diff --git a/external/OntoRXN.ofn b/external/OntoRXN.ofn new file mode 100644 index 0000000..e4a5541 --- /dev/null +++ b/external/OntoRXN.ofn @@ -0,0 +1,488 @@ +Prefix(:=) +Prefix(dc:=) +Prefix(gc:=) +Prefix(ns:=) +Prefix(mop:=) +Prefix(ns2:=) +Prefix(obo:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(qudt:=) +Prefix(rdfs:=) +Prefix(terms:=) +Prefix(terms1:=) +Prefix(oboInOwl:=) +Prefix(ontospecies:=) + + +Ontology( + +Import() +Annotation(dc:description "OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies."@en) +Annotation(dc:title "OntoRXN"@en) +Annotation(terms:license "https://creativecommons.org/licenses/by/4.0/") + +Declaration(Class(obo:MOP_0000543)) +Declaration(Class(gc:VectorValue)) +Declaration(Class(ontospecies:Species)) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class(:ChemSpecies)) +Declaration(Class(:CompCalculation)) +Declaration(Class(:NetworkStage)) +Declaration(Class(:ReactionStep)) +Declaration(Class(:ThermoCondition)) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty(:hasCalculation)) +Declaration(ObjectProperty(:hasElecEnergy)) +Declaration(ObjectProperty(:hasEnergy)) +Declaration(ObjectProperty(:hasFreqList)) +Declaration(ObjectProperty(:hasGibbsFreeEnergy)) +Declaration(ObjectProperty(:hasMolMass)) +Declaration(ObjectProperty(:hasMomentInertia)) +Declaration(ObjectProperty(:hasNode)) +Declaration(ObjectProperty(:hasPressure)) +Declaration(ObjectProperty(:hasReactionType)) +Declaration(ObjectProperty(:hasRotTemps)) +Declaration(ObjectProperty(:hasSolventPolarity)) +Declaration(ObjectProperty(:hasSpecies)) +Declaration(ObjectProperty(:hasTS)) +Declaration(ObjectProperty(:hasTemperature)) +Declaration(ObjectProperty(:hasThermoConditions)) +Declaration(ObjectProperty(:isCalculationOf)) +Declaration(ObjectProperty(:isConnectedWith)) +Declaration(ObjectProperty(:isNodeOf)) +Declaration(ObjectProperty(:isSpeciesOf)) +Declaration(ObjectProperty(:isTSOf)) +Declaration(DataProperty(:hasAnnotation)) +Declaration(DataProperty(:hasInChI)) +Declaration(DataProperty(:hasSolvent)) +Declaration(DataProperty(:hasSymmetryNumber)) +Declaration(DataProperty(:hasXYZGeometry)) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty(qudt:description)) +Declaration(AnnotationProperty(dc:description)) +Declaration(AnnotationProperty(dc:title)) +Declaration(AnnotationProperty(terms:description)) +Declaration(AnnotationProperty(terms:hasVersion)) +Declaration(AnnotationProperty(terms:issued)) +Declaration(AnnotationProperty(terms:license)) +Declaration(Datatype(xsd:date)) + +############################ +# Object Properties +############################ + +# Object Property: :hasCalculation (has calculation) + +AnnotationAssertion(rdfs:comment :hasCalculation "Links a given chemical entity in the reaction network to the calculation(s) defined for that entity."@en) +AnnotationAssertion(rdfs:label :hasCalculation "has calculation") +InverseObjectProperties(:hasCalculation :isCalculationOf) +ObjectPropertyDomain(:hasCalculation :ChemSpecies) +ObjectPropertyRange(:hasCalculation :CompCalculation) + +# Object Property: :hasElecEnergy (has electronic energy) + +AnnotationAssertion(rdfs:comment :hasElecEnergy "Property defining the electronic energy of a calculation") +AnnotationAssertion(rdfs:label :hasElecEnergy "has electronic energy") +SubObjectPropertyOf(:hasElecEnergy :hasEnergy) + +# Object Property: :hasEnergy (has energy) + +AnnotationAssertion(rdfs:comment :hasEnergy "Parent property for energies in a calculation.") +AnnotationAssertion(rdfs:label :hasEnergy "has energy") +FunctionalObjectProperty(:hasEnergy) +ObjectPropertyDomain(:hasEnergy gc:CalculationResult) +ObjectPropertyRange(:hasEnergy gc:FloatValue) + +# Object Property: :hasFreqList (has freqlist) + +AnnotationAssertion(rdfs:comment :hasFreqList "Property defining the list of frequencies (in cm-1) for a calculation.") +AnnotationAssertion(rdfs:label :hasFreqList "has freqlist") +FunctionalObjectProperty(:hasFreqList) +ObjectPropertyDomain(:hasFreqList gc:CalculationResult) +ObjectPropertyRange(:hasFreqList gc:VectorValue) + +# Object Property: :hasGibbsFreeEnergy (has Gibbs free energy) + +AnnotationAssertion(rdfs:comment :hasGibbsFreeEnergy "Property defining the Gibbs free energy of a calculation.") +AnnotationAssertion(rdfs:label :hasGibbsFreeEnergy "has Gibbs free energy") +SubObjectPropertyOf(:hasGibbsFreeEnergy :hasEnergy) + +# Object Property: :hasMolMass (:hasMolMass) + +ObjectPropertyDomain(:hasMolMass gc:CalculationResult) +ObjectPropertyRange(:hasMolMass gc:FloatValue) + +# Object Property: :hasMomentInertia (:hasMomentInertia) + +ObjectPropertyDomain(:hasMomentInertia gc:CalculationResult) +ObjectPropertyRange(:hasMomentInertia gc:VectorValue) + +# Object Property: :hasNode (has node) + +AnnotationAssertion(rdfs:comment :hasNode "Links a reaction step in the reaction network with the stage corresponding to an intermediate."@en) +AnnotationAssertion(rdfs:label :hasNode "has node") +InverseObjectProperties(:hasNode :isNodeOf) +ObjectPropertyDomain(:hasNode :ReactionStep) +ObjectPropertyRange(:hasNode :NetworkStage) + +# Object Property: :hasPressure (has pressure) + +AnnotationAssertion(rdfs:comment :hasPressure "Property defining the pressure for determining thermodynamic properties") +AnnotationAssertion(rdfs:label :hasPressure "has pressure") +ObjectPropertyDomain(:hasPressure :ThermoCondition) +ObjectPropertyRange(:hasPressure gc:FloatValue) + +# Object Property: :hasReactionType (has reaction type) + +AnnotationAssertion(rdfs:comment :hasReactionType "Property that links a named molecular process to a ReactionStep entity") +AnnotationAssertion(rdfs:label :hasReactionType "has reaction type") +ObjectPropertyDomain(:hasReactionType :ReactionStep) +ObjectPropertyRange(:hasReactionType obo:MOP_0000543) + +# Object Property: :hasRotTemps (:hasRotTemps) + +ObjectPropertyDomain(:hasRotTemps gc:CalculationResult) +ObjectPropertyRange(:hasRotTemps gc:VectorValue) + +# Object Property: :hasSolventPolarity (has solvent polarity) + +AnnotationAssertion(rdfs:label :hasSolventPolarity "has solvent polarity") +ObjectPropertyDomain(:hasSolventPolarity gc:CalculationResult) +ObjectPropertyRange(:hasSolventPolarity gc:FloatValue) + +# Object Property: :hasSpecies (has species) + +AnnotationAssertion(rdfs:comment :hasSpecies "Links a given stage in the reaction network to the chemical entities collected by that stage."@en) +AnnotationAssertion(rdfs:label :hasSpecies "has species") +InverseObjectProperties(:hasSpecies :isSpeciesOf) +ObjectPropertyDomain(:hasSpecies :NetworkStage) +ObjectPropertyRange(:hasSpecies :ChemSpecies) + +# Object Property: :hasTS (has TS) + +AnnotationAssertion(rdfs:comment :hasTS "Links a reaction step in the reaction network with the stage corresponding to a transition state."@en) +AnnotationAssertion(rdfs:label :hasTS "has TS") +InverseObjectProperties(:hasTS :isTSOf) +FunctionalObjectProperty(:hasTS) +ObjectPropertyDomain(:hasTS :ReactionStep) +ObjectPropertyRange(:hasTS :NetworkStage) + +# Object Property: :hasTemperature (has temperature) + +AnnotationAssertion(rdfs:comment :hasTemperature "Property defining the temperature for determining thermodynamic properties") +AnnotationAssertion(rdfs:label :hasTemperature "has temperature") +ObjectPropertyDomain(:hasTemperature :ThermoCondition) +ObjectPropertyRange(:hasTemperature gc:FloatValue) + +# Object Property: :hasThermoConditions (has thermodynamic conditions) + +AnnotationAssertion(rdfs:comment :hasThermoConditions "Property to link calculations with the corresponding thermodynamic conditions") +AnnotationAssertion(rdfs:label :hasThermoConditions "has thermodynamic conditions") +ObjectPropertyDomain(:hasThermoConditions :CompCalculation) +ObjectPropertyRange(:hasThermoConditions :ThermoCondition) + +# Object Property: :isCalculationOf (is calculation of) + +AnnotationAssertion(rdfs:comment :isCalculationOf "Links a calculation to the chemical entity to which it refers."@en) +AnnotationAssertion(rdfs:label :isCalculationOf "is calculation of") + +# Object Property: :isConnectedWith (is connected with) + +AnnotationAssertion(rdfs:comment :isConnectedWith "Links two reaction steps having some common intermediate."@en) +AnnotationAssertion(rdfs:label :isConnectedWith "is connected with") +ObjectPropertyDomain(:isConnectedWith :ReactionStep) +ObjectPropertyRange(:isConnectedWith :ReactionStep) + +# Object Property: :isNodeOf (is node of) + +AnnotationAssertion(rdfs:comment :isNodeOf "Links the stage corresponding to an intermediate in the reaction network to the reaction step(s) it participates in."@en) +AnnotationAssertion(rdfs:label :isNodeOf "is node of") + +# Object Property: :isSpeciesOf (is species of) + +AnnotationAssertion(rdfs:comment :isSpeciesOf "Links a given chemical entity in the reaction network to the stage(s) in which it is contained."@en) +AnnotationAssertion(rdfs:label :isSpeciesOf "is species of") + +# Object Property: :isTSOf (is TS of) + +AnnotationAssertion(rdfs:comment :isTSOf "Links the stage corresponding to a transition state in the reaction network to the reaction step it participates in."@en) +AnnotationAssertion(rdfs:label :isTSOf "is TS of") + +# Object Property: (has environment) + +ObjectPropertyDomain( ) + +# Object Property: (has initialization.) + +ObjectPropertyDomain( ) + +# Object Property: (has unique species) + +ObjectPropertyDomain( ) + + +############################ +# Data Properties +############################ + +# Data Property: :hasAnnotation (has annotation) + +AnnotationAssertion(rdfs:comment :hasAnnotation "Property defining string annotations"@en) +AnnotationAssertion(rdfs:label :hasAnnotation "has annotation") +DataPropertyRange(:hasAnnotation xsd:string) + +# Data Property: :hasInChI (has InChI) + +AnnotationAssertion(rdfs:label :hasInChI "has InChI") +DataPropertyDomain(:hasInChI :ChemSpecies) +DataPropertyDomain(:hasInChI :CompCalculation) + +# Data Property: :hasSolvent (has solvent) + +AnnotationAssertion(rdfs:comment :hasSolvent "Property defining the solvent modelled for a calculation."@en) +AnnotationAssertion(rdfs:label :hasSolvent "has solvent") +FunctionalDataProperty(:hasSolvent) +DataPropertyDomain(:hasSolvent :CompCalculation) +DataPropertyRange(:hasSolvent xsd:string) + +# Data Property: :hasSymmetryNumber (:hasSymmetryNumber) + +DataPropertyDomain(:hasSymmetryNumber :CompCalculation) +DataPropertyRange(:hasSymmetryNumber xsd:integer) + +# Data Property: :hasXYZGeometry (has XYZ geometry) + +AnnotationAssertion(rdfs:comment :hasXYZGeometry "Property defining the string corresponding to the XYZ coordinates of a calculation."@en) +AnnotationAssertion(rdfs:label :hasXYZGeometry "has XYZ geometry") +DataPropertyDomain(:hasXYZGeometry :CompCalculation) +DataPropertyRange(:hasXYZGeometry xsd:string) + + + +############################ +# Classes +############################ + +# Class: gc:VectorValue (gc:VectorValue) + +SubClassOf(gc:VectorValue gc:Value) + +# Class: :ChemSpecies (chemical species) + +AnnotationAssertion(rdfs:comment :ChemSpecies "Individual molecular entity participating at some point of a reaction network."@en) +AnnotationAssertion(rdfs:label :ChemSpecies "chemical species") +SubClassOf(:ChemSpecies owl:Thing) + +# Class: :CompCalculation (computational calculation) + +AnnotationAssertion(rdfs:comment :CompCalculation "Collection of computational data from an electronic structure calculation."@en) +AnnotationAssertion(rdfs:label :CompCalculation "computational calculation") +EquivalentClasses(:CompCalculation ) +SubClassOf(:CompCalculation owl:Thing) + +# Class: :NetworkStage (network stage) + +AnnotationAssertion(rdfs:comment :NetworkStage "Collection of structures that must be combined to define a point in a reaction network, so as the corresponding energy of the molecule set matches the chosen reference state."@en) +AnnotationAssertion(rdfs:label :NetworkStage "network stage") +SubClassOf(:NetworkStage owl:Thing) +SubClassOf(:NetworkStage ObjectMinCardinality(1 :hasSpecies :ChemSpecies)) + +# Class: :ReactionStep (reaction step) + +AnnotationAssertion(rdfs:comment :ReactionStep "Non-directed step in a reaction network containing two intermediates and (possibly) the corresponding transition state between them."@en) +AnnotationAssertion(rdfs:label :ReactionStep "reaction step") +SubClassOf(:ReactionStep owl:Thing) +SubClassOf(:ReactionStep ObjectExactCardinality(2 :hasNode :NetworkStage)) + +# Class: :ThermoCondition (thermodynamic condition) + +AnnotationAssertion(rdfs:comment :ThermoCondition "A class representing the thermodynamic conditions for a calculation") +AnnotationAssertion(rdfs:label :ThermoCondition "thermodynamic condition") +SubClassOf(:ThermoCondition gc:AuxiliaryConcept) + +# Class: (base calculation) + +AnnotationAssertion(rdfs:comment "General class for computational chemistry calculations") +AnnotationAssertion(rdfs:label "base calculation") + +# Class: (Gaussian calculation) + +SubClassOf( ) + +# Class: (generic calculation) + +AnnotationAssertion(rdfs:comment "Calculations performed by unspecified software.") +AnnotationAssertion(rdfs:label "generic calculation") +SubClassOf( ) + + +) \ No newline at end of file diff --git a/external/OntoRXN.yaml b/external/OntoRXN.yaml new file mode 100644 index 0000000..56d4485 --- /dev/null +++ b/external/OntoRXN.yaml @@ -0,0 +1,271 @@ +id: http://www.semanticweb.com/OntoRxn +name: OntoRxn +description: OntoRxn +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + OntoRxn: https://w3id.org/None/ +default_prefix: OntoRxn +types: {} +classes: + MOP_0000543: + class_uri: obo:MOP_0000543 + VectorValue: + class_uri: gc:VectorValue + is_a: Value + Species: + class_uri: ontospecies:Species + Block: + class_uri: http://www.daml.org/2003/01/periodictable/PeriodicTable.owl#Block + Classification: + class_uri: http://www.daml.org/2003/01/periodictable/PeriodicTable.owl#Classification + Element: + class_uri: http://www.daml.org/2003/01/periodictable/PeriodicTable.owl#Element + Group: + class_uri: http://www.daml.org/2003/01/periodictable/PeriodicTable.owl#Group + Period: + class_uri: http://www.daml.org/2003/01/periodictable/PeriodicTable.owl#Period + StandardState: + class_uri: http://www.daml.org/2003/01/periodictable/PeriodicTable.owl#StandardState + ChemSpecies: + class_uri: OntoRxn:ChemSpecies + slots: + - hasCalculation + - hasInChI + is_a: Thing + comments: + - Individual molecular entity participating at some point of a reaction network.@en + CompCalculation: + class_uri: OntoRxn:CompCalculation + slots: + - hasThermoConditions + - hasInChI + - hasSolvent + - hasSymmetryNumber + - hasXYZGeometry + is_a: Thing + comments: + - Collection of computational data from an electronic structure calculation.@en + NetworkStage: + class_uri: OntoRxn:NetworkStage + slots: + - hasSpecies + is_a: Thing + comments: + - Collection of structures that must be combined to define a point in a reaction + network, so as the corresponding energy of the molecule set matches the chosen + reference state.@en + slot_usage: + hasSpecies: + required: true + ReactionStep: + class_uri: OntoRxn:ReactionStep + slots: + - hasNode + - hasReactionType + - hasTS + - isConnectedWith + is_a: Thing + comments: + - Non-directed step in a reaction network containing two intermediates and (possibly) + the corresponding transition state between them.@en + slot_usage: + hasNode: + multivalued: true + ThermoCondition: + class_uri: OntoRxn:ThermoCondition + slots: + - hasPressure + - hasTemperature + is_a: AuxiliaryConcept + comments: + - A class representing the thermodynamic conditions for a calculation + BaseCalculation: + class_uri: http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#BaseCalculation + slots: + - hasEnvironment + - hasInitialization + - hasUniqueSpecies + comments: + - General class for computational chemistry calculations + GenericCalculation: + class_uri: http://www.theworldavatar.com/ontology/ontocompchem/ontocompchem.owl#GenericCalculation + is_a: BaseCalculation + comments: + - Calculations performed by unspecified software. + NodeShape: + class_uri: http://www.w3.org/ns/shacl#NodeShape + CalculationResult: + slots: + - hasEnergy + - hasFreqList + - hasMolMass + - hasMomentInertia + - hasRotTemps + - hasSolventPolarity + GaussianCalculation: + is_a: BaseCalculation +slots: + hasCalculation: + slot_uri: OntoRxn:hasCalculation + range: CompCalculation + comments: + - Links a given chemical entity in the reaction network to the calculation(s) + defined for that entity.@en + multivalued: true + hasElecEnergy: + slot_uri: OntoRxn:hasElecEnergy + is_a: hasEnergy + comments: + - Property defining the electronic energy of a calculation + multivalued: true + hasEnergy: + slot_uri: OntoRxn:hasEnergy + range: FloatValue + comments: + - Parent property for energies in a calculation. + multivalued: true + hasFreqList: + slot_uri: OntoRxn:hasFreqList + range: VectorValue + comments: + - Property defining the list of frequencies (in cm-1) for a calculation. + multivalued: true + hasGibbsFreeEnergy: + slot_uri: OntoRxn:hasGibbsFreeEnergy + is_a: hasEnergy + comments: + - Property defining the Gibbs free energy of a calculation. + multivalued: true + hasMolMass: + slot_uri: OntoRxn:hasMolMass + range: FloatValue + multivalued: true + hasMomentInertia: + slot_uri: OntoRxn:hasMomentInertia + range: VectorValue + multivalued: true + hasNode: + slot_uri: OntoRxn:hasNode + range: NetworkStage + comments: + - Links a reaction step in the reaction network with the stage corresponding to + an intermediate.@en + multivalued: true + hasPressure: + slot_uri: OntoRxn:hasPressure + range: FloatValue + comments: + - Property defining the pressure for determining thermodynamic properties + multivalued: true + hasReactionType: + slot_uri: OntoRxn:hasReactionType + range: MOP_0000543 + comments: + - Property that links a named molecular process to a ReactionStep entity + multivalued: true + hasRotTemps: + slot_uri: OntoRxn:hasRotTemps + range: VectorValue + multivalued: true + hasSolventPolarity: + slot_uri: OntoRxn:hasSolventPolarity + range: FloatValue + multivalued: true + hasSpecies: + slot_uri: OntoRxn:hasSpecies + range: ChemSpecies + comments: + - Links a given stage in the reaction network to the chemical entities collected + by that stage.@en + multivalued: true + hasTS: + slot_uri: OntoRxn:hasTS + range: NetworkStage + comments: + - Links a reaction step in the reaction network with the stage corresponding to + a transition state.@en + multivalued: true + hasTemperature: + slot_uri: OntoRxn:hasTemperature + range: FloatValue + comments: + - Property defining the temperature for determining thermodynamic properties + multivalued: true + hasThermoConditions: + slot_uri: OntoRxn:hasThermoConditions + range: ThermoCondition + comments: + - Property to link calculations with the corresponding thermodynamic conditions + multivalued: true + isCalculationOf: + slot_uri: OntoRxn:isCalculationOf + comments: + - Links a calculation to the chemical entity to which it refers.@en + multivalued: true + isConnectedWith: + slot_uri: OntoRxn:isConnectedWith + range: ReactionStep + comments: + - Links two reaction steps having some common intermediate.@en + multivalued: true + isNodeOf: + slot_uri: OntoRxn:isNodeOf + comments: + - Links the stage corresponding to an intermediate in the reaction network to + the reaction step(s) it participates in.@en + multivalued: true + isSpeciesOf: + slot_uri: OntoRxn:isSpeciesOf + comments: + - Links a given chemical entity in the reaction network to the stage(s) in which + it is contained.@en + multivalued: true + isTSOf: + slot_uri: OntoRxn:isTSOf + comments: + - Links the stage corresponding to a transition state in the reaction network + to the reaction step it participates in.@en + multivalued: true + hasAnnotation: + slot_uri: OntoRxn:hasAnnotation + comments: + - Property defining string annotations@en + multivalued: true + hasInChI: + slot_uri: OntoRxn:hasInChI + multivalued: true + hasSolvent: + slot_uri: OntoRxn:hasSolvent + comments: + - Property defining the solvent modelled for a calculation.@en + multivalued: true + hasSymmetryNumber: + slot_uri: OntoRxn:hasSymmetryNumber + multivalued: true + hasXYZGeometry: + slot_uri: OntoRxn:hasXYZGeometry + comments: + - Property defining the string corresponding to the XYZ coordinates of a calculation.@en + multivalued: true + isAbstract: + slot_uri: isAbstract + multivalued: true + description: + slot_uri: terms:description + multivalued: true + title: + slot_uri: dc:title + multivalued: true + hasVersion: + slot_uri: terms:hasVersion + multivalued: true + issued: + slot_uri: terms:issued + multivalued: true + license: + slot_uri: terms:license + multivalued: true +enums: {} + diff --git a/external/catalog-v001.xml b/external/catalog-v001.xml new file mode 100644 index 0000000..83ebb19 --- /dev/null +++ b/external/catalog-v001.xml @@ -0,0 +1,6 @@ + + + + + + diff --git a/external/daml-periodic-table.ttl b/external/daml-periodic-table.ttl new file mode 100644 index 0000000..ec6b664 --- /dev/null +++ b/external/daml-periodic-table.ttl @@ -0,0 +1,2549 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + rdfs:comment "Periodic Table of the Elements" ; + owl:versionInfo "$Id: PeriodicTable.owl,v 1.10 2004/02/05 15:49:58 mdean Exp $" . + +################################################################# +# Object Properties +################################################################# + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#block +:block rdf:type owl:ObjectProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#classification +:classification rdf:type owl:ObjectProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#element +:element rdf:type owl:ObjectProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group +:group rdf:type owl:ObjectProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period +:period rdf:type owl:ObjectProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#standardState +:standardState rdf:type owl:ObjectProperty . + + +################################################################# +# Data properties +################################################################# + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#atomicNumber +:atomicNumber rdf:type owl:DatatypeProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#atomicWeight +:atomicWeight rdf:type owl:DatatypeProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#casRegistryID +:casRegistryID rdf:type owl:DatatypeProperty ; + rdfs:comment "Chemical Abstracts Service (CAS) related information" ; + rdfs:seeAlso . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#color +:color rdf:type owl:DatatypeProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#name +:name rdf:type owl:DatatypeProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#number +:number rdf:type owl:DatatypeProperty . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#symbol +:symbol rdf:type owl:DatatypeProperty . + + +################################################################# +# Classes +################################################################# + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Block +:Block rdf:type owl:Class ; + owl:equivalentClass [ rdf:type owl:Class ; + owl:oneOf ( :d-block + :f-block + :p-block + :s-block + ) + ] . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Classification +:Classification rdf:type owl:Class ; + owl:equivalentClass [ rdf:type owl:Class ; + owl:oneOf ( :Metallic + :Non-metallic + :Semi-metallic + ) + ] . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Element +:Element rdf:type owl:Class ; + rdfs:subClassOf [ rdf:type owl:Restriction ; + owl:onProperty :block ; + owl:allValuesFrom :Block + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :classification ; + owl:allValuesFrom :Classification + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :group ; + owl:allValuesFrom :Group + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :period ; + owl:allValuesFrom :Period + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :standardState ; + owl:allValuesFrom :StandardState + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :block ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :group ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :period ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :atomicNumber ; + owl:allValuesFrom xsd:integer + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :atomicWeight ; + owl:allValuesFrom xsd:float + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :color ; + owl:allValuesFrom xsd:string + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :name ; + owl:allValuesFrom xsd:string + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :symbol ; + owl:allValuesFrom xsd:string + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :atomicNumber ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :atomicWeight ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :name ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :symbol ; + owl:cardinality "1"^^xsd:nonNegativeInteger + ] . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Group +:Group rdf:type owl:Class ; + rdfs:subClassOf [ rdf:type owl:Restriction ; + owl:onProperty :element ; + owl:allValuesFrom :Element + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :name ; + owl:allValuesFrom xsd:string + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :number ; + owl:allValuesFrom xsd:integer + ] . