EnzymeMlDocumentShape
type: NodeShape
target class: EnzymeMlDocument
property:
  path: version
  datatype: string
  min count: 1
  max count: 1
  description: The version of the EnzymeML Document.
property:
  path: description
  datatype: string
  min count: 0
  max count: 1
  description: Description of the EnzymeML Document.
property:
  or:
    path: name
  or:
    path: title
  datatype: string
  min count: 1
  max count: 1
  description: Title of the EnzymeML Document.
property:
  or:
    path: created
  or:
    path: dateCreated
  datatype: string
  min count: 0
  max count: 1
  description: Date the EnzymeML Document was created.
property:
  or:
    path: modified
  or:
    path: dateModified
  datatype: string
  min count: 0
  max count: 1
  description: Date the EnzymeML Document was modified.
property:
  or:
    path: creators
  or:
    path: creator
  node: CreatorShape
  min count: 1
  description: Contains descriptions of all authors that are part of the experiment.
property:
  path: vessels
  node: VesselShape
  min count: 1
  description: Contains descriptions of all vessels that are part of the experiment.
property:
  path: proteins
  node: ProteinShape
  min count: 0
  description: Contains descriptions of all proteins that are part of the experiment that may be referenced in reactions, measurements, and equations.
property:
  path: complexes
  node: ComplexShape
  min count: 0
  description: Contains descriptions of all complexes that are part of the experiment that may be referenced in reactions, measurements, and equations.
property:
  path: small molecules
  node: SmallMoleculeShape
  min count: 0
  description: Contains descriptions of all reactants that are part of the experiment that may be referenced in reactions, measurements, and equations.
property:
  path: reactions
  node: ReactionShape
  min count: 0
  description: Contains descriptions of all reactions that are part of the experiment.
property:
  path: measurements
  node: MeasurementShape
  min count: 0
  description: Contains descriptions of all measurements that are part of the experiment.
property:
  path: equations
  node: EquationShape
  min count: 0
  description: Contains descriptions of all equations that are part of the experiment.
property:
  path: parameters
  node: ParameterShape
  min count: 0
  description: Contains descriptions of all parameters that are part of the experiment and may be used in equations.
property:
  or:
    path: references
  or:
    path: citation
  datatype: string
  min count: 0
  description: Contains references to publications, databases, and arbitrary links to the web.

CreatorShape
type: NodeShape
target class: Creator
property:
  or:
    path: given name
  or:
    path: givenName
  datatype: string
  min count: 1
  max count: 1
  description: Given name of the author or contributor.
property:
  or:
    path: family name
  or:
    path: familyName
  datatype: string
  min count: 1
  max count: 1
  description: Family name of the author or contributor.
property:
  or:
    path: mail
  or:
    path: email
  datatype: string
  min count: 1
  max count: 1
  description: Email address of the author or contributor.

VesselShape
type: NodeShape
target class: Vessel
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Unique identifier of the vessel.
property:
  or:
    path: name
  or:
    path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the used vessel.
property:
  or:
    path: volume
  or:
    path: OBI_0002139
  datatype: decimal
  min count: 1
  max count: 1
  description: Volumetric value of the vessel.
property:
  path: unit
  node: UnitDefinitionShape
  min count: 1
  max count: 1
  description: Volumetric unit of the vessel.
property:
  path: constant
  datatype: boolean
  min count: 1
  max count: 1
  description: Whether the volume of the vessel is constant or not. Default is True.

ProteinShape
type: NodeShape
target class: Protein
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Identifier of the protein, such as a UniProt ID, or a custom identifier.
property:
  or:
    path: name
  or:
    path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the protein.
property:
  path: constant
  datatype: boolean
  min count: 1
  max count: 1
  description: Whether the concentration of the protein is constant through the experiment or not. Default is True.
property:
  or:
    path: sequence
  or:
    path: GSSO_007262
  datatype: string
  min count: 0
  max count: 1
  description: Amino acid sequence of the protein
property:
  or:
    path: vessel id
  or:
    path: identifier
  datatype: string
  min count: 0
  max count: 1
  description: Identifier of the vessel this protein has been applied to.
property:
  path: ecnumber
  datatype: string
  min count: 0
  max count: 1
  description: EC number of the protein.
property:
  or:
    path: organism
  or:
    path: OBI_0100026
  datatype: string
  min count: 0
  max count: 1
  description: Expression host organism of the protein.
property:
  path: organism tax id
  datatype: string
  min count: 0
  max count: 1
  description: Taxonomy identifier of the expression host.
property:
  or:
    path: references
  or:
    path: citation
  datatype: string
  min count: 0
  description: List of references to publications, database entries, etc. that describe or reference the protein.

