ontokin.owl
type: Ontology
version info: 1.0
comment: OntoSpecies is an ontology developed for representing chemical species.
date: 27 January 2020

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

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

belongsToPhase
type: ObjectProperty
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
comment: A relation between a site phase or bulk phase and a material in which they exist.

extractedFrom
type: ObjectProperty
domain: ReactionMechanism
range: MechanismRepresentationLanguage
type: NamedIndividual
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
type: NamedIndividual
comment: A relation that defines that a reaction has coefficients for an Arrhenius reaction rate model.

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

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

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

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

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

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

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

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

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

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

hasReactionOrder
type: ObjectProperty
type: NamedIndividual
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: ReactionMechanism
  union of: ThermoModel
range: Reference
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
comment: A relation between a species and its metadata.

hasStickingCoefficient
type: ObjectProperty
type: NamedIndividual
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
type: NamedIndividual
comment: A relation between a species and its thermo(dynamic) data model.

hasThirdBodyEfficiency
type: ObjectProperty
type: NamedIndividual
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
type: NamedIndividual
comment: A relation between a species and its transport data model.

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

hasCommit
type: DatatypeProperty
domain: MechanismRepresentationLanguage
range: string
type: NamedIndividual
comment: test comment

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

ArrheniusCoefficient
type: Class
subclass of: RateCoefficient
type: NamedIndividual
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
type: NamedIndividual
comment: A reaction that has an Arrhenius reaction rate model.

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

CHEBRateCoefficient
type: Class
subclass of: RateCoefficient
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
comment: An atom or isotope.

ElementMetadata
type: Class
type: NamedIndividual
comment: Metadata of an element.

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

FallOffModelCoefficient
type: Class
subclass of: RateCoefficient
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
comment: A continuous gaseous phase.

GasPhaseReaction
type: Class
subclass of: ChemicalReaction
subclass of: Restriction
  on property: belongsToPhase
  all values from: GasPhase
type: NamedIndividual
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
type: NamedIndividual
comment: Specification of a journal describing the page number and volume.

LandauTellerRateCoefficient
type: Class
subclass of: RateCoefficient
type: NamedIndividual
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
type: NamedIndividual
comment: A reaction that has a Landau-Teller reaction rate model.

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

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

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

NASA
type: Class
subclass of: ThermoModel
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
comment: A distinct and homogeneous form of matter (i.e. a particular solid, liquid, or gas) separated by its surface from other forms (Oxford Living Dictionary).

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

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

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

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

RateCoefficient
type: Class
equivalent class: ReactionRateCoefficient
type: NamedIndividual
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
type: NamedIndividual
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
type: NamedIndividual
comment: A collection of species and reactions together with the specification of thermodynamic data, transport data and rate coefficients.

ReactionMetadata
type: Class
type: NamedIndividual
comment: Metadata of a reaction.

ReactionOrder
type: Class
subclass of: Restriction
  on property: appliesTo
  all values from: Class
    union of: Product
    union of: Reactant
type: NamedIndividual
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
type: NamedIndividual
comment: A note describing the journal, conference proceedings or preprint where a document was published.

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

SRIReaction
type: Class
subclass of: FallOffReaction
type: NamedIndividual
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
type: NamedIndividual
comment: A phase that exists at the interface between the gas phase and a bulk phase.

Species
type: Class
equivalent class: ChemicalSpecies
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
type: NamedIndividual
comment: An ensemble of chemically identical molecular entities (McNaught & Wilkinson, 1997).

SpeciesMetadata
type: Class
type: NamedIndividual
comment: Metadata of a species.

StickingCoefficient
type: Class
subclass of: RateCoefficient
type: NamedIndividual
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
type: NamedIndividual
comment: A surface reaction that has a sticking coefficient reaction rate model.

SurfaceCoverageReaction
type: Class
subclass of: SurfaceReaction
subclass of: Restriction
  on property: hasCoverageDependency
  all values from: CoverageDependency
type: NamedIndividual
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
type: NamedIndividual
comment: A chemical reaction that occurs on a surface. Such reactions typically include species that belong to site or bulk phase(s) and the gas phase.

ThirdBodyEfficiency
type: Class
type: NamedIndividual
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: Species
    union of: ChemicalReaction
subclass of: Restriction
  on property: hasThirdBodyEfficiency
  all values from: ThirdBodyEfficiency
type: NamedIndividual
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
type: NamedIndividual
comment: Specifies the transport model used to calculate quantities such as viscosity, thermal conductivity and diffusion coefficients.

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

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