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Period +:Period rdf:type owl:Class ; + rdfs:subClassOf [ rdf:type owl:Restriction ; + owl:onProperty :element ; + owl:allValuesFrom :Element + ] , + [ rdf:type owl:Restriction ; + owl:onProperty :number ; + owl:allValuesFrom xsd:integer + ] . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#StandardState +:StandardState rdf:type owl:Class ; + owl:equivalentClass [ rdf:type owl:Class ; + owl:oneOf ( :gas + :liquid + :solid + :state_unknown + ) + ] . + + +################################################################# +# Individuals +################################################################# + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ac +:Ac rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 89 ; + :atomicWeight "227.0"^^xsd:float ; + :casRegistryID "7440-34-8"^^xsd:string ; + :color "silvery"^^xsd:string ; + :name "actinium"^^xsd:string ; + :symbol "Ac"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ag +:Ag rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_11 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 47 ; + :atomicWeight "107.8682"^^xsd:float ; + :casRegistryID "7440-22-4"^^xsd:string ; + :color "silver"^^xsd:string ; + :name "silver"^^xsd:string ; + :symbol "Ag"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Al +:Al rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_13 ; + :period :period_3 ; + :standardState :solid ; + :atomicNumber 13 ; + :atomicWeight "26.981539"^^xsd:float ; + :casRegistryID "7429-90-5"^^xsd:string ; + :color "silvery"^^xsd:string ; + :name "aluminium"^^xsd:string ; + :symbol "Al"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Am +:Am rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 95 ; + :atomicWeight "243.0"^^xsd:float ; + :casRegistryID "7440-35-9"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "americium"^^xsd:string ; + :symbol "Am"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ar +:Ar rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_3 ; + :standardState :gas ; + :atomicNumber 18 ; + :atomicWeight "39.948"^^xsd:float ; + :casRegistryID "7440-37-1"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "argon"^^xsd:string ; + :symbol "Ar"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#As +:As rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_15 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 33 ; + :atomicWeight "74.9216"^^xsd:float ; + :casRegistryID "7440-38-2"^^xsd:string ; + :color "metallic grey"^^xsd:string ; + :name "arsenic"^^xsd:string ; + :symbol "As"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#At +:At rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_17 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 85 ; + :atomicWeight "210.0"^^xsd:float ; + :casRegistryID "7440-68-8"^^xsd:string ; + :color "metallic"^^xsd:string ; + :name "astatine"^^xsd:string ; + :symbol "At"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Au +:Au rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_11 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 79 ; + :atomicWeight "196.96655"^^xsd:float ; + :casRegistryID "7440-57-5"^^xsd:string ; + :color "gold"^^xsd:string ; + :name "gold"^^xsd:string ; + :symbol "Au"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#B +:B rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_13 ; + :period :period_2 ; + :standardState :solid ; + :atomicNumber 5 ; + :atomicWeight "10.811"^^xsd:float ; + :casRegistryID "7440-42-8"^^xsd:string ; + :color "black"^^xsd:string ; + :name "boron"^^xsd:string ; + :symbol "B"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ba +:Ba rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_2 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 56 ; + :atomicWeight "137.327"^^xsd:float ; + :casRegistryID "7440-39-3"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "barium"^^xsd:string ; + :symbol "Ba"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Be +:Be rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_2 ; + :period :period_2 ; + :standardState :solid ; + :atomicNumber 4 ; + :atomicWeight "9.012182"^^xsd:float ; + :casRegistryID "7440-41-7"^^xsd:string ; + :color "lead gray"^^xsd:string ; + :name "beryllium"^^xsd:string ; + :symbol "Be"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Bh +:Bh rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_7 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 107 ; + :atomicWeight "264.0"^^xsd:float ; + :casRegistryID "54037-14-8"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "bohrium"^^xsd:string ; + :symbol "Bh"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Bi +:Bi rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_15 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 83 ; + :atomicWeight "208.98038"^^xsd:float ; + :casRegistryID "7440-69-9"^^xsd:string ; + :color "lustrous reddish white"^^xsd:string ; + :name "bismuth"^^xsd:string ; + :symbol "Bi"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Bk +:Bk rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 97 ; + :atomicWeight "247.0"^^xsd:float ; + :casRegistryID "7440-40-6"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "berkelium"^^xsd:string ; + :symbol "Bk"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Br +:Br rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_17 ; + :period :period_4 ; + :standardState :liquid ; + :atomicNumber 35 ; + :atomicWeight "79.904"^^xsd:float ; + :casRegistryID "7726-95-6"^^xsd:string ; + :color "red-brown, metallic lustre when solid"^^xsd:string ; + :name "bromine"^^xsd:string ; + :symbol "Br"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#C +:C rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_14 ; + :period :period_2 ; + :standardState :solid ; + :atomicNumber 6 ; + :atomicWeight "12.0107"^^xsd:float ; + :casRegistryID "7440-44-0"^^xsd:string ; + :color "graphite is black, diamond is colourless"^^xsd:string ; + :name "carbon"^^xsd:string ; + :symbol "C"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ca +:Ca rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_2 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 20 ; + :atomicWeight "40.078"^^xsd:float ; + :casRegistryID "7440-70-2"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "calcium"^^xsd:string ; + :symbol "Ca"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cd +:Cd rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_12 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 48 ; + :atomicWeight "112.411"^^xsd:float ; + :casRegistryID "7440-43-9"^^xsd:string ; + :color "silvery grey metallic"^^xsd:string ; + :name "cadmium"^^xsd:string ; + :symbol "Cd"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ce +:Ce rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 58 ; + :atomicWeight "140.116"^^xsd:float ; + :casRegistryID "7440-45-1"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "cerium"^^xsd:string ; + :symbol "Ce"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cf +:Cf rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 98 ; + :atomicWeight "251.0"^^xsd:float ; + :casRegistryID "7440-71-3"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "californium"^^xsd:string ; + :symbol "Cf"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cl +:Cl rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_17 ; + :period :period_3 ; + :standardState :gas ; + :atomicNumber 17 ; + :atomicWeight "35.453"^^xsd:float ; + :casRegistryID "7782-50-5"^^xsd:string ; + :color "yellowish green"^^xsd:string ; + :name "chlorine"^^xsd:string ; + :symbol "Cl"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cm +:Cm rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 96 ; + :atomicWeight "247.0"^^xsd:float ; + :casRegistryID "7440-51-9"^^xsd:string ; + :color "silver"^^xsd:string ; + :name "curium"^^xsd:string ; + :symbol "Cm"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Co +:Co rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_9 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 27 ; + :atomicWeight "58.9332"^^xsd:float ; + :casRegistryID "7440-48-4"^^xsd:string ; + :color "lustrous, metallic, greyish tinge"^^xsd:string ; + :name "cobalt"^^xsd:string ; + :symbol "Co"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cr +:Cr rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_6 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 24 ; + :atomicWeight "51.9961"^^xsd:float ; + :casRegistryID "7440-47-3"^^xsd:string ; + :color "silvery metallic"^^xsd:string ; + :name "chromium"^^xsd:string ; + :symbol "Cr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cs +:Cs rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_1 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 55 ; + :atomicWeight "132.90546"^^xsd:float ; + :casRegistryID "7440-46-2"^^xsd:string ; + :color "silvery gold"^^xsd:string ; + :name "caesium"^^xsd:string ; + :symbol "Cs"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Cu +:Cu rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_11 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 29 ; + :atomicWeight "63.546"^^xsd:float ; + :casRegistryID "7440-50-8"^^xsd:string ; + :color "copper, metallic"^^xsd:string ; + :name "copper"^^xsd:string ; + :symbol "Cu"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Db +:Db rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_5 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 105 ; + :atomicWeight "262.0"^^xsd:float ; + :casRegistryID "53850-35-4"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "dubnium"^^xsd:string ; + :symbol "Db"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Dy +:Dy rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 66 ; + :atomicWeight "162.5"^^xsd:float ; + :casRegistryID "7429-91-6"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "dysprosium"^^xsd:string ; + :symbol "Dy"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Er +:Er rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 68 ; + :atomicWeight "167.259"^^xsd:float ; + :casRegistryID "7440-52-0"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "erbium"^^xsd:string ; + :symbol "Er"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Es +:Es rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 99 ; + :atomicWeight "252.0"^^xsd:float ; + :casRegistryID "7429-92-7"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "einsteinium"^^xsd:string ; + :symbol "Es"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Eu +:Eu rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 63 ; + :atomicWeight "151.964"^^xsd:float ; + :casRegistryID "7440-53-1"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "europium"^^xsd:string ; + :symbol "Eu"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#F +:F rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_17 ; + :period :period_2 ; + :standardState :gas ; + :atomicNumber 9 ; + :atomicWeight "18.998404"^^xsd:float ; + :casRegistryID "7782-41-4"^^xsd:string ; + :color "pale yellow"^^xsd:string ; + :name "fluorine"^^xsd:string ; + :symbol "F"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Fe +:Fe rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_8 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 26 ; + :atomicWeight "55.845"^^xsd:float ; + :casRegistryID "7439-89-6"^^xsd:string ; + :color "lustrous, metallic, greyish tinge"^^xsd:string ; + :name "iron"^^xsd:string ; + :symbol "Fe"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Fm +:Fm rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 100 ; + :atomicWeight "257.0"^^xsd:float ; + :casRegistryID "7440-72-4"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "fermium"^^xsd:string ; + :symbol "Fm"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Fr +:Fr rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_1 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 87 ; + :atomicWeight "223.0"^^xsd:float ; + :casRegistryID "7440-73-5"^^xsd:string ; + :color "metallic"^^xsd:string ; + :name "francium"^^xsd:string ; + :symbol "Fr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ga +:Ga rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_13 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 31 ; + :atomicWeight "69.723"^^xsd:float ; + :casRegistryID "7440-55-3"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "gallium"^^xsd:string ; + :symbol "Ga"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Gd +:Gd rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 64 ; + :atomicWeight "157.25"^^xsd:float ; + :casRegistryID "7440-54-2"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "gadolinium"^^xsd:string ; + :symbol "Gd"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ge +:Ge rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_14 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 32 ; + :atomicWeight "72.64"^^xsd:float ; + :casRegistryID "7440-56-4"^^xsd:string ; + :color "greyish white"^^xsd:string ; + :name "germanium"^^xsd:string ; + :symbol "Ge"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#H +:H rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Non-metallic ; + :group :group_1 ; + :period :period_1 ; + :standardState :gas ; + :atomicNumber 1 ; + :atomicWeight "1.00794"^^xsd:float ; + :casRegistryID "1333-74-0"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "hydrogen"^^xsd:string ; + :symbol "H"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#He +:He rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_1 ; + :standardState :gas ; + :atomicNumber 2 ; + :atomicWeight "4.002602"^^xsd:float ; + :casRegistryID "7440-59-7"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "helium"^^xsd:string ; + :symbol "He"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Hf +:Hf rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_4 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 72 ; + :atomicWeight "178.49"^^xsd:float ; + :casRegistryID "7440-58-6"^^xsd:string ; + :color "grey steel"^^xsd:string ; + :name "hafnium"^^xsd:string ; + :symbol "Hf"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Hg +:Hg rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_12 ; + :period :period_6 ; + :standardState :liquid ; + :atomicNumber 80 ; + :atomicWeight "200.59"^^xsd:float ; + :casRegistryID "7439-97-6"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "mercury"^^xsd:string ; + :symbol "Hg"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ho +:Ho rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 67 ; + :atomicWeight "164.93031"^^xsd:float ; + :casRegistryID "7440-60-0"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "holmium"^^xsd:string ; + :symbol "Ho"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Hs +:Hs rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_8 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 108 ; + :atomicWeight "269.0"^^xsd:float ; + :casRegistryID "54037-57-9"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "hassium"^^xsd:string ; + :symbol "Hs"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#I +:I rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_17 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 53 ; + :atomicWeight "126.90447"^^xsd:float ; + :casRegistryID "7553-56-2"^^xsd:string ; + :color "violet-dark grey, lustrous"^^xsd:string ; + :name "iodine"^^xsd:string ; + :symbol "I"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#In +:In rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_13 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 49 ; + :atomicWeight "114.818"^^xsd:float ; + :casRegistryID "7440-74-6"^^xsd:string ; + :color "silvery lustrous grey"^^xsd:string ; + :name "indium"^^xsd:string ; + :symbol "In"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ir +:Ir rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_9 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 77 ; + :atomicWeight "192.217"^^xsd:float ; + :casRegistryID "7439-88-5"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "iridium"^^xsd:string ; + :symbol "Ir"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#K +:K rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_1 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 19 ; + :atomicWeight "39.0983"^^xsd:float ; + :casRegistryID "7440-09-7"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "potassium"^^xsd:string ; + :symbol "K"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Kr +:Kr rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_4 ; + :standardState :gas ; + :atomicNumber 36 ; + :atomicWeight "83.798"^^xsd:float ; + :casRegistryID "7439-90-9"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "krypton"^^xsd:string ; + :symbol "Kr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#La +:La rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 57 ; + :atomicWeight "138.9055"^^xsd:float ; + :casRegistryID "7439-91-0"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "lanthanum"^^xsd:string ; + :symbol "La"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Li +:Li rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_1 ; + :period :period_2 ; + :standardState :solid ; + :atomicNumber 3 ; + :atomicWeight "6.941"^^xsd:float ; + :casRegistryID "7439-93-2"^^xsd:string ; + :color "silvery white/grey"^^xsd:string ; + :name "lithium"^^xsd:string ; + :symbol "Li"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Lr +:Lr rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_3 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 103 ; + :atomicWeight "262.0"^^xsd:float ; + :casRegistryID "22537-19-5"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "lawrencium"^^xsd:string ; + :symbol "Lr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Lu +:Lu rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_3 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 71 ; + :atomicWeight "174.967"^^xsd:float ; + :casRegistryID "7439-94-3"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "lutetium"^^xsd:string ; + :symbol "Lu"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Md +:Md rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 101 ; + :atomicWeight "258.0"^^xsd:float ; + :casRegistryID "7440-11-1"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "mendelevium"^^xsd:string ; + :symbol "Md"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Metallic +:Metallic rdf:type owl:NamedIndividual , + :Classification . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Mg +:Mg rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_2 ; + :period :period_3 ; + :standardState :solid ; + :atomicNumber 12 ; + :atomicWeight "24.305"^^xsd:float ; + :casRegistryID "7439-95-4"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "magnesium"^^xsd:string ; + :symbol "Mg"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Mn +:Mn rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_7 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 25 ; + :atomicWeight "54.93805"^^xsd:float ; + :casRegistryID "7439-96-5"^^xsd:string ; + :color "silvery metallic"^^xsd:string ; + :name "manganese"^^xsd:string ; + :symbol "Mn"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Mo +:Mo rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_6 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 42 ; + :atomicWeight "95.94"^^xsd:float ; + :casRegistryID "7439-98-7"^^xsd:string ; + :color "grey metallic"^^xsd:string ; + :name "molybdenum"^^xsd:string ; + :symbol "Mo"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Mt +:Mt rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_9 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 109 ; + :atomicWeight "268.0"^^xsd:float ; + :casRegistryID "54038-01-6"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "meitnerium"^^xsd:string ; + :symbol "Mt"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#N +:N rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_15 ; + :period :period_2 ; + :standardState :gas ; + :atomicNumber 7 ; + :atomicWeight "14.0067"^^xsd:float ; + :casRegistryID "7727-37-9"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "nitrogen"^^xsd:string ; + :symbol "N"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Na +:Na rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_1 ; + :period :period_3 ; + :standardState :solid ; + :atomicNumber 11 ; + :atomicWeight "22.98977"^^xsd:float ; + :casRegistryID "7440-23-5"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "sodium"^^xsd:string ; + :symbol "Na"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Nb +:Nb rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_5 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 41 ; + :atomicWeight "92.90638"^^xsd:float ; + :casRegistryID "7440-03-1"^^xsd:string ; + :color "grey metallic"^^xsd:string ; + :name "niobium"^^xsd:string ; + :symbol "Nb"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Nd +:Nd rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 60 ; + :atomicWeight "144.24"^^xsd:float ; + :casRegistryID "7440-00-8"^^xsd:string ; + :color "silvery white, yellowish tinge"^^xsd:string ; + :name "neodymium"^^xsd:string ; + :symbol "Nd"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ne +:Ne rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_2 ; + :standardState :gas ; + :atomicNumber 10 ; + :atomicWeight "20.1797"^^xsd:float ; + :casRegistryID "7440-01-9"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "neon"^^xsd:string ; + :symbol "Ne"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ni +:Ni rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_10 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 28 ; + :atomicWeight "58.6934"^^xsd:float ; + :casRegistryID "7440-02-0"^^xsd:string ; + :color "lustrous, metallic, silvery tinge"^^xsd:string ; + :name "nickel"^^xsd:string ; + :symbol "Ni"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#No +:No rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 102 ; + :atomicWeight "259.0"^^xsd:float ; + :casRegistryID "10028-14-5"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "nobelium"^^xsd:string ; + :symbol "No"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Non-metallic +:Non-metallic rdf:type owl:NamedIndividual , + :Classification . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Np +:Np rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 93 ; + :atomicWeight "237.0"^^xsd:float ; + :casRegistryID "7439-99-8"^^xsd:string ; + :color "silvery metallic"^^xsd:string ; + :name "neptunium"^^xsd:string ; + :symbol "Np"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#O +:O rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_16 ; + :period :period_2 ; + :standardState :gas ; + :atomicNumber 8 ; + :atomicWeight "15.9994"^^xsd:float ; + :casRegistryID "7782-44-7"^^xsd:string ; + :color "colourless as a gas, liquid is pale blue"^^xsd:string ; + :name "oxygen"^^xsd:string ; + :symbol "O"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Os +:Os rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_8 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 76 ; + :atomicWeight "190.23"^^xsd:float ; + :casRegistryID "7440-04-2"^^xsd:string ; + :color "bluish grey"^^xsd:string ; + :name "osmium"^^xsd:string ; + :symbol "Os"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#P +:P rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_15 ; + :period :period_3 ; + :standardState :solid ; + :atomicNumber 15 ; + :atomicWeight "30.97376"^^xsd:float ; + :casRegistryID "7723-14-0"^^xsd:string ; + :color "colourless/red/silvery white"^^xsd:string ; + :name "phosphorus"^^xsd:string ; + :symbol "P"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pa +:Pa rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 91 ; + :atomicWeight "231.03587"^^xsd:float ; + :casRegistryID "7440-13-3"^^xsd:string ; + :color "silvery metallic"^^xsd:string ; + :name "protactinium"^^xsd:string ; + :symbol "Pa"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pb +:Pb rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_14 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 82 ; + :atomicWeight "207.2"^^xsd:float ; + :casRegistryID "7439-92-1"^^xsd:string ; + :color "bluish white"^^xsd:string ; + :name "lead"^^xsd:string ; + :symbol "Pb"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pd +:Pd rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_10 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 46 ; + :atomicWeight "106.42"^^xsd:float ; + :casRegistryID "7440-05-3"^^xsd:string ; + :color "silvery white metallic"^^xsd:string ; + :name "palladium"^^xsd:string ; + :symbol "Pd"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pm +:Pm rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 61 ; + :atomicWeight "145.0"^^xsd:float ; + :casRegistryID "7440-12-2"^^xsd:string ; + :color "metallic"^^xsd:string ; + :name "promethium"^^xsd:string ; + :symbol "Pm"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Po +:Po rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_16 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 84 ; + :atomicWeight "209.0"^^xsd:float ; + :casRegistryID "7440-08-6"^^xsd:string ; + :color "silvery"^^xsd:string ; + :name "polonium"^^xsd:string ; + :symbol "Po"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pr +:Pr rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 59 ; + :atomicWeight "140.90765"^^xsd:float ; + :casRegistryID "7440-10-0"^^xsd:string ; + :color "silvery white, yellowish tinge"^^xsd:string ; + :name "praseodymium"^^xsd:string ; + :symbol "Pr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pt +:Pt rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_10 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 78 ; + :atomicWeight "195.078"^^xsd:float ; + :casRegistryID "7440-06-4"^^xsd:string ; + :color "greyish white"^^xsd:string ; + :name "platinum"^^xsd:string ; + :symbol "Pt"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Pu +:Pu rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 94 ; + :atomicWeight "244.0"^^xsd:float ; + :casRegistryID "7440-07-5"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "plutonium"^^xsd:string ; + :symbol "Pu"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ra +:Ra rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_2 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 88 ; + :atomicWeight "226.0"^^xsd:float ; + :casRegistryID "7440-14-4"^^xsd:string ; + :color "metallic"^^xsd:string ; + :name "radium"^^xsd:string ; + :symbol "Ra"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Rb +:Rb rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_1 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 37 ; + :atomicWeight "85.4678"^^xsd:float ; + :casRegistryID "7440-17-7"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "rubidium"^^xsd:string ; + :symbol "Rb"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Re +:Re rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_7 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 75 ; + :atomicWeight "186.207"^^xsd:float ; + :casRegistryID "7440-15-5"^^xsd:string ; + :color "greyish white"^^xsd:string ; + :name "rhenium"^^xsd:string ; + :symbol "Re"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Rf +:Rf rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_4 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 104 ; + :atomicWeight "261.0"^^xsd:float ; + :casRegistryID "53850-36-5"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "rutherfordium"^^xsd:string ; + :symbol "Rf"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Rh +:Rh rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_9 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 45 ; + :atomicWeight "102.9055"^^xsd:float ; + :casRegistryID "7440-16-6"^^xsd:string ; + :color "silvery white metallic"^^xsd:string ; + :name "rhodium"^^xsd:string ; + :symbol "Rh"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Rn +:Rn rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_6 ; + :standardState :gas ; + :atomicNumber 86 ; + :atomicWeight "222.0"^^xsd:float ; + :casRegistryID "10043-92-2"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "radon"^^xsd:string ; + :symbol "Rn"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ru +:Ru rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_8 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 44 ; + :atomicWeight "101.07"^^xsd:float ; + :casRegistryID "7440-18-8"^^xsd:string ; + :color "silvery white metallic"^^xsd:string ; + :name "ruthenium"^^xsd:string ; + :symbol "Ru"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#S +:S rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_16 ; + :period :period_3 ; + :standardState :solid ; + :atomicNumber 16 ; + :atomicWeight "32.065"^^xsd:float ; + :casRegistryID "7704-34-9"^^xsd:string ; + :color "lemon yellow"^^xsd:string ; + :name "sulpher"^^xsd:string ; + :symbol "S"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Sb +:Sb rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_15 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 51 ; + :atomicWeight "121.76"^^xsd:float ; + :casRegistryID "7440-36-0"^^xsd:string ; + :color "silvery lustrous grey"^^xsd:string ; + :name "antimony"^^xsd:string ; + :symbol "Sb"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Sc +:Sc rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_3 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 21 ; + :atomicWeight "44.95591"^^xsd:float ; + :casRegistryID "7440-20-2"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "scandium"^^xsd:string ; + :symbol "Sc"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Se +:Se rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_16 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 34 ; + :atomicWeight "78.96"^^xsd:float ; + :casRegistryID "7782-49-2"^^xsd:string ; + :color "grey, metallic lustre"^^xsd:string ; + :name "selenium"^^xsd:string ; + :symbol "Se"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Semi-metallic +:Semi-metallic rdf:type owl:NamedIndividual , + :Classification . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Sg +:Sg rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_6 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 106 ; + :atomicWeight "266.0"^^xsd:float ; + :casRegistryID "54038-81-2"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "seaborgium"^^xsd:string ; + :symbol "Sg"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Si +:Si rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_14 ; + :period :period_3 ; + :standardState :solid ; + :atomicNumber 14 ; + :atomicWeight "28.0855"^^xsd:float ; + :casRegistryID "7440-21-3"^^xsd:string ; + :color "dark grey with a bluish tinge"^^xsd:string ; + :name "silicon"^^xsd:string ; + :symbol "Si"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Sm +:Sm rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 62 ; + :atomicWeight "150.36"^^xsd:float ; + :casRegistryID "7440-19-9"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "samarium"^^xsd:string ; + :symbol "Sm"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Sn +:Sn rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_14 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 50 ; + :atomicWeight "118.71"^^xsd:float ; + :casRegistryID "7440-31-5"^^xsd:string ; + :color "silvery lustrous grey"^^xsd:string ; + :name "tin"^^xsd:string ; + :symbol "Sn"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Sr +:Sr rdf:type owl:NamedIndividual , + :Element ; + :block :s-block ; + :classification :Metallic ; + :group :group_2 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 38 ; + :atomicWeight "87.62"^^xsd:float ; + :casRegistryID "7440-24-6"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "strontium"^^xsd:string ; + :symbol "Sr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ta +:Ta rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_5 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 73 ; + :atomicWeight "180.9479"^^xsd:float ; + :casRegistryID "7440-25-7"^^xsd:string ; + :color "grey blue"^^xsd:string ; + :name "tantalum"^^xsd:string ; + :symbol "Ta"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Tb +:Tb rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 65 ; + :atomicWeight "158.92534"^^xsd:float ; + :casRegistryID "7440-27-9"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "terbium"^^xsd:string ; + :symbol "Tb"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Tc +:Tc rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_7 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 43 ; + :atomicWeight "98.0"^^xsd:float ; + :casRegistryID "7440-26-8"^^xsd:string ; + :color "silvery grey metallic"^^xsd:string ; + :name "technetium"^^xsd:string ; + :symbol "Tc"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Te +:Te rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Semi-metallic ; + :group :group_16 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 52 ; + :atomicWeight "127.6"^^xsd:float ; + :casRegistryID "13494-80-9"^^xsd:string ; + :color "silvery lustrous grey"^^xsd:string ; + :name "tellurium"^^xsd:string ; + :symbol "Te"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Th +:Th rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 90 ; + :atomicWeight "232.0381"^^xsd:float ; + :casRegistryID "7440-29-1"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "thorium"^^xsd:string ; + :symbol "Th"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Ti +:Ti rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_4 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 22 ; + :atomicWeight "47.867"^^xsd:float ; + :casRegistryID "7440-32-6"^^xsd:string ; + :color "silvery metallic"^^xsd:string ; + :name "titanium"^^xsd:string ; + :symbol "Ti"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Tl +:Tl rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_13 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 81 ; + :atomicWeight "204.3833"^^xsd:float ; + :casRegistryID "7440-28-0"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "thallium"^^xsd:string ; + :symbol "Tl"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Tm +:Tm rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 69 ; + :atomicWeight "168.9342"^^xsd:float ; + :casRegistryID "7440-30-4"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "thulium"^^xsd:string ; + :symbol "Tm"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#U +:U rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_actinoid ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 92 ; + :atomicWeight "238.02892"^^xsd:float ; + :casRegistryID "7440-61-1"^^xsd:string ; + :color "metallic grey"^^xsd:string ; + :name "uranium"^^xsd:string ; + :symbol "U"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uub +:Uub rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_12 ; + :period :period_7 ; + :standardState :liquid ; + :atomicNumber 112 ; + :atomicWeight "285.0"^^xsd:float ; + :casRegistryID "54084-26-3"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "ununbium"^^xsd:string ; + :symbol "Uub"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uuh +:Uuh rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_16 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 116 ; + :casRegistryID "54100-71-9"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "ununhexium"^^xsd:string ; + :symbol "Uuh"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uun +:Uun rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_10 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 110 ; + :atomicWeight "271.0"^^xsd:float ; + :casRegistryID "54083-77-1"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "ununnilium"^^xsd:string ; + :symbol "Uun"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uuo +:Uuo rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_7 ; + :standardState :gas ; + :atomicNumber 118 ; + :casRegistryID "54144-19-3"^^xsd:string ; + :color "unknown, but probably a colourless gas"^^xsd:string ; + :name "ununoctium"^^xsd:string ; + :symbol "Uuo"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uup +:Uup rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :group :group_15 ; + :period :period_7 ; + :standardState :state_unknown ; + :atomicNumber 115 ; + :name "ununpentium"^^xsd:string ; + :symbol "Uup"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uuq +:Uuq rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Metallic ; + :group :group_14 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 114 ; + :atomicWeight "289.0"^^xsd:float ; + :casRegistryID "54085-16-4"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "ununquadium"^^xsd:string ; + :symbol "Uuq"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uus +:Uus rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :group :group_17 ; + :period :period_7 ; + :standardState :state_unknown ; + :atomicNumber 117 ; + :name "ununseptium"^^xsd:string ; + :symbol "Uus"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uut +:Uut rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :group :group_13 ; + :period :period_7 ; + :standardState :state_unknown ; + :atomicNumber 113 ; + :name "ununtrium"^^xsd:string ; + :symbol "Uut"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Uuu +:Uuu rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_11 ; + :period :period_7 ; + :standardState :solid ; + :atomicNumber 111 ; + :atomicWeight "272.0"^^xsd:float ; + :casRegistryID "54386-24-2"^^xsd:string ; + :color "unknown, but probably metallic and silvery white or grey in appearance"^^xsd:string ; + :name "unununium"^^xsd:string ; + :symbol "Uuu"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#V +:V rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_5 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 23 ; + :atomicWeight "50.9415"^^xsd:float ; + :casRegistryID "7440-62-2"^^xsd:string ; + :color "silvery grey metallic"^^xsd:string ; + :name "vanadium"^^xsd:string ; + :symbol "V"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#W +:W rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_6 ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 74 ; + :atomicWeight "183.84"^^xsd:float ; + :casRegistryID "7440-33-7"^^xsd:string ; + :color "greyish white, lustrous"^^xsd:string ; + :name "tungsten"^^xsd:string ; + :symbol "W"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Xe +:Xe rdf:type owl:NamedIndividual , + :Element ; + :block :p-block ; + :classification :Non-metallic ; + :group :group_18 ; + :period :period_5 ; + :standardState :gas ; + :atomicNumber 54 ; + :atomicWeight "131.293"^^xsd:float ; + :casRegistryID "7440-63-3"^^xsd:string ; + :color "colourless"^^xsd:string ; + :name "xenon"^^xsd:string ; + :symbol "Xe"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Y +:Y rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_3 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 39 ; + :atomicWeight "88.90585"^^xsd:float ; + :casRegistryID "7440-65-5"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "yttrium"^^xsd:string ; + :symbol "Y"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Yb +:Yb rdf:type owl:NamedIndividual , + :Element ; + :block :f-block ; + :classification :Metallic ; + :group :group_lanthanoid ; + :period :period_6 ; + :standardState :solid ; + :atomicNumber 70 ; + :atomicWeight "173.04"^^xsd:float ; + :casRegistryID "7440-64-4"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "ytterbium"^^xsd:string ; + :symbol "Yb"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Zn +:Zn rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_12 ; + :period :period_4 ; + :standardState :solid ; + :atomicNumber 30 ; + :atomicWeight "65.409"^^xsd:float ; + :casRegistryID "7440-66-6"^^xsd:string ; + :color "bluish pale grey"^^xsd:string ; + :name "zinc"^^xsd:string ; + :symbol "Zn"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#Zr +:Zr rdf:type owl:NamedIndividual , + :Element ; + :block :d-block ; + :classification :Metallic ; + :group :group_4 ; + :period :period_5 ; + :standardState :solid ; + :atomicNumber 40 ; + :atomicWeight "91.224"^^xsd:float ; + :casRegistryID "7440-67-7"^^xsd:string ; + :color "silvery white"^^xsd:string ; + :name "zirconium"^^xsd:string ; + :symbol "Zr"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#d-block +:d-block rdf:type owl:NamedIndividual , + :Block . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#f-block +:f-block rdf:type owl:NamedIndividual , + :Block . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#gas +:gas rdf:type owl:NamedIndividual , + :StandardState . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_1 +:group_1 rdf:type owl:NamedIndividual , + :Group ; + :element :Cs , + :Fr , + :H , + :K , + :Li , + :Na , + :Rb ; + :name "Alkali metal"^^xsd:string ; + :number 1 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_10 +:group_10 rdf:type owl:NamedIndividual , + :Group ; + :element :Ni , + :Pd , + :Pt , + :Uun ; + :number 10 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_11 +:group_11 rdf:type owl:NamedIndividual , + :Group ; + :element :Ag , + :Au , + :Cu , + :Uuu ; + :name "Coinage metal"^^xsd:string ; + :number 11 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_12 +:group_12 rdf:type owl:NamedIndividual , + :Group ; + :element :Cd , + :Hg , + :Uub , + :Zn ; + :number 12 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_13 +:group_13 rdf:type owl:NamedIndividual , + :Group ; + :element :Al , + :B , + :Ga , + :In , + :Tl , + :Uut ; + :number 13 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_14 +:group_14 rdf:type owl:NamedIndividual , + :Group ; + :element :C , + :Ge , + :Pb , + :Si , + :Sn , + :Uuq ; + :number 14 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_15 +:group_15 rdf:type owl:NamedIndividual , + :Group ; + :element :As , + :Bi , + :N , + :P , + :Sb , + :Uup ; + :name "Pnictogen"^^xsd:string ; + :number 15 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_16 +:group_16 rdf:type owl:NamedIndividual , + :Group ; + :element :O , + :Po , + :S , + :Se , + :Te , + :Uuh ; + :name "Chalcogen"^^xsd:string ; + :number 16 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_17 +:group_17 rdf:type owl:NamedIndividual , + :Group ; + :element :At , + :Br , + :Cl , + :F , + :I , + :Uus ; + :name "Halogen"^^xsd:string ; + :number 17 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_18 +:group_18 rdf:type owl:NamedIndividual , + :Group ; + :element :Ar , + :He , + :Kr , + :Ne , + :Rn , + :Uuo , + :Xe ; + :name "Noble gas"^^xsd:string ; + :number 18 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_2 +:group_2 rdf:type owl:NamedIndividual , + :Group ; + :element :Ba , + :Be , + :Ca , + :Mg , + :Ra , + :Sr ; + :name "Alkaline earth metal"^^xsd:string ; + :number 2 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_3 +:group_3 rdf:type owl:NamedIndividual , + :Group ; + :element :Lr , + :Lu , + :Sc , + :Y ; + :number 3 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_4 +:group_4 rdf:type owl:NamedIndividual , + :Group ; + :element :Hf , + :Rf , + :Ti , + :Zr ; + :number 4 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_5 +:group_5 rdf:type owl:NamedIndividual , + :Group ; + :element :Db , + :Nb , + :Ta , + :V ; + :number 5 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_6 +:group_6 rdf:type owl:NamedIndividual , + :Group ; + :element :Cr , + :Mo , + :Sg , + :W ; + :number 6 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_7 +:group_7 rdf:type owl:NamedIndividual , + :Group ; + :element :Bh , + :Mn , + :Re , + :Tc ; + :number 7 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_8 +:group_8 rdf:type owl:NamedIndividual , + :Group ; + :element :Fe , + :Hs , + :Os , + :Ru ; + :number 8 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_9 +:group_9 rdf:type owl:NamedIndividual , + :Group ; + :element :Co , + :Ir , + :Mt , + :Rh ; + :number 9 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_actinoid +:group_actinoid rdf:type owl:NamedIndividual , + :Group ; + :element :Ac , + :Am , + :Bk , + :Cf , + :Cm , + :Es , + :Fm , + :Md , + :No , + :Np , + :Pa , + :Pu , + :Th , + :U ; + :name "Actinoid"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#group_lanthanoid +:group_lanthanoid rdf:type owl:NamedIndividual , + :Group ; + :element :Ce , + :Dy , + :Er , + :Eu , + :Gd , + :Ho , + :La , + :Nd , + :Pm , + :Pr , + :Sm , + :Tb , + :Tm , + :Yb ; + :name "Lanthanoid"^^xsd:string . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#liquid +:liquid rdf:type owl:NamedIndividual , + :StandardState . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#p-block +:p-block rdf:type owl:NamedIndividual , + :Block . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_1 +:period_1 rdf:type owl:NamedIndividual , + :Period ; + :element :H , + :He ; + :number 1 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_2 +:period_2 rdf:type owl:NamedIndividual , + :Period ; + :element :B , + :Be , + :C , + :F , + :Li , + :N , + :Ne , + :O ; + :number 2 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_3 +:period_3 rdf:type owl:NamedIndividual , + :Period ; + :element :Al , + :Ar , + :Cl , + :Mg , + :Na , + :P , + :S , + :Si ; + :number 3 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_4 +:period_4 rdf:type owl:NamedIndividual , + :Period ; + :element :As , + :Br , + :Ca , + :Co , + :Cr , + :Cu , + :Fe , + :Ga , + :Ge , + :K , + :Kr , + :Mn , + :Ni , + :Sc , + :Se , + :Ti , + :V , + :Zn ; + :number 4 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_5 +:period_5 rdf:type owl:NamedIndividual , + :Period ; + :element :Ag , + :Cd , + :I , + :In , + :Mo , + :Nb , + :Pd , + :Rb , + :Rh , + :Ru , + :Sb , + :Sn , + :Sr , + :Tc , + :Te , + :Xe , + :Y , + :Zr ; + :number 5 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_6 +:period_6 rdf:type owl:NamedIndividual , + :Period ; + :element :At , + :Au , + :Ba , + :Bi , + :Ce , + :Cs , + :Dy , + :Er , + :Eu , + :Gd , + :Hf , + :Hg , + :Ho , + :Ir , + :La , + :Lu , + :Nd , + :Os , + :Pb , + :Pm , + :Po , + :Pr , + :Pt , + :Re , + :Rn , + :Sm , + :Ta , + :Tb , + :Tl , + :Tm , + :W , + :Yb ; + :number 6 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#period_7 +:period_7 rdf:type owl:NamedIndividual , + :Period ; + :element :Ac , + :Am , + :Bh , + :Bk , + :Cf , + :Cm , + :Db , + :Es , + :Fm , + :Fr , + :Hs , + :Lr , + :Md , + :Mt , + :No , + :Np , + :Pa , + :Pu , + :Ra , + :Rf , + :Sg , + :Th , + :U , + :Uub , + :Uuh , + :Uun , + :Uuo , + :Uup , + :Uuq , + :Uus , + :Uut , + :Uuu ; + :number 7 . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#s-block +:s-block rdf:type owl:NamedIndividual , + :Block . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#solid +:solid rdf:type owl:NamedIndividual , + :StandardState . + + +### http://www.daml.org/2003/01/periodictable/PeriodicTable#state_unknown +:state_unknown rdf:type owl:NamedIndividual , + :StandardState . + + +### Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi diff --git a/external/gc07.owl b/external/gc07.owl new file mode 100644 index 0000000..8f996e8 --- /dev/null +++ b/external/gc07.owl @@ -0,0 +1,6015 @@ + + + + + + 0.7.0 + An ontology for publishing results of computational chemistry. + Chemical Semantics, Inc. + + + GNVC: Gainesville Core Ontology - standard for publishing results of computational chemistry. + 2015-03-04 + This ontology aims at complete description of typical Computational Chemistry experiment. + + Gainesville Core describes: + - Molecular Publications + - Molecular Systems + - Molecular Calculations +   + Molecular Systems contains Molecules + The Molecules may have Residues (for biopolymers and polymers) + Molecular Calculations contain Initial Data and Results + The Initial Data may have Methods, Basis Sets, Functionals, etc. + The Results may have Energies, Wave Functions and Spectra, etc. + Gainesville Core Ontology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This annotation should be used to mark entities as abstract. + Abstract entity is a defined OWL resource that from a data model should never be defined explicitly. + + NOTE! + Since it's only a annotation property, it doesn't impact a logical definition of an Entity. Such a property should be treated as a "side note". + + is abstract + + + + + + + + + Such a annotation contains information about defined in DMS ontology Axiom status. + Since it's a text based value, follwing enumerations should be used as values: + + - STABLE (Entity was tested during QA process and is stable) + - UNSTABLE (Entity is unstable due to some reasone - shouldn't be use till fixed) + - TESTING (Entity is under testing process) + - ARCHAIC (old and unused definition - probably will be removed in comming iterations) + - DEPRECATED (Entity is deprecated due to some reason - should not be used) + - NEW (new definition) + - FIX (definition that was made to bring fix for some issue) + + NOTE! + Since it's only a annotation property, it doesn't impact a logical definition of an Entity. Such a property should be treated as a "side note". + + term status + + + + + + + + + This property is a status description of a particular Entity. Combined with log:termStatus contains information aboud current status of an Entity, with a information about history, changes, etc. + + NOTE! + Since it's only a annotation property, it doesn't impact a logical definition of an Entity. Such a property should be treated as a "side note". + + term status note + + + + + + + + + + + + + + + + + + + + + A generic atomic property + Atom Property + + + + + + + + + A generic system property + System Property + + + + + + + + + + + A property that tells which atoms are bonded. + + the act of binding of atoms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes atoms comprised by a molecule or residue + + has atom + + + + + + + + + + + + A property that describes Atom X coordinate + Atom Coordinate X + + + + + + + + + + + + A property that describes Atom Y coordinate + Atom Coordinate Y + + + + + + + + + + + + A property that describes Atom Z coordinate + Atom Coordinate Z + + + + + + + + + + + + + + + + + + + + + A property that describes teh author + Author + + + + + + + + + + The upper property for various properties related to publications + + Generic Auxiliary Property + + + + + + + + + A property that specifies the Basis Count. + The Basis Count + + + + + + + + + + + + + + + + + + + + + + + + A property that allows to assign the Binding Energy to the molecular system + + has binding energy + + + + + + + + + + + A property that allows the bond to be assigned to atoms. + + has bond + + + + + + + + + + + A property that allows bond length to be assigned the a bond. + + has bond length + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes the atom charge calculated by a specific methodology. + + has calculated atom charge + + + + + + + + + A property that specifies the calculation. + Calculation + + + + + + + + + + A property that tells whether the molecular system has calculations done. + + has calculation on + + + + + + + + + A property that specifies the Collection Entry. + Collection Entry + + + + + + + + + + + A property that describes atom coordinates. + + has coordinates + + + + + + + + + + + A property that describes system correlation energy. + + has correlation Energy + + + + + + + + + + + A property that describes the correlation functional for the given methodology. + + + + + + + + + + + + A property that describes specific approximations to exchange-correlation functionals in the Density Functional Theory. + + + + + + + + + + + + A property that describes DFT Functionals for the given methodology. + + + + + + + + + + + + A property that describes molecular dipole moment. + + has dipole moment + + + + + + + + + + + A property that describes the average molecular dipole moment. + + has dipole moment average + + + + + + + + + + + + A property that reports dipole moment X component + Dipole Moment X component + + + + + + + + + + + + A property ... + Dipole Moment Y component + + + + + + + + + + + + A property ... + Dipole Moment Z component + + + + + + + + + true + A property that describes molecular dipole moment. + + has dipole result + + + + + + + + + + + A property that describes the dispersion correction + + + + + + + + + + + + A property that describes the electronic energy. + + has electronic energy + + + + + + + + + A property that describes the electronic spectra. + + has electronic spectra result + + + + + + + + + + + A property that describes electronic transition energies. + + has electronic transitions + + + + + + + + + + + A property that describes the exchange functionals. + + has exchange functional + + + + + + + + + + + + + + + + + + + + A property that describes a specific feature of given methodology. + has feature + + + + + + + + + + + + + + + + + + + A property that specifies the Float Vector. + Float Vector + + + + + + + + + + + + + + + + + + + + + + + A property that descibes the formal charge. The formal charge is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity. + + has formal charge + + + + + + + + + + + A property that describes the value of a frequency at the peak of the spectrum. + + has frequency + + + + + + + + + + + + + A property that describes the value of a frequency peak of the vibrational spectrum. + + has frequency peak + + + + + + + + + A property that specifies the Group Property. + Group Property + + + + + + + + + + + A property that describes the value of a the Heat of Formation. + + has heat of formation + + + + + + + + + + A property that describes Molecular System + IR Spectrum + + + + + + + + + A property that specifies the Integer Vector. + Integer Vector + + + + + + + + + + + A property that describes the value of the intensity of a peak of a spectrum. + + has Intensity + + + + + + + + + A property describes keywords for running QC jobs + Keyword + + + + + + + + + + + + + + + + + + + + + + A property that specifies MathML object. + Math ML + + + + + + + + + + A property that specifies MathML Equation. + Math ML Equation + + + + + + + + + + + + + + + + + + + A property that specifies the Molecular Collection. + Molecular Collection + + + + + + + + + + + A property that describes Molecular Computation + Molecular Computation + + + + + + + + + + + + + + + + + + The upper property for various properties related to molecular systems + + Generic Molecular Property + + + + + + + + + + + A property ... + Molecular System + + + + + + + + + A property that specifies a molecule. + Molecule + + + + + + + + + A property that specifies the Molecule Property. + Molecule Property + + + + + + + + + + + A property that describes computed Mulliken Charges. + + has Mulliken charges + + + + + + + + + + + + + + + + + + + A property that describes Multiple Reference State + Multiple Reference State + + + + + + + + + + + A property that describes computed NMR Shielding Anisotropic component. + + has nmr shielding anisotropy + + + + + + + + + + + A property that describes computed NMR Shielding Isotropic component + + has nmr shielding isotropic + + + + + + + + + + + A property that describes the normal mode of a vibration + + has normal mode + + + + + + + + + + + A property that describes the potential energy arising from Coulombic nuclei-nuclei repulsions + + has nuclear repulsion energy + + + + + + + + + + + A property that describes the number of basis functions. + + + + + + + + + + + + A property that describes the occupancy of the orbital + + has occupancy + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes the orbital. + + has orbital + + + + + + + + + + + + + + + + + + + A property that describes the orbital energy. + + has orbital energy + + + + + + + + + + + + + + + + + + + + A property that defines oscillator strengths of electronic spectra. + + has oscillator strength + + + + + + + + + A property that specifies the Output file. + Output File + + + + + + + + + A property that specifies a parameter. + Parameter + + + + + + + + + + + + + + + + + + + + + A property Value + Property Value + + + + + + + + + + + A property that relates publication to publisher + Publisher of the publication + + + + + + + + + A property that defines quantity + Quantity + + + + + + + + + + + + + + + + + + + A property that describes RMS gradient of the computations. + + has RMS Gradient + + + + + + + + + + + + A property that describes the residue in a molecule. + + has residue + + + + + + + + + A property that specifies the Residue Property. + Residue Property + + + + + + + + + + A property that describes generic results of the computations. + + has result + + + + + + + + + + A property ... + Scope of something (??) + + + + + + + + + + + A property that describes an NMR shielding of an atom. + + has shielding + + + + + + + + + + A property ... + Single Determinant Type + + + + + + + + + + A property ... + Single Reference State + + + + + + + + + + A property that describes Reference State Type + Single Reference State Type + + + + + + + + + + + + + + + + + + + + A property that defines relations that allows to describe Source Package for Publication. + + has source package + + + + + + + + + + + + + + + + + + + + + + A property that describes molecular system charge. + + has system charge + + + + + + + + + true + A property that describes system energies. + + has system energies result + + + + + + + + + + + + + + + + + + + + A property ... + System Property + + + + + + + + + + + A property that describes system temperature. + + has system temperature + + + + + + + + + + + A property that describes Total Potential Energy. + + has total potential energy + + + + + + + + + + + + + + + + + + + + + A property that describes a unit of the value. + + has unit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes Wave Function Coefficients. + + has wave function coefficients + + + + + + + + + A property that specifies the XY Point. + XY Point + + + + + + + + + A property that defines objects held by a container. + + holds + + + + + + + + + A property that specifies the object of the calculation. + Calculation On + + + + + + + + + + + A property that describes what element the given atom is. + + is element + + + + + + + + + + A property that describes related entity. + + related entity + + + + + + + + + A property that specifies the use of Molecular Calculation. + The use of Molecular Calculation + + + + + + + + + A property that specifies the use of Molecular System. + The use of Molecular System + + + + + + + + + + A property that describes what is on xAxis + x Axis + + + + + + + + + A property that describes Units of X Axis + X Axis Unit + + + + + + + + + + A property that describes what is on Axis + Y Axis + + + + + + + + + + A property that describes Units of X Axis + Y Axis Unit + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that allows to declare total count of atoms in a given structure - Molecular System or Molecule or Residue. + + has number of atoms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that determinates the count of bonds into Molecule, Residue or Atom. + + has bond count + + + + + + + + + + + + + + + + + + + + + + + + + A property that determines a category of the publication. + + has category + + + + + + + + + + + A property that defines chain number in the molecule. + + has chain number + + + + + + + + + + + + A property that defines the Symbol of the element of an atom. + + has element symbol + + + + + + + + + + + A property that describes the email address of corresponding author. + has email + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes the first name of corresponding author. + has first name + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes the InChI Key - the condensed, 27 character hashed version of the InChI String. + + has InChI key + + + + + + + + + + + + A property that describes the InChI String - International Chemical Identifier - a textual identifier for chemical substances. + + has InChI string + + + + + + + + + + A property that defines a sequential arrangement of material in numerical order, i.e. Frequency Peak, Orbital or a sequence number in residue. + + has index + + + + + + + + + + + A property that defines the contents of the input file of the calculation. + + has input + + + + + + + + + + + A property that specifies input file for calculations. + Input File + + + + + + + + + + A property that defines the insertion code for residue numbering. + + has insertion code + + + + + + + + + + + + A property that describes Integer Value. + + has integer value + + + + + + + + + + + A property that defines the security key of the publication. + + has key + + + + + + + + + + + A property that describes the last name of corresponding author. + has last name + + + + + + + + + + + + + + + + + + + A property that defines the calculation method for given technology. + + has method + + + + + + + + The upper property for various properties related to computational methods + + Generic Datatype Property for Molecular Features related to methods of computations + + + + + + + + + + + + + + + + + The upper property for various properties related to Molecular Data + + Generic Datatype Property for Molecular Data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that defines the name of molecular system elements, i.e. atom or residue. + The name of an entity. + + has name + + + + + + + + + + + + A property that defines natural value. + + has natural value + + + + + + + + + A property of having a number + Number + + + + + + + + + + A property that determines the number of atoms in a given collection + A property that determines the number of atoms in a given collection + Number of Atoms + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes the organization of corresponding author. + has organization + + + + + + + + + + + The property that defines the contents of the output file of the calculation. + + has output + + + + + + + + + + + + + + + + + + + + + + + A property that determinates the count of peaks in a spectrum. + + Peak Count + has Peak Count + + + + + + + + + + + A property that reports property count + Property Count + + + + + + + + The upper property for various properties related to the publication data + + Generic Datatype Property for Publication data + + + + + + + + + + + + + + + + + + + A property that defines the three-dimensional form of local segments of biopolymers. + + has secondary structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + A property that describes the status of the publication. + has status + + + + + + + + + + + + + + + + + + + A property that reports tags assigned to publication + Tag for the calculation + + + + + + + + + + + A property that describes the calculation's technology for molecular system. + + has technology + + + + + + + + + A property ... + Text Value + + + + + + + + + + + + + + + + + + + + + + + + + + + + A Superproperty of typed numerical values. + + has value + + + + + + + + + + + + A property that describes the vector values. + + has vector value + + + + + + + + + + + A property that describes the version of the software package used. + + has version + + + + + + + + + + + + + + + + + + + A property that defines the allowed visibility of the publication. + + has visibility + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A class for Self Consistent Field methods (Hartree-Fock methods) for approximate solution of Schrödinger equation for quantum many body system. + Ab initio SCF + + + + + + + + + A class for AbinitioScf. + + AbinitioScf + + + + + + + + + A class for the Correlation Consistent basis sets. + + Ahlrichs Basis Set + + + + + + + + + A class for AlphaOrbital. + + AlphaOrbital + + + + + + + + + A class for bonds with aromatic character + + Aromatic Bond + + + + + + + + + + + + A class for Atom. + A class for atoms, the basic unit of matter. + + Atom + Atoms + + + + + + + + + A class for AtomCoordinateX. + + AtomCoordinateX + + + + + + + + + A class for AtomCoordinateY. + + AtomCoordinateY + + + + + + + + + A class for AtomCoordinateZ. + + AtomCoordinateZ + + + + + + + + + A class for AtomCoordinates. + + AtomCoordinates + + + + + + + + + A class for AtomProperty. + + AtomProperty + + + + + + + + + A class for AtomicMass. + + AtomicMass + + + + + + + + + A class for all authors of this publication. + + Author + + + + + + + + A generic class representing Auxiliary concepts. + Auxiliary Concept + + + + + + + + + Becke-Lee-Yang-Parr hybrid functional. + + B3LYP + + + + + + + + + The Becke 1997 hybrid functional. + + B97 + + + + + + + + + Becke-Lee-Yang-Parr functional. + + BLYP + + + + + + + + + A class for the Born-Oppenheimer molecular dynamics computations on molecular systems. + + Born-Oppenheimer Molecular Dynamics Computation + + + + + + + + + Becke-Perdew86 functional. + + BP86 + + + + + + + + + A class for the basis set. In computational chemistry basis set is a set of functions which are combined to create molecular orbitals. + + Basis Set + + + + + + + + + Becke 1988 exchange functional + + Becke88 + + + + + + + + + A class for BetaOrbital. + + BetaOrbital + + + + + + + + + + + + + + + + + + + + + + + A class for the complete active space perturbation theory methods. + + CASPT2 + + + + + + + + + A class for the Complete Active Space Multiconfiguration SCF (CASSCF) method. + + CASSCF + + + + + + + + + A class for the coupled cluster method. + + CC + + + + + + + + + A class for the coupled cluster method with a treatment singles, doubles. + + CC(2) + + + + + + + + + A class for the coupled cluster method with a treatment singles, doubles, and triples. + + CC(3) + + + + + + + + + A class for the coupled cluster method with a treatment singles, doubles. + + CC2 + + + + + + + + + A class for the coupled cluster method with a treatment singles, doubles, and triples. + + CC3 + + + + + + + + + A class for the coupled cluster method with double substitutions. + + CCD + + + + + + + + + A class for the CCDZ Correlation Consistent Double Zeta basis sets. + + CC-DoubleZeta Basis Set + + + + + + + + + A class for the CCQZ Correlation Consistent Quadrupole Zeta basis sets. + + CC-QuadrupleZeta Basis Set + + + + + + + + + A class for the CC5Z Correlation Consistent Quintuple Zeta basis sets. + + CC-QuintupleZeta Basis Set + + + + + + + + + A class for the coupled cluster method with a full treatment singles and doubles. + + CCSD + + + + + + + + + A class for the coupled cluster method with a full treatment singles, doubles and approximate treatment of triple excitations. + + CCSD[T] + + + + + + + + + A class for the coupled cluster method with a full treatment singles and doubles and approximate treatment of triple excitations. + + CCSD(T) + + + + + + + + + A class for the coupled cluster method with a full treatment singles, doubles, and triples. + + CCSDT + + + + + + + + + A class for the coupled cluster method with a full treatment singles, doubles and approximate treatment of triple excitations. + + CCSDT-1A + + + + + + + + + A class for the coupled cluster method with a full treatment singles, doubles and approximate treatment of triple excitations. + + CCSDT-1B + + + + + + + + + A class for the second-order coupled cluster method. + + CCSecondOrder + + + + + + + + + A class for the third-order coupled cluster method. + + CCThirdOrder + + + + + + + + + A class for the third-order perturbative coupled cluster method. + + CCThirdOrderPerturbative + + + + + + + + + A class for the third-order self-consistent coupled cluster method. + + CCThirdOrderSelfConsistent + + + + + + + + + A class for the CCTZ Correlation Consistent Triple Zeta basis sets. + + CC-TripleZeta Basis Set + + + + + + + + + A class for the configuration interaction (CI) method. + + CI + + + + + + + + + A class for the configuration interaction (CI) method with single substitutions. + + CIS + + + + + + + + + A class for the configuration interaction (CI) method with single and double substitutions. + + CISD + + + + + + + + + A class for the Car-Parinello type of molecular dynamics computations on molecular systems. + + Car-Pariinello Molecular Dynamics Computation + + + + + + + + + CSXVersion class. + CSXVersion + + + + + + + + + A class for the properties of the intersection of two atoms calculated in the course of computational chemistry procedure, such as spin-spin coupling + + Calculated Atom-Atom Properties + + + + + + + + + A class for CalculatedAtomCharge. + + CalculatedAtomCharge + + + + + + + + + A class for the properties of an atom calculated in the course of computational chemistry procedure. + + Calculated Atomic Properties + + + + + + + + + A class for the properties of a molecule calculated in the course of computational chemistry procedure. + + Calculated Properties of a molecule + + + + + + + + + A class for the properties of calculated in the course of computational chemistry procedure. + + Calculated Properties + + + + + + + + + A class for CalculatedProperty. + + CalculatedProperty + + + + + + + + + A class for the properties of molecular system calculated in the course of computational chemistry procedure. + + Calculated System Properties + + + + + + + + A class for generic concepts that describe calculations in computational chemistry. + + Calculation Concept + + + + + + + + + A class for specific concepts related to the results of computational chemistry procedures. + + Calculation Result + + + + + + + + + + A class for NMR chemical shifts. + + Chemical Shift + + + + + + + + + + A class for ComputationalChemistryPublication. + A class for publication of the results of the computional chemistry programs. + + Computational Chemistry Publication + ComputationalChemistryPublication + + + + + + + + + A class for the classical energy of the core (possibly nucleus-nucleus repulsion) energy in the Born-Oppenheimer approx. of Schroedinger equation. The Core Energy plus the Electronic Energy constitute the TotalBOPotentialEnergy. + + Core Energy + + + + + + + + + A class for the Correlation Consistent basis sets. + + Correlation-consistent(cc) Basis Set + + + + + + + + + A class for correlation functionals in Density Functional Theories. + + Correlation Functional + + + + + + + + + A class for principal author of this publication. + + Corresponding Author + + + + + + + + + A class for the Dunning DZ double zeta basis set. + + DZ Basis Set + + + + + + + + + A class for dative covalent bond. + + DativeBond + + + + + + + + + A class for all density functionals in Density Functional Theories. + + Density Functional + + + + + + + + + A class for methods from the family of Density Functional Theories. + + Dft + + + + + + + + + A class for specific approximations to exchange-correlation functionals in the Density Functional Theory. + + Dft Flavor + + + + + + + + + A class for DFT Functional. + + DFT Functional + + + + + + + + + A class for the Pople basis sets with diffuse functions. + + Diffuse Basis Set + + + + + + + + + + A class for molecular dipole moment. + + Dipole Moment + + + + + + + + + A class for Dipole Moment Average. + + Dipole Moment Average + + + + + + + + + A class for Dipole Moment X coordinate. + + Dipole Moment X coordinate + + + + + + + + + A class for Dipole Moment Y coordinate. + + Dipole Moment Y coordinate + + + + + + + + + A class for Dipole Moment Z coordinate. + + Dipole Moment Z coordinate + + + + + + + + + A class for the dispersion correction in the Density Functional Theory. + + Dispersion Correction + + + + + + + + + + A class for Double. + A class for double covalent bonds. + + Double + + + + + + + + + A class for the older Dunning basis sets. + + Dunning Basis Set + + + + + + + + + A class for Electronic. + + Electronic + + + + + + + + + A class for the total energy of electrons in the Born-Oppenheimer approx of Schroedinger equation. + + Electronic Energy + + + + + + + + + + A class for ElectronicSpectra. + A class for spectra resulting from the molecular electronic transitions. + + Electronic Spectra + ElectronicSpectra + + + + + + + + + A class for ElectronicTransitions. + + ElectronicTransitions + + + + + + + + + A class for exchange functionals in Density Functional Theories. + + Exchange Functional + + + + + + + + + A class for the computations of the excited states of molecules. + + Excited States Computation + + + + + + + + + A class for publication of the results of an experimental measurement. + + Experimental Chemistry Publication + + + + + + + + + A class for the full configuration interaction (CI) method. + + FCI + + + + + + + + + A class for float value, containing value and unit. + + Float Value + + + + + + + + + A class for the classical mechanical methods based on the concept of the Force Field. + + Force Field + + + + + + + + + A class for FormalAtomCharge. + + FormalAtomCharge + + + + + + + + + A class for Frequency. + + Frequency + + + + + + + + + + A class for FrequencyPeak. + A class representing frequency peak of the spectrum. + + Frequency Peak + FrequencyPeak + + + + + + + + + A version of Gaussian-n composite calculations. + + G1 + + + + + + + + + A version of Gaussian-n composite calculations. + + G2 + + + + + + + + + A version of Gaussian-n composite calculations. + + G3 + + + + + + + + + A version of Gaussian-n composite calculations. + + G4 + + + + + + + + + A class for the Complete Generalized Valence Bond Method (CASSCF) method. + + GVB + + + + + + + + + + + + + + + A collection of composite calculations (mainly quadratic CI plus others) that try to approximate full CI. + + Gaussian-n + + + + + + + + + A class for the generalized (e.g. Hybrid) density functionals in the Density Functional Theory. + + GeneralizedDFTFunctional + + + + + + + + + A class for GGA approximations of density functionals. + + GeneralizedGradientApprox-GGA + + + + + + + + + A class for calculations in computational chemistry that aim to find molecular geometry of lowest energy. + + Geometry optimization + + + + + + + + + Gill 1996 exchange functional. + + Gill96 + + + + + + + + + Grimme's parameterization of Becke 1997 functional. + + B97 + + + + + + + + + + A class for energy gradient of molecular system. + + Gradient + + + + + + + + + + + A class for Group. + A class for generic collection of atoms in molecules and residues + + Group + + + + + + + + + A class for GroupProperty. + + GroupProperty + + + + + + + + + Hamprecht-Cohen-Tozer-Handy GGA functional for 120 cases. + + HCTH120 + + + + + + + + + Hamprecht-Cohen-Tozer-Handy GGA functional for 147 cases. + + HCTH147 + + + + + + + + + Hamprecht-Cohen-Tozer-Handy GGA functional for 407 cases. + + HCTH407 + + + + + + + + + Hamprecht-Cohen-Tozer-Handy 1993 GGA functional. + + HCTH93 + + + + + + + + + A class for Hybrid approximations of density functionals. + + Hybrids + + + + + + + + + A class for hydrogen bond - the electrostatic interaction between polar molecules (strong dipole-dipole attraction). + + Hydrogen Bond + + + + + + + + + A class for IRDataPoint. + + IRDataPoint + + + + + + + + + A class for vibrational spectra resulting from IR intensities. + + InfraRed Spectra + + + + + + + + + A class for InfraRed Spectrum. + + Infra Red Spectrum + + + + + + + + + A class for InfraredSpectrum. + + InfraredSpectrum + + + + + + + + + A class that represents integer value, containing value and unit. + + Integer Value + + + + + + + + + A class for Intensity. + + Intensity + + + + + + + + + A class for perturbation theory method applied to the intermolecular interactions of quantum chemistry. + + InterMolecularPT + + + + + + + + + Lee-Yang-Parr correlation functional + + LYP + + + + + + + + + A class for LDA approximations of density functionals. + + LocalDensityApprox-LDA + + + + + + + + + Minnesota (Truhlar) Functional 2005. + + M05 + + + + + + + + + Minnesota (Truhlar) Version of Functional 5. + + M05-2X + + + + + + + + + Minnesota (Truhlar) Functional 2006. + + M06 + + + + + + + + + Minnesota (Truhlar) Version of Functional 2006. + + M06-HF + + + + + + + + + Minnesota (Truhlar) Version of Functional 6. + + M06-L + + + + + + + + + Minnesota (Truhlar) Version of Functional 6. + + M06-X + + + + + + + + + Minnesota (Truhlar) Version of Functional 2008. + + M08-HX + + + + + + + + + Minnesota (Truhlar) Version of Functional 2008. + + M08-SO + + + + + + + + + Minnesota (Truhlar) Version of Functional 2011. + + M11 + + + + + + + + + Minnesota (Truhlar) Version of Functional 11. + Minnesota (Truhlar) Version of Functional 2011. + + M11-L + + + + + + + + + Minnesota (Truhlar) Version of Functional 2011. + + M11-SO + + + + + + + + + A class for the perturbation of single determinant wave functions such as