examples/sbtab/SBtab.py
# Schema automatically generated at 2020-05-29 00:27:56
import obj_tables
__all__ = [
'Compartment',
'Compound',
'Definition',
'Enzyme',
'FbcObjective',
'Gene',
'Layout',
'Measurement',
'PbConfig',
'Position',
'Protein',
'Quantity',
'QuantityInfo',
'QuantityMatrix',
'Reaction',
'ReactionStoichiometry',
'Regulator',
'Relation',
'Relationship',
'SparseMatrix',
'SparseMatrixColumn',
'SparseMatrixOrdered',
'SparseMatrixRow',
'StoichiometricMatrix',
'rxnconContingencyList',
'rxnconReactionList',
]
class Reaction(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
modifier = obj_tables.StringAttribute(verbose_name='Modifier')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
s_b_m_l_reaction_id = obj_tables.StringAttribute(verbose_name='SBML:reaction:id')
reaction_formula = obj_tables.LongStringAttribute(verbose_name='ReactionFormula')
location = obj_tables.StringAttribute(verbose_name='Location')
enzyme = obj_tables.StringAttribute(verbose_name='Enzyme')
model = obj_tables.StringAttribute(verbose_name='Model')
pathway = obj_tables.StringAttribute(verbose_name='Pathway')
subreaction_of = obj_tables.StringAttribute(verbose_name='SubreactionOf')
is_complete = obj_tables.BooleanAttribute(verbose_name='IsComplete')
is_reversible = obj_tables.BooleanAttribute(verbose_name='IsReversible')
is_in_equilibrium = obj_tables.BooleanAttribute(verbose_name='IsInEquilibrium')
is_exchange_reaction = obj_tables.BooleanAttribute(verbose_name='IsExchangeReaction')
flux = obj_tables.FloatAttribute(verbose_name='Flux')
is_non_enzymatic = obj_tables.BooleanAttribute(verbose_name='IsNonEnzymatic')
kinetic_law = obj_tables.LongStringAttribute(verbose_name='KineticLaw')
kinetic_law_name = obj_tables.StringAttribute(verbose_name='KineticLaw:Name')
kinetic_law_formula = obj_tables.StringAttribute(verbose_name='KineticLaw:Formula')
gene = obj_tables.StringAttribute(verbose_name='Gene')
gene_symbol = obj_tables.StringAttribute(verbose_name='Gene:Symbol')
operon = obj_tables.StringAttribute(verbose_name='Operon')
enzyme_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='Enzyme:SBML:species:id')
enzyme_s_b_m_l_parameter_id = obj_tables.StringAttribute(verbose_name='Enzyme:SBML:parameter:id')
build_reaction = obj_tables.BooleanAttribute(verbose_name='BuildReaction')
build_enzyme = obj_tables.BooleanAttribute(verbose_name='BuildEnzyme')
build_enzyme_production = obj_tables.BooleanAttribute(verbose_name='BuildEnzymeProduction')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_kegg_reaction = obj_tables.StringAttribute(verbose_name='Identifiers:kegg.reaction')
identifiers_obo_sbo = obj_tables.StringAttribute(verbose_name='Identifiers:obo.sbo')
identifiers_ec_code = obj_tables.StringAttribute(verbose_name='Identifiers:ec-code')
s_b_m_l_fbc_gene_association = obj_tables.LongStringAttribute(verbose_name='SBML:fbc:GeneAssociation')
s_b_m_l_fbc_lower_bound = obj_tables.StringAttribute(verbose_name='SBML:fbc:LowerBound')
s_b_m_l_fbc_upper_bound = obj_tables.StringAttribute(verbose_name='SBML:fbc:UpperBound')
regulator = obj_tables.StringAttribute(verbose_name='Regulator')
name_for_plots = obj_tables.StringAttribute(verbose_name='NameForPlots')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'modifier',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
's_b_m_l_reaction_id',
'reaction_formula',
'location',
'enzyme',
'model',
'pathway',
'subreaction_of',
'is_complete',
'is_reversible',
'is_in_equilibrium',
'is_exchange_reaction',
'flux',
'is_non_enzymatic',
'kinetic_law',
'kinetic_law_name',
'kinetic_law_formula',
'gene',
'gene_symbol',
'operon',
'enzyme_s_b_m_l_species_id',
'enzyme_s_b_m_l_parameter_id',
'build_reaction',
'build_enzyme',
'build_enzyme_production',
's_b_o_term',
'identifiers',
'identifiers_kegg_reaction',
'identifiers_obo_sbo',
'identifiers_ec_code',
's_b_m_l_fbc_gene_association',
