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EnzymeML V2

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

The EnzymeMLDocument is the root object that serves as a container for all components of an enzymatic experiment. It includes essential metadata about the document itself, such as its title and creation/modification dates, as well as references to related publications and databases. Additionally, it contains comprehensive information about the experimental setup, including reaction vessels, proteins, complexes, small molecules, reactions, measurements, equations, and parameters.

name* string

  • Title of the EnzymeML Document.

created string

  • Date the EnzymeML Document was created.

modified string

  • Date the EnzymeML Document was modified.

creators list[Creator]

  • Contains descriptions of all authors that are part of the experiment.

vessels list[Vessel]

  • Contains descriptions of all vessels that are part of the experiment.

proteins list[Protein]

  • Contains descriptions of all proteins that are part of the experiment that may be referenced in reactions, measurements, and equations.

complexes list[Complex]

  • Contains descriptions of all complexes that are part of the experiment that may be referenced in reactions, measurements, and equations.

small_molecules list[SmallMolecule]

  • Contains descriptions of all reactants that are part of the experiment that may be referenced in reactions, measurements, and equations.

reactions list[Reaction]

  • Contains descriptions of all reactions that are part of the experiment.

measurements list[Measurement]

  • Contains descriptions of all measurements that are part of the experiment.

equations list[Equation]

  • Contains descriptions of all equations that are part of the experiment.

parameters list[Parameter]

  • Contains descriptions of all parameters that are part of the experiment and may be used in equations.

references list[string]

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

Creator

The Creator object represents an individual author or contributor who has participated in creating or modifying the EnzymeML Document. It captures essential personal information such as their name and contact details, allowing proper attribution and enabling communication with the document's creators.

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

The Vessel object represents containers used to conduct experiments, such as reaction vessels, microplates, or bioreactors. It captures key properties like volume and whether the volume remains constant during the experiment.

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 is True.

  • Default: true

Protein

The Protein object represents enzymes and other proteins involved in the experiment.

id* string

  • Identifier of the protein, such as a UniProt ID, or a custom identifier.

name* string

  • Name of the protein.

constant* boolean

  • Whether the concentration of the protein is constant through the experiment or not. Default is True.

  • Default: true

sequence string

  • Amino acid sequence of the protein

vessel_id string

  • Identifier of the vessel this protein has been applied to.

ecnumber string

  • EC number of the protein.

organism string

  • Expression host organism of the protein.

organism_tax_id string

  • Taxonomy identifier of the expression host.

references list[string]

  • List of references to publications, database entries, etc. that describe or reference the protein.

Complex

The Complex object allows the grouping of multiple species using their . This enables the representation of protein-small molecule complexes (e.g., enzyme-substrate complexes) as well as buffer or solvent mixtures (combinations of SmallMolecule species).

id* string

  • Unique identifier of the complex.

name* string

  • Name of the complex.

constant* boolean

  • Whether the concentration of the complex is constant through the experiment or not. Default is False.

  • 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

The SmallMolecule object represents small chemical compounds that participate in the experiment as substrates, products, or modifiers. It captures key molecular identifiers like SMILES and InChI.

id* string

  • Identifier of the small molecule, such as a Pubchem ID, ChEBI ID, or a custom identifier.

name* string

  • Name of the small molecule.

constant* boolean

  • Whether the concentration of the small molecule is constant through the experiment or not. Default is False.

  • Default: false

vessel_id string

  • 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 small molecule.

inchi string

  • International Chemical Identifier (InChI) encoding of the small molecule.

inchikey string

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

references list[string]

  • List of references to publications, database entries, etc. that describe or reference the small molecule.

Reaction

The Reaction object represents a chemical or enzymatic reaction and holds the different species and modifiers that are part of the reaction.

id* string

  • Unique identifier of the reaction.

name* string

  • Name of the reaction.

reversible* boolean

  • Whether the reaction is reversible or irreversible. Default is False.

  • 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 object and describes a species (SmallMolecule, Protein, Complex) participating in the reaction. The stochiometry is of the species is specified in the field, whereas negative values indicate that the species is a reactant and positive values indicate that the species is a product of the reaction.

species_id* string

  • Internal identifier to either a protein or reactant defined in the EnzymeML Document.

stoichiometry* float

  • Float number representing the associated stoichiometry. Negative values indicate that the species is a reactant and positive values indicate that the species is a product of the reaction.

Equation

The Equation object describes a mathematical equation used to model parts of a reaction system.

species_id* string

  • Identifier of a defined species (SmallMolecule, Protein, Complex). Represents the left hand side of the equation.

equation* string

  • Mathematical expression of the equation. Represents the right hand side of the equation.

equation_type* EquationType

  • Type of the 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. Variables can represent species concentrations, time, or other quantities that appear in mathematical expressions. Each variable must have a unique identifier, name, and symbol that is used in equations.

id* string

  • Identifier of the variable.

name* string

  • Name of the variable.

symbol* string

  • Equation symbol of the variable.

Parameter

This object describes parameters used in kinetic models, including estimated values, bounds, and associated uncertainties. Parameters can represent rate constants, binding constants, or other numerical values that appear in rate equations or other mathematical expressions.

id* string

  • Identifier of the parameter.

name* string

  • Name of the parameter.

symbol* string

  • Equation 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_bound float

  • Upper bound for the parameter value that was used for the parameter estimation

lower_bound float

  • Lower bound for the parameter value that was used for the parameter estimation

stderr float

  • Standard error of the estimated parameter.

constant boolean

  • Specifies if this parameter is constant. Default is True.

  • Default: true

Measurement

This object describes a single measurement, which includes time course data of any type defined in DataTypes. It contains initial concentrations and measurement data for all species involved in the experiment. Multiple measurements can be grouped together using the group_id field to indicate they are part of the same experimental series.

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 refers to a Protein, Complex, or SmallMolecule.

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 (Protein, Complex, SmallMolecule). It contains time course data for that species, including the initial amount, prepared amount, and measured data points over time. Endpoint data is treated as a time course data point with only one data point.

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 array.

data_unit* UnitDefinition

  • SI unit of the data that was measured.

data_type* DataTypes

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

prepared float

  • Amount of the the species before starting the measurement. This field can be used for specifying the prepared amount of a species in the reaction mix. Not to be confused with , specifying the concentration of a species at the first data point from the array.

data list[float]

  • Data that was measured.

time list[float]

  • Corresponding time points of the .

time_unit UnitDefinition

  • Unit of the time points of the .

is_simulated* boolean

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

  • 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 absorbance
CONCENTRATION concentration
CONVERSION conversion
FLUORESCENCE fluorescence
PEAK_AREA peakarea
TRANSMITTANCE transmittance

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