MP2, etc. + + MBPerturbationTheory + + + + + + + + + A class for the multi-configurational self-consistent field (MCSCF) method. + + MCSCF + + + + + + + + + Minnesota Nonseparable (Truhlar) Version of Functional 12. + + MN12-L + + + + + + + + + Minnesota Nonseparable (Truhlar) Version of Functional 12. + + MN12-SX + + + + + + + + + A class for a Multi-reference coupled cluster calculation. + + MRCC + + + + + + + + + A class for a Multi-reference configuration interaction calculation. + + MRCI + + + + + + + + + A class for Meta-GGA approximations of density functionals. + + Meta-GGA + + + + + + + + + A class for the specific methodology used to conduct computational chemistry calculations. + + Methodology + + + + + + + + + A class for specific features or properties of a given methodology. + + Methodology Feature + + + + + + + + + A class for the Pople minimal basis sets. + + Minimal PopleBasis Set + + + + + + + + + A class for Molecular Calculation. + + Molecular Calculation + + + + + + + + + + A class for MolecularComputation. + A class for the specific type of calculation (like optimization, single point, etc) conducted by a computational chemistry program. + + Molecular Computation + MolecularComputation + + + + + + + + A generic class of various concepts related to molecular systems. + + Molecular Concept + + + + + + + + + A class for the molecular dynamics computations on molecular systems. + + Molecular Dynamics Computation + + + + + + + + + A class for the classical methodologies of computational chemistry. + + Molecular Mechanics + + + + + + + + + + A class for MolecularMethodology. + A class for general methodologies of computational chemistry. + + Molecular Methodology + MolecularMethodology + + + + + + + + + A class that represents objects of molecular structure (atoms, molecules etc). + + Molecular Structure Object + + + + + + + + + + A class for MolecularSystem. + A class for objects related to molecular systems. + + Molecular System + MolecularSystem + + + + + + + + + + + A class for Molecule. + A class for molecule - electrically neutral group (or polyatomic ion) of two or more atoms held together by chemical bonds. + + Molecule + + + + + + + + + A class for MoleculeProperty. + + MoleculeProperty + + + + + + + + + A class for Møller–Plesset perturbation theory method of quantum chemistry. + + MollerPlesset + + + + + + + + + A class for the Monte Carlo computations on molecular systems. + + Monte Carlo Computation + + + + + + + + + A class for the second order Møller–Plesset perturbation theory method of quantum chemistry. + + Mp2 + + + + + + + + + A class for the third order Møller–Plesset perturbation theory method of quantum chemistry. + + Mp3 + + + + + + + + + A class for the fourth order Møller–Plesset perturbation theory method of quantum chemistry. + + Mp4 + + + + + + + + + + A class for Mulliken atom charges. + + Mulliken Charge + + + + + + + + + A class for Mulliken Charges. + + Mulliken Charges + + + + + + + + + + A class for the methods of quantum chemistry using multiple Slater determinants. + Multiple Determinant + + + + + + + + + + A class representing methods of quantum chemistry using multiple reference state determinants. + + Multiple Reference State + + + + + + + + + A class for methods of computational chemistry combining different methodologies (e.g. quantum and classical) for large molecular systems. + + Multiscale Methods + + + + + + + + + A class for nuclear magentic resonance spectra. + + NMR Spectra + + + + + + + + + A class for natural values, containing value and unit. + + Natural Value + + + + + + + + + A class for NMR Shielding Anisotropy. + + NMR Shielding Anisotropy + + + + + + + + + A class for NMR Shielding Isotropic. + + NMR Shielding Isotropic + + + + + + + + + + A class for NormalBond. + A class for covalent bond in molecules. + + Normal Bond + NormalBond + + + + + + + + + A class for NormalMode. + + NormalMode + + + + + + + + + A class for NuclearRepulsion. + + NuclearRepulsion + + + + + + + + + A particular class for residues - monomers of RNA, DNA, etc. + + NucleicAcidResidue + + + + + + + + + A class representing the number of basis set functions used in calculations. + + Number Basis Func + + + + + + + + + Handy-Cohen exchange functional + + OPTX + + + + + + + + + + A class for Orbital. + A class for molecular orbital (MO) - a mathematical function describing an electron in a molecule. + + Orbital + Orbital (1-electron wavefunction) + + + + + + + + + A class for OrbitalEnergy. + + OrbitalEnergy + + + + + + + + + A class for OrbitalOccupancy. + + OrbitalOccupancy + + + + + + + + + A class for OrbitalSymmetry. + + OrbitalSymmetry + + + + + + + + + A class for OscillatorStrength. + + OscillatorStrength + + + + + + + + + A particular class for residue - monomers of some sort - example polymer. + + OtherResidue + + + + + + + + + Perdew-Burke-Ernzerhof functional. + + PBE + + + + + + + + + Perdew-Burke-Ernzerhof hybrid functional. + + PBE0 + + + + + + + + + Perdew-Burke-Ernzerhof 1996 correlation functional + + PBE96C + + + + + + + + + Perdew-Burke-Ernzerhof 1996 exchange functional. + + PBE96X + + + + + + + + + Perdew-Wang functional. + + PW + + + + + + + + + Perdew-Wang 1991 functional. + + PW91 + + + + + + + + + Perdew-Wang 1991 correlation functional + + PW91C + + + + + + + + + Perdew-Wang 1991 exchange functional. + + PW91X + + + + + + + + + Perdew-Zunger functional. + + PZ + + + + + + + + + Perdew-Zunger 1981 correlation functional + + PZ81 + + + + + + + + + A class representing a specific set of parameters used by the Force Field calculations (Molecular Mechanics). + + Parameter Set + + + + + + + + + A particular class for residues - monomers of polypeptide and protein + + PeptideResidue + + + + + + + + + Perdew 1996 correlation functional + + Perdew86 + + + + + + + + + A class for the Pople basis sets with polarization functions. + + Polarized split Valence Basis Set + + + + + + + + + A class for the Pople basis sets. + + Pople Basis Set + + + + + + + + + A generic class for objects related to the publication of results of computational chemistry calculations. + + Publication + + + + + + + + A generic class representing concepts related to publications. + Publication Concept + + + + + + + + + A class for the quadratic configuration interaction (QCI) method with single and double substitutions. + + QCISD + + + + + + + + + A class for the quadratic configuration interaction (QCI) method with single, double, and approximate triple substitutions. + + QCISD(T) + + + + + + + + + A class for the quadratic configuration interaction (QCI) method. + + QuadraticCI + + + + + + + + + ??? !!! + + Quadruple + + + + + + + + + + A class for Quantum Mechanical methods. + A class for QuantumMechanics. + + Quantum Mechanics + QuantumMechanics + + + + + + + + + A class for the restricted active space perturbation theory methods. + + RASPT2 + + + + + + + + + A class for the Restricted Active Space Multiconfiguration SCF (RASSCF) method. + + RASSCF + + + + + + + + + + + + + + + + + A class for vibrational spectra resulting from Raman intensities. + + Raman Spectra + + + + + + + + + A class for Møller–Plesset perturbation theory method of quantum chemistry. + + RayleighSchroedinger + + + + + + + + + A class for a reference. + Reference + + + + + + + + + + + A class for Residue. + A class for residues - monomers of polysaccharide, protein, nucleic acid or polymer + + Residue + + + + + + + + + A class for ResidueProperty. + + ResidueProperty + + + + + + + + + A class for Rms Gradient. + + Rms Gradient + + + + + + + + + A class for the symmetry-adapted perturbation theory for intermolecular interactions. + + SAPT + + + + + + + + + A class for a sub-class of symmetry-adapted perturbation theory for intermolecular interactions. + + SAPT0 + + + + + + + + + A class for a sub-class of symmetry-adapted perturbation theory for intermolecular interactions. + + SAPT2 + + + + + + + + + A class for a sub-class of symmetry-adapted perturbation theory for intermolecular interactions. + + SAPT2+ + + + + + + + + + A class for a sub-class of symmetry-adapted perturbation theory for intermolecular interactions. + + SAPT2+3 + + + + + + + + + A class for a sub-class of symmetry-adapted perturbation theory for intermolecular interactions. + + SAPT2+(3) + + + + + + + + + A class for the Pople minimal STO-2G basis set. + + STO-2G Basis Set + + + + + + + + + A class for the Pople minimal STO-3G basis set. + + STO-3G Basis Set + + + + + + + + + + A class for the Pople minimal STO-3G basis set with polarization functions. + + STO-3G* Basis Set + + + + + + + + + A class for the Pople minimal STO-4G basis set. + + STO-4G Basis Set + + + + + + + + + A class for the Pople minimal STO-5G basis set. + + STO-5G Basis Set + + + + + + + + + A class for the Pople minimal STO-6G basis set. + + STO-6G Basis Set + + + + + + + + + A class for SemiEmpirical Methods of Quantum Chemistry + + Semi-empirical Scf + + + + + + + + + + A class for Single. + A class for single covalent bonds. + + Single + + + + + + + + + A class for Single Determinant methods of Quantum Chemistry. + + Single Determinant + + + + + + + + + A class for Single Point calculations - computation of the energy of molecular system for given geometry. + + Single Point + + + + + + + + + A class for Single Reference (SR) coupled-cluster methods. + + Single Reference State + + + + + + + + + Slater exchange functional. + + Slater + + + + + + + + + + A class for SourcePackage. + A class for quantum chemistry packages used to peform computations. + + Source Package + SourcePackage + + + + + + + + + A class for general spectra. + + Generic Spectra Class + + + + + + + + + A class for general spectra. + + Features of Spectra + + + + + + + + + + A class for NMR coupling constants. + + Spin-Spin Coupling Constant + + + + + + + + + A class for method for spin treatment in quantum chemical calculations (rhf,uhf,rohf). + + Spin Type + + + + + + + + + A class for the Pople split valence basis sets. + + Split Valence Basis Set + + + + + + + + + A class for author submitting this publication. + + Submitting Author + + + + + + + + + A class for perturbation theory method applied to whole molecular systems of quantum chemistry. + + SupraMolecularPT + + + + + + + + + A class for SystemCharge. + + SystemCharge + + + + + + + + + A class for various types of energies associated with molecular system. + + System Energies + + + + + + + + + A class for SystemMultiplicity. + + SystemMultiplicity + + + + + + + + + A class for systemProperty. + + systemProperty + + + + + + + + + A class for SystemTemperature. + + SystemTemperature + + + + + + + + + An N-electron wave function describing the whole molecular system. + + The system N-electron wavefunction + + + + + + + + + Tao-Perdew-Staroverov-Scuseria functional. + + TPSS + + + + + + + + + Tao-Perdew-Staroverov-Scuseria hybrid functional. + + TPSSh + + + + + + + + + A class for the Dunning TZ triple zeta basis set. + + TZ Basis Set + + + + + + + + + A class for methods for excited states and response properties from the family of Density Functional Theories. + + Tddft + + + + + + + + + A class for the Born-Oppenheimer Total Energy (Electronic plus Nuclear Repulsion) (i.e. potential energy for subsequent MD and other statistical mechanics uses). + + Total Born-Oppenheimer Potential Energy + + + + + + + + + A class for TotalPotential. + + TotalPotential + + + + + + + + + A class for triple covalent bond. + + Triple + + + + + + + + + A class for UVVis Spectrum. + + UVVis Spectrum + + + + + + + + + A class for the ahlrichs VDZ double zeta basis set. + + VDZ Basis Set + + + + + + + + + A class for the ahlrichs VDZ double zeta basis set. + + VTZ Basis Set + + + + + + + + + Vosco-Wilks-Nusair functional. + + VWN + + + + + + + + + Vosco-Wilks-Nusair Formula 3 correlation functional + + VWN3 + + + + + + + + + Vosco-Wilks-Nusair Formula 5 correlation functional + + VWN5 + + + + + + + + + This is super class for the expression of various types of values. + + Value + + + + + + + + + A class for vector type of data, containing value and unit. + + Vector Value + + + + + + + + + + A class for VibrationalAnalysis. + A class for the computations of vibrational spectrum of molecules. + + Vibrational Analysis + VibrationalAnalysis + + + + + + + + + A class for spectra resulting from the molecular vibrations. + + Vibrational Spectra + + + + + + + + + + A class for WaveFunction. + A class for the mathematical description of a quantum particle, in most practical cases of the electron. + + Wave Function + WaveFunction + + + + + + + + + A class for WaveFunctionCoefficient. + + WaveFunctionCoefficient + + + + + + + + + A class for the aug-cc-pV5Z Correlation Consistent Quintuple Zeta basis set. + + aug-cc-pV5Z Basis Set + + + + + + + + + A class for the aug-cc-pVDZ Correlation Consistent Double Zeta basis set. + + aug-cc-pVDZ Basis Set + + + + + + + + + A class for the aug-cc-pVQZ Correlation Consistent Quadruple Zeta basis set. + + aug-cc-pVQZ Basis Set + + + + + + + + + A class for the aug-cc-pVTZ Correlation Consistent Triple Zeta basis set. + + aug-cc-pVTZ Basis Set + + + + + + + + + A class for the aug-cc-pV(D+d)Z Correlation Consistent Double Zeta basis set. + + aug-cc-pV(D+d)Z Basis Set + + + + + + + + + A class for the cc-pV5Z Correlation Consistent Quintuple Zeta basis set. + + cc-pV5Z Basis Set + + + + + + + + + A class for the cc-pVDZ Correlation Consistent Double Zeta basis set. + + cc-pVDZ Basis Set + + + + + + + + + A class for the cc-pVQZ Correlation Consistent Quadruple Zeta basis set. + + cc-pVQZ Basis Set + + + + + + + + + A class for the cc-pVTZ Correlation Consistent Triple Zeta basis set. + + cc-pVTZ Basis Set + + + + + + + + + A class for the d-aug-cc-pVDZ Correlation Consistent Double Zeta basis set. + + d-aug-cc-pVDZ Basis Set + + + + + + + + + + + + + + + A class for the jun-cc-pVDZ Correlation Consistent Double Zeta basis set. + + jun-cc-pVDZ Basis Set + + + + + + + + + A class for the Pople split valence 3-21G basis set. + + 3-21G Basis Set + + + + + + + + + + A class for the Pople polarization split valence 3-21G* basis set. + A class for the Pople split valence 3-21G* basis set. + + 3-21G* Basis Set + + + + + + + + + + A class for the Pople split valence 3-21+G basis set. + + 3-21+G Basis Set + + + + + + + + + + + A class for the Pople split valence 3-21+G* basis set. + + 3-21+G* Basis Set + + + + + + + + + A class for the Pople split valence 4-31G basis set. + + 4-31G Basis Set + + + + + + + + + A class for the Pople split valence 6-31G basis set. + + 6-31G Basis Set + + + + + + + + + + A class for the Pople polarization split valence 6-31G* basis set. + + 6-31G* Basis Set + + + + + + + + + + A class for the Pople polarization split valence 6-31G** basis set. + + 6-31G** Basis Set + + + + + + + + + + + A class for the Pople polarization split valence 6-31+G* basis set. + + 6-31+G* Basis Set + + + + + + + + + A class for the Pople split valence 6-311G basis set. + + 6-311G Basis Set + + + + + + + + + + A class for the Pople split valence 6-311G* basis set. + + 6-311G* Basis Set + + + + + + + + + + + A class for the Pople split valence 6-311+G* basis set. + + 6-311+G* Basis Set + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a unit of temperature. + + Kelvin + + + + + + + + + a unit of length + + nano meter + + + + + + + + + The Amber force field. + Amber + + + + + + + + + + + 2 + + + + + + + + + + + The Charmm force field. + Charmm + + + + + + + + + Default Amber parameter set. + Default Amber Parameter Set + + + + + + + + + Default Charmm parameter set. + Default Charmm Parameter Set + + + + + + + + + Default MM plus parameter set + Default MMP Parameter Set + + + + + + + + + Default OPLS parameter set. + Default OPLS Parameter Set + + + + + + + + + A normal methodology. + Normal + + + + + + + + + The OPLS force field. + Opls + + + + + + + + + + + + + + + + + Open-shell restricted Hartree-Fock method. + ROHF + + + + + + + + + Unrestricted Hartree-Fock method. + UHF + + + + + + + + + A unit of length. + + angstrom + + + + + + + + + Atomic Unit this is measure in units of elementary atomic charge called atomicUnits (a.u) . + The elementary unit of charge (e) is called an atomic unit (a.u.) of charge and is so many Coulombs (1.6 *10**(-19) Coulombs. (float) + + Atomic Unit + + + + + + + + + + A wavenumber - the unit of frequency. + + cm-1 + + + + + + + + + + + debye + + + + + + + + + the unit of energy. + + electron volts + + + + + + + + + the unit of energy. + + hartree + + + + + + + + + + the unit of energy + + kilo calories + + + + + + + + + ??? + + kilo calories per angstrom + + + + + + + + + a unit of energy + + kilo joules + + + + + + + + + + kilo grap per mol + + + + + + + + + MM+ force field. + Mm+ + + + + + + + + A class for generic chemical bond. + Bond + + + + A class for RHF. + RHF + + Restricted Hartree-Fock method. + + + Generic property of atoms + Atom Property + A property that allows to describe an atom, like NMR Shielding + A property that allows to declare a general property for an atom. + + + A property that allows Basis Sets to be assigned to a given quantum methodology + has basis set + + A property that allows to define Basis Set - finite set of functions used to approximately express the Molecular Orbital wavefunction(s) of system, normally atom centered, consisting of AOs differing in local angular momentum for each atom. + + + Bond order + A property that specifies bond order. + + + A property that describes bond type@en + A property that describes Bond Type + Bond Type + + + A property that defines the method for the calculation of the excited states of molecules. + has excited state method + + + + + A property that describes the attachment file. + has file + A property that describes the reference to the attachment file. + + + A property that describes floating point value. + has float value + + + + A property that describes a specific force field for given Molecular Mechanics method. + + has force field + A property that describes Force Field. + + + Mass of a molecular entity + A property ... + + + has methodology + + A property that describes a methodology of computations. + A property that describes the methodology of the computations. + + + + Generic Datatype Property for Molecular Features related to computations + The upper property for various properties related to Molecular Data + + + A property that says (true/false) if there is MM calculation + There is Molecular Mechanical Calculation + + + Multiple Determinant + A property that specifies Multiple Determinant. + + + A property that describes the inclusion of occupied orbitals in electronic spectra calculations. + + has occupied orbitals included + + + + A property that describes the treatment of open shell systems. + has open shell treatment + + + + has orbital count + A property that defines the number of electron orbitals + + + has orbital symmetry + + A property that defines Orbital symmetry + + + A property that defines the parametr set for calculations. + has parameter set + + A property that describes a specific parameter set for Molecular Mechanics calculations. + + + There is Quantum Mechanical Calculation + A property that says (true/false) if there is QM calculation + + + Source of calculations (software) + A property that describes softare package + A property that reports what software package was used + Source + + + + has spin type + A property that defines the spin type. + A property that describes handling of spins by the methodology (RHF,UHF,ROHF). + + + + has system multiplicity + A property that describes the system spin multiplicity. + + + A property that describes the number of the electronic transitions in spectral calculations. + has transition count + + + + A property that describes the inclusion of occupied orbitals in electronic spectra calculations. + + has unoccupied orbitals included + + + A property that describes the number of vibrational frequencies. + has vibration count + + + + + + + + diff --git a/external/gc07.yaml b/external/gc07.yaml new file mode 100644 index 0000000..e519db3 --- /dev/null +++ b/external/gc07.yaml @@ -0,0 +1,2991 @@ +id: http://purl.org/gc/ +name: gc +description: gc +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + gc: http://purl.org/gc/ +default_prefix: gc +types: {} +classes: + AtomicPhysicsQuantityKind: + class_uri: qudt:AtomicPhysicsQuantityKind + ChemistryUnit: + class_uri: qudt:ChemistryUnit + is_a: AuxiliaryConcept + DerivedUnit: + class_uri: qudt:DerivedUnit + is_a: AuxiliaryConcept + ElectricDipoleMomentUnit: + class_uri: qudt:ElectricDipoleMomentUnit + is_a: AuxiliaryConcept + EnergyAndWorkUnit: + class_uri: qudt:EnergyAndWorkUnit + is_a: AuxiliaryConcept + FrequencyUnit: + class_uri: qudt:FrequencyUnit + is_a: AuxiliaryConcept + LengthUnit: + class_uri: qudt:LengthUnit + is_a: AuxiliaryConcept + TemperatureUnit: + class_uri: qudt:TemperatureUnit + is_a: AuxiliaryConcept + BFO_0000027: + class_uri: bfo:BFO_0000027 + BFO_0000030: + class_uri: bfo:BFO_0000030 + publisher: + class_uri: dc:publisher + AbInitioScf: + class_uri: gc:AbInitioScf + is_a: SingleDeterminant + comments: + - "A class for Self Consistent Field methods (Hartree-Fock methods) for approximate\ + \ solution of Schr\xF6dinger equation for quantum many body system.@en" + AbinitioScf: + class_uri: gc:AbinitioScf + is_a: GainesvilleCoreTerm + comments: + - A class for AbinitioScf.@en + AhlrichsBasisSet: + class_uri: gc:AhlrichsBasisSet + is_a: BasisSet + comments: + - A class for the Correlation Consistent basis sets.@en + AlphaOrbital: + class_uri: gc:AlphaOrbital + is_a: GainesvilleCoreTerm + comments: + - A class for AlphaOrbital.@en + Aromatic: + class_uri: gc:Aromatic + is_a: NormalBond + comments: + - A class for bonds with aromatic character@en + Atom: + class_uri: gc:Atom + slots: + - hasAtomCoordinateX + - hasAtomCoordinateY + - hasAtomCoordinateZ + - hasAtomProperty + - hasBasisSet + - hasBond + - hasCalculatedAtomCharge + - hasCoordinates + - hasFormalCharge + - hasMass + - hasShielding + - isElement + - hasBondCount + - hasElementSymbol + is_a: MolecularStructureObject + mixins: + - BFO_0000030 + - GainesvilleCoreTerm + comments: + - A class for Atom.@en + - A class for atoms, the basic unit of matter.@en + AtomCoordinateX: + class_uri: gc:AtomCoordinateX + is_a: GainesvilleCoreTerm + comments: + - A class for AtomCoordinateX.@en + AtomCoordinateY: + class_uri: gc:AtomCoordinateY + is_a: GainesvilleCoreTerm + comments: + - A class for AtomCoordinateY.@en + AtomCoordinateZ: + class_uri: gc:AtomCoordinateZ + is_a: GainesvilleCoreTerm + comments: + - A class for AtomCoordinateZ.@en + AtomCoordinates: + class_uri: gc:AtomCoordinates + is_a: GainesvilleCoreTerm + comments: + - A class for AtomCoordinates.@en + AtomProperty: + class_uri: gc:AtomProperty + is_a: GainesvilleCoreTerm + comments: + - A class for AtomProperty.@en + AtomicMass: + class_uri: gc:AtomicMass + is_a: GainesvilleCoreTerm + comments: + - A class for AtomicMass.@en + Author: + class_uri: gc:Author + slots: + - hasEmail + - hasFirstName + - hasLastName + - hasOrganization + is_a: PublicationConcept + comments: + - A class for all authors of this publication.@en + AuxiliaryConcept: + class_uri: gc:AuxiliaryConcept + comments: + - A generic class representing Auxiliary concepts.@en + B3LYP: + class_uri: gc:B3LYP + is_a: Hybrids + comments: + - Becke-Lee-Yang-Parr hybrid functional.@en + B97: + class_uri: gc:B97 + is_a: Hybrids + comments: + - The Becke 1997 hybrid functional.@en + BLYP: + class_uri: gc:BLYP + is_a: GeneralizedGradientApprox-GGA + comments: + - Becke-Lee-Yang-Parr functional.@en + BOMolecularDynamics: + class_uri: gc:BOMolecularDynamics + is_a: MolecularDynamics + comments: + - A class for the Born-Oppenheimer molecular dynamics computations on molecular + systems.@en + BP86: + class_uri: gc:BP86 + is_a: GeneralizedGradientApprox-GGA + comments: + - Becke-Perdew86 functional.@en + BasisSet: + class_uri: gc:BasisSet + is_a: MethodologyFeature + comments: + - A class for the basis set. In computational chemistry basis set is a set of + functions which are combined to create molecular orbitals.@en + Becke88: + class_uri: gc:Becke88 + is_a: ExchangeFunctional + comments: + - Becke 1988 exchange functional@en + BetaOrbital: + class_uri: gc:BetaOrbital + is_a: GainesvilleCoreTerm + comments: + - A class for BetaOrbital.@en + Bond: + class_uri: gc:Bond + slots: + - binds + - hasBondLength + - hasBondOrder + - hasBondType + - hasMultipleDeterminant + is_a: MolecularStructureObject + comments: + - A class for generic chemical bond.@en + BondTypes: + class_uri: gc:BondTypes + CASPT2: + class_uri: gc:CASPT2 + is_a: MCSCF + comments: + - A class for the complete active space perturbation theory methods.@en + CASSCF: + class_uri: gc:CASSCF + is_a: MCSCF + comments: + - A class for the Complete Active Space Multiconfiguration SCF (CASSCF) method.@en + CC: + class_uri: gc:CC + is_a: MultipleDeterminant + comments: + - A class for the coupled cluster method.@en + CC-2: + class_uri: gc:CC-2 + is_a: CCSecondOrder + comments: + - A class for the coupled cluster method with a treatment singles, doubles.@en + CC-3: + class_uri: gc:CC-3 + is_a: CCThirdOrderSelfConsistent + comments: + - A class for the coupled cluster method with a treatment singles, doubles, and + triples.@en + CC2: + class_uri: gc:CC2 + is_a: CCSecondOrder + comments: + - A class for the coupled cluster method with a treatment singles, doubles.