Transformer 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:

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