's_b_m_l_fbc_lower_bound',
's_b_m_l_fbc_upper_bound',
'regulator',
'name_for_plots',
)
verbose_name = 'Reaction'
verbose_name_plural = 'Reaction'
class Compound(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='SBML:species:id')
s_b_m_l_speciestype_id = obj_tables.StringAttribute(verbose_name='SBML:speciestype:id')
initial_value = obj_tables.FloatAttribute(verbose_name='InitialValue')
initial_concentration = obj_tables.FloatAttribute(verbose_name='InitialConcentration')
unit = obj_tables.StringAttribute(verbose_name='Unit')
location = obj_tables.StringAttribute(verbose_name='Location')
state = obj_tables.StringAttribute(verbose_name='State')
compound_sum_formula = obj_tables.StringAttribute(verbose_name='CompoundSumFormula')
structure_formula = obj_tables.StringAttribute(verbose_name='StructureFormula')
charge = obj_tables.IntegerAttribute(verbose_name='Charge')
mass = obj_tables.FloatAttribute(verbose_name='Mass')
is_constant = obj_tables.BooleanAttribute(verbose_name='IsConstant')
enzyme_role = obj_tables.StringAttribute(verbose_name='EnzymeRole')
regulator_role = obj_tables.StringAttribute(verbose_name='RegulatorRole')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_sbo_kegg = obj_tables.StringAttribute(verbose_name='Identifiers:sbo.kegg')
identifiers_kegg_compound = obj_tables.StringAttribute(verbose_name='Identifiers:kegg.compound')
identifiers_obo_chebi = obj_tables.StringAttribute(verbose_name='Identifiers:obo.chebi')
s_b_m_l_fbc_chemical_formula = obj_tables.StringAttribute(verbose_name='SBML:fbc:ChemicalFormula')
s_b_m_l_fbc_charge = obj_tables.FloatAttribute(verbose_name='SBML:fbc:Charge')
has_only_substance_units = obj_tables.BooleanAttribute(verbose_name='HasOnlySubstanceUnits')
name_for_plots = obj_tables.StringAttribute(verbose_name='NameForPlots')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
's_b_m_l_species_id',
's_b_m_l_speciestype_id',
'initial_value',
'initial_concentration',
'unit',
'location',
'state',
'compound_sum_formula',
'structure_formula',
'charge',
'mass',
'is_constant',
'enzyme_role',
'regulator_role',
's_b_o_term',
'identifiers',
'identifiers_sbo_kegg',
'identifiers_kegg_compound',
'identifiers_obo_chebi',
's_b_m_l_fbc_chemical_formula',
's_b_m_l_fbc_charge',
'has_only_substance_units',
'name_for_plots',
)
verbose_name = 'Compound'
verbose_name_plural = 'Compound'
class Enzyme(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
catalysed_reaction = obj_tables.StringAttribute(verbose_name='CatalysedReaction')
kinetic_law = obj_tables.StringAttribute(verbose_name='KineticLaw')
kinetic_law_name = obj_tables.StringAttribute(verbose_name='KineticLaw:Name')
kinetic_law_formula = obj_tables.StringAttribute(verbose_name='KineticLaw:Formula')
pathway = obj_tables.StringAttribute(verbose_name='Pathway')
gene = obj_tables.StringAttribute(verbose_name='Gene')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'catalysed_reaction',
'kinetic_law',
'kinetic_law_name',
'kinetic_law_formula',
'pathway',
'gene',
'identifiers',
)
verbose_name = 'Enzyme'
verbose_name_plural = 'Enzyme'
class Protein(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
gene = obj_tables.StringAttribute(verbose_name='Gene')
mass = obj_tables.FloatAttribute(verbose_name='Mass')
size = obj_tables.FloatAttribute(verbose_name='Size')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'gene',
'mass',
'size',
)
verbose_name = 'Protein'
verbose_name_plural = 'Protein'
class Compartment(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
s_b_m_l_compartment_id = obj_tables.StringAttribute(verbose_name='SBML:compartment:id')
outer_compartment = obj_tables.StringAttribute(verbose_name='OuterCompartment')
outer_compartment_s_b_m_l_compartment_id = obj_tables.StringAttribute(verbose_name='OuterCompartment:SBML:compartment:id')
size = obj_tables.FloatAttribute(verbose_name='Size')
unit = obj_tables.StringAttribute(verbose_name='Unit')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_sbo_go = obj_tables.StringAttribute(verbose_name='Identifiers:sbo.go')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
's_b_m_l_compartment_id',
'outer_compartment',
'outer_compartment_s_b_m_l_compartment_id',
'size',
'unit',
's_b_o_term',
'identifiers',
'identifiers_sbo_go',
)
verbose_name = 'Compartment'
verbose_name_plural = 'Compartment'
class Quantity(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
quantity = obj_tables.StringAttribute(verbose_name='Quantity')
reference = obj_tables.StringAttribute(verbose_name='Reference')
quantity_name = obj_tables.StringAttribute(verbose_name='QuantityName')
quantity_type = obj_tables.StringAttribute(verbose_name='QuantityType')
value = obj_tables.FloatAttribute(verbose_name='Value')
mean = obj_tables.FloatAttribute(verbose_name='Mean')
std = obj_tables.FloatAttribute(verbose_name='Std')
min = obj_tables.FloatAttribute(verbose_name='Min')
max = obj_tables.FloatAttribute(verbose_name='Max')
median = obj_tables.FloatAttribute(verbose_name='Median')
geometric_mean = obj_tables.FloatAttribute(verbose_name='GeometricMean')
sign = obj_tables.EnumAttribute(['+', '-', '0'], default='0', verbose_name='Sign')
prob_dist = obj_tables.StringAttribute(verbose_name='ProbDist')
s_b_m_l_parameter_id = obj_tables.StringAttribute(verbose_name='SBML:parameter:id')
unit = obj_tables.StringAttribute(verbose_name='Unit')
scale = obj_tables.StringAttribute(verbose_name='Scale')
time = obj_tables.FloatAttribute(verbose_name='Time')
time_point = obj_tables.StringAttribute(verbose_name='TimePoint')
condition = obj_tables.StringAttribute(verbose_name='Condition')
p_h = obj_tables.FloatAttribute(verbose_name='pH')
temperature = obj_tables.FloatAttribute(verbose_name='Temperature')
location = obj_tables.StringAttribute(verbose_name='Location')
location_s_b_m_l_compartment_id = obj_tables.StringAttribute(verbose_name='Location:SBML:compartment:id')
compound = obj_tables.StringAttribute(verbose_name='Compound')
compound_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='Compound:SBML:species:id')
reaction = obj_tables.StringAttribute(verbose_name='Reaction')
reaction_s_b_m_l_reaction_id = obj_tables.StringAttribute(verbose_name='Reaction:SBML:reaction:id')
enyzme = obj_tables.StringAttribute(verbose_name='Enyzme')
enyzme_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='Enyzme:SBML:species:id')
enyzme_s_b_m_l_parameter_id = obj_tables.StringAttribute(verbose_name='Enyzme:SBML:parameter:id')
gene = obj_tables.StringAttribute(verbose_name='Gene')
organism = obj_tables.StringAttribute(verbose_name='Organism')
provenance = obj_tables.StringAttribute(verbose_name='Provenance')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_kegg_reaction = obj_tables.StringAttribute(verbose_name='Identifiers:kegg.reaction')
identifiers_kegg_compound = obj_tables.StringAttribute(verbose_name='Identifiers:kegg.compound')
identifiers_obo_chebi = obj_tables.StringAttribute(verbose_name='Identifiers:obo.chebi')
reaction_identifiers_kegg_reaction = obj_tables.StringAttribute(verbose_name='Reaction:Identifiers:kegg.reaction')
compound_identifiers_kegg_compound = obj_tables.StringAttribute(verbose_name='Compound:Identifiers:kegg.compound')
biological_element = obj_tables.StringAttribute(verbose_name='BiologicalElement')
mathematical_type = obj_tables.StringAttribute(verbose_name='MathematicalType')
data_geometric_std = obj_tables.FloatAttribute(verbose_name='DataGeometricStd')
prior_median = obj_tables.FloatAttribute(verbose_name='PriorMedian')
prior_std = obj_tables.FloatAttribute(verbose_name='PriorStd')
prior_geometric_std = obj_tables.FloatAttribute(verbose_name='PriorGeometricStd')
lower_bound = obj_tables.FloatAttribute(verbose_name='LowerBound')