@en + CC3: + class_uri: gc:CC3 + is_a: CCThirdOrderSelfConsistent + comments: + - A class for the coupled cluster method with a treatment singles, doubles, and + triples.@en + CCD: + class_uri: gc:CCD + is_a: CCSecondOrder + comments: + - A class for the coupled cluster method with double substitutions.@en + CCDoubleZeta: + class_uri: gc:CCDoubleZeta + is_a: CorrelationConsistentBasisSet + comments: + - A class for the CCDZ Correlation Consistent Double Zeta basis sets.@en + CCQuadrupleZeta: + class_uri: gc:CCQuadrupleZeta + is_a: CorrelationConsistentBasisSet + comments: + - A class for the CCQZ Correlation Consistent Quadrupole Zeta basis sets.@en + CCQuintupleZeta: + class_uri: gc:CCQuintupleZeta + is_a: CorrelationConsistentBasisSet + comments: + - A class for the CC5Z Correlation Consistent Quintuple Zeta basis sets.@en + CCSD: + class_uri: gc:CCSD + is_a: CCSecondOrder + comments: + - A class for the coupled cluster method with a full treatment singles and doubles.@en + CCSD--T: + class_uri: gc:CCSD--T + is_a: CCThirdOrderPerturbative + comments: + - A class for the coupled cluster method with a full treatment singles, doubles + and approximate treatment of triple excitations.@en + CCSD-T: + class_uri: gc:CCSD-T + is_a: CCThirdOrderPerturbative + comments: + - A class for the coupled cluster method with a full treatment singles and doubles + and approximate treatment of triple excitations.@en + CCSDT: + class_uri: gc:CCSDT + is_a: CCThirdOrderSelfConsistent + comments: + - A class for the coupled cluster method with a full treatment singles, doubles, + and triples.@en + CCSDT-1A: + class_uri: gc:CCSDT-1A + is_a: CCThirdOrderSelfConsistent + comments: + - A class for the coupled cluster method with a full treatment singles, doubles + and approximate treatment of triple excitations.@en + CCSDT-1B: + class_uri: gc:CCSDT-1B + is_a: CCThirdOrderSelfConsistent + comments: + - A class for the coupled cluster method with a full treatment singles, doubles + and approximate treatment of triple excitations.@en + CCSecondOrder: + class_uri: gc:CCSecondOrder + is_a: CC + comments: + - A class for the second-order coupled cluster method.@en + CCThirdOrder: + class_uri: gc:CCThirdOrder + is_a: CC + comments: + - A class for the third-order coupled cluster method.@en + CCThirdOrderPerturbative: + class_uri: gc:CCThirdOrderPerturbative + is_a: CCThirdOrder + comments: + - A class for the third-order perturbative coupled cluster method.@en + CCThirdOrderSelfConsistent: + class_uri: gc:CCThirdOrderSelfConsistent + is_a: CCThirdOrder + comments: + - A class for the third-order self-consistent coupled cluster method.@en + CCTripleZeta: + class_uri: gc:CCTripleZeta + is_a: CorrelationConsistentBasisSet + comments: + - A class for the CCTZ Correlation Consistent Triple Zeta basis sets.@en + CI: + class_uri: gc:CI + is_a: MultipleDeterminant + comments: + - A class for the configuration interaction (CI) method.@en + CIS: + class_uri: gc:CIS + is_a: CI + comments: + - A class for the configuration interaction (CI) method with single substitutions.@en + CISD: + class_uri: gc:CISD + is_a: CI + comments: + - A class for the configuration interaction (CI) method with single and double + substitutions.@en + CPMolecularDynamics: + class_uri: gc:CPMolecularDynamics + is_a: MolecularDynamics + comments: + - A class for the Car-Parinello type of molecular dynamics computations on molecular + systems.@en + CSXVersion: + class_uri: gc:CSXVersion + is_a: GainesvilleCoreTerm + comments: + - CSXVersion class.@en + CalculatedAtomAtomProperties: + class_uri: gc:CalculatedAtomAtomProperties + is_a: CalculatedProperties + comments: + - A class for the properties of the intersection of two atoms calculated in the + course of computational chemistry procedure, such as spin-spin coupling@en + CalculatedAtomCharge: + class_uri: gc:CalculatedAtomCharge + is_a: GainesvilleCoreTerm + comments: + - A class for CalculatedAtomCharge.@en + CalculatedAtomProperties: + class_uri: gc:CalculatedAtomProperties + slots: + - hasMullikenCharges + is_a: CalculatedProperties + comments: + - A class for the properties of an atom calculated in the course of computational + chemistry procedure.@en + CalculatedMoleculeProperties: + class_uri: gc:CalculatedMoleculeProperties + is_a: CalculatedProperties + comments: + - A class for the properties of a molecule calculated in the course of computational + chemistry procedure.@en + CalculatedProperties: + class_uri: gc:CalculatedProperties + slots: + - hasNmrShieldingAnisotropy + - hasNmrShieldingIsotropic + - hasRMSGradient + is_a: CalculationResult + comments: + - A class for the properties of calculated in the course of computational chemistry + procedure.@en + CalculatedProperty: + class_uri: gc:CalculatedProperty + slots: + - hasSystemProperty + is_a: GainesvilleCoreTerm + comments: + - A class for CalculatedProperty.@en + CalculatedSystemProperties: + class_uri: gc:CalculatedSystemProperties + slots: + - hasDipoleMoment + - hasDipoleMomentAverage + - hasDipoleMomentX + - hasDipoleMomentY + - hasDipoleMomentZ + is_a: CalculatedProperties + comments: + - A class for the properties of molecular system calculated in the course of computational + chemistry procedure.@en + CalculationConcept: + class_uri: gc:CalculationConcept + comments: + - A class for generic concepts that describe calculations in computational chemistry.@en + CalculationResult: + class_uri: gc:CalculationResult + is_a: CalculationConcept + comments: + - A class for specific concepts related to the results of computational chemistry + procedures.@en + ChemicalShift: + class_uri: gc:ChemicalShift + is_a: CalculatedAtomProperties + comments: + - '@en' + - A class for NMR chemical shifts.@en + ComputationalChemistryPublication: + class_uri: gc:ComputationalChemistryPublication + slots: + - hasFile + - hasMathML + - hasMathMLEquation + - hasPublisher + - hasSource + - hasSourcePackage + - hasCategory + - hasInputFile + - hasKey + - hasStatus + - hasTag + - hasVisibility + is_a: Publication + mixins: + - GainesvilleCoreTerm + comments: + - A class for ComputationalChemistryPublication.@en + - A class for publication of the results of the computional chemistry programs.@en + CoreEnergy: + class_uri: gc:CoreEnergy + is_a: SystemEnergies + comments: + - A class for the classical energy of the core (possibly nucleus-nucleus repulsion) + energy in the Born-Oppenheimer approx. of Schroedinger equation. The Core Energy + plus the Electronic Energy constitute the TotalBOPotentialEnergy.@en + CorrelationConsistentBasisSet: + class_uri: gc:CorrelationConsistentBasisSet + is_a: BasisSet + comments: + - A class for the Correlation Consistent basis sets.@en + CorrelationFunctional: + class_uri: gc:CorrelationFunctional + is_a: DensityFunctional + comments: + - A class for correlation functionals in Density Functional Theories.@en + CorrespondingAuthor: + class_uri: gc:CorrespondingAuthor + is_a: Author + comments: + - A class for principal author of this publication.@en + DZ: + class_uri: gc:DZ + is_a: DunningBasisSet + comments: + - A class for the Dunning DZ double zeta basis set.@en + DativeBond: + class_uri: gc:DativeBond + is_a: Bond + comments: + - A class for dative covalent bond.@en + DensityFunctional: + class_uri: gc:DensityFunctional + is_a: MethodologyFeature + comments: + - A class for all density functionals in Density Functional Theories.@en + Dft: + class_uri: gc:Dft + is_a: SingleDeterminant + comments: + - A class for methods from the family of Density Functional Theories.@en + DftFlavor: + class_uri: gc:DftFlavor + is_a: MethodologyFeature + comments: + - A class for specific approximations to exchange-correlation functionals in the + Density Functional Theory.@en + DftFunctional: + class_uri: gc:DftFunctional + is_a: GainesvilleCoreTerm + comments: + - A class for DFT Functional.@en + DiffusePopleBasisSet: + class_uri: gc:DiffusePopleBasisSet + is_a: PopleBasisSet + comments: + - A class for the Pople basis sets with diffuse functions.@en + DipoleMoment: + class_uri: gc:DipoleMoment + is_a: CalculatedSystemProperties + comments: + - '@en' + - A class for molecular dipole moment.@en + DipoleMomentAverage: + class_uri: gc:DipoleMomentAverage + is_a: GainesvilleCoreTerm + comments: + - A class for Dipole Moment Average.@en + DipoleMomentX: + class_uri: gc:DipoleMomentX + is_a: GainesvilleCoreTerm + comments: + - A class for Dipole Moment X coordinate.@en + DipoleMomentY: + class_uri: gc:DipoleMomentY + is_a: GainesvilleCoreTerm + comments: + - A class for Dipole Moment Y coordinate.@en + DipoleMomentZ: + class_uri: gc:DipoleMomentZ + is_a: GainesvilleCoreTerm + comments: + - A class for Dipole Moment Z coordinate.@en + DispersionCorrection: + class_uri: gc:DispersionCorrection + is_a: MethodologyFeature + comments: + - A class for the dispersion correction in the Density Functional Theory.@en + Double: + class_uri: gc:Double + is_a: GainesvilleCoreTerm + mixins: + - NormalBond + comments: + - A class for Double.@en + - A class for double covalent bonds.@en + DunningBasisSet: + class_uri: gc:DunningBasisSet + is_a: BasisSet + comments: + - A class for the older Dunning basis sets.@en + Electronic: + class_uri: gc:Electronic + is_a: GainesvilleCoreTerm + comments: + - A class for Electronic.@en + ElectronicEnergy: + class_uri: gc:ElectronicEnergy + is_a: SystemEnergies + comments: + - A class for the total energy of electrons in the Born-Oppenheimer approx of + Schroedinger equation.@en + ElectronicSpectra: + class_uri: gc:ElectronicSpectra + slots: + - hasElectronicTransitions + - hasExcitedStateMethod + - hasFrequencyPeak + - hasOccupiedOrbitalsIncluded + - hasOscillatorStrength + - hasTransitionCount + - hasUnoccupiedOrbitalsIncluded + - hasPeakCount + is_a: GainesvilleCoreTerm + mixins: + - Spectra + comments: + - A class for ElectronicSpectra.@en + - A class for spectra resulting from the molecular electronic transitions.@en + ElectronicTransitions: + class_uri: gc:ElectronicTransitions + is_a: GainesvilleCoreTerm + comments: + - A class for ElectronicTransitions.@en + ExchangeFunctional: + class_uri: gc:ExchangeFunctional + is_a: DensityFunctional + comments: + - A class for exchange functionals in Density Functional Theories.@en + ExcitedStates: + class_uri: gc:ExcitedStates + is_a: MolecularComputation + comments: + - A class for the computations of the excited states of molecules.@en + ExperimentalChemistryPublication: + class_uri: gc:ExperimentalChemistryPublication + is_a: Publication + comments: + - A class for publication of the results of an experimental measurement.@en + FCI: + class_uri: gc:FCI + is_a: CI + comments: + - A class for the full configuration interaction (CI) method.@en + FloatValue: + class_uri: gc:FloatValue + slots: + - hasFloatValue + is_a: Value + comments: + - A class for float value, containing value and unit.@en + ForceField: + class_uri: gc:ForceField + is_a: MethodologyFeature + comments: + - A class for the classical mechanical methods based on the concept of the Force + Field.@en + FormalAtomCharge: + class_uri: gc:FormalAtomCharge + is_a: GainesvilleCoreTerm + comments: + - A class for FormalAtomCharge.@en + Frequency: + class_uri: gc:Frequency + is_a: GainesvilleCoreTerm + comments: + - A class for Frequency.@en + FrequencyPeak: + class_uri: gc:FrequencyPeak + slots: + - hasFrequency + - hasIntensity + - hasNormalMode + is_a: GainesvilleCoreTerm + mixins: + - SpectralFeatures + comments: + - A class for FrequencyPeak.@en + - A class representing frequency peak of the spectrum.@en + G1: + class_uri: gc:G1 + is_a: Gaussian-n + comments: + - A version of Gaussian-n composite calculations.@en + G2: + class_uri: gc:G2 + is_a: Gaussian-n + comments: + - A version of Gaussian-n composite calculations.@en + G3: + class_uri: gc:G3 + is_a: Gaussian-n + comments: + - A version of Gaussian-n composite calculations.@en + G4: + class_uri: gc:G4 + is_a: Gaussian-n + comments: + - A version of Gaussian-n composite calculations.@en + GVB: + class_uri: gc:GVB + is_a: MultipleReferenceState + comments: + - A class for the Complete Generalized Valence Bond Method (CASSCF) method.@en + GainesvilleCoreTerm: + class_uri: gc:GainesvilleCoreTerm + Gaussian-n: + class_uri: gc:Gaussian-n + is_a: MultipleDeterminant + comments: + - A collection of composite calculations (mainly quadratic CI plus others) that + try to approximate full CI.@en + GeneralizedDFTFunctional: + class_uri: gc:GeneralizedDFTFunctional + is_a: DensityFunctional + comments: + - A class for the generalized (e.g. Hybrid) density functionals in the Density + Functional Theory.@en + GeneralizedGradientApprox-GGA: + class_uri: gc:GeneralizedGradientApprox-GGA + is_a: GeneralizedDFTFunctional + comments: + - A class for GGA approximations of density functionals.@en + GeometryOptimization: + class_uri: gc:GeometryOptimization + is_a: MolecularComputation + comments: + - A class for calculations in computational chemistry that aim to find molecular + geometry of lowest energy.@en + Gill96: + class_uri: gc:Gill96 + is_a: ExchangeFunctional + comments: + - Gill 1996 exchange functional.@en + GrB97: + class_uri: gc:GrB97 + is_a: GeneralizedGradientApprox-GGA + comments: + - Grimme's parameterization of Becke 1997 functional.@en + Gradient: + class_uri: gc:Gradient + is_a: CalculatedSystemProperties + comments: + - '@en' + - A class for energy gradient of molecular system.@en + Group: + class_uri: gc:Group + is_a: MolecularStructureObject + mixins: + - GainesvilleCoreTerm + - BFO_0000027 + comments: + - A class for Group.@en + - A class for generic collection of atoms in molecules and residues@en + GroupProperty: + class_uri: gc:GroupProperty + is_a: GainesvilleCoreTerm + comments: + - A class for GroupProperty.@en + HCTH120: + class_uri: gc:HCTH120 + is_a: GeneralizedGradientApprox-GGA + comments: + - Hamprecht-Cohen-Tozer-Handy GGA functional for 120 cases.@en + HCTH147: + class_uri: gc:HCTH147 + is_a: GeneralizedGradientApprox-GGA + comments: + - Hamprecht-Cohen-Tozer-Handy GGA functional for 147 cases.@en + HCTH407: + class_uri: gc:HCTH407 + is_a: GeneralizedGradientApprox-GGA + comments: + - Hamprecht-Cohen-Tozer-Handy GGA functional for 407 cases.@en + HCTH93: + class_uri: gc:HCTH93 + is_a: GeneralizedGradientApprox-GGA + comments: + - Hamprecht-Cohen-Tozer-Handy 1993 GGA functional.@en + Hybrids: + class_uri: gc:Hybrids + is_a: GeneralizedDFTFunctional + comments: + - A class for Hybrid approximations of density functionals.@en + HydrogenBond: + class_uri: gc:HydrogenBond + is_a: Bond + comments: + - A class for hydrogen bond - the electrostatic interaction between polar molecules + (strong dipole-dipole attraction).@en + IRDataPoint: + class_uri: gc:IRDataPoint + is_a: GainesvilleCoreTerm + comments: + - A class for IRDataPoint.@en + InfraRedSpectra: + class_uri: gc:InfraRedSpectra + is_a: VibrationalSpectra + comments: + - A class for vibrational spectra resulting from IR intensities.@en + InfraRedSpectrum: + class_uri: gc:InfraRedSpectrum + slots: + - xAxis + - yAxis + - yAxisUnit + is_a: GainesvilleCoreTerm + comments: + - A class for InfraRed Spectrum.@en + InfraredSpectrum: + class_uri: gc:InfraredSpectrum + is_a: GainesvilleCoreTerm + comments: + - A class for InfraredSpectrum.@en + IntegerValue: + class_uri: gc:IntegerValue + slots: + - hasIntegerValue + is_a: Value + comments: + - A class that represents integer value, containing value and unit.@en + Intensity: + class_uri: gc:Intensity + is_a: GainesvilleCoreTerm + comments: + - A class for Intensity.@en + InterMolecularPT: + class_uri: gc:InterMolecularPT + is_a: MBPerturbationTheory + comments: + - A class for perturbation theory method applied to the intermolecular interactions + of quantum chemistry.@en + LYP: + class_uri: gc:LYP + is_a: CorrelationFunctional + comments: + - Lee-Yang-Parr correlation functional@en + LocalDensityApprox-LDA: + class_uri: gc:LocalDensityApprox-LDA + is_a: GeneralizedDFTFunctional + comments: + - A class for LDA approximations of density functionals.@en + M05: + class_uri: gc:M05 + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Functional 2005.@en + M05-2X: + class_uri: gc:M05-2X + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 5.@en + M06: + class_uri: gc:M06 + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Functional 2006.@en + M06-HF: + class_uri: gc:M06-HF + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 2006.@en + M06-L: + class_uri: gc:M06-L + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 6.@en + M06-X: + class_uri: gc:M06-X + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 6.@en + M08-HX: + class_uri: gc:M08-HX + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 2008.@en + M08-SO: + class_uri: gc:M08-SO + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 2008.@en + M11: + class_uri: gc:M11 + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 2011.@en + M11-L: + class_uri: gc:M11-L + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 11.@en + - Minnesota (Truhlar) Version of Functional 2011.@en + M11-SO: + class_uri: gc:M11-SO + is_a: Meta-GGA + comments: + - Minnesota (Truhlar) Version of Functional 2011.@en + MBPerturbationTheory: + class_uri: gc:MBPerturbationTheory + is_a: SingleDeterminant + comments: + - A class for the perturbation of single determinant wave functions such as MP2, + etc.@en + MCSCF: + class_uri: gc:MCSCF + is_a: MultipleReferenceState + comments: + - A class for the multi-configurational self-consistent field (MCSCF) method.@en + MN12-L: + class_uri: gc:MN12-L + is_a: Meta-GGA + comments: + - Minnesota Nonseparable (Truhlar) Version of Functional 12.@en + MN12-SX: + class_uri: gc:MN12-SX + is_a: Meta-GGA + comments: + - Minnesota Nonseparable (Truhlar) Version of Functional 12.@en + MRCC: + class_uri: gc:MRCC + is_a: MultipleReferenceState + comments: + - A class for a Multi-reference coupled cluster calculation.@en + MRCI: + class_uri: gc:MRCI + is_a: MultipleReferenceState + comments: + - A class for a Multi-reference configuration interaction calculation.@en + Meta-GGA: + class_uri: gc:Meta-GGA + is_a: GeneralizedDFTFunctional + comments: + - A class for Meta-GGA approximations of density functionals.@en + Methodology: + class_uri: gc:Methodology + is_a: MethodologyFeature + comments: + - A class for the specific methodology used to conduct computational chemistry + calculations.@en + MethodologyFeature: + class_uri: gc:MethodologyFeature + is_a: CalculationConcept + comments: + - A class for specific features or properties of a given methodology.@en + MinimalPopleBasisSet: + class_uri: gc:MinimalPopleBasisSet + is_a: PopleBasisSet + comments: + - A class for the Pople minimal basis sets.@en + MolecularCalculation: + class_uri: gc:MolecularCalculation + slots: + - hasMolecularSystem + is_a: GainesvilleCoreTerm + comments: + - A class for Molecular Calculation.@en + MolecularComputation: + class_uri: gc:MolecularComputation + slots: + - hasResult + is_a: CalculationConcept + mixins: + - GainesvilleCoreTerm + comments: + - A class for MolecularComputation.@en + - A class for the specific type of calculation (like optimization, single point, + etc) conducted by a computational chemistry program.@en + MolecularConcept: + class_uri: gc:MolecularConcept + comments: + - A generic class of various concepts related to molecular systems.@en + MolecularDynamics: + class_uri: gc:MolecularDynamics + is_a: MolecularComputation + comments: + - A class for the molecular dynamics computations on molecular systems.@en + MolecularMechanics: + class_uri: gc:MolecularMechanics + slots: + - hasForceField + - hasParameterSet + is_a: MolecularMethodology + comments: + - A class for the classical methodologies of computational chemistry.@en + MolecularMethodology: + class_uri: gc:MolecularMethodology + slots: + - hasBasisSet + - hasCorrelationFunctional + - hasDftFlavor + - hasDftFunctional + - hasDispersionCorrection + - hasExchangeFunctional + - hasFeature + - hasForceField + - hasMethodology + - hasNumberBasisFunc + - hasParameterSet + - hasSpinType + is_a: CalculationConcept + mixins: + - GainesvilleCoreTerm + comments: + - A class for MolecularMethodology.@en + - A class for general methodologies of computational chemistry.@en + MolecularStructureObject: + class_uri: gc:MolecularStructureObject + is_a: MolecularConcept + comments: + - A class that represents objects of molecular structure (atoms, molecules etc).@en + MolecularSystem: + class_uri: gc:MolecularSystem + slots: + - hasCalculationOn + - hasIRSpectrum + - hasMass + - hasMolecularComputation + - hasMultipleReferenceState + - hasSystemCharge + - hasSystemMultiplicity + - hasSystemTemperature + - hasAtomCount + is_a: MolecularStructureObject + mixins: + - GainesvilleCoreTerm + comments: + - A class for MolecularSystem.@en + - A class for objects related to molecular systems.@en + Molecule: + class_uri: gc:Molecule + slots: + - hasAtom + - hasMass + - hasResidue + - hasAtomCount + - hasBondCount + - hasInChIKey + - hasInChIString + is_a: MolecularStructureObject + mixins: + - BFO_0000030 + - GainesvilleCoreTerm + comments: + - A class for Molecule.@en + - A class for molecule - electrically neutral group (or polyatomic ion) of two + or more atoms held together by chemical bonds.@en + MoleculeProperty: + class_uri: gc:MoleculeProperty + is_a: GainesvilleCoreTerm + comments: + - A class for MoleculeProperty.@en + MollerPlesset: + class_uri: gc:MollerPlesset + is_a: SupraMolecularPT + comments: + - "A class for M\xF8ller\u2013Plesset perturbation theory method of quantum chemistry.@en" + MonteCarlo: + class_uri: gc:MonteCarlo + is_a: MolecularComputation + comments: + - A class for the Monte Carlo computations on molecular systems.@en + Mp2: + class_uri: gc:Mp2 + is_a: MollerPlesset + comments: + - "A class for the second order M\xF8ller\u2013Plesset perturbation theory method\ + \ of quantum chemistry.@en" + Mp3: + class_uri: gc:Mp3 + is_a: MollerPlesset + comments: + - "A class for the third order M\xF8ller\u2013Plesset perturbation theory method\ + \ of quantum chemistry.@en" + Mp4: + class_uri: gc:Mp4 + is_a: MollerPlesset + comments: + - "A class for the fourth order M\xF8ller\u2013Plesset perturbation theory method\ + \ of quantum chemistry.@en" + MullikenCharge: + class_uri: gc:MullikenCharge + is_a: CalculatedAtomProperties + comments: + - '@en' + - A class for Mulliken atom charges.@en + MullikenCharges: + class_uri: gc:MullikenCharges + is_a: GainesvilleCoreTerm + comments: + - A class for Mulliken Charges.@en + MultipleDeterminant: + class_uri: gc:MultipleDeterminant + is_a: SingleReferenceState + comments: + - A class for the methods of quantum chemistry using multiple Slater determinants.@en + MultipleReferenceState: + class_uri: gc:MultipleReferenceState + is_a: QuantumMechanics + comments: + - A class representing methods of quantum chemistry using multiple reference state + determinants.@en + Multiscale: + class_uri: gc:Multiscale + is_a: MolecularMethodology + comments: + - A class for methods of computational chemistry combining different methodologies + (e.g. quantum and classical) for large molecular systems.@en + NMRSpectra: + class_uri: gc:NMRSpectra + slots: + - hasFrequencyPeak + - hasPeakCount + is_a: Spectra + comments: + - A class for nuclear magentic resonance spectra.@en + NaturalValue: + class_uri: gc:NaturalValue + slots: + - hasNaturalValue + is_a: Value + comments: + - A class for natural values, containing value and unit.@en + NmrShieldingAnisotropy: + class_uri: gc:NmrShieldingAnisotropy + is_a: GainesvilleCoreTerm + comments: + - A class for NMR Shielding Anisotropy.@en + NmrShieldingIsotropic: + class_uri: gc:NmrShieldingIsotropic + is_a: GainesvilleCoreTerm + comments: + - A class for NMR Shielding Isotropic.@en + NormalBond: + class_uri: gc:NormalBond + is_a: GainesvilleCoreTerm + mixins: + - Bond + comments: + - A class for NormalBond.@en + - A class for covalent bond in molecules.@en + NormalMode: + class_uri: gc:NormalMode + is_a: GainesvilleCoreTerm + comments: + - A class for NormalMode.@en + NuclearRepulsion: + class_uri: gc:NuclearRepulsion + is_a: GainesvilleCoreTerm + comments: + - A class for NuclearRepulsion.@en + NucleicAcidResidue: + class_uri: gc:NucleicAcidResidue + is_a: Residue + comments: + - A particular class for residues - monomers of RNA, DNA, etc.@en + NumberBasisFunc: + class_uri: gc:NumberBasisFunc + is_a: MethodologyFeature + comments: + - A class representing the number of basis set functions used in calculations.@en + OPTX: + class_uri: gc:OPTX + is_a: ExchangeFunctional + comments: + - Handy-Cohen exchange functional@en + Orbital: + class_uri: gc:Orbital + slots: + - hasOccupancy + - hasOrbitalEnergy + - hasOrbitalSymmetry + - hasWaveFunctionCoefficients + is_a: GainesvilleCoreTerm + mixins: + - WaveFunction + comments: + - A class for Orbital.@en + - A class for molecular orbital (MO) - a mathematical function describing an electron + in a molecule.@en + OrbitalEnergy: + class_uri: gc:OrbitalEnergy + is_a: GainesvilleCoreTerm + comments: + - A class for OrbitalEnergy.@en + OrbitalOccupancy: + class_uri: gc:OrbitalOccupancy + is_a: GainesvilleCoreTerm + comments: + - A class for OrbitalOccupancy.@en + OrbitalSymmetry: + class_uri: gc:OrbitalSymmetry + is_a: GainesvilleCoreTerm + comments: + - A class for OrbitalSymmetry.@en + OscillatorStrength: + class_uri: gc:OscillatorStrength + is_a: GainesvilleCoreTerm + comments: + - A class for OscillatorStrength.