examples/sbtab/simple_examples/2.yml
Compartment: []
Compound:
- __id: 0
__type: Compound
charge: null
comment: ''
compound_sum_formula: ''
description: ''
enzyme_role: ''
has_only_substance_units: false
i_d: F6P
identifiers: ''
identifiers_kegg_compound: C05345
identifiers_obo_chebi: ''
identifiers_sbo_kegg: ''
initial_concentration: .nan
initial_value: .nan
is_constant: false
location: ''
mass: .nan
miriam_annotations: ''
name: Fructose 6-phosphate
name_for_plots: ''
position_x: .nan
position_y: .nan
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator_role: ''
s_b_m_l_fbc_charge: .nan
s_b_m_l_fbc_chemical_formula: ''
s_b_m_l_species_id: f6p
s_b_m_l_speciestype_id: ''
s_b_o_term: ''
state: ''
structure_formula: ''
symbol: ''
type: ''
unit: ''
- __id: 1
__type: Compound
charge: null
comment: ''
compound_sum_formula: ''
description: ''
enzyme_role: ''
has_only_substance_units: false
i_d: ATP
identifiers: ''
identifiers_kegg_compound: C00002
identifiers_obo_chebi: ''
identifiers_sbo_kegg: ''
initial_concentration: .nan
initial_value: .nan
is_constant: false
location: ''
mass: .nan
miriam_annotations: ''
name: ATP
name_for_plots: ''
position_x: .nan
position_y: .nan
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator_role: ''
s_b_m_l_fbc_charge: .nan
s_b_m_l_fbc_chemical_formula: ''
s_b_m_l_species_id: atp
s_b_m_l_speciestype_id: ''
s_b_o_term: ''
state: ''
structure_formula: ''
symbol: ''
type: ''
unit: ''
- __id: 2
__type: Compound
charge: null
comment: ''
compound_sum_formula: ''
description: ''
enzyme_role: ''
has_only_substance_units: false
i_d: ADP
identifiers: ''
identifiers_kegg_compound: C00008
identifiers_obo_chebi: ''
identifiers_sbo_kegg: ''
initial_concentration: .nan
initial_value: .nan
is_constant: false
location: ''
mass: .nan
miriam_annotations: ''
name: ADP
name_for_plots: ''
position_x: .nan
position_y: .nan
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator_role: ''
s_b_m_l_fbc_charge: .nan
s_b_m_l_fbc_chemical_formula: ''
s_b_m_l_species_id: adp
s_b_m_l_speciestype_id: ''
s_b_o_term: ''
state: ''
structure_formula: ''
symbol: ''
type: ''
unit: ''
Definition: []
Enzyme: []
FbcObjective: []
Gene: []
Layout: []
Measurement: []
PbConfig: []
Position: []
Protein: []
Quantity:
- __id: 3
__type: Quantity
abbreviation: ''
biological_element: ''
comment: ''
compound: ''
compound_identifiers_kegg_compound: ''
compound_s_b_m_l_species_id: atp
concentration_max: .nan
concentration_min: .nan
condition: ''
data_geometric_std: .nan
data_std: .nan
dependence: ''
description: ''
enyzme: ''
enyzme_s_b_m_l_parameter_id: ''
enyzme_s_b_m_l_species_id: ''
gene: ''
geometric_mean: .nan
i_d: MyData 1
identifiers: ''
identifiers_kegg_compound: ''
identifiers_kegg_reaction: ''
identifiers_obo_chebi: ''
location: ''
location_s_b_m_l_compartment_id: ''
lower_bound: .nan
mathematical_type: ''
matrix_info: ''
max: .nan
mean: .nan
median: .nan
min: .nan
miriam_annotations: ''
name: ''
organism: ''
p_h: .nan
parameter_s_b_m_l_parameter_id: ''
physical_type: ''
position_x: .nan
position_y: .nan
prior_geometric_std: .nan
prior_median: .nan
prior_std: .nan
prob_dist: ''
provenance: ''
quantity: ''
quantity_name: ''
quantity_type: equilibrium constant
reaction: ''
reaction_identifiers_kegg_reaction: ''
reaction_s_b_m_l_reaction_id: r1
reference: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_element: ''
s_b_m_l_parameter_id: ''
s_b_o_concentration: .nan
s_b_o_concentration_m_m_log10_median: .nan
s_b_o_equilibrium_constant: .nan
s_b_o_identifiers_obo_sbo: ''
s_b_o_term: ''
scale: ''
sign: '0'
std: .nan
symbol: ''
temperature: .nan
time: .nan
time_point: ''
type: ''
unit: dimensionless
upper_bound: .nan
use_as_prior_information: false
value: 156.0
value_type: ''
- __id: 4
__type: Quantity
abbreviation: ''
biological_element: ''
comment: ''
compound: ''
compound_identifiers_kegg_compound: ''