ComplexShape
type: NodeShape
target class: Complex
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Unique identifier of the complex.
property:
  or:
    path: name
  or:
    path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the complex.
property:
  path: constant
  datatype: boolean
  min count: 1
  max count: 1
  description: Whether the concentration of the complex is constant through the experiment or not. Default is False.
property:
  or:
    path: vessel id
  or:
    path: identifier
  datatype: string
  min count: 0
  max count: 1
  description: Unique identifier of the vessel this complex has been used in.
property:
  path: participants
  datatype: string
  min count: 0
  description: Array of IDs the complex contains

SmallMoleculeShape
type: NodeShape
target class: SmallMolecule
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Identifier of the small molecule, such as a Pubchem ID, ChEBI ID, or a custom identifier.
property:
  or:
    path: name
  or:
    path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the small molecule.
property:
  path: constant
  datatype: boolean
  min count: 1
  max count: 1
  description: Whether the concentration of the small molecule is constant through the experiment or not. Default is False.
property:
  or:
    path: vessel id
  or:
    path: identifier
  datatype: string
  min count: 0
  max count: 1
  description: Identifier of the vessel this small molecule has been used in.
property:
  path: canonical smiles
  datatype: string
  min count: 0
  max count: 1
  description: Canonical Simplified Molecular-Input Line-Entry System (SMILES) encoding of the small molecule.
property:
  path: inchi
  datatype: string
  min count: 0
  max count: 1
  description: International Chemical Identifier (InChI) encoding of the small molecule.
property:
  path: inchikey
  datatype: string
  min count: 0
  max count: 1
  description: Hashed International Chemical Identifier (InChIKey) encoding of the small molecule.
property:
  path: synonymous names
  datatype: string
  min count: 0
  description: List of synonymous names for the small molecule.
property:
  or:
    path: references
  or:
    path: citation
  datatype: string
  min count: 0
  description: List of references to publications, database entries, etc. that describe or reference the small molecule.

ReactionShape
type: NodeShape
target class: Reaction
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Unique identifier of the reaction.
property:
  path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the reaction.
property:
  path: reversible
  datatype: boolean
  min count: 1
  max count: 1
  description: Whether the reaction is reversible or irreversible. Default is False.
property:
  path: kinetic law
  node: EquationShape
  min count: 0
  max count: 1
  description: Mathematical expression of the reaction.
property:
  path: reactants
  node: ReactionElementShape
  min count: 0
  description: List of reactants that are part of the reaction.
property:
  path: products
  node: ReactionElementShape
  min count: 0
  description: List of products that are part of the reaction.
property:
  path: modifiers
  node: ModifierElementShape
  min count: 0
  description: List of reaction elements that are not part of the reaction but influence it.

ReactionElementShape
type: NodeShape
target class: ReactionElement
property:
  or:
    path: species id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Internal identifier to either a protein or reactant defined in the EnzymeML Document.
property:
  path: stoichiometry
  datatype: decimal
  min count: 1
  max count: 1
  description: Float number representing the associated stoichiometry.

ModifierElementShape
type: NodeShape
target class: ModifierElement
property:
  or:
    path: species id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Internal identifier to either a protein or reactant defined in the EnzymeML Document.
property:
  path: role
  class: ModifierRole
  min count: 1
  max count: 1
  description: Role of the modifier in the reaction.