@en + OtherResidue: + class_uri: gc:OtherResidue + is_a: Residue + comments: + - A particular class for residue - monomers of some sort - example polymer.@en + PBE: + class_uri: gc:PBE + is_a: GeneralizedGradientApprox-GGA + comments: + - Perdew-Burke-Ernzerhof functional.@en + PBE0: + class_uri: gc:PBE0 + is_a: Hybrids + comments: + - Perdew-Burke-Ernzerhof hybrid functional.@en + PBE96C: + class_uri: gc:PBE96C + is_a: CorrelationFunctional + comments: + - Perdew-Burke-Ernzerhof 1996 correlation functional@en + PBE96X: + class_uri: gc:PBE96X + is_a: ExchangeFunctional + comments: + - Perdew-Burke-Ernzerhof 1996 exchange functional.@en + PW: + class_uri: gc:PW + is_a: LocalDensityApprox-LDA + comments: + - Perdew-Wang functional.@en + PW91: + class_uri: gc:PW91 + is_a: GeneralizedGradientApprox-GGA + comments: + - Perdew-Wang 1991 functional.@en + PW91C: + class_uri: gc:PW91C + is_a: CorrelationFunctional + comments: + - Perdew-Wang 1991 correlation functional@en + PW91X: + class_uri: gc:PW91X + is_a: ExchangeFunctional + comments: + - Perdew-Wang 1991 exchange functional.@en + PZ: + class_uri: gc:PZ + is_a: LocalDensityApprox-LDA + comments: + - Perdew-Zunger functional.@en + PZ81: + class_uri: gc:PZ81 + is_a: CorrelationFunctional + comments: + - Perdew-Zunger 1981 correlation functional@en + ParameterSet: + class_uri: gc:ParameterSet + is_a: MethodologyFeature + comments: + - A class representing a specific set of parameters used by the Force Field calculations + (Molecular Mechanics).@en + PeptideResidue: + class_uri: gc:PeptideResidue + is_a: Residue + comments: + - A particular class for residues - monomers of polypeptide and protein@en + Perdew86: + class_uri: gc:Perdew86 + is_a: CorrelationFunctional + comments: + - Perdew 1996 correlation functional@en + PolarizedPopleBasisSet: + class_uri: gc:PolarizedPopleBasisSet + is_a: PopleBasisSet + comments: + - A class for the Pople basis sets with polarization functions.@en + PopleBasisSet: + class_uri: gc:PopleBasisSet + is_a: BasisSet + comments: + - A class for the Pople basis sets.@en + Publication: + class_uri: gc:Publication + slots: + - hasAuthor + is_a: PublicationConcept + comments: + - A generic class for objects related to the publication of results of computational + chemistry calculations.@en + PublicationConcept: + class_uri: gc:PublicationConcept + comments: + - A generic class representing concepts related to publications.@en + QCISD: + class_uri: gc:QCISD + is_a: QuadraticCI + comments: + - A class for the quadratic configuration interaction (QCI) method with single + and double substitutions.@en + QCISD-T: + class_uri: gc:QCISD-T + is_a: QuadraticCI + comments: + - A class for the quadratic configuration interaction (QCI) method with single, + double, and approximate triple substitutions.@en + QuadraticCI: + class_uri: gc:QuadraticCI + is_a: MultipleDeterminant + comments: + - A class for the quadratic configuration interaction (QCI) method.@en + Quadruple: + class_uri: gc:Quadruple + is_a: NormalBond + comments: + - ??? !!!@en + QuantumMechanics: + class_uri: gc:QuantumMechanics + slots: + - hasSingleDeterminantType + - hasSingleReferenceState + - hasSingleReferenceStateType + is_a: GainesvilleCoreTerm + mixins: + - MolecularMethodology + comments: + - A class for Quantum Mechanical methods.@en + - A class for QuantumMechanics.@en + RASPT2: + class_uri: gc:RASPT2 + is_a: MCSCF + comments: + - A class for the restricted active space perturbation theory methods.@en + RASSCF: + class_uri: gc:RASSCF + is_a: MCSCF + comments: + - A class for the Restricted Active Space Multiconfiguration SCF (RASSCF) method.@en + RHF: + class_uri: gc:RHF + is_a: GainesvilleCoreTerm + comments: + - A class for RHF.@en + - Restricted Hartree-Fock method.@en + RamanSpectra: + class_uri: gc:RamanSpectra + is_a: VibrationalSpectra + comments: + - A class for vibrational spectra resulting from Raman intensities.@en + RayleighSchroedinger: + class_uri: gc:RayleighSchroedinger + is_a: SupraMolecularPT + comments: + - "A class for M\xF8ller\u2013Plesset perturbation theory method of quantum chemistry.@en" + Reference: + class_uri: gc:Reference + is_a: GainesvilleCoreTerm + comments: + - A class for a reference.@en + Residue: + class_uri: gc:Residue + slots: + - hasAtom + - hasAtomCount + - hasBondCount + - hasChainNumber + - hasInsertion + - hasSecondaryStructure + is_a: MolecularStructureObject + mixins: + - BFO_0000030 + - GainesvilleCoreTerm + comments: + - A class for Residue.@en + - A class for residues - monomers of polysaccharide, protein, nucleic acid or + polymer@en + ResidueProperty: + class_uri: gc:ResidueProperty + is_a: GainesvilleCoreTerm + comments: + - A class for ResidueProperty.@en + RmsGradient: + class_uri: gc:RmsGradient + is_a: GainesvilleCoreTerm + comments: + - A class for Rms Gradient.@en + SAPT: + class_uri: gc:SAPT + is_a: InterMolecularPT + comments: + - A class for the symmetry-adapted perturbation theory for intermolecular interactions.@en + SAPT0: + class_uri: gc:SAPT0 + is_a: SAPT + comments: + - A class for a sub-class of symmetry-adapted perturbation theory for intermolecular + interactions.@en + SAPT2: + class_uri: gc:SAPT2 + is_a: SAPT + comments: + - A class for a sub-class of symmetry-adapted perturbation theory for intermolecular + interactions.@en + SAPT2p: + class_uri: gc:SAPT2p + is_a: SAPT + comments: + - A class for a sub-class of symmetry-adapted perturbation theory for intermolecular + interactions.@en + SAPT2p3: + class_uri: gc:SAPT2p3 + is_a: SAPT + comments: + - A class for a sub-class of symmetry-adapted perturbation theory for intermolecular + interactions.@en + SAPT2p_3_: + class_uri: gc:SAPT2p_3_ + is_a: SAPT + comments: + - A class for a sub-class of symmetry-adapted perturbation theory for intermolecular + interactions.@en + STO-2G: + class_uri: gc:STO-2G + is_a: MinimalPopleBasisSet + comments: + - A class for the Pople minimal STO-2G basis set.@en + STO-3G: + class_uri: gc:STO-3G + is_a: MinimalPopleBasisSet + comments: + - A class for the Pople minimal STO-3G basis set.@en + STO-3GS: + class_uri: gc:STO-3GS + is_a: PolarizedPopleBasisSet + mixins: + - MinimalPopleBasisSet + comments: + - A class for the Pople minimal STO-3G basis set with polarization functions.@en + STO-4G: + class_uri: gc:STO-4G + is_a: MinimalPopleBasisSet + comments: + - A class for the Pople minimal STO-4G basis set.@en + STO-5G: + class_uri: gc:STO-5G + is_a: MinimalPopleBasisSet + comments: + - A class for the Pople minimal STO-5G basis set.@en + STO-6G: + class_uri: gc:STO-6G + is_a: MinimalPopleBasisSet + comments: + - A class for the Pople minimal STO-6G basis set.@en + SemiEmpiricalScf: + class_uri: gc:SemiEmpiricalScf + is_a: SingleDeterminant + comments: + - A class for SemiEmpirical Methods of Quantum Chemistry@en + Single: + class_uri: gc:Single + is_a: GainesvilleCoreTerm + mixins: + - NormalBond + comments: + - A class for Single.@en + - A class for single covalent bonds.@en + SingleDeterminant: + class_uri: gc:SingleDeterminant + is_a: SingleReferenceState + comments: + - A class for Single Determinant methods of Quantum Chemistry.@en + SinglePoint: + class_uri: gc:SinglePoint + is_a: MolecularComputation + comments: + - A class for Single Point calculations - computation of the energy of molecular + system for given geometry.@en + SingleReferenceState: + class_uri: gc:SingleReferenceState + is_a: QuantumMechanics + comments: + - A class for Single Reference (SR) coupled-cluster methods.@en + Slater: + class_uri: gc:Slater + is_a: ExchangeFunctional + comments: + - Slater exchange functional.@en + SourcePackage: + class_uri: gc:SourcePackage + slots: + - hasInput + - hasOutput + - hasVersion + is_a: PublicationConcept + mixins: + - GainesvilleCoreTerm + comments: + - A class for SourcePackage.@en + - A class for quantum chemistry packages used to peform computations.@en + Spectra: + class_uri: gc:Spectra + is_a: CalculationResult + comments: + - A class for general spectra.@en + SpectralFeatures: + class_uri: gc:SpectralFeatures + is_a: CalculationResult + comments: + - A class for general spectra.@en + SpinSpinCouplingConstant: + class_uri: gc:SpinSpinCouplingConstant + is_a: CalculatedAtomAtomProperties + comments: + - '@en' + - A class for NMR coupling constants.@en + SpinType: + class_uri: gc:SpinType + is_a: MethodologyFeature + comments: + - A class for method for spin treatment in quantum chemical calculations (rhf,uhf,rohf).@en + SplitValencePopleBasisSet: + class_uri: gc:SplitValencePopleBasisSet + is_a: PopleBasisSet + comments: + - A class for the Pople split valence basis sets.@en + SubmittingAuthor: + class_uri: gc:SubmittingAuthor + is_a: Author + comments: + - A class for author submitting this publication.@en + SupraMolecularPT: + class_uri: gc:SupraMolecularPT + is_a: MBPerturbationTheory + comments: + - A class for perturbation theory method applied to whole molecular systems of + quantum chemistry.@en + SystemCharge: + class_uri: gc:SystemCharge + is_a: GainesvilleCoreTerm + comments: + - A class for SystemCharge.@en + SystemEnergies: + class_uri: gc:SystemEnergies + slots: + - hasBindingEnergy + - hasCorrelationEnergy + - hasElectronicEnergy + - hasHeatOfFormation + - hasNuclearRepulsionEnergy + - hasTotalPotentialEnergy + is_a: CalculationResult + comments: + - A class for various types of energies associated with molecular system.@en + SystemMultiplicity: + class_uri: gc:SystemMultiplicity + is_a: GainesvilleCoreTerm + comments: + - A class for SystemMultiplicity.@en + SystemProperty: + class_uri: gc:SystemProperty + slots: + - hasPropertyCount + is_a: GainesvilleCoreTerm + comments: + - A class for systemProperty.@en + SystemTemperature: + class_uri: gc:SystemTemperature + is_a: GainesvilleCoreTerm + comments: + - A class for SystemTemperature.@en + SystemWaveFunction: + class_uri: gc:SystemWaveFunction + is_a: WaveFunction + comments: + - An N-electron wave function describing the whole molecular system.@en + TPSS: + class_uri: gc:TPSS + is_a: Meta-GGA + comments: + - Tao-Perdew-Staroverov-Scuseria functional.@en + TPSSh: + class_uri: gc:TPSSh + is_a: Hybrids + comments: + - Tao-Perdew-Staroverov-Scuseria hybrid functional.@en + TZ: + class_uri: gc:TZ + is_a: DunningBasisSet + comments: + - A class for the Dunning TZ triple zeta basis set.@en + Tddft: + class_uri: gc:Tddft + is_a: SingleDeterminant + comments: + - A class for methods for excited states and response properties from the family + of Density Functional Theories.@en + TotalBOPotentialEnergy: + class_uri: gc:TotalBOPotentialEnergy + is_a: SystemEnergies + comments: + - A class for the Born-Oppenheimer Total Energy (Electronic plus Nuclear Repulsion) + (i.e. potential energy for subsequent MD and other statistical mechanics uses).@en + TotalPotential: + class_uri: gc:TotalPotential + is_a: GainesvilleCoreTerm + comments: + - A class for TotalPotential.@en + Triple: + class_uri: gc:Triple + is_a: NormalBond + comments: + - A class for triple covalent bond.@en + UVVisSpectrum: + class_uri: gc:UVVisSpectrum + is_a: GainesvilleCoreTerm + comments: + - A class for UVVis Spectrum.@en + VDZ: + class_uri: gc:VDZ + is_a: AhlrichsBasisSet + comments: + - A class for the ahlrichs VDZ double zeta basis set.@en + VTZ: + class_uri: gc:VTZ + is_a: AhlrichsBasisSet + comments: + - A class for the ahlrichs VDZ double zeta basis set.@en + VWN: + class_uri: gc:VWN + is_a: LocalDensityApprox-LDA + comments: + - Vosco-Wilks-Nusair functional.@en + VWN3: + class_uri: gc:VWN3 + is_a: CorrelationFunctional + comments: + - Vosco-Wilks-Nusair Formula 3 correlation functional@en + VWN5: + class_uri: gc:VWN5 + is_a: CorrelationFunctional + comments: + - Vosco-Wilks-Nusair Formula 5 correlation functional@en + Value: + class_uri: gc:Value + slots: + - hasUnit + - relatedEntity + - hasValue + is_a: AuxiliaryConcept + comments: + - This is super class for the expression of various types of values.@en + VectorValue: + class_uri: gc:VectorValue + slots: + - hasVectorValue + is_a: Value + comments: + - A class for vector type of data, containing value and unit.@en + VibrationalAnalysis: + class_uri: gc:VibrationalAnalysis + is_a: GainesvilleCoreTerm + mixins: + - MolecularComputation + comments: + - A class for VibrationalAnalysis.@en + - A class for the computations of vibrational spectrum of molecules.@en + VibrationalSpectra: + class_uri: gc:VibrationalSpectra + slots: + - hasFrequencyPeak + - hasPeakCount + is_a: Spectra + comments: + - A class for spectra resulting from the molecular vibrations.@en + WaveFunction: + class_uri: gc:WaveFunction + slots: + - hasOrbital + is_a: GainesvilleCoreTerm + mixins: + - CalculationResult + comments: + - A class for WaveFunction.@en + - A class for the mathematical description of a quantum particle, in most practical + cases of the electron.@en + WaveFunctionCoefficient: + class_uri: gc:WaveFunctionCoefficient + is_a: GainesvilleCoreTerm + comments: + - A class for WaveFunctionCoefficient.@en + aug-cc-pV5Z: + class_uri: gc:aug-cc-pV5Z + is_a: CCQuintupleZeta + comments: + - A class for the aug-cc-pV5Z Correlation Consistent Quintuple Zeta basis set.@en + aug-cc-pVDZ: + class_uri: gc:aug-cc-pVDZ + is_a: CCDoubleZeta + comments: + - A class for the aug-cc-pVDZ Correlation Consistent Double Zeta basis set.@en + aug-cc-pVQZ: + class_uri: gc:aug-cc-pVQZ + is_a: CCQuadrupleZeta + comments: + - A class for the aug-cc-pVQZ Correlation Consistent Quadruple Zeta basis set.@en + aug-cc-pVTZ: + class_uri: gc:aug-cc-pVTZ + is_a: CCTripleZeta + comments: + - A class for the aug-cc-pVTZ Correlation Consistent Triple Zeta basis set.@en + aug-cc-pV_DPD_Z: + class_uri: gc:aug-cc-pV_DPD_Z + is_a: CCDoubleZeta + comments: + - A class for the aug-cc-pV(D+d)Z Correlation Consistent Double Zeta basis set.@en + cc-pV5Z: + class_uri: gc:cc-pV5Z + is_a: CCQuintupleZeta + comments: + - A class for the cc-pV5Z Correlation Consistent Quintuple Zeta basis set.@en + cc-pVDZ: + class_uri: gc:cc-pVDZ + is_a: CCDoubleZeta + comments: + - A class for the cc-pVDZ Correlation Consistent Double Zeta basis set.@en + cc-pVQZ: + class_uri: gc:cc-pVQZ + is_a: CCQuadrupleZeta + comments: + - A class for the cc-pVQZ Correlation Consistent Quadruple Zeta basis set.@en + cc-pVTZ: + class_uri: gc:cc-pVTZ + is_a: CCTripleZeta + comments: + - A class for the cc-pVTZ Correlation Consistent Triple Zeta basis set.@en + d-aug-cc-pVDZ: + class_uri: gc:d-aug-cc-pVDZ + is_a: CCDoubleZeta + comments: + - A class for the d-aug-cc-pVDZ Correlation Consistent Double Zeta basis set.@en + hasFloatValue: + class_uri: gc:hasFloatValue + comments: + - A property that describes floating point value.@en + jun-cc-pVDZ: + class_uri: gc:jun-cc-pVDZ + is_a: CCDoubleZeta + comments: + - A class for the jun-cc-pVDZ Correlation Consistent Double Zeta basis set.@en + 3-21G: + class_uri: http://purl.org/gc/3-21G + is_a: SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 3-21G basis set.@en + 3-21GS: + class_uri: http://purl.org/gc/3-21GS + is_a: PolarizedPopleBasisSet + mixins: + - SplitValencePopleBasisSet + comments: + - A class for the Pople polarization split valence 3-21G* basis set.@en + - A class for the Pople split valence 3-21G* basis set.@en + 3-21pG: + class_uri: http://purl.org/gc/3-21pG + is_a: SplitValencePopleBasisSet + mixins: + - DiffusePopleBasisSet + comments: + - A class for the Pople split valence 3-21+G basis set.@en + 3-21pGS: + class_uri: http://purl.org/gc/3-21pGS + is_a: PolarizedPopleBasisSet + mixins: + - DiffusePopleBasisSet + - SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 3-21+G* basis set.@en + 4-31G: + class_uri: http://purl.org/gc/4-31G + is_a: SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 4-31G basis set.@en + 6-31G: + class_uri: http://purl.org/gc/6-31G + is_a: SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 6-31G basis set.@en + 6-31GS: + class_uri: http://purl.org/gc/6-31GS + is_a: PolarizedPopleBasisSet + mixins: + - SplitValencePopleBasisSet + comments: + - A class for the Pople polarization split valence 6-31G* basis set.@en + 6-31GSS: + class_uri: http://purl.org/gc/6-31GSS + is_a: PolarizedPopleBasisSet + mixins: + - SplitValencePopleBasisSet + comments: + - A class for the Pople polarization split valence 6-31G** basis set.@en + 6-31pGS: + class_uri: http://purl.org/gc/6-31pGS + is_a: PolarizedPopleBasisSet + mixins: + - DiffusePopleBasisSet + - SplitValencePopleBasisSet + comments: + - A class for the Pople polarization split valence 6-31+G* basis set.@en + 6-311G: + class_uri: http://purl.org/gc/6-311G + is_a: SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 6-311G basis set.@en + 6-311GS: + class_uri: http://purl.org/gc/6-311GS + is_a: PolarizedPopleBasisSet + mixins: + - SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 6-311G* basis set.@en + 6-311pGS: + class_uri: http://purl.org/gc/6-311pGS + is_a: PolarizedPopleBasisSet + mixins: + - DiffusePopleBasisSet + - SplitValencePopleBasisSet + comments: + - A class for the Pople split valence 6-311+G* basis set.@en + Element: + class_uri: pt:Element + is_a: MolecularConcept + Class: + class_uri: owl:Class + slots: + - hasAuxiliaryProperty + - hasMolecularProperty + ObjectProperty: + class_uri: owl:ObjectProperty + kelvin: + comments: + - a unit of temperature.@en + nano_meter: + comments: + - a unit of length@en + Amber: + comments: + - The Amber force field.@en + Charmm: + comments: + - The Charmm force field.@en + DefaultAmberParameterSet: + comments: + - Default Amber parameter set.@en + DefaultCharmmParameterSet: + comments: + - Default Charmm parameter set.@en + DefaultMMPParameterSet: + comments: + - Default MM plus parameter set@en + DefaultOPLSParameterSet: + comments: + - Default OPLS parameter set.@en + NormalMethodology: + comments: + - A normal methodology.@en + Opls: + comments: + - The OPLS force field.@en + ROHF: + comments: + - Open-shell restricted Hartree-Fock method.@en + UHF: + comments: + - Unrestricted Hartree-Fock method.@en + angstrom: + comments: + - A unit of length.@en + atomicUnit: + comments: + - "Atomic Unit this is measure in units of elementary atomic charge called atomicUnits\ + \ (a.u) .\n\tThe elementary unit of charge (e) is called an atomic unit (a.u.)\ + \ of charge and is so many Coulombs (1.6 *10**(-19) Coulombs. (float)@en" + cm-1: + comments: + - A wavenumber - the unit of frequency.@en + debye: + comments: + - '@en' + electronVolts: + comments: + - the unit of energy.@en + hartree: + comments: + - the unit of energy.@en + kiloCalories: + comments: + - the unit of energy@en + kiloCaloriesPerAngstrom: + comments: + - ???@en + kiloJoules: + comments: + - a unit of energy@en + Mm+: + comments: + - MM+ force field.@en +slots: + BFO_0000124: + slot_uri: bfo:BFO_0000124 + multivalued: true + IsAtomProperty: + slot_uri: gc:IsAtomProperty + is_a: extraGCObjectProperty + comments: + - A generic atomic property@en + multivalued: true + IsSystemProperty: + slot_uri: gc:IsSystemProperty + is_a: extraGCObjectProperty + comments: + - A generic system property@en + multivalued: true + binds: + slot_uri: gc:binds + range: Atom + is_a: hasMolecularProperty + comments: + - A property that tells which atoms are bonded.@en + multivalued: true + extraGCObjectProperty: + slot_uri: gc:extraGCObjectProperty + multivalued: true + hasAtom: + slot_uri: gc:hasAtom + range: Atom + is_a: hasMolecularProperty + mixins: + - BFO_0000124 + comments: + - A property that describes atoms comprised by a molecule or residue@en + multivalued: true + hasAtomCoordinateX: + slot_uri: gc:hasAtomCoordinateX + range: FloatValue + is_a: extraGCObjectProperty + mixins: + - hasCoordinates + comments: + - A property that describes Atom X coordinate@en + multivalued: true + hasAtomCoordinateY: + slot_uri: gc:hasAtomCoordinateY + range: FloatValue + is_a: extraGCObjectProperty + mixins: + - hasCoordinates + comments: + - A property that describes Atom Y coordinate@en + multivalued: true + hasAtomCoordinateZ: + slot_uri: gc:hasAtomCoordinateZ + range: FloatValue + is_a: extraGCObjectProperty + mixins: + - hasCoordinates + comments: + - A property that describes Atom Z coordinate@en + multivalued: true + hasAtomProperty: + slot_uri: gc:hasAtomProperty + range: ObjectProperty + is_a: extraGCObjectProperty + mixins: + - hasMolecularData + comments: + - A property that allows to declare a general property for an atom.@en + - A property that allows to describe an atom, like NMR Shielding@en + multivalued: true + hasAuthor: + slot_uri: gc:hasAuthor + range: Author + is_a: extraGCObjectProperty + comments: + - A property that describes teh author@en + multivalued: true + hasAuxiliaryProperty: + slot_uri: gc:hasAuxiliaryProperty + range: Class + comments: + - The upper property for various properties related to publications + multivalued: true + hasBasisCount: + slot_uri: gc:hasBasisCount + is_a: extraGCObjectProperty + comments: + - A property that specifies the Basis Count.@en + multivalued: true + hasBasisSet: + slot_uri: gc:hasBasisSet + range: BasisSet + is_a: hasMolecularFeature + mixins: + - hasFeature + comments: + - A property that allows Basis Sets to be assigned to a given quantum methodology@en + - A property that allows to define Basis Set - finite set of functions used to + approximately express the Molecular Orbital wavefunction(s) of system, normally + atom centered, consisting of AOs differing in local angular momentum for each + atom.@en + multivalued: true + hasBindingEnergy: + slot_uri: gc:hasBindingEnergy + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that allows to assign the Binding Energy to the molecular system@en + multivalued: true + hasBond: + slot_uri: gc:hasBond + range: Bond + is_a: hasMolecularProperty + comments: + - A property that allows the bond to be assigned to atoms.@en + multivalued: true + hasBondLength: + slot_uri: gc:hasBondLength + range: FloatValue + is_a: hasMolecularProperty + comments: + - A property that allows bond length to be assigned the a bond.@en + multivalued: true + hasBondOrder: + slot_uri: gc:hasBondOrder + is_a: extraGCObjectProperty + comments: + - A property that specifies bond order.@en + multivalued: true + hasBondType: + slot_uri: gc:hasBondType + range: BondTypes + is_a: extraGCObjectProperty + comments: + - A property that describes Bond Type@en + - 'A property that describes bond type@en ' + multivalued: true + hasCalculatedAtomCharge: + slot_uri: gc:hasCalculatedAtomCharge + range: FloatValue + is_a: hasResult + comments: + - A property that describes the atom charge calculated by a specific methodology.@en + multivalued: true + hasCalculation: + slot_uri: gc:hasCalculation + is_a: extraGCObjectProperty + comments: + - A property that specifies the calculation.@en + multivalued: true + hasCalculationOn: + slot_uri: gc:hasCalculationOn + is_a: hasResult + comments: + - A property that tells whether the molecular system has calculations done.@en + multivalued: true + hasCollectionEntry: + slot_uri: gc:hasCollectionEntry + is_a: extraGCObjectProperty + comments: + - A property that specifies the Collection Entry.@en + multivalued: true + hasCoordinates: + slot_uri: gc:hasCoordinates + range: VectorValue + is_a: hasMolecularProperty + comments: + - A property that describes atom coordinates.@en + multivalued: true + hasCorrelationEnergy: + slot_uri: gc:hasCorrelationEnergy + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that describes system correlation energy.@en + multivalued: true + hasCorrelationFunctional: + slot_uri: gc:hasCorrelationFunctional + range: CorrelationFunctional + is_a: hasFeature + comments: + - A property that describes the correlation functional for the given methodology.@en + multivalued: true + hasDftFlavor: + slot_uri: gc:hasDftFlavor + range: DftFlavor + is_a: hasFeature + comments: + - A property that describes specific approximations to exchange-correlation functionals + in the Density Functional Theory.@en + multivalued: true + hasDftFunctional: + slot_uri: gc:hasDftFunctional + range: DensityFunctional + is_a: hasFeature + comments: + - A property that describes DFT Functionals for the given methodology.@en + multivalued: true + hasDipoleMoment: + slot_uri: gc:hasDipoleMoment + range: VectorValue + is_a: hasDipoleResult + comments: + - A property that describes molecular dipole moment.@en + multivalued: true + hasDipoleMomentAverage: + slot_uri: gc:hasDipoleMomentAverage + range: FloatValue + is_a: hasDipoleResult + comments: + - A property that describes the average molecular dipole moment.@en + multivalued: true + hasDipoleMomentX: + slot_uri: gc:hasDipoleMomentX + range: FloatValue + is_a: extraGCObjectProperty + mixins: + - hasDipoleMoment + comments: + - A property that reports dipole moment X component@en + multivalued: true + hasDipoleMomentY: + slot_uri: gc:hasDipoleMomentY + range: FloatValue + is_a: extraGCObjectProperty + mixins: + - hasDipoleMoment + comments: + - A property ... @en + multivalued: true + hasDipoleMomentZ: + slot_uri: gc:hasDipoleMomentZ + range: FloatValue + is_a: extraGCObjectProperty + mixins: + - hasDipoleMoment + comments: + - A property ... @en + multivalued: true + hasDipoleResult: + slot_uri: gc:hasDipoleResult + is_a: hasResult + comments: + - A property that describes molecular dipole moment.@en + multivalued: true + hasDispersionCorrection: + slot_uri: gc:hasDispersionCorrection + range: DispersionCorrection + is_a: hasFeature + comments: + - A property that describes the dispersion correction@en + multivalued: true + hasElectronicEnergy: + slot_uri: gc:hasElectronicEnergy + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that describes the electronic energy.