compound_s_b_m_l_species_id: atp
concentration_max: .nan
concentration_min: .nan
condition: ''
data_geometric_std: .nan
data_std: .nan
dependence: ''
description: ''
enyzme: ''
enyzme_s_b_m_l_parameter_id: ''
enyzme_s_b_m_l_species_id: ''
gene: ''
geometric_mean: .nan
i_d: MyData 2
identifiers: ''
identifiers_kegg_compound: ''
identifiers_kegg_reaction: ''
identifiers_obo_chebi: ''
location: ''
location_s_b_m_l_compartment_id: ''
lower_bound: .nan
mathematical_type: ''
matrix_info: ''
max: .nan
mean: .nan
median: .nan
min: .nan
miriam_annotations: ''
name: ''
organism: ''
p_h: .nan
parameter_s_b_m_l_parameter_id: ''
physical_type: ''
position_x: .nan
position_y: .nan
prior_geometric_std: .nan
prior_median: .nan
prior_std: .nan
prob_dist: ''
provenance: ''
quantity: ''
quantity_name: ''
quantity_type: Michaelis constant
reaction: ''
reaction_identifiers_kegg_reaction: ''
reaction_s_b_m_l_reaction_id: r1
reference: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_element: ''
s_b_m_l_parameter_id: ''
s_b_o_concentration: .nan
s_b_o_concentration_m_m_log10_median: .nan
s_b_o_equilibrium_constant: .nan
s_b_o_identifiers_obo_sbo: ''
s_b_o_term: ''
scale: ''
sign: '0'
std: .nan
symbol: ''
temperature: .nan
time: .nan
time_point: ''
type: ''
unit: mM
upper_bound: .nan
use_as_prior_information: false
value: 0.96
value_type: ''
- __id: 5
__type: Quantity
abbreviation: ''
biological_element: ''
comment: ''
compound: ''
compound_identifiers_kegg_compound: ''
compound_s_b_m_l_species_id: atp
concentration_max: .nan
concentration_min: .nan
condition: ''
data_geometric_std: .nan
data_std: .nan
dependence: ''
description: ''
enyzme: ''
enyzme_s_b_m_l_parameter_id: ''
enyzme_s_b_m_l_species_id: ''
gene: ''
geometric_mean: .nan
i_d: MyData 3
identifiers: ''
identifiers_kegg_compound: ''
identifiers_kegg_reaction: ''
identifiers_obo_chebi: ''
location: ''
location_s_b_m_l_compartment_id: ''
lower_bound: .nan
mathematical_type: ''
matrix_info: ''
max: .nan
mean: .nan
median: .nan
min: .nan
miriam_annotations: ''
name: ''
organism: ''
p_h: .nan
parameter_s_b_m_l_parameter_id: ''
physical_type: ''
position_x: .nan
position_y: .nan
prior_geometric_std: .nan
prior_median: .nan
prior_std: .nan
prob_dist: ''
provenance: ''
quantity: ''
quantity_name: ''
quantity_type: inhibition constant
reaction: ''
reaction_identifiers_kegg_reaction: ''
reaction_s_b_m_l_reaction_id: r1
reference: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_element: ''
s_b_m_l_parameter_id: ''
s_b_o_concentration: .nan
s_b_o_concentration_m_m_log10_median: .nan
s_b_o_equilibrium_constant: .nan
s_b_o_identifiers_obo_sbo: ''
s_b_o_term: ''
scale: ''
sign: '0'
std: .nan
symbol: ''
temperature: .nan
time: .nan
time_point: ''
type: ''
unit: mM
upper_bound: .nan
use_as_prior_information: false
value: 0.13
value_type: ''
- __id: 6
__type: Quantity
abbreviation: ''
biological_element: ''
comment: ''
compound: ''
compound_identifiers_kegg_compound: ''
compound_s_b_m_l_species_id: '...'
concentration_max: .nan
concentration_min: .nan
condition: ''
data_geometric_std: .nan
data_std: .nan
dependence: ''
description: ''
enyzme: ''
enyzme_s_b_m_l_parameter_id: ''
enyzme_s_b_m_l_species_id: ''
gene: ''
geometric_mean: .nan
i_d: MyData 4
identifiers: ''
identifiers_kegg_compound: ''
identifiers_kegg_reaction: ''
identifiers_obo_chebi: ''
location: ''
location_s_b_m_l_compartment_id: ''
lower_bound: .nan
mathematical_type: ''
matrix_info: ''
max: .nan
mean: .nan
median: .nan
min: .nan
miriam_annotations: ''
name: ''
organism: ''
p_h: .nan
parameter_s_b_m_l_parameter_id: ''
physical_type: ''
position_x: .nan
position_y: .nan
prior_geometric_std: .nan
prior_median: .nan
prior_std: .nan
prob_dist: ''
provenance: ''
quantity: ''
quantity_name: ''
quantity_type: concentration
reaction: ''
reaction_identifiers_kegg_reaction: ''
reaction_s_b_m_l_reaction_id: '...'