EquationShape
type: NodeShape
target class: Equation
property:
  or:
    path: species id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Identifier of a defined species (SmallMolecule, Protein, Complex). Represents the left hand side of the equation.
property:
  path: equation
  datatype: string
  min count: 1
  max count: 1
  description: Mathematical expression of the equation. Represents the right hand side of the equation.
property:
  path: equation type
  class: EquationType
  min count: 1
  max count: 1
  description: Type of the equation.
property:
  path: variables
  node: VariableShape
  min count: 0
  description: List of variables that are part of the equation

VariableShape
type: NodeShape
target class: Variable
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Identifier of the variable.
property:
  path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the variable.
property:
  path: symbol
  datatype: string
  min count: 1
  max count: 1
  description: Equation symbol of the variable.

ParameterShape
type: NodeShape
target class: Parameter
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Identifier of the parameter.
property:
  path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the parameter.
property:
  path: symbol
  datatype: string
  min count: 1
  max count: 1
  description: Equation symbol of the parameter.
property:
  path: value
  datatype: decimal
  min count: 0
  max count: 1
  description: Numerical value of the estimated parameter.
property:
  path: unit
  node: UnitDefinitionShape
  min count: 0
  max count: 1
  description: Unit of the estimated parameter.
property:
  path: initial value
  datatype: decimal
  min count: 0
  max count: 1
  description: Initial value that was used for the parameter estimation.
property:
  path: upper bound
  datatype: decimal
  min count: 0
  max count: 1
  description: Upper bound for the parameter value that was used for the parameter estimation
property:
  path: lower bound
  datatype: decimal
  min count: 0
  max count: 1
  description: Lower bound for the parameter value that was used for the parameter estimation
property:
  path: fit
  datatype: boolean
  min count: 0
  max count: 1
  description: Whether this parameter should be varied or not in the context of an optimization.
property:
  path: stderr
  datatype: decimal
  min count: 0
  max count: 1
  description: Standard error of the estimated parameter.
property:
  path: constant
  datatype: boolean
  min count: 0
  max count: 1
  description: Specifies if this parameter is constant. Default is True.

MeasurementShape
type: NodeShape
target class: Measurement
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 1
  max count: 1
  description: Unique identifier of the measurement.
property:
  path: name
  datatype: string
  min count: 1
  max count: 1
  description: Name of the measurement
property:
  path: species data
  min count: 0
  description: Measurement data of all species that were part of the measurement. A species refers to a Protein, Complex, or SmallMolecule.
property:
  path: group id
  datatype: string
  min count: 0
  max count: 1
  description: User-defined group ID to signal relationships between measurements.
property:
  path: ph
  datatype: decimal
  min count: 0
  max count: 1
  description: pH value of the measurement.
property:
  path: temperature
  datatype: decimal
  min count: 0
  max count: 1
  description: Temperature of the measurement.
property:
  path: temperature unit
  node: UnitDefinitionShape
  min count: 0
  max count: 1
  description: Unit of the temperature of the measurement.

UnitDefinitionShape
type: NodeShape
target class: UnitDefinition
property:
  or:
    path: id
  or:
    path: identifier
  datatype: string
  min count: 0
  max count: 1
  description: Unique identifier of the unit definition.
property:
  or:
    path: name
  or:
    path: label
  datatype: string
  min count: 0
  max count: 1
  description: Common or human-readable name of the unit definition.
property:
  or:
    path: base units
  or:
    path: factorUnit
  node: BaseUnitShape
  min count: 0
  description: Base or factor units that define this unit.

BaseUnitShape
type: NodeShape
target class: BaseUnit
property:
  or:
    path: kind
  or:
    path: unit
  class: UnitType
  min count: 1
  max count: 1
  description: Kind of the base unit (e.g., meter, kilogram, second).
property:
  or:
    path: exponent
  or:
    path: exponent
  datatype: integer
  min count: 1
  max count: 1
  description: Exponent of the base unit in the unit definition.
property:
  or:
    path: multiplier
  or:
    path: multiplier
  datatype: decimal
  min count: 0
  max count: 1
  description: Multiplier applied to the base unit.
property:
  or:
    path: scale
  or:
    path: scale
  datatype: decimal
  min count: 0
  max count: 1
  description: Power-of-ten scale applied to the base unit.