OntoKin.owl
type: Ontology
date: 08 February 2022
comment: OntoKin is an ontology developed for representing chemical kinetic reaction mechanisms.
version info: 1

appliesTo
type: ObjectProperty
comment: A relation from a reaction order to a reactant/product to which the order is applicable.

belongsToMaterial
type: ObjectProperty
comment: A relation between a surface reaction and the material that is involved in the reaction.

belongsToPhase
type: ObjectProperty
comment: A relation between a gas-phase reaction and the gas-phase that is involved in the reaction.

containedIn
type: ObjectProperty
domain: Class
  union of: GasPhase
  union of: Material
comment: A relation that identifies that a gas phase or material is contained in a reaction mechanism.

existsIn
type: ObjectProperty
domain: Class
  union of: BulkPhase
  union of: SitePhase
comment: A relation between a site phase or bulk phase and a material in which they exist.

extractedFrom
type: ObjectProperty
domain: ReactionMechanism
range: MechanismRepresentationLanguage
comment: A relation between a chemical kinetic reaction mechanism and the language from which the mechanism is extracted (to represent this using OWL).

hasArrheniusCoefficient
type: ObjectProperty
comment: A relation that defines that a reaction has coefficients for an Arrhenius reaction rate model.

hasCHEBRateCoefficient
type: ObjectProperty
comment: A relation that defines that a reaction has coefficients for a CHEB (Chebyshev) reaction rate model.

hasCoverageDependency
type: ObjectProperty
comment: A relation that defines that a surface reaction has coefficients for a coverage-dependent reaction rate model.

hasCreator
type: ObjectProperty
comment: A relation between a chemical kinetic reaction mechanism and the agent that created the mechanism.

hasElement
type: ObjectProperty
comment: A relation that defines that a species or molecular entity contains a chemical element.

hasElementMetadata
type: ObjectProperty
comment: A relation between an element and its metadata.

hasElementNumber
type: ObjectProperty
comment: A relation that defines the number of atoms of a given element contained in a species or molecular entity.

hasFallOffModelCoefficient
type: ObjectProperty
comment: A relation that defines that a reaction has coefficients for a fall-off reaction rate model.

hasLandauTellerDependency
type: ObjectProperty
comment: A relation that defines that a reaction has coefficients for a Landau-Teller reaction rate model.

hasNamedThirdBody
type: ObjectProperty
comment: A relation that defines that a fall-off reaction rate model is defined in terms of a named third body.

hasPublicationSpecification
type: ObjectProperty
comment: A relation between a reference and a publication specification that can be a journal specification, a proceedings specification or a preprint specification.

hasReactionMetadata
type: ObjectProperty
comment: A relation between a chemical reaction and its metadata.

hasReactionOrder
type: ObjectProperty
comment: A relation between a species that participates in a chemical reaction and the reaction order with respect to the species.

hasReference
type: ObjectProperty
domain: Class
  union of: ThermoModel
  union of: ReactionMechanism
range: Reference
comment: Connects a reaction mechanism to a reference that describes where the mechanism was published.

hasSpecies
type: ObjectProperty
domain: Class
  union of: CoverageDependency
  union of: StickingCoefficient
  union of: ThirdBodyEfficiency
range: Species
comment: A relation that connects a coverage-dependent reaction rate model, sticking coefficient reaction rate model or third body efficiency to a species that participates in the (coverage-dependent, sticking coefficient or third body efficiency) model.

hasSpeciesMetadata
type: ObjectProperty
comment: A relation between a species and its metadata.

hasStickingCoefficient
type: ObjectProperty
comment: A relation that defines that a surface reaction has coefficients for a sticking coefficient reaction rate model.

hasThermoModel
type: ObjectProperty
domain: Species
range: ThermoModel
comment: A relation between a species and its thermo(dynamic) data model.

hasThirdBodyEfficiency
type: ObjectProperty
comment: A relation between a species that participates in a chemical reaction and the third body efficiency of the species in the reaction.

hasTransportModel
type: ObjectProperty
domain: Species
range: TransportModel
comment: A relation between a species and its transport data model.

indicatesNumberOf
type: ObjectProperty
comment: A relation that defines the number of atoms of a given element contained in a species or molecular entity.

participatesIn
type: ObjectProperty
domain: Product
range: ReverseReaction
comment: A relation that defines that a species participates as a reactant in a reaction. The relationship can also exist between a species that is a product (of the forward reaction) that participates in the reverse reaction.

specifies
type: ObjectProperty
comment: A relation between a journal specification that describes the page number and volume, and the journal that describes its title and ISSN.

hasUniqueSpecies
type: ObjectProperty
domain: Species
range: Species
comment: A relation that identifies the unique chemical species the OntoKin Species is referring to.

Journal
type: Class
comment: Describes the title and ISSN of a journal.