reference: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_element: ''
s_b_m_l_parameter_id: ''
s_b_o_concentration: .nan
s_b_o_concentration_m_m_log10_median: .nan
s_b_o_equilibrium_constant: .nan
s_b_o_identifiers_obo_sbo: ''
s_b_o_term: ''
scale: ''
sign: '0'
std: .nan
symbol: ''
temperature: .nan
time: .nan
time_point: ''
type: ''
unit: mM
upper_bound: .nan
use_as_prior_information: false
value: 1.5
value_type: ''
QuantityInfo: []
QuantityMatrix:
- __id: 7
__type: QuantityMatrix
_concentration_fructose: .nan
_concentration_glucose: .nan
_document_table_column: ''
_sample_t0: .nan
_sample_t1: .nan
_t_p_t0_mean: .nan
_t_p_t0_std: .nan
_t_p_t1_mean: .nan
_t_p_t1_std: .nan
_table_column: ''
comment: ''
compound: ''
compound_s_b_m_l_species_id: ''
description: ''
enyzme: ''
enyzme_s_b_m_l_parameter_id: ''
enyzme_s_b_m_l_species_id: ''
gene: ''
geometric_mean: .nan
i_d: ''
identifiers_obo_chebi: ''
max: .nan
mean: .nan
median: .nan
min: .nan
miriam_annotations: ''
name: ''
position_x: .nan
position_y: .nan
prob_dist: ''
protein: ''
protein_s_b_m_l_species_id: ''
quantity_name: ''
quantity_type: ''
reaction: ''
reaction_s_b_m_l_reaction_id: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_parameter_id: ''
scale: ''
sign: '0'
std: .nan
symbol: ''
time: 0.0
time_point: ''
type: ''
unit: ''
value: .nan
- __id: 8
__type: QuantityMatrix
_concentration_fructose: .nan
_concentration_glucose: .nan
_document_table_column: ''
_sample_t0: .nan
_sample_t1: .nan
_t_p_t0_mean: .nan
_t_p_t0_std: .nan
_t_p_t1_mean: .nan
_t_p_t1_std: .nan
_table_column: ''
comment: ''
compound: ''
compound_s_b_m_l_species_id: ''
description: ''
enyzme: ''
enyzme_s_b_m_l_parameter_id: ''
enyzme_s_b_m_l_species_id: ''
gene: ''
geometric_mean: .nan
i_d: ''
identifiers_obo_chebi: ''
max: .nan
mean: .nan
median: .nan
min: .nan
miriam_annotations: ''
name: ''
position_x: .nan
position_y: .nan
prob_dist: ''
protein: ''
protein_s_b_m_l_species_id: ''
quantity_name: ''
quantity_type: ''
reaction: ''
reaction_s_b_m_l_reaction_id: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_parameter_id: ''
scale: ''
sign: '0'
std: .nan
symbol: ''
time: 0.5
time_point: ''
type: ''
unit: ''
value: .nan
Reaction:
- __id: 9
__type: Reaction
build_enzyme: false
build_enzyme_production: false
build_reaction: false
comment: ''
description: ''
enzyme: ''
enzyme_s_b_m_l_parameter_id: ''
enzyme_s_b_m_l_species_id: ''
flux: .nan
gene: ''
gene_symbol: ''
i_d: R1
identifiers: ''
identifiers_ec_code: ''
identifiers_kegg_reaction: R00658
identifiers_obo_sbo: ''
is_complete: false
is_exchange_reaction: false
is_in_equilibrium: false
is_non_enzymatic: false
is_reversible: false
kinetic_law: ''
kinetic_law_formula: ''
kinetic_law_name: ''
location: ''
miriam_annotations: ''
model: ''
modifier: ''
name: ''
name_for_plots: ''
operon: ''
pathway: ''
position_x: .nan
position_y: .nan
reaction_formula: ATP + F6P <=> ADP + F16P
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator: ''
s_b_m_l_fbc_gene_association: ''
s_b_m_l_fbc_lower_bound: ''
s_b_m_l_fbc_upper_bound: ''
s_b_m_l_reaction_id: r1
s_b_o_term: ''
subreaction_of: ''
symbol: ''
type: ''
- __id: 10
__type: Reaction
build_enzyme: false
build_enzyme_production: false
build_reaction: false
comment: ''
description: ''
enzyme: ''
enzyme_s_b_m_l_parameter_id: ''
enzyme_s_b_m_l_species_id: ''
flux: .nan
gene: ''
gene_symbol: ''
i_d: R2
identifiers: ''