@en + multivalued: true + hasElectronicSpectraResult: + slot_uri: gc:hasElectronicSpectraResult + is_a: hasResult + comments: + - A property that describes the electronic spectra.@en + multivalued: true + hasElectronicTransitions: + slot_uri: gc:hasElectronicTransitions + range: VectorValue + is_a: hasElectronicSpectraResult + comments: + - A property that describes electronic transition energies.@en + multivalued: true + hasExchangeFunctional: + slot_uri: gc:hasExchangeFunctional + range: ExchangeFunctional + is_a: hasFeature + comments: + - A property that describes the exchange functionals.@en + multivalued: true + hasExcitedStateMethod: + slot_uri: gc:hasExcitedStateMethod + is_a: hasMolecularFeature + comments: + - A property that defines the method for the calculation of the excited states + of molecules.@en + multivalued: true + hasFeature: + slot_uri: gc:hasFeature + range: MethodologyFeature + comments: + - A property that describes a specific feature of given methodology.@en + - has feature + multivalued: true + hasFile: + slot_uri: gc:hasFile + is_a: hasPublicationData + mixins: + - hasAuxiliaryProperty + comments: + - A property that describes the attachment file.@en + - A property that describes the reference to the attachment file.@en + multivalued: true + hasFloatVector: + slot_uri: gc:hasFloatVector + is_a: extraGCObjectProperty + comments: + - A property that specifies the Float Vector.@en + multivalued: true + hasForceField: + slot_uri: gc:hasForceField + range: ForceField + is_a: hasMolecularFeature + mixins: + - hasFeature + comments: + - A property that describes Force Field.@en + - A property that describes a specific force field for given Molecular Mechanics + method.@en + multivalued: true + hasFormalCharge: + slot_uri: gc:hasFormalCharge + range: IntegerValue + is_a: hasMolecularProperty + comments: + - A property that descibes the formal charge. The formal charge is the charge + assigned to an atom in a molecule, assuming that electrons in a chemical bond + are shared equally between atoms, regardless of relative electronegativity.@en + multivalued: true + hasFrequency: + slot_uri: gc:hasFrequency + range: FloatValue + is_a: hasResult + comments: + - A property that describes the value of a frequency at the peak of the spectrum.@en + multivalued: true + hasFrequencyPeak: + slot_uri: gc:hasFrequencyPeak + range: FrequencyPeak + is_a: hasResult + comments: + - A property that describes the value of a frequency peak of the vibrational spectrum.@en + multivalued: true + hasGroupProperty: + slot_uri: gc:hasGroupProperty + is_a: extraGCObjectProperty + comments: + - A property that specifies the Group Property.@en + multivalued: true + hasHeatOfFormation: + slot_uri: gc:hasHeatOfFormation + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that describes the value of a the Heat of Formation.@en + multivalued: true + hasIRSpectrum: + slot_uri: gc:hasIRSpectrum + is_a: extraGCObjectProperty + comments: + - A property that describes Molecular System@en + multivalued: true + hasIntegerVector: + slot_uri: gc:hasIntegerVector + is_a: extraGCObjectProperty + comments: + - A property that specifies the Integer Vector.@en + multivalued: true + hasIntensity: + slot_uri: gc:hasIntensity + range: FloatValue + is_a: hasResult + comments: + - A property that describes the value of the intensity of a peak of a spectrum.@en + multivalued: true + hasKeyword: + slot_uri: gc:hasKeyword + is_a: extraGCObjectProperty + comments: + - A property describes keywords for running QC jobs@en + multivalued: true + hasMass: + slot_uri: gc:hasMass + range: hasFloatValue + is_a: extraGCObjectProperty + mixins: + - hasMolecularData + comments: + - A property ...@en + multivalued: true + hasMathML: + slot_uri: gc:hasMathML + is_a: extraGCObjectProperty + comments: + - A property that specifies MathML object.@en + multivalued: true + hasMathMLEquation: + slot_uri: gc:hasMathMLEquation + is_a: extraGCObjectProperty + comments: + - A property that specifies MathML Equation.@en + multivalued: true + hasMethodology: + slot_uri: gc:hasMethodology + range: Methodology + is_a: hasMethodFeature + mixins: + - hasFeature + comments: + - A property that describes a methodology of computations.@en + - A property that describes the methodology of the computations.@en + multivalued: true + hasMolecularCollection: + slot_uri: gc:hasMolecularCollection + is_a: extraGCObjectProperty + comments: + - A property that specifies the Molecular Collection.@en + multivalued: true + hasMolecularComputation: + slot_uri: gc:hasMolecularComputation + range: MolecularComputation + is_a: extraGCObjectProperty + comments: + - A property that describes Molecular Computation@en + multivalued: true + hasMolecularMechanics: + slot_uri: gc:hasMolecularMechanics + range: boolean + is_a: hasCalculationOn + mixins: + - extraGCDataProperty + comments: + - A property that says (true/false) if there is MM calculation@en + multivalued: true + hasMolecularProperty: + slot_uri: gc:hasMolecularProperty + range: Class + comments: + - The upper property for various properties related to molecular systems + multivalued: true + hasMolecularSystem: + slot_uri: gc:hasMolecularSystem + range: MolecularSystem + is_a: extraGCObjectProperty + comments: + - A property ...@en + multivalued: true + hasMolecule: + slot_uri: gc:hasMolecule + is_a: extraGCObjectProperty + comments: + - A property that specifies a molecule.@en + multivalued: true + hasMoleculeProperty: + slot_uri: gc:hasMoleculeProperty + is_a: extraGCObjectProperty + comments: + - A property that specifies the Molecule Property.@en + multivalued: true + hasMullikenCharges: + slot_uri: gc:hasMullikenCharges + range: FloatValue + is_a: hasResult + comments: + - A property that describes computed Mulliken Charges.@en + multivalued: true + hasMultipleDeterminant: + slot_uri: gc:hasMultipleDeterminant + is_a: extraGCObjectProperty + comments: + - A property that specifies Multiple Determinant.@en + multivalued: true + hasMultipleReferenceState: + slot_uri: gc:hasMultipleReferenceState + is_a: extraGCObjectProperty + comments: + - A property that describes Multiple Reference State@en + multivalued: true + hasNmrShieldingAnisotropy: + slot_uri: gc:hasNmrShieldingAnisotropy + range: FloatValue + is_a: hasShielding + comments: + - A property that describes computed NMR Shielding Anisotropic component.@en + multivalued: true + hasNmrShieldingIsotropic: + slot_uri: gc:hasNmrShieldingIsotropic + range: FloatValue + is_a: hasShielding + comments: + - A property that describes computed NMR Shielding Isotropic component@en + multivalued: true + hasNormalMode: + slot_uri: gc:hasNormalMode + range: VectorValue + is_a: hasResult + comments: + - A property that describes the normal mode of a vibration@en + multivalued: true + hasNuclearRepulsionEnergy: + slot_uri: gc:hasNuclearRepulsionEnergy + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that describes the potential energy arising from Coulombic nuclei-nuclei + repulsions@en + multivalued: true + hasNumberBasisFunc: + slot_uri: gc:hasNumberBasisFunc + range: NumberBasisFunc + is_a: hasFeature + comments: + - A property that describes the number of basis functions.@en + multivalued: true + hasOccupancy: + slot_uri: gc:hasOccupancy + range: FloatValue + is_a: hasResult + comments: + - A property that describes the occupancy of the orbital@en + multivalued: true + hasOccupiedOrbitalsIncluded: + slot_uri: gc:hasOccupiedOrbitalsIncluded + is_a: hasMolecularFeature + comments: + - A property that describes the inclusion of occupied orbitals in electronic spectra + calculations.@en + multivalued: true + hasOpenShellTreatment: + slot_uri: gc:hasOpenShellTreatment + is_a: hasMolecularFeature + comments: + - A property that describes the treatment of open shell systems.@en + multivalued: true + hasOrbital: + slot_uri: gc:hasOrbital + range: Orbital + is_a: hasResult + comments: + - A property that describes the orbital.@en + multivalued: true + hasOrbitalCount: + slot_uri: gc:hasOrbitalCount + is_a: hasMolecularFeature + comments: + - A property that defines the number of electron orbitals@en + multivalued: true + hasOrbitalEnergy: + slot_uri: gc:hasOrbitalEnergy + range: FloatValue + is_a: hasResult + comments: + - A property that describes the orbital energy.@en + multivalued: true + hasOrbitalSymmetry: + slot_uri: gc:hasOrbitalSymmetry + is_a: hasMolecularFeature + comments: + - A property that defines Orbital symmetry@en + multivalued: true + hasOscillatorStrength: + slot_uri: gc:hasOscillatorStrength + range: VectorValue + is_a: hasElectronicSpectraResult + comments: + - A property that defines oscillator strengths of electronic spectra.@en + multivalued: true + hasOutputFile: + slot_uri: gc:hasOutputFile + is_a: extraGCObjectProperty + comments: + - A property that specifies the Output file.@en + multivalued: true + hasParameter: + slot_uri: gc:hasParameter + is_a: extraGCObjectProperty + comments: + - A property that specifies a parameter.@en + multivalued: true + hasParameterSet: + slot_uri: gc:hasParameterSet + range: ParameterSet + is_a: hasMolecularFeature + mixins: + - hasFeature + comments: + - A property that defines the parametr set for calculations.@en + - A property that describes a specific parameter set for Molecular Mechanics calculations.@en + multivalued: true + hasPropertyValue: + slot_uri: gc:hasPropertyValue + is_a: extraGCObjectProperty + comments: + - A property Value@en + multivalued: true + hasPublisher: + slot_uri: gc:hasPublisher + range: publisher + is_a: extraGCObjectProperty + comments: + - A property that relates publication to publisher@en + multivalued: true + hasQuantity: + slot_uri: gc:hasQuantity + is_a: extraGCObjectProperty + comments: + - A property that defines quantity@en + multivalued: true + hasQuantumMechanics: + slot_uri: gc:hasQuantumMechanics + range: boolean + is_a: hasCalculationOn + mixins: + - extraGCDataProperty + comments: + - A property that says (true/false) if there is QM calculation@en + multivalued: true + hasRMSGradient: + slot_uri: gc:hasRMSGradient + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that describes RMS gradient of the computations.@en + multivalued: true + hasResidue: + slot_uri: gc:hasResidue + range: Residue + is_a: hasMolecularProperty + mixins: + - BFO_0000124 + comments: + - A property that describes the residue in a molecule.@en + multivalued: true + hasResidueProperty: + slot_uri: gc:hasResidueProperty + is_a: extraGCObjectProperty + comments: + - A property that specifies the Residue Property.@en + multivalued: true + hasResult: + slot_uri: gc:hasResult + range: CalculationResult + comments: + - A property that describes generic results of the computations.@en + multivalued: true + hasScope: + slot_uri: gc:hasScope + range: MolecularSystem + is_a: extraGCObjectProperty + comments: + - A property ...@en + multivalued: true + hasShielding: + slot_uri: gc:hasShielding + range: FloatValue + is_a: hasResult + comments: + - A property that describes an NMR shielding of an atom.@en + multivalued: true + hasSingleDeterminantType: + slot_uri: gc:hasSingleDeterminantType + is_a: extraGCObjectProperty + comments: + - A property ...@en + multivalued: true + hasSingleReferenceState: + slot_uri: gc:hasSingleReferenceState + is_a: extraGCObjectProperty + comments: + - A property ...@en + multivalued: true + hasSingleReferenceStateType: + slot_uri: gc:hasSingleReferenceStateType + is_a: extraGCObjectProperty + comments: + - A property that describes Reference State Type@en + multivalued: true + hasSource: + slot_uri: gc:hasSource + is_a: extraGCObjectProperty + mixins: + - extraGCDataProperty + comments: + - A property that describes softare package@en + - A property that reports what software package was used + multivalued: true + hasSourcePackage: + slot_uri: gc:hasSourcePackage + range: SourcePackage + is_a: hasAuxiliaryProperty + comments: + - A property that defines relations that allows to describe Source Package for + Publication.@en + multivalued: true + hasSpinType: + slot_uri: gc:hasSpinType + range: SpinType + is_a: hasMolecularFeature + mixins: + - hasFeature + comments: + - A property that defines the spin type.@en + - A property that describes handling of spins by the methodology (RHF,UHF,ROHF).@en + multivalued: true + hasSystemCharge: + slot_uri: gc:hasSystemCharge + range: FloatValue + is_a: hasMolecularProperty + comments: + - A property that describes molecular system charge.@en + multivalued: true + hasSystemEnergiesResult: + slot_uri: gc:hasSystemEnergiesResult + is_a: hasResult + comments: + - A property that describes system energies.@en + multivalued: true + hasSystemMultiplicity: + slot_uri: gc:hasSystemMultiplicity + is_a: hasMolecularFeature + comments: + - A property that describes the system spin multiplicity.@en + multivalued: true + hasSystemProperty: + slot_uri: gc:hasSystemProperty + range: CalculatedSystemProperties + is_a: extraGCObjectProperty + comments: + - A property ...@en + multivalued: true + hasSystemTemperature: + slot_uri: gc:hasSystemTemperature + range: FloatValue + is_a: hasMolecularProperty + comments: + - A property that describes system temperature.@en + multivalued: true + hasTotalPotentialEnergy: + slot_uri: gc:hasTotalPotentialEnergy + range: FloatValue + is_a: hasSystemEnergiesResult + comments: + - A property that describes Total Potential Energy.@en + multivalued: true + hasTransitionCount: + slot_uri: gc:hasTransitionCount + is_a: hasMolecularFeature + comments: + - A property that describes the number of the electronic transitions in spectral + calculations.@en + multivalued: true + hasUnit: + slot_uri: gc:hasUnit + is_a: hasAuxiliaryProperty + comments: + - A property that describes a unit of the value.@en + multivalued: true + hasUnoccupiedOrbitalsIncluded: + slot_uri: gc:hasUnoccupiedOrbitalsIncluded + is_a: hasMolecularFeature + comments: + - A property that describes the inclusion of occupied orbitals in electronic spectra + calculations.@en + multivalued: true + hasVibrationCount: + slot_uri: gc:hasVibrationCount + is_a: hasMolecularFeature + comments: + - A property that describes the number of vibrational frequencies.@en + multivalued: true + hasWaveFunctionCoefficients: + slot_uri: gc:hasWaveFunctionCoefficients + range: VectorValue + is_a: hasResult + comments: + - A property that describes Wave Function Coefficients.@en + multivalued: true + hasXYPoint: + slot_uri: gc:hasXYPoint + is_a: extraGCObjectProperty + comments: + - A property that specifies the XY Point.@en + multivalued: true + holds: + slot_uri: gc:holds + is_a: hasAuxiliaryProperty + comments: + - A property that defines objects held by a container.@en + multivalued: true + isCalculationOn: + slot_uri: gc:isCalculationOn + is_a: extraGCObjectProperty + comments: + - A property that specifies the object of the calculation.@en + multivalued: true + isElement: + slot_uri: gc:isElement + range: Element + is_a: hasMolecularProperty + comments: + - A property that describes what element the given atom is.@en + multivalued: true + relatedEntity: + slot_uri: gc:relatedEntity + is_a: hasAuxiliaryProperty + comments: + - A property that describes related entity.@en + multivalued: true + usesMolecularCalculation: + slot_uri: gc:usesMolecularCalculation + is_a: extraGCObjectProperty + comments: + - A property that specifies the use of Molecular Calculation.@en + multivalued: true + usesMolecularSystem: + slot_uri: gc:usesMolecularSystem + is_a: extraGCObjectProperty + comments: + - A property that specifies the use of Molecular System.@en + multivalued: true + xAxis: + slot_uri: gc:xAxis + is_a: extraGCObjectProperty + comments: + - A property that describes what is on xAxis@en + multivalued: true + xAxisUnit: + slot_uri: gc:xAxisUnit + is_a: extraGCObjectProperty + comments: + - A property that describes Units of X Axis@en + multivalued: true + yAxis: + slot_uri: gc:yAxis + is_a: extraGCObjectProperty + comments: + - A property that describes what is on Axis@en + multivalued: true + yAxisUnit: + slot_uri: gc:yAxisUnit + is_a: extraGCObjectProperty + comments: + - A property that describes Units of X Axis@en + multivalued: true + extraGCDataProperty: + slot_uri: gc:extraGCDataProperty + multivalued: true + hasAtomCount: + slot_uri: gc:hasAtomCount + is_a: hasMolecularData + comments: + - A property that allows to declare total count of atoms in a given structure + - Molecular System or Molecule or Residue.@en + multivalued: true + hasBondCount: + slot_uri: gc:hasBondCount + is_a: hasMolecularData + comments: + - A property that determinates the count of bonds into Molecule, Residue or Atom.@en + multivalued: true + hasCategory: + slot_uri: gc:hasCategory + is_a: hasPublicationData + comments: + - A property that determines a category of the publication.@en + multivalued: true + hasChainNumber: + slot_uri: gc:hasChainNumber + is_a: hasMolecularData + comments: + - A property that defines chain number in the molecule.@en + multivalued: true + hasElementSymbol: + slot_uri: gc:hasElementSymbol + is_a: hasMolecularData + comments: + - A property that defines the Symbol of the element of an atom.@en + multivalued: true + hasEmail: + slot_uri: gc:hasEmail + is_a: hasPublicationData + comments: + - A property that describes the email address of corresponding author.@en + multivalued: true + hasFirstName: + slot_uri: gc:hasFirstName + is_a: hasPublicationData + comments: + - A property that describes the first name of corresponding author.@en + multivalued: true + hasFloatValue: + slot_uri: gc:hasFloatValue + is_a: hasValue + multivalued: true + hasInChIKey: + slot_uri: gc:hasInChIKey + is_a: hasMolecularData + comments: + - A property that describes the InChI Key - the condensed, 27 character hashed + version of the InChI String.@en + multivalued: true + hasInChIString: + slot_uri: gc:hasInChIString + is_a: hasMolecularData + comments: + - A property that describes the InChI String - International Chemical Identifier + - a textual identifier for chemical substances.@en + multivalued: true + hasIndex: + slot_uri: gc:hasIndex + is_a: hasMolecularData + comments: + - A property that defines a sequential arrangement of material in numerical order, + i.e. Frequency Peak, Orbital or a sequence number in residue.@en + multivalued: true + hasInput: + slot_uri: gc:hasInput + is_a: hasPublicationData + comments: + - A property that defines the contents of the input file of the calculation.@en + multivalued: true + hasInputFile: + slot_uri: gc:hasInputFile + is_a: extraGCDataProperty + comments: + - A property that specifies input file for calculations.@en + multivalued: true + hasInsertion: + slot_uri: gc:hasInsertion + is_a: hasMolecularData + comments: + - A property that defines the insertion code for residue numbering.@en + multivalued: true + hasIntegerValue: + slot_uri: gc:hasIntegerValue + is_a: hasValue + comments: + - A property that describes Integer Value.@en + multivalued: true + hasKey: + slot_uri: gc:hasKey + is_a: hasPublicationData + comments: + - A property that defines the security key of the publication.@en + multivalued: true + hasLastName: + slot_uri: gc:hasLastName + is_a: hasPublicationData + comments: + - A property that describes the last name of corresponding author.@en + multivalued: true + hasMethod: + slot_uri: gc:hasMethod + is_a: hasMethodFeature + comments: + - A property that defines the calculation method for given technology.@en + multivalued: true + hasMethodFeature: + slot_uri: gc:hasMethodFeature + comments: + - The upper property for various properties related to computational methods + multivalued: true + hasMolecularData: + slot_uri: gc:hasMolecularData + comments: + - The upper property for various properties related to Molecular Data + multivalued: true + hasMolecularFeature: + slot_uri: gc:hasMolecularFeature + comments: + - The upper property for various properties related to Molecular Data + multivalued: true + hasName: + slot_uri: gc:hasName + is_a: hasMolecularData + comments: + - A property that defines the name of molecular system elements, i.e. atom or + residue.@en + - The name of an entity. + multivalued: true + hasNaturalValue: + slot_uri: gc:hasNaturalValue + is_a: hasValue + comments: + - A property that defines natural value.@en + multivalued: true + hasNumber: + slot_uri: gc:hasNumber + is_a: extraGCDataProperty + comments: + - A property of having a number@en + multivalued: true + hasNumberOfAtoms: + slot_uri: gc:hasNumberOfAtoms + is_a: extraGCDataProperty + mixins: + - hasMolecularData + comments: + - A property that determines the number of atoms in a given collection@en + multivalued: true + hasOrganization: + slot_uri: gc:hasOrganization + is_a: hasPublicationData + comments: + - A property that describes the organization of corresponding author.@en + multivalued: true + hasOutput: + slot_uri: gc:hasOutput + is_a: hasPublicationData + comments: + - The property that defines the contents of the output file of the calculation.@en + multivalued: true + hasPeakCount: + slot_uri: gc:hasPeakCount + is_a: extraGCDataProperty + mixins: + - hasMolecularData + comments: + - A property that determinates the count of peaks in a spectrum.@en + multivalued: true + hasPropertyCount: + slot_uri: gc:hasPropertyCount + is_a: extraGCDataProperty + comments: + - A property that reports property count@en + multivalued: true + hasPublicationData: + slot_uri: gc:hasPublicationData + comments: + - The upper property for various properties related to the publication data + multivalued: true + hasSecondaryStructure: + slot_uri: gc:hasSecondaryStructure + is_a: hasMolecularData + comments: + - A property that defines the three-dimensional form of local segments of biopolymers.@en + multivalued: true + hasStatus: + slot_uri: gc:hasStatus + is_a: hasPublicationData + comments: + - A property that describes the status of the publication.@en + multivalued: true + hasTag: + slot_uri: gc:hasTag + is_a: extraGCDataProperty + comments: + - A property that reports tags assigned to publication@en + multivalued: true + hasTechnology: + slot_uri: gc:hasTechnology + is_a: hasMethodFeature + comments: + - A property that describes the calculation's technology for molecular system.@en + multivalued: true + hasTextValue: + slot_uri: gc:hasTextValue + is_a: extraGCDataProperty + comments: + - A property ...@en + multivalued: true + hasValue: + slot_uri: gc:hasValue + comments: + - A Superproperty of typed numerical values.@en + multivalued: true + hasVectorValue: + slot_uri: gc:hasVectorValue + is_a: hasValue + comments: + - A property that describes the vector values.@en + multivalued: true + hasVersion: + slot_uri: gc:hasVersion + is_a: hasPublicationData + comments: + - A property that describes the version of the software package used.@en + multivalued: true + hasVisibility: + slot_uri: gc:hasVisibility + is_a: hasPublicationData + comments: + - A property that defines the allowed visibility of the publication.@en + multivalued: true + license: + slot_uri: cc:license + multivalued: true + contributor: + slot_uri: dc:contributor + multivalued: true + created: + slot_uri: dc:created + multivalued: true + creator: + slot_uri: dcterms:creator + multivalued: true + date: + slot_uri: dc:date + multivalued: true + description: + slot_uri: dc:description + multivalued: true + rights: + slot_uri: dc:rights + multivalued: true + subject: + slot_uri: dc:subject + multivalued: true + title: + slot_uri: dcterms:title + multivalued: true + isAbstract: + slot_uri: gc:isAbstract + range: boolean + comments: + - "This annotation should be used to mark entities as abstract.\n\tAbstract entity\ + \ is a defined OWL resource that from a data model should never be defined explicitly.\n\ + \n\tNOTE!\n\tSince it's only a annotation property, it doesn't impact a logical\ + \ definition of an Entity. Such a property should be treated as a \\\"side note\\\ + \".\t@en" + multivalued: true + termStatus: + slot_uri: gc:termStatus + range: string + comments: + - "Such a annotation contains information about defined in DMS ontology Axiom\ + \ status.\n\tSince it's a text based value, follwing enumerations should be\ + \ used as values:\n\n\t- STABLE (Entity was tested during QA process and is\ + \ stable)\n\t- UNSTABLE (Entity is unstable due to some reasone - shouldn't\ + \ be use till fixed)\n\t- TESTING (Entity is under testing process)\n\t- ARCHAIC\ + \ (old and unused definition - probably will be removed in comming iterations)\n\ + \t- DEPRECATED (Entity is deprecated due to some reason - should not be used)\n\ + \t- NEW (new definition)\n\t- FIX (definition that was made to bring fix for\ + \ some issue)\n\n\tNOTE!\n\tSince it's only a annotation property, it doesn't\ + \ impact a logical definition of an Entity. Such a property should be treated\ + \ as a \\\"side note\\\".\t@en" + multivalued: true + termStatusNote: + slot_uri: gc:termStatusNote + range: string + comments: + - "This property is a status description of a particular Entity. Combined with\ + \ log:termStatus contains information aboud current status of an Entity, with\ + \ a information about history, changes, etc.\n\n\tNOTE!\n\tSince it's only a\ + \ annotation property, it doesn't impact a logical definition of an Entity.\ + \ Such a property should be treated as a \\\"side note\\\".\t@en" + multivalued: true +enums: {} +