Chemical Semantics, Inc.

The Gainesville Core Ontology 0.5.5

Namespace Document 09 April 2015

This version:
http://ontologies.makolab.com/gc06/gc.html (OWL)
Latest version:
http://purl.org/gc/ (OWL)
Previous version:
http://purl.org/gc/0.2 (OWL)
Authors:
Dominik Kuzinski, Gniewko Rzepka (MakoLab SA)
Dr Mirek Sopek, Dr Neil Ostlund (Chemical Semantics, Inc.)

Valid XHTML + RDFa Example Licencing Information Creative Commons License This work is licensed under a Creative Commons Attribution License. This copyright applies to the Gainesville Core Ontology Specification and accompanying documentation in RDF. Regarding underlying technology, the Gainesville Core Ontology uses W3C's RDF technology, an open Web standard that can be freely used by anyone.


Abstract

The Gainesville Core Ontology Ontology aims at complete description of typical Computational Chemistry experiment.

Gainesville Core describes:
- Molecular Publications
- Molecular Systems
- Molecular Calculations
  Molecular Systems contain 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.

Table of Contents

The Gainesville Core Ontology at a glance

An a-z index of Gainesville Core Ontology terms, by class (categories or types) and by property.

Classes: | AbInitioScf | Aromatic | Atom | AuxiliaryConcept | BasisSet | Bond | CalculatedProperties | CalculationConcept | CalculationResult | Caspt2 | Ccd | Ccsd | Ccsd-t | Cis | Cisd | ComputationalChemistryPublication | CorrelationFunctional | Dft | DftFlavor | DftFunctional | DipoleMoment | DispersionCorrection | Double | ElectronicSpectra | ExchangeFunctional | FloatValue | ForceField | FrequencyPeak | GeometryOptimization | Group | HydrogenBond | IntegerValue | Mcscf | Methodology | MethodologyFeature | MolecularComputation | MolecularConcept | MolecularMechanics | MolecularMethodology | MolecularStructureObject | MolecularSystem | Molecule | Mp2 | Mp3 | Mp4 | MultipleDeterminant | MultipleReferenceState | Multiscale | NaturalValue | NormalBond | NumberBasisFunc | Orbital | ParameterSet | Publication | PublicationConcept | Quadruple | QuantumMechanics | Residue | Scf | SemiEmpiricalScf | Single | SingleDeterminant | SinglePoint | SingleReferenceState | SourcePackage | SpinType | SystemEnergies | Triple | Value | VectorValue | VibrationalAnalysis | VibrationalFrequencies | WaveFunction
Properties: | hasAtom | hasAtomCount | hasBasisSet | hasBindingEnergy | hasBond | hasBondCount | hasBondLength | hasCalculatedAtomCharge | hasCalculationOn | hasCategory | hasChainNumber | hasCoordinates | hasCorrelation | hasDipoleMoment | hasDipoleMomentAverage | hasDipoleResult | hasElectronicEnergy | hasElectronicSpectraResult | hasElectronicTransitions | hasElementSymbol | hasExchangeFunctional | hasExcitedStateMethod | hasFile | hasFloatValue | hasForceField | hasFormalCharge | hasFrequency | hasFrequencyPeak | hasHeatOfFormation | hasInChIKey | hasInChIString | hasIndex | hasInput | hasInsertion | hasIntegerValue | hasIntensity | hasKey | hasMethod | hasMethodology | hasMullikenCharges | hasName | hasNaturalValue | hasNmrShieldingAnisotropy | hasNmrShