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EnzymeML

This page provides comprehensive information about the structure and components of the data model, including detailed descriptions of the types and their properties, information on enumerations, and an overview of the ontologies used and their associated prefixes. Below, you will find a graph that visually represents the overall structure of the data model.

Graph 
flowchart TB
    enzymemldocument(EnzymeMLDocument)
    creator(Creator)
    vessel(Vessel)
    protein(Protein)
    complex(Complex)
    smallmolecule(SmallMolecule)
    reaction(Reaction)
    reactionelement(ReactionElement)
    equation(Equation)
    variable(Variable)
    parameter(Parameter)
    measurement(Measurement)
    measurementdata(MeasurementData)
    unitdefinition(UnitDefinition)
    baseunit(BaseUnit)
    equationtype(EquationType)
    datatypes(DataTypes)
    unittype(UnitType)
    enzymemldocument(EnzymeMLDocument) --> creator(Creator)
    enzymemldocument(EnzymeMLDocument) --> vessel(Vessel)
    enzymemldocument(EnzymeMLDocument) --> protein(Protein)
    enzymemldocument(EnzymeMLDocument) --> complex(Complex)
    enzymemldocument(EnzymeMLDocument) --> smallmolecule(SmallMolecule)
    enzymemldocument(EnzymeMLDocument) --> reaction(Reaction)
    enzymemldocument(EnzymeMLDocument) --> measurement(Measurement)
    enzymemldocument(EnzymeMLDocument) --> equation(Equation)
    enzymemldocument(EnzymeMLDocument) --> parameter(Parameter)
    vessel(Vessel) --> unitdefinition(UnitDefinition)
    reaction(Reaction) --> equation(Equation)
    reaction(Reaction) --> reactionelement(ReactionElement)
    equation(Equation) --> equationtype(EquationType)
    equation(Equation) --> variable(Variable)
    parameter(Parameter) --> unitdefinition(UnitDefinition)
    measurement(Measurement) --> measurementdata(MeasurementData)
    measurement(Measurement) --> unitdefinition(UnitDefinition)
    measurementdata(MeasurementData) --> unitdefinition(UnitDefinition)
    measurementdata(MeasurementData) --> datatypes(DataTypes)
    measurementdata(MeasurementData) --> unitdefinition(UnitDefinition)
    unitdefinition(UnitDefinition) --> baseunit(BaseUnit)
    baseunit(BaseUnit) --> unittype(UnitType)

    click enzymemldocument "#enzymemldocument" "Go to EnzymeMLDocument"
    click creator "#creator" "Go to Creator"
    click vessel "#vessel" "Go to Vessel"
    click protein "#protein" "Go to Protein"
    click complex "#complex" "Go to Complex"
    click smallmolecule "#smallmolecule" "Go to SmallMolecule"
    click reaction "#reaction" "Go to Reaction"
    click reactionelement "#reactionelement" "Go to ReactionElement"
    click equation "#equation" "Go to Equation"
    click variable "#variable" "Go to Variable"
    click parameter "#parameter" "Go to Parameter"
    click measurement "#measurement" "Go to Measurement"
    click measurementdata "#measurementdata" "Go to MeasurementData"
    click unitdefinition "#unitdefinition" "Go to UnitDefinition"
    click baseunit "#baseunit" "Go to BaseUnit"
    click equationtype "#equationtype" "Go to EquationType"
    click datatypes "#datatypes" "Go to DataTypes"
    click unittype "#unittype" "Go to UnitType"

Ontologies

Types

EnzymeMLDocument

This is the root object that composes all objects found in an EnzymeML document. It also includes general metadata such as the name of the document, when it was created/modified, and references to publications, databases, and arbitrary links to the web.

name* string

  • Title of the EnzymeML Document.

references list[string]

  • Contains references to publications, databases, and arbitrary links to the web.

created string

  • Date the EnzymeML document was created.

modified string

  • Date the EnzymeML document was modified.

creators list[Creator]

  • Contains all authors that are part of the experiment.

vessels list[Vessel]

  • Contains all vessels that are part of the experiment.

proteins list[Protein]