upper_bound = obj_tables.FloatAttribute(verbose_name='UpperBound')
data_std = obj_tables.FloatAttribute(verbose_name='DataStd')
physical_type = obj_tables.StringAttribute(verbose_name='PhysicalType')
dependence = obj_tables.StringAttribute(verbose_name='Dependence')
use_as_prior_information = obj_tables.BooleanAttribute(verbose_name='UseAsPriorInformation')
s_b_m_l_element = obj_tables.StringAttribute(verbose_name='SBMLElement')
abbreviation = obj_tables.StringAttribute(verbose_name='Abbreviation')
matrix_info = obj_tables.StringAttribute(verbose_name='MatrixInfo')
s_b_o_equilibrium_constant = obj_tables.FloatAttribute(verbose_name='SBO:equilibrium_constant')
s_b_o_identifiers_obo_sbo = obj_tables.StringAttribute(verbose_name='SBO:Identifiers:obo.sbo')
s_b_o_concentration = obj_tables.FloatAttribute(verbose_name='SBO:concentration')
s_b_o_concentration_m_m_log10_median = obj_tables.FloatAttribute(verbose_name='SBO:concentration [mM:Log10]:Median')
value_type = obj_tables.StringAttribute(verbose_name='ValueType')
concentration_min = obj_tables.FloatAttribute(verbose_name='Concentration:Min')
concentration_max = obj_tables.FloatAttribute(verbose_name='Concentration:Max')
parameter_s_b_m_l_parameter_id = obj_tables.StringAttribute(verbose_name='Parameter:SBML:parameter:id')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'quantity',
'reference',
'quantity_name',
'quantity_type',
'value',
'mean',
'std',
'min',
'max',
'median',
'geometric_mean',
'sign',
'prob_dist',
's_b_m_l_parameter_id',
'unit',
'scale',
'time',
'time_point',
'condition',
'p_h',
'temperature',
'location',
'location_s_b_m_l_compartment_id',
'compound',
'compound_s_b_m_l_species_id',
'reaction',
'reaction_s_b_m_l_reaction_id',
'enyzme',
'enyzme_s_b_m_l_species_id',
'enyzme_s_b_m_l_parameter_id',
'gene',
'organism',
'provenance',
's_b_o_term',
'identifiers',
'identifiers_kegg_reaction',
'identifiers_kegg_compound',
'identifiers_obo_chebi',
'reaction_identifiers_kegg_reaction',
'compound_identifiers_kegg_compound',
'biological_element',
'mathematical_type',
'data_geometric_std',
'prior_median',
'prior_std',
'prior_geometric_std',
'lower_bound',
'upper_bound',
'data_std',
'physical_type',
'dependence',
'use_as_prior_information',
's_b_m_l_element',
'abbreviation',
'matrix_info',
's_b_o_equilibrium_constant',
's_b_o_identifiers_obo_sbo',
's_b_o_concentration',
's_b_o_concentration_m_m_log10_median',
'value_type',
'concentration_min',
'concentration_max',
'parameter_s_b_m_l_parameter_id',
)
verbose_name = 'Quantity'
verbose_name_plural = 'Quantity'
class Regulator(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
state = obj_tables.StringAttribute(verbose_name='State')
target_gene = obj_tables.StringAttribute(verbose_name='TargetGene')
target_operon = obj_tables.StringAttribute(verbose_name='TargetOperon')
target_promoter = obj_tables.StringAttribute(verbose_name='TargetPromoter')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'state',
'target_gene',
'target_operon',
'target_promoter',
'identifiers',
)
verbose_name = 'Regulator'
verbose_name_plural = 'Regulator'
class Gene(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
locus_name = obj_tables.StringAttribute(verbose_name='LocusName')
gene_product = obj_tables.StringAttribute(verbose_name='GeneProduct')
gene_product_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='GeneProduct:SBML:species:id')
operon = obj_tables.StringAttribute(verbose_name='Operon')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
s_b_m_l_fbc_i_d = obj_tables.StringAttribute(verbose_name='SBML:fbc:ID')
s_b_m_l_fbc_name = obj_tables.StringAttribute(verbose_name='SBML:fbc:Name')
s_b_m_l_fbc_gene_product = obj_tables.BooleanAttribute(verbose_name='SBML:fbc:GeneProduct')
s_b_m_l_fbc_gene_association = obj_tables.BooleanAttribute(verbose_name='SBML:fbc:GeneAssociation')
