KarrLab/obj_tables

!!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,