  • Contains all proteins that are part of the experiment.

complexes list[Complex]

  • Contains all complexes that are part of the experiment.

small_molecules list[SmallMolecule]

  • Contains all reactants that are part of the experiment.

reactions list[Reaction]

  • Dictionary mapping from reaction IDs to reaction-describing objects.

measurements list[Measurement]

  • Contains measurements that describe outcomes of an experiment.

equations list[Equation]

  • Contains ordinary differential equations that describe the kinetic model.

parameters list[Parameter]

  • List of parameters that are part of the equation

Creator

The creator object contains all information about authors that contributed to the resulting document.

given_name* string

  • Given name of the author or contributor.

family_name* string

  • Family name of the author or contributor.

mail* string

  • Email address of the author or contributor.

Vessel

This object describes vessels in which the experiment has been carried out. These can include any type of vessel used in biocatalytic experiments.

id* string

  • Unique identifier of the vessel.

name* string

  • Name of the used vessel.

volume* float

  • Volumetric value of the vessel.

unit* UnitDefinition

  • Volumetric unit of the vessel.

constant* boolean

  • Whether the volume of the vessel is constant or not.

  • Default: true

Protein

This object describes the proteins that were used or formed throughout the experiment.

id* string

  • Unique internal identifier of the protein.
  • Schema: identifier

name* string

constant* boolean

  • Default: false

sequence string

  • Amino acid sequence of the protein

vessel_id string

  • Unique identifier of the vessel this protein has been used in.

ecnumber string

  • EC number of the protein.

organism string

  • Organism the protein was expressed in.

organism_tax_id string

  • Taxonomy identifier of the expression host.

references list[string]

  • Array of references to publications, database entries, etc. that describe the protein.

Complex

This object describes complexes made of reactants and/or proteins that were used or produced in the course of the experiment.

id* string

  • Unique identifier of the complex.

name* string

constant* boolean

  • Default: false

vessel_id string

  • Unique identifier of the vessel this complex has been used in.

participants list[string]

  • Array of IDs the complex contains

SmallMolecule

This object describes the reactants that were used or produced in the course of the experiment.

id* string

  • Unique identifier of the small molecule.

name* string

constant* boolean

  • Default: false

vessel_id string

  • Unique identifier of the vessel this small molecule has been used in.

canonical_smiles string

  • Canonical Simplified Molecular-Input Line-Entry System (SMILES) encoding of the reactant.

inchi string

  • International Chemical Identifier (InChI) encoding of the reactant.

inchikey string

  • Hashed International Chemical Identifier (InChIKey) encoding of the reactant.

references list[string]

  • Array of references to publications, database entries, etc. that describe the reactant.

Reaction

This object describes a chemical or enzymatic reaction that was investigated in the course of the experiment. All species used within this object need to be part of the data model.

id* string

  • Unique identifier of the reaction.

name* string

  • Name of the reaction.

reversible* boolean

  • Whether the reaction is reversible or irreversible

  • Default: false

kinetic_law Equation

  • Mathematical expression of the reaction.

species list[ReactionElement]

  • List of reaction elements that are part of the reaction.

modifiers list[string]

  • List of reaction elements that are not part of the reaction but influence it.

ReactionElement

This object is part of the Reaction object and describes either an educt, product or modifier. The latter includes buffers, counter-ions as well as proteins/enzymes.

species_id* string

  • Internal identifier to either a protein or reactant defined in the EnzymeMLDocument.
  • Schema: identifier

stoichiometry* float

  • Float number representing the associated stoichiometry.

Equation

This object describes an equation that can be used to model the kinetics of a reaction. There are different types of equations that can be used to model the kinetics of a reaction. The equation can be an ordinary differential equation, a rate law or assignment rule.

equation* string

  • Mathematical expression of the equation.

equation_type* EquationType

  • Type of the equation.

species_id string

  • Internal identifier to a species defined in the EnzymeMLDocument, given it is a rate equation.

variables list[Variable]

  • List of variables that are part of the equation

Variable

This object describes a variable that is part of an equation.

id* string

  • Unique identifier of the variable.

name* string

  • Name of the variable.

symbol* string

  • Symbol of the variable.