s_b_m_l_fbc_label = obj_tables.StringAttribute(verbose_name='SBML:fbc:Label')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'locus_name',
'gene_product',
'gene_product_s_b_m_l_species_id',
'operon',
'identifiers',
's_b_m_l_fbc_i_d',
's_b_m_l_fbc_name',
's_b_m_l_fbc_gene_product',
's_b_m_l_fbc_gene_association',
's_b_m_l_fbc_label',
)
verbose_name = 'Gene'
verbose_name_plural = 'Gene'
class Relation(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
i_d = obj_tables.StringAttribute(verbose_name='ID')
from_object = obj_tables.StringAttribute(verbose_name='FromObject')
to_object = obj_tables.StringAttribute(verbose_name='ToObject')
is_symmetric = obj_tables.BooleanAttribute(verbose_name='IsSymmetric')
value_quantity_type = obj_tables.FloatAttribute(verbose_name='Value:QuantityType')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'i_d',
'from_object',
'to_object',
'is_symmetric',
'value_quantity_type',
)
verbose_name = 'Relation'
verbose_name_plural = 'Relation'
class Definition(obj_tables.Model):
component_name = obj_tables.StringAttribute(verbose_name='ComponentName')
component_type = obj_tables.StringAttribute(verbose_name='ComponentType')
is_part_of = obj_tables.StringAttribute(verbose_name='IsPartOf')
format = obj_tables.StringAttribute(verbose_name='Format')
description = obj_tables.StringAttribute(verbose_name='Description')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'component_name',
'component_type',
'is_part_of',
'format',
'description',
)
verbose_name = 'Definition'
verbose_name_plural = 'Definition'
class QuantityMatrix(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
time = obj_tables.FloatAttribute(verbose_name='Time')
time_point = obj_tables.StringAttribute(verbose_name='TimePoint')
_table_column = obj_tables.StringAttribute(verbose_name='>Table:Column')
_document_table_column = obj_tables.StringAttribute(verbose_name='>Document:Table:Column')
i_d = obj_tables.StringAttribute(verbose_name='ID')
quantity_name = obj_tables.StringAttribute(verbose_name='QuantityName')
quantity_type = obj_tables.StringAttribute(verbose_name='QuantityType')
value = obj_tables.FloatAttribute(verbose_name='Value')
mean = obj_tables.FloatAttribute(verbose_name='Mean')
std = obj_tables.FloatAttribute(verbose_name='Std')
min = obj_tables.FloatAttribute(verbose_name='Min')
max = obj_tables.FloatAttribute(verbose_name='Max')
median = obj_tables.FloatAttribute(verbose_name='Median')
geometric_mean = obj_tables.FloatAttribute(verbose_name='GeometricMean')
sign = obj_tables.EnumAttribute(['+', '-', '0'], default='0', verbose_name='Sign')
prob_dist = obj_tables.StringAttribute(verbose_name='ProbDist')
s_b_m_l_parameter_id = obj_tables.StringAttribute(verbose_name='SBML:parameter:id')
unit = obj_tables.StringAttribute(verbose_name='Unit')
scale = obj_tables.StringAttribute(verbose_name='Scale')
compound = obj_tables.StringAttribute(verbose_name='Compound')
compound_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='Compound:SBML:species:id')
reaction = obj_tables.StringAttribute(verbose_name='Reaction')
reaction_s_b_m_l_reaction_id = obj_tables.StringAttribute(verbose_name='Reaction:SBML:reaction:id')
enyzme = obj_tables.StringAttribute(verbose_name='Enyzme')
enyzme_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='Enyzme:SBML:species:id')
enyzme_s_b_m_l_parameter_id = obj_tables.StringAttribute(verbose_name='Enyzme:SBML:parameter:id')
protein = obj_tables.StringAttribute(verbose_name='Protein')
protein_s_b_m_l_species_id = obj_tables.StringAttribute(verbose_name='Protein:SBML:species:id')
gene = obj_tables.StringAttribute(verbose_name='Gene')
identifiers_obo_chebi = obj_tables.StringAttribute(verbose_name='Identifiers:obo.chebi')
_concentration_glucose = obj_tables.FloatAttribute(verbose_name='>Concentration:Glucose')
_concentration_fructose = obj_tables.FloatAttribute(verbose_name='>Concentration:Fructose')
_sample_t0 = obj_tables.FloatAttribute(verbose_name='>Sample:t0')
_sample_t1 = obj_tables.FloatAttribute(verbose_name='>Sample:t1')
_t_p_t0_mean = obj_tables.FloatAttribute(verbose_name='>TP:t0:mean')
_t_p_t0_std = obj_tables.FloatAttribute(verbose_name='>TP:t0:std')
_t_p_t1_mean = obj_tables.FloatAttribute(verbose_name='>TP:t1:mean')
_t_p_t1_std = obj_tables.FloatAttribute(verbose_name='>TP:t1:std')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'time',
'time_point',
'_table_column',
'_document_table_column',
'i_d',
'quantity_name',
'quantity_type',
'value',
'mean',
'std',
'min',
'max',
'median',
'geometric_mean',
'sign',
'prob_dist',
's_b_m_l_parameter_id',
'unit',
'scale',
'compound',
'compound_s_b_m_l_species_id',
'reaction',
'reaction_s_b_m_l_reaction_id',
'enyzme',
'enyzme_s_b_m_l_species_id',
'enyzme_s_b_m_l_parameter_id',
'protein',
'protein_s_b_m_l_species_id',
'gene',
'identifiers_obo_chebi',
'_concentration_glucose',
'_concentration_fructose',
'_sample_t0',
'_sample_t1',
'_t_p_t0_mean',
'_t_p_t0_std',
'_t_p_t1_mean',
'_t_p_t1_std',
)
verbose_name = 'QuantityMatrix'
verbose_name_plural = 'QuantityMatrix'
class StoichiometricMatrix(obj_tables.Model):
reaction_i_d = obj_tables.StringAttribute(verbose_name='ReactionID')
stoichiometry = obj_tables.StringAttribute(verbose_name='Stoichiometry')
substrate = obj_tables.StringAttribute(verbose_name='Substrate')
product = obj_tables.StringAttribute(verbose_name='Product')
location = obj_tables.StringAttribute(verbose_name='Location')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'reaction_i_d',
'stoichiometry',
'substrate',
'product',
'location',
)
verbose_name = 'StoichiometricMatrix'
verbose_name_plural = 'StoichiometricMatrix'
class Measurement(obj_tables.Model):
sample = obj_tables.StringAttribute(verbose_name='Sample')
time = obj_tables.StringAttribute(verbose_name='Time')
unit = obj_tables.StringAttribute(verbose_name='Unit')
value_type = obj_tables.StringAttribute(verbose_name='ValueType')
description = obj_tables.StringAttribute(verbose_name='Description')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'sample',
'time',
'unit',
'value_type',
'description',
)
verbose_name = 'Measurement'
verbose_name_plural = 'Measurement'
class QuantityInfo(obj_tables.Model):
quantity_type = obj_tables.StringAttribute(verbose_name='QuantityType')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
unit = obj_tables.StringAttribute(verbose_name='Unit')
constant = obj_tables.StringAttribute(verbose_name='Constant')
element = obj_tables.StringAttribute(verbose_name='Element')
related_element = obj_tables.StringAttribute(verbose_name='RelatedElement')
scaling = obj_tables.StringAttribute(verbose_name='Scaling')
dependence = obj_tables.StringAttribute(verbose_name='Dependence')
prior_median = obj_tables.FloatAttribute(verbose_name='PriorMedian')
prior_std = obj_tables.FloatAttribute(verbose_name='PriorStd')
lower_bound = obj_tables.FloatAttribute(verbose_name='LowerBound')
upper_bound = obj_tables.FloatAttribute(verbose_name='UpperBound')
error_std = obj_tables.FloatAttribute(verbose_name='ErrorStd')
data_std = obj_tables.FloatAttribute(verbose_name='DataStd')
s_b_m_l_element = obj_tables.StringAttribute(verbose_name='SBMLElement')
s_b_m_l_element_type = obj_tables.StringAttribute(verbose_name='SBMLElementType')
abbreviation = obj_tables.StringAttribute(verbose_name='Abbreviation')
i_d = obj_tables.StringAttribute(verbose_name='ID')
matrix_info = obj_tables.StringAttribute(verbose_name='MatrixInfo')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'quantity_type',
'symbol',
'unit',
'constant',
'element',
'related_element',
'scaling',
'dependence',
'prior_median',
'prior_std',
'lower_bound',
'upper_bound',
'error_std',
'data_std',
's_b_m_l_element',
's_b_m_l_element_type',
'abbreviation',
'i_d',
'matrix_info',
)
verbose_name = 'QuantityInfo'
verbose_name_plural = 'QuantityInfo'
class PbConfig(obj_tables.Model):
option = obj_tables.StringAttribute(verbose_name='Option')
value = obj_tables.StringAttribute(verbose_name='Value')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'option',
'value',
)
verbose_name = 'PbConfig'
verbose_name_plural = 'PbConfig'
class rxnconContingencyList(obj_tables.Model):
u_i_d_contingency = obj_tables.IntegerAttribute(verbose_name='UID:Contingency')
target = obj_tables.StringAttribute(verbose_name='Target')
contingency = obj_tables.StringAttribute(verbose_name='Contingency')
modifier = obj_tables.StringAttribute(verbose_name='Modifier')
reference_identifiers_pubmed = obj_tables.StringAttribute(verbose_name='Reference:Identifiers:pubmed')
quality = obj_tables.StringAttribute(verbose_name='Quality')
comment = obj_tables.StringAttribute(verbose_name='Comment')
internal_complex_i_d = obj_tables.StringAttribute(verbose_name='InternalComplexID')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'u_i_d_contingency',
'target',
'contingency',
'modifier',
'reference_identifiers_pubmed',
'quality',
'comment',
'internal_complex_i_d',
)
verbose_name = 'rxnconContingencyList'
verbose_name_plural = 'rxnconContingencyList'
class rxnconReactionList(obj_tables.Model):
i_d = obj_tables.IntegerAttribute(verbose_name='ID')
u_i_d_reaction = obj_tables.StringAttribute(verbose_name='UID:Reaction')
component_a_name = obj_tables.StringAttribute(verbose_name='ComponentA:Name')
component_a_domain = obj_tables.StringAttribute(verbose_name='ComponentA:Domain')
component_a_residue = obj_tables.StringAttribute(verbose_name='ComponentA:Residue')
reaction = obj_tables.StringAttribute(verbose_name='Reaction')
component_b_name = obj_tables.StringAttribute(verbose_name='ComponentB:Name')
component_b_domain = obj_tables.StringAttribute(verbose_name='ComponentB:Domain')
component_b_residue = obj_tables.StringAttribute(verbose_name='ComponentB:Residue')
quality = obj_tables.StringAttribute(verbose_name='Quality')
literature_identifiers_pubmed = obj_tables.StringAttribute(verbose_name='Literature:Identifiers:pubmed')
comment = obj_tables.StringAttribute(verbose_name='Comment')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'u_i_d_reaction',
'component_a_name',
'component_a_domain',
'component_a_residue',
'reaction',
'component_b_name',
'component_b_domain',
'component_b_residue',
'quality',
'literature_identifiers_pubmed',
'comment',
)
verbose_name = 'rxnconReactionList'
verbose_name_plural = 'rxnconReactionList'
class FbcObjective(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
name = obj_tables.StringAttribute(verbose_name='Name')
s_b_m_l_fbc_type = obj_tables.StringAttribute(verbose_name='SBML:fbc:type')
s_b_m_l_fbc_active = obj_tables.BooleanAttribute(verbose_name='SBML:fbc:active')
s_b_m_l_fbc_objective = obj_tables.StringAttribute(verbose_name='SBML:fbc:objective')
s_b_m_l_fbc_reaction = obj_tables.StringAttribute(verbose_name='SBML:fbc:reaction')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'name',
's_b_m_l_fbc_type',
's_b_m_l_fbc_active',
's_b_m_l_fbc_objective',
's_b_m_l_fbc_reaction',
)
verbose_name = 'FbcObjective'
verbose_name_plural = 'FbcObjective'
class Layout(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
name = obj_tables.StringAttribute(verbose_name='Name')
s_b_m_l_layout_model_entity = obj_tables.StringAttribute(verbose_name='SBML:layout:modelEntity')
s_b_m_l_layout_compartment_id = obj_tables.StringAttribute(verbose_name='SBML:layout:compartment:id')
s_b_m_l_layout_reaction_id = obj_tables.StringAttribute(verbose_name='SBML:layout:reaction:id')
s_b_m_l_layout_species_id = obj_tables.StringAttribute(verbose_name='SBML:layout:species:id')
s_b_m_l_layout_curve_segment = obj_tables.StringAttribute(verbose_name='SBML:layout:curveSegment')
s_b_m_l_layout_x = obj_tables.FloatAttribute(verbose_name='SBML:layout:X')
