

Initial table
2d excel like table

Output

Table
2d excel like table

Configuration

entity_id_column

Optional

The name of the column of entity ids

Type : stringDefault value : id

target_column

Optional

The name of the target column

Type : stringDefault value : target

lower_bound_column

Optional

The name of the lower-bound column

Type : stringDefault value : lower_bound

upper_bound_column

Optional

The name of the upper-bound column

Type : stringDefault value : upper_bound

confidence_score_column

Optional

The name of the confidence score column

Type : stringDefault value : confidence_score