Parameter

This object describes the parameters of the kinetic model and can include all estimated values.

id* string

  • Unique identifier of the parameter.

name* string

  • Name of the parameter.

symbol* string

  • Symbol of the parameter.

value float

  • Numerical value of the estimated parameter.

unit UnitDefinition

  • Unit of the estimated parameter.

initial_value float

  • Initial value that was used for the parameter estimation.

upper float

  • Upper bound of the estimated parameter.

lower float

  • Lower bound of the estimated parameter.

stderr float

  • Standard error of the estimated parameter.

constant boolean

  • Specifies if this parameter is constant

  • Default: true

Measurement

This object describes the result of a measurement, which includes time course data of any type defined in DataTypes. It includes initial concentrations of all species used in a single measurement.

id* string

  • Unique identifier of the measurement.

name* string

  • Name of the measurement

species_data list[MeasurementData]

  • Measurement data of all species that were part of the measurement. A species can refer to a protein, complex, or small molecule.

group_id string

  • User-defined group ID to signal relationships between measurements.

ph float

  • PH value of the measurement.
  • Minimum: 0- Maximum: 14

temperature float

  • Temperature of the measurement.

temperature_unit UnitDefinition

  • Unit of the temperature of the measurement.

MeasurementData

This object describes a single entity of a measurement, which corresponds to one species. It also holds replicates that contain time course data.

species_id* string

  • The identifier for the described reactant.

initial* float

  • Initial amount of the measurement data. This must be the same as the first data point in the

data_unit* UnitDefinition

  • SI unit of the data that was measured.

data_type* DataTypes

  • Type of data that was measured (e.g. concentration)

prepared float

  • Amount of the reactant before the measurement. This field should be used for specifying the prepared amount of a species in the reaction mix. Not to be confused with

data list[float]

  • Data that was measured.

time list[float]

  • Time steps of the replicate.

time_unit UnitDefinition

  • Time unit of the replicate.

is_simulated* boolean

  • Whether or not the data has been generated by simulation.

  • Default: false

UnitDefinition

Represents a unit definition that is based on the SI unit system.

id string

  • Unique identifier of the unit definition.

name string

  • Common name of the unit definition.

base_units list[BaseUnit]

  • Base units that define the unit.

BaseUnit

Represents a base unit in the unit definition.

kind* UnitType

  • Kind of the base unit (e.g., meter, kilogram, second).

exponent* integer

  • Exponent of the base unit in the unit definition.

multiplier float

  • Multiplier of the base unit in the unit definition.

scale float

  • Scale of the base unit in the unit definition.

Enumerations

EquationType

Alias Value
ASSIGNMENT assignment
INITIAL_ASSIGNMENT initialAssignment
ODE ode
RATE_LAW rateLaw

DataTypes

Alias Value
ABSORBANCE http://purl.allotrope.org/ontologies/quality#AFQ_0000061
CONCENTRATION http://purl.obolibrary.org/obo/PATO_0000033
CONVERSION http://purl.allotrope.org/ontologies/quality#AFQ_0000226
FLUORESCENCE http://purl.obolibrary.org/obo/PATO_0000018
PEAK_AREA http://purl.allotrope.org/ontologies/result#AFR_0001073
TRANSMITTANCE http://purl.allotrope.org/ontologies/result#AFR_0002261

UnitType

Alias Value
AMPERE ampere
AVOGADRO avogadro
BECQUEREL becquerel
CANDELA candela
CELSIUS celsius
COULOMB coulomb
DIMENSIONLESS dimensionless
FARAD farad
GRAM gram
GRAY gray
HENRY henry
HERTZ hertz
ITEM item
JOULE joule
KATAL katal
KELVIN kelvin
KILOGRAM kilogram
LITRE litre
LUMEN lumen
LUX lux
METRE metre
MOLE mole
NEWTON newton
OHM ohm
PASCAL pascal
RADIAN radian
SECOND second
SIEMENS siemens
SIEVERT sievert
STERADIAN steradian
TESLA tesla
VOLT volt
WATT watt
WEBER weber