examples/kinetic_metabolic_model/schema.tsv
!!ObjTables type='Schema' tableFormat='row' description='Table/model and column/attribute definitions' date='2020-05-14 17:04:33' objTablesVersion='1.0.0'
!Name !Type !Parent !Format !Verbose name !Verbose name plural
Compartment Class row Compartment Compartments
id Attribute Compartment String(primary=True, unique=True)
name Attribute Compartment String(none=True, default=None, default_cleaned_value=None)
Metabolite Class row Metabolite Metabolites
id Attribute Metabolite String(primary=True, unique=True)
name Attribute Metabolite String(none=True, default=None, default_cleaned_value=None)
formula Attribute Metabolite chem.ChemicalFormula
Kinetics Class cell Kinetics Kinetics
value Attribute Kinetics Range
molecule Attribute Kinetics String
organism Attribute Kinetics String
uniprot_ids Attribute Kinetics List UniProt ids
comments Attribute Kinetics LongString
pubmed_ids Attribute Kinetics List PubMed ids
image Attribute Kinetics Enum(['2D-image'], none=True)
Reaction Class row Reaction Reactions
id Attribute Reaction String(primary=True, unique=True)
id_iAF1260 Attribute Reaction String(none=True, default=None, default_cleaned_value=None) Id (iAF1260 [Ref1])
name Attribute Reaction String(none=True, default=None, default_cleaned_value=None)
equation Attribute Reaction chem.ReactionEquation(species_cls='Metabolite', compartment_cls='Compartment')
reversible Attribute Reaction Boolean
subsystem Attribute Reaction String(none=True, default=None, default_cleaned_value=None)
ec_number Attribute Reaction Regex(pattern='\d+\.\d+\.\d+\.\d+', none=True, default=None, default_cleaned_value=None) EC number
gene_rule Attribute Reaction String(none=True, default=None, default_cleaned_value=None)
obs_k_ms Attribute Reaction ManyToMany('Kinetics', related_name='k_m_reactions', cell_dialect='tsv') Measured Km (mM) [Ref2, Ref3]
obs_range_k_ms Attribute Reaction LongString Measured Km range (mM) [Ref2, Ref3]
est_range_k_ms Attribute Reaction LongString Estimated Km range (mM)
obs_k_cats Attribute Reaction ManyToMany('Kinetics', related_name='k_cat_reactions', cell_dialect='tsv') Measured kcat (s^-1) [Ref2, Ref3]
min_obs_for_k_cat Attribute Reaction Float Minimum measured forward kcat (s^-1) [Ref2, Ref3]
max_obs_for_k_cat Attribute Reaction Float Maximum measured forward kcat (s^-1) [Ref2, Ref3]
min_obs_back_k_cat Attribute Reaction Float Minimum measured backward kcat (s^-1) [Ref2, Ref3]
max_obs_back_k_cat Attribute Reaction Float Maximum measured backward kcat (s^-1) [Ref2, Ref3]
min_est_for_k_cat Attribute Reaction Float Minimum estimated forward kcat (s^-1)
max_est_for_k_cat Attribute Reaction Float Maximum estimated forward kcat (s^-1)
min_est_back_k_cat Attribute Reaction Float Minimum estimated backward kcat (s^-1)
max_est_back_k_cat Attribute Reaction Float Maximum estimated backward kcat (s^-1)
obs_k_cat_k_ms Attribute Reaction ManyToMany('Kinetics', related_name='k_cat_k_m_reactions', cell_dialect='tsv') Measured kcat/Km (mM^-1 s^-1) [Ref2, Ref3]
obs_k_is Attribute Reaction ManyToMany('Kinetics', related_name='k_i_reactions', cell_dialect='tsv') Measured Ki (mM) [Ref2, Ref3]
coupled_to_biomass Attribute Reaction Boolean
Regulation Class row Regulation Regulations
reaction Attribute Regulation ManyToOne('Reaction', related_name='regulations')
regulator Attribute Regulation ManyToOne('Metabolite', related_name='regulated_reactions')
regulator_compartment Attribute Regulation ManyToOne('Compartment', related_name='regulated_reactions')
type Attribute Regulation Enum(['activation', 'competitive inhibition', 'mixed inhibition']) Type [Ref2, Ref3]
Reference Class row Reference References
id Attribute Reference String(primary=True, unique=True)
title Attribute Reference LongString
authors Attribute Reference LongString
journal Attribute Reference String
volume Attribute Reference PositiveInteger
issue Attribute Reference PositiveInteger
start_page Attribute Reference PositiveInteger
end_page Attribute Reference PositiveInteger
pubmed_id Attribute Reference PositiveInteger PubMed id