id: enzml name: EnzymeML-V2 title: EnzymeML V2 prefixes: OBO: http://purl.obolibrary.org/obo/ schema: https://schema.org/ default_prefix: enzml default_range: string imports: - linkml:types classes: EnzymeMLDocument: description: 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. tree_root: true slot_usage: version: pattern: '"^(\d+)\.\d+$"' attributes: name: description: Title of the EnzymeML Document. slot_uri: schema:title required: true version: description: The version of the EnzymeML Document. required: true description: description: Description of the EnzymeML Document. created: description: Date the EnzymeML Document was created. slot_uri: schema:dateCreated modified: description: Date the EnzymeML Document was modified. slot_uri: schema:dateModified creators: description: Contains descriptions of all authors that are part of the experiment. slot_uri: schema:creator required: true range: Creator multivalued: true vessels: description: Contains descriptions of all vessels that are part of the experiment. required: true range: Vessel multivalued: true proteins: description: Contains descriptions of all proteins that are part of the experiment that may be referenced in reactions, measurements, and equations. range: Protein multivalued: true complexes: description: Contains descriptions of all complexes that are part of the experiment that may be referenced in reactions, measurements, and equations. range: Complex multivalued: true small_molecules: description: Contains descriptions of all reactants that are part of the experiment that may be referenced in reactions, measurements, and equations. range: SmallMolecule multivalued: true reactions: description: Contains descriptions of all reactions that are part of the experiment. range: Reaction multivalued: true measurements: description: Contains descriptions of all measurements that are part of the experiment. range: Measurement multivalued: true equations: description: Contains descriptions of all equations that are part of the experiment. range: Equation multivalued: true parameters: description: Contains descriptions of all parameters that are part of the experiment and may be used in equations. range: Parameter multivalued: true references: description: Contains references to publications, databases, and arbitrary links to the web. slot_uri: schema:citation identifier: true multivalued: true Creator: description: 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. class_uri: schema:person attributes: given_name: description: Given name of the author or contributor. slot_uri: schema:givenName required: true family_name: description: Family name of the author or contributor. slot_uri: schema:familyName required: true mail: description: Email address of the author or contributor. slot_uri: schema:email required: true Vessel: description: 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. class_uri: OBO:OBI_0400081 attributes: id: description: Unique identifier of the vessel. slot_uri: schema:identifier identifier: true required: true name: description: Name of the used vessel. slot_uri: schema:name required: true volume: description: Volumetric value of the vessel. slot_uri: OBO:OBI_0002139 required: true range: float unit: description: Volumetric unit of the vessel. required: true range: UnitDefinition constant: description: Whether the volume of the vessel is constant or not. Default is True. required: true range: boolean Protein: description: The Protein object represents enzymes and other proteins involved in the experiment. class_uri: OBO:PR_000000001 attributes: id: description: Identifier of the protein, such as a UniProt ID, or a custom identifier. slot_uri: schema:identifier identifier: true required: true name: description: Name of the protein. slot_uri: schema:name required: true constant: description: Whether the concentration of the protein is constant through the experiment or not. Default is True. required: true range: boolean sequence: description: Amino acid sequence of the protein slot_uri: OBO:GSSO_007262 vessel_id: description: Identifier of the vessel this protein has been applied to. slot_uri: schema:identifier identifier: true ecnumber: description: EC number of the protein. organism: description: Expression host organism of the protein. slot_uri: OBO:OBI_0100026 organism_tax_id: description: Taxonomy identifier of the expression host. identifier: true references: description: List of references to publications, database entries, etc. that describe or reference the protein. slot_uri: schema:citation identifier: true multivalued: true Complex: description: 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). attributes: id: description: Unique identifier of the complex. slot_uri: schema:identifier identifier: true required: true name: description: Name of the complex. slot_uri: schema:name required: true constant: description: Whether the concentration of the complex is constant through the experiment or not. Default is False. required: true range: boolean vessel_id: description: Unique identifier of the vessel this complex has been used in. slot_uri: schema:identifier identifier: true participants: description: Array of IDs the complex contains identifier: true multivalued: true SmallMolecule: description: 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. attributes: id: description: Identifier of the small molecule, such as a Pubchem ID, ChEBI ID, or a custom identifier. slot_uri: schema:identifier identifier: true required: true name: description: Name of the small molecule. slot_uri: schema:name required: true constant: description: Whether the concentration of the small molecule is constant through the experiment or not. Default is False. required: true range: boolean vessel_id: description: Identifier of the vessel this small molecule has been used in. slot_uri: schema:identifier identifier: true canonical_smiles: description: Canonical Simplified Molecular-Input Line-Entry System (SMILES) encoding of the small molecule. inchi: description: International Chemical Identifier (InChI) encoding of the small molecule. inchikey: description: Hashed International Chemical Identifier (InChIKey) encoding of the small molecule. synonymous_names: description: List of synonymous names for the small molecule. multivalued: true references: description: List of references to publications, database entries, etc. that describe or reference the small molecule. slot_uri: schema:citation identifier: true multivalued: true Reaction: description: The Reaction object represents a chemical or enzymatic reaction and holds the different species and modifiers that are part of the reaction. attributes: id: description: Unique identifier of the reaction. slot_uri: schema:identifier identifier: true required: true name: description: Name of the reaction. required: true reversible: description: Whether the reaction is reversible or irreversible. Default is False. required: true range: boolean kinetic_law: description: Mathematical expression of the reaction. range: Equation reactants: description: List of reactants that are part of the reaction. range: ReactionElement multivalued: true products: description: List of products that are part of the reaction. range: ReactionElement multivalued: true modifiers: description: List of reaction elements that are not part of the reaction but influence it. range: ModifierElement multivalued: true ReactionElement: description: 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. attributes: species_id: description: Internal identifier to either a protein or reactant defined in the EnzymeML Document. slot_uri: schema:identifier identifier: true required: true stoichiometry: description: Float number representing the associated stoichiometry. required: true range: float ModifierElement: description: The ModifierElement object represents a species that is not part of the reaction but influences it. attributes: species_id: description: Internal identifier to either a protein or reactant defined in the EnzymeML Document. slot_uri: schema:identifier identifier: true required: true role: description: Role of the modifier in the reaction. required: true range: ModifierRole Equation: description: The Equation object describes a mathematical equation used to model parts of a reaction system. attributes: species_id: description: Identifier of a defined species (SmallMolecule, Protein, Complex). Represents the left hand side of the equation. slot_uri: schema:identifier identifier: true required: true equation: description: Mathematical expression of the equation. Represents the right hand side of the equation. required: true equation_type: description: Type of the equation. required: true range: EquationType variables: description: List of variables that are part of the equation range: Variable multivalued: true Variable: description: 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. attributes: id: description: Identifier of the variable. slot_uri: schema:identifier identifier: true required: true name: description: Name of the variable. required: true symbol: description: Equation symbol of the variable. required: true Parameter: description: 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. attributes: id: description: Identifier of the parameter. slot_uri: schema:identifier identifier: true required: true name: description: Name of the parameter. required: true symbol: description: Equation symbol of the parameter. required: true value: description: Numerical value of the estimated parameter. range: float unit: description: Unit of the estimated parameter. range: UnitDefinition initial_value: description: Initial value that was used for the parameter estimation. range: float upper_bound: description: Upper bound for the parameter value that was used for the parameter estimation range: float lower_bound: description: Lower bound for the parameter value that was used for the parameter estimation range: float fit: description: Whether this parameter should be varied or not in the context of an optimization. range: boolean stderr: description: Standard error of the estimated parameter. range: float constant: description: Specifies if this parameter is constant. Default is True. range: boolean Measurement: description: 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. attributes: id: description: Unique identifier of the measurement. slot_uri: schema:identifier identifier: true required: true name: description: Name of the measurement required: true species_data: description: Measurement data of all species that were part of the measurement. A species refers to a Protein, Complex, or SmallMolecule. range: MeasurementData multivalued: true group_id: description: User-defined group ID to signal relationships between measurements. identifier: true ph: description: pH value of the measurement. range: float minimum_value: 0 maximum_value: 14 temperature: description: Temperature of the measurement. range: float temperature_unit: description: Unit of the temperature of the measurement. range: UnitDefinition MeasurementData: description: 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. attributes: species_id: description: The identifier for the described reactant. identifier: true required: true prepared: description: 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. range: float initial: description: Initial amount of the measurement data. This must be the same as the first data point in the array. range: float data_unit: description: SI unit of the data that was measured. range: UnitDefinition data: description: Data that was measured. range: float multivalued: true time: description: Corresponding time points of the . range: float multivalued: true time_unit: description: Unit of the time points of the . range: UnitDefinition data_type: description: Type of data that was measured (e.g. concentration, absorbance, etc.) range: DataTypes is_simulated: description: Whether or not the data has been generated by simulation. Default is False. range: boolean UnitDefinition: description: Represents a unit definition that is based on the SI unit system. attributes: id: description: Unique identifier of the unit definition. name: description: Common name of the unit definition. base_units: description: Base units that define the unit. range: BaseUnit multivalued: true BaseUnit: description: Represents a base unit in the unit definition. attributes: kind: description: Kind of the base unit (e.g., meter, kilogram, second). required: true range: UnitType exponent: description: Exponent of the base unit in the unit definition. required: true range: integer multiplier: description: Multiplier of the base unit in the unit definition. range: float scale: description: Scale of the base unit in the unit definition. range: float enums: ModifierRole: permissible_values: ACTIVATOR: meaning: activator description: activator ADDITIVE: meaning: additive description: additive BIOCATALYST: meaning: biocatalyst description: biocatalyst BUFFER: meaning: buffer description: buffer CATALYST: meaning: catalyst description: catalyst INHIBITOR: meaning: inhibitor description: inhibitor SOLVENT: meaning: solvent description: solvent EquationType: permissible_values: ASSIGNMENT: meaning: assignment description: assignment INITIAL_ASSIGNMENT: meaning: initialAssignment description: initialAssignment ODE: meaning: ode description: ode RATE_LAW: meaning: rateLaw description: rateLaw DataTypes: permissible_values: ABSORBANCE: meaning: absorbance description: absorbance AMOUNT: meaning: amount description: amount CONCENTRATION: meaning: concentration description: concentration CONVERSION: meaning: conversion description: conversion FLUORESCENCE: meaning: fluorescence description: fluorescence PEAK_AREA: meaning: peakarea description: peakarea TRANSMITTANCE: meaning: transmittance description: transmittance TURNOVER: meaning: turnover description: turnover YIELD: meaning: yield description: yield UnitType: permissible_values: AMPERE: meaning: ampere description: ampere AVOGADRO: meaning: avogadro description: avogadro BECQUEREL: meaning: becquerel description: becquerel CANDELA: meaning: candela description: candela CELSIUS: meaning: celsius description: celsius COULOMB: meaning: coulomb description: coulomb DIMENSIONLESS: meaning: dimensionless description: dimensionless FARAD: meaning: farad description: farad GRAM: meaning: gram description: gram GRAY: meaning: gray description: gray HENRY: meaning: henry description: henry HERTZ: meaning: hertz description: hertz ITEM: meaning: item description: item JOULE: meaning: joule description: joule KATAL: meaning: katal description: katal KELVIN: meaning: kelvin description: kelvin KILOGRAM: meaning: kilogram description: kilogram LITRE: meaning: litre description: litre LUMEN: meaning: lumen description: lumen LUX: meaning: lux description: lux METRE: meaning: metre description: metre MOLE: meaning: mole description: mole NEWTON: meaning: newton description: newton OHM: meaning: ohm description: ohm PASCAL: meaning: pascal description: pascal RADIAN: meaning: radian description: radian SECOND: meaning: second description: second SIEMENS: meaning: siemens description: siemens SIEVERT: meaning: sievert description: sievert STERADIAN: meaning: steradian description: steradian TESLA: meaning: tesla description: tesla VOLT: meaning: volt description: volt WATT: meaning: watt description: watt WEBER: meaning: weber description: weber