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Definition of SBtab table types

The definition of all predefined SBtab table types, their corresponding columns and contents, can be found in the definitions.tsv. This file can also be employed if you want to define an individual table type for types of data that SBtab does not cover so far. Simply download the definitions, add your table type and the columns to the end of the file, and upload it on the SBtab customiser. Then, you can validate SBtab files whether they adhere to your individual table type definition on the SBtab validator.

SBtab Example Files

Example 1: The first two reactions of yeast glycolysis. Entire model in one file:

  1. BIOMD0000000061.tsv

Tables in separate files:

  1. BIOMD0000000061_Compartment.tsv
  2. BIOMD0000000061_Compound.tsv
  3. BIOMD0000000061_Enzyme.tsv
  4. BIOMD0000000061_Quantity-concentration.tsv
  5. BIOMD0000000061_Quantity-parameters.tsv
  6. BIOMD0000000061_Reaction.tsv

The two reactions stem from a model of yeast glycolysis, published in Hynne et al. (2001), Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys. Chem. (1-2): 121-163). The original SBML file has been retrieved from Biomodels Database and automatically been converted into SBtab tables.

Example 4: Standard Gibbs free energies of reactions for chemical reactions listed in the KEGG database. The values have been computed using the eQuilibrator web tool.

  1. kegg_reactions_CC_ph7.0.tsv