identifiers_ec_code: ''
identifiers_kegg_reaction: R01015
identifiers_obo_sbo: ''
is_complete: false
is_exchange_reaction: false
is_in_equilibrium: false
is_non_enzymatic: false
is_reversible: false
kinetic_law: ''
kinetic_law_formula: ''
kinetic_law_name: ''
location: ''
miriam_annotations: ''
model: ''
modifier: ''
name: ''
name_for_plots: ''
operon: ''
pathway: ''
position_x: .nan
position_y: .nan
reaction_formula: F16P + H2O <=> F6P + Pi
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator: ''
s_b_m_l_fbc_gene_association: ''
s_b_m_l_fbc_lower_bound: ''
s_b_m_l_fbc_upper_bound: ''
s_b_m_l_reaction_id: r2
s_b_o_term: ''
subreaction_of: ''
symbol: ''
type: ''
- __id: 11
__type: Reaction
build_enzyme: false
build_enzyme_production: false
build_reaction: false
comment: ''
description: ''
enzyme: ''
enzyme_s_b_m_l_parameter_id: ''
enzyme_s_b_m_l_species_id: ''
flux: .nan
gene: ''
gene_symbol: ''
i_d: '% That''s a comment.'
identifiers: ''
identifiers_ec_code: ''
identifiers_kegg_reaction: ''
identifiers_obo_sbo: ''
is_complete: false
is_exchange_reaction: false
is_in_equilibrium: false
is_non_enzymatic: false
is_reversible: false
kinetic_law: ''
kinetic_law_formula: ''
kinetic_law_name: ''
location: ''
miriam_annotations: ''
model: ''
modifier: ''
name: ''
name_for_plots: ''
operon: ''
pathway: ''
position_x: .nan
position_y: .nan
reaction_formula: ''
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator: ''
s_b_m_l_fbc_gene_association: ''
s_b_m_l_fbc_lower_bound: ''
s_b_m_l_fbc_upper_bound: ''
s_b_m_l_reaction_id: ''
s_b_o_term: ''
subreaction_of: ''
symbol: ''
type: ''
ReactionStoichiometry: []
Regulator: []
Relation: []
Relationship: []
SparseMatrix: []
SparseMatrixColumn: []
SparseMatrixOrdered: []
SparseMatrixRow: []
StoichiometricMatrix: []
_classMetadata:
Compartment:
class: Compartment
name: Compartment
Compound:
class: Compound
description: Ex 4 - Compound
name: Compound
Definition:
class: Definition
name: Definition
Enzyme:
class: Enzyme
name: Enzyme
FbcObjective:
class: FbcObjective
name: FbcObjective
Gene:
class: Gene
name: Gene
Layout:
class: Layout
name: Layout
Measurement:
class: Measurement
name: Measurement
PbConfig:
class: PbConfig
name: PbConfig
Position:
class: Position
name: Position
Protein:
class: Protein
name: Protein
Quantity:
class: Quantity
description: Ex 6 - Quantity
name: Quantity
QuantityInfo:
class: QuantityInfo
name: QuantityInfo
QuantityMatrix:
class: QuantityMatrix
description: Ex 16 - Metabolomics
name: QuantityMatrix
Reaction:
class: Reaction
description: Ex 3 - Reaction
name: Reaction
ReactionStoichiometry:
class: ReactionStoichiometry
name: ReactionStoichiometry
Regulator:
class: Regulator
name: Regulator
Relation:
class: Relation
name: Relation
Relationship:
class: Relationship
name: Relationship
SparseMatrix:
class: SparseMatrix
name: SparseMatrix
SparseMatrixColumn:
class: SparseMatrixColumn
name: SparseMatrixColumn
SparseMatrixOrdered:
class: SparseMatrixOrdered
name: SparseMatrixOrdered
SparseMatrixRow:
class: SparseMatrixRow
name: SparseMatrixRow
StoichiometricMatrix:
class: StoichiometricMatrix
name: StoichiometricMatrix
rxnconContingencyList:
class: rxnconContingencyList
name: rxnconContingencyList
rxnconReactionList:
class: rxnconReactionList
name: rxnconReactionList
_documentMetadata:
date: '2020-07-18 12:17:39'
objTablesVersion: 1.0.5
schema: SBtab
rxnconContingencyList: []
rxnconReactionList: []