s_b_m_l_layout_y = obj_tables.FloatAttribute(verbose_name='SBML:layout:Y')
s_b_m_l_layout_width = obj_tables.FloatAttribute(verbose_name='SBML:layout:width')
s_b_m_l_layout_height = obj_tables.FloatAttribute(verbose_name='SBML:layout:height')
s_b_m_l_layout_text = obj_tables.StringAttribute(verbose_name='SBML:layout:text')
s_b_m_l_layout_species_role = obj_tables.StringAttribute(verbose_name='SBML:layout:speciesRole')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'name',
's_b_m_l_layout_model_entity',
's_b_m_l_layout_compartment_id',
's_b_m_l_layout_reaction_id',
's_b_m_l_layout_species_id',
's_b_m_l_layout_curve_segment',
's_b_m_l_layout_x',
's_b_m_l_layout_y',
's_b_m_l_layout_width',
's_b_m_l_layout_height',
's_b_m_l_layout_text',
's_b_m_l_layout_species_role',
)
verbose_name = 'Layout'
verbose_name_plural = 'Layout'
class ReactionStoichiometry(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
stoichiometry = obj_tables.StringAttribute(verbose_name='Stoichiometry')
substrate = obj_tables.StringAttribute(verbose_name='Substrate')
product = obj_tables.StringAttribute(verbose_name='Product')
location = obj_tables.StringAttribute(verbose_name='Location')
reaction = obj_tables.StringAttribute(verbose_name='Reaction')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'stoichiometry',
'substrate',
'product',
'location',
'reaction',
)
verbose_name = 'ReactionStoichiometry'
verbose_name_plural = 'ReactionStoichiometry'
class SparseMatrixOrdered(obj_tables.Model):
row_number = obj_tables.IntegerAttribute(verbose_name='RowNumber')
column_number = obj_tables.IntegerAttribute(verbose_name='ColumnNumber')
value = obj_tables.FloatAttribute(verbose_name='Value')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'row_number',
'column_number',
'value',
)
verbose_name = 'SparseMatrixOrdered'
verbose_name_plural = 'SparseMatrixOrdered'
class SparseMatrix(obj_tables.Model):
row_i_d = obj_tables.StringAttribute(verbose_name='RowID')
column_i_d = obj_tables.StringAttribute(verbose_name='ColumnID')
value = obj_tables.FloatAttribute(verbose_name='Value')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'row_i_d',
'column_i_d',
'value',
)
verbose_name = 'SparseMatrix'
verbose_name_plural = 'SparseMatrix'
class SparseMatrixRow(obj_tables.Model):
row_i_d = obj_tables.StringAttribute(verbose_name='RowID')
row_string = obj_tables.StringAttribute(verbose_name='RowString')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'row_i_d',
'row_string',
)
verbose_name = 'SparseMatrixRow'
verbose_name_plural = 'SparseMatrixRow'
class SparseMatrixColumn(obj_tables.Model):
column_i_d = obj_tables.StringAttribute(verbose_name='ColumnID')
column_string = obj_tables.StringAttribute(verbose_name='ColumnString')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'column_i_d',
'column_string',
)
verbose_name = 'SparseMatrixColumn'
verbose_name_plural = 'SparseMatrixColumn'
class Relationship(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
from_object = obj_tables.StringAttribute(verbose_name='FromObject')
to_object = obj_tables.StringAttribute(verbose_name='ToObject')
value = obj_tables.IntegerAttribute(verbose_name='Value')
is_symmetric = obj_tables.BooleanAttribute(verbose_name='IsSymmetric')
sign = obj_tables.EnumAttribute(['+', '-', '0'], default='0', verbose_name='Sign')
relation = obj_tables.StringAttribute(verbose_name='Relation')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'from_object',
'to_object',
'value',
'is_symmetric',
'sign',
'relation',
)
verbose_name = 'Relationship'
verbose_name_plural = 'Relationship'
class Position(obj_tables.Model):
element = obj_tables.StringAttribute(verbose_name='Element')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'element',
'position_x',
'position_y',
)
verbose_name = 'Position'
verbose_name_plural = 'Position'