ChemicalReaction
type: Class
subclass of: Restriction
  on property: hasProduct
  all values from: Product
subclass of: Restriction
  on property: hasReactant
  all values from: Reactant
subclass of: Restriction
  on property: hasStoichiometricCoefficient
  all values from: StoichiometricCoefficient
subclass of: Restriction
  on property: hasReactionMetadata
  all values from: ReactionMetadata
subclass of: Restriction
  on property: hasReactionOrder
  all values from: ReactionOrder
comment: A process in which one or more substances, the reactants, are converted to one or more new and entirely different substances, the products. In chemistry, substances are either chemical elements or compounds. A chemical reaction rearranges the constituent atoms of the reactants to create different substances as products.

StoichiometricCoefficient
type: Class
subclass of: Restriction
  on property: indicatesMultiplicityOf
  all values from: Class
    union of: Product
    union of: Reactant
comment: The ratio in which the reactants combine and the corresponding proportion of products participating in a chemical reaction are modelled using a stoichiometric coefficient.

ThermoModel
type: Class
comment: Specifies the thermodynamic model used to calculate quantities such as heat capacity, enthalpy and entropy.

ArrheniusCoefficient
type: Class
subclass of: RateCoefficient
comment: The coefficients used to evaluate the Arrhenius part of a reaction rate model.

ArrheniusReaction
type: Class
subclass of: GasPhaseReaction
subclass of: Restriction
  on property: hasArrheniusCoefficient
  all values from: ArrheniusCoefficient
comment: A gas-phase reaction that is described by an Arrhenius law.

BulkPhase
type: Class
subclass of: Phase
subclass of: Restriction
  on property: existsIn
  all values from: Material
comment: A solid phase that is contiguous with site phases and remote from the gas phase.

CHEBRateCoefficient
type: Class
subclass of: RateCoefficient
comment: The coefficients used to evaluate the CHEB (Chebyshev) part of a reaction rate model.

CHEBReaction
type: Class
subclass of: PressureDependentReaction
subclass of: Restriction
  on property: hasCHEBRateCoefficient
  all values from: CHEBRateCoefficient
comment: A reaction that has a CHEB (Chebyshev) reaction rate model. The CHEB reaction rate model can be used to describe pressure-dependent reaction rates.

CoverageDependency
type: Class
subclass of: RateCoefficient
comment: The coefficients used to evaluate the coverage-dependent part of a surface reaction rate model.

Element
type: Class
subclass of: Restriction
  on property: hasElementMetadata
  all values from: ElementMetadata
comment: An atom or isotope.

ElementMetadata
type: Class
comment: Metadata of an element.

ElementNumber
type: Class
subclass of: Restriction
  on property: indicatesNumberOf
  all values from: Element
comment: A number indicating the multiplicity of an element in a species.

FallOffModelCoefficient
type: Class
subclass of: RateCoefficient
comment: The coefficients used to evaluate the fall-off part of a reaction rate model.

FallOffReaction
type: Class
subclass of: PressureDependentReaction
subclass of: Restriction
  on property: hasFallOffModelCoefficient
  all values from: FallOffModelCoefficient
comment: A reaction that has a fall-off reaction rate model. The fall-off model can be used to describe pressure-dependent reaction rates.

ForwardReaction
type: Class
subclass of: ChemicalReaction
comment: A chemical reaction that proceeds in the forward direction, so producing products from reactants.

GasPhase
type: Class
subclass of: Phase
subclass of: Restriction
  on property: containedIn
  qualified cardinality: 1
  on class: ReactionMechanism
comment: A continuous gaseous phase.

GasPhaseReaction
type: Class
subclass of: ChemicalReaction
subclass of: Restriction
  on property: belongsToPhase
  all values from: GasPhase
comment: A chemical reaction that occurs in the gas phase.

JournalSpecification
type: Class
subclass of: PublicationSpecification
subclass of: Restriction
  on property: specifies
  all values from: Journal
comment: Specification of a journal describing the page number and volume.

LandauTellerRateCoefficient
type: Class
subclass of: RateCoefficient
comment: The coefficients used to evaluate the Landau-Teller part of a reaction rate model.

LandauTellerReaction
type: Class
subclass of: GasPhaseReaction
subclass of: Restriction
  on property: hasLandauTellerDependency
  all values from: LandauTellerRateCoefficient
comment: A reaction that has a Landau-Teller reaction rate model.

LindemannReaction
type: Class
subclass of: FallOffReaction
comment: A reaction that includes a Lindemann fall-off reaction rate model.

LiquidPhase
type: Class
subclass of: Phase
comment: The structural phase�of matter in which the thermal mobility of molecules or atoms is comparable with the cohesiveness, having them connected but fluid in a mass [Wikitionary].

Material
type: Class
subclass of: Restriction
  on property: containedIn
  qualified cardinality: 1
  on class: ReactionMechanism
comment: A substance that contains at least one site or bulk phase.

MechanismRepresentationLanguage
type: Class
comment: A representation language specialised for the codification of chemical kinetic reaction mechanisms.

NASA
type: Class
subclass of: ThermoModel
comment: The NASA polynomial parameterisation used to compute the reference-state thermodynamic properties of a species within a specified temperature range.

PLOGReaction
type: Class
subclass of: PressureDependentReaction
comment: A reaction that has a PLOG reaction rate model. The PLOG reaction rate model can be used to describe pressure-dependent reaction rates.

Phase
type: Class
comment: A phase of a substance is a form of matter that is uniform throughout in chemical composition and state (i.e. a particular solid, liquid, or gas).

PreprintSpecification
type: Class
subclass of: PublicationSpecification
comment: Specification of a preprint.

PressureDependentReaction
type: Class
subclass of: ThreeBodyReaction
comment: A reaction that includes a pressure-dependent reaction rate model.

ProceedingsSpecification
type: Class
subclass of: PublicationSpecification
comment: Specification of a conference.

Product
type: Class
subclass of: Species
comment: A name-quantity pair that defines the name and corresponding stoichiometric coefficient of a chemical species or molecular entity participating in the reverse reaction.

PublicationSpecification
type: Class
comment: Specification of a publication for describing its author(s), title, year of publication, journal or conference, publisher, etc.

RateCoefficient
type: Class
comment: The coefficients used to evaluate the reaction rate expression.

Reactant
type: Class
subclass of: Species
subclass of: Restriction
  on property: participatesIn
  all values from: ForwardReaction
comment: A name-quantity pair that defines the name and corresponding stoichiometric coefficient of a chemical species or molecular entity participating in the forward reaction.

ReactionMechanism
type: Class
subclass of: Restriction
  on property: hasCreator
  all values from: Agent
comment: A reaction mechanism refers to a set of elementary reactions with specific rate laws, for example to model the combustion of hydrogen.

ReactionMetadata
type: Class
comment: Metadata of a reaction.

ReactionOrder
type: Class
subclass of: Restriction
  on property: appliesTo
  all values from: Class
    union of: Product
    union of: Reactant
comment: The order of reaction with resepct to a species. The value of the reaction order for the species is exactly the same as its stoichometric coefficient in mass-action kinetics.

Reference
type: Class
subclass of: Restriction
  on property: contributor
  all values from: Agent
subclass of: Restriction
  on property: hasPublicationSpecification
  all values from: PublicationSpecification
comment: A note describing the journal, conference proceedings or preprint where a document was published.

ReverseReaction
type: Class
subclass of: ChemicalReaction
comment: A chemical reaction that proceeds in the reverse direction, so producing reactants from products.

SRIReaction
type: Class
subclass of: FallOffReaction
comment: A reaction that includes an SRI fall-off reaction rate model.

SitePhase
type: Class
subclass of: Phase
subclass of: Restriction
  on property: existsIn
  all values from: Material
comment: A phase that exists at the interface between the gas phase and a bulk phase.

SolidPhase
type: Class
subclass of: Phase
comment: The�structural�phase�of matter in which the�cohesive force�of matter is strong enough to keep the molecules or atoms in the given positions, restraining the�thermal mobility [Wikitionary].

Species
type: Class
subclass of: Restriction
  on property: belongsToPhase
  all values from: Phase
subclass of: Restriction
  on property: hasElement
  all values from: Element
subclass of: Restriction
  on property: hasElementNumber
  all values from: ElementNumber
subclass of: Restriction
  on property: hasSpeciesMetadata
  all values from: SpeciesMetadata
comment: An ensemble of chemically identical molecular entities (McNaught & Wilkinson, 1997).

SpeciesMetadata
type: Class
comment: Metadata of a species.

StickingCoefficient
type: Class
subclass of: RateCoefficient
comment: The coefficients used to evaluate the sticking coefficient part of a surface reaction rate model.

StickingCoefficientReaction
type: Class
subclass of: SurfaceReaction
subclass of: Restriction
  on property: hasStickingCoefficient
  all values from: StickingCoefficient
comment: A surface reaction that is described by a sticking coefficient rate model.

SurfaceCoverageReaction
type: Class
subclass of: SurfaceReaction
subclass of: Restriction
  on property: hasCoverageDependency
  all values from: CoverageDependency
comment: A surface reaction that has a coverage-dependent reaction rate model.

SurfaceReaction
type: Class
subclass of: ChemicalReaction
subclass of: Restriction
  on property: belongsToMaterial
  all values from: Material
subclass of: Restriction
  on property: belongsToPhase
  all values from: Class
    union of: BulkPhase
    union of: SitePhase
comment: A chemical reaction that involves an adsorbed species or desorption of products into the gas phase, or adsorption of reactants from the gas phase onto the surface.

ThirdBodyEfficiency
type: Class
comment: An efficiency that indicates the effectiveness of a species that acts as a third body in a pressure dependent reaction.

ThreeBodyReaction
type: Class
subclass of: GasPhaseReaction
subclass of: Restriction
  on property: hasNamedThirdBody
  all values from: Class
    union of: ChemicalReaction
    union of: Species
subclass of: Restriction
  on property: hasThirdBodyEfficiency
  all values from: ThirdBodyEfficiency
comment: A gas-phase reaction that involves an inert third body. The third body is required to ensure conservation of both energy and momentum in a reaction in which two species react to form a single product.

TransportModel
type: Class
comment: Specifies the transport model used to calculate quantities such as viscosity, thermal conductivity and diffusion coefficients.

TroeReaction
type: Class
subclass of: FallOffReaction
comment: A reaction that includes a Troe fall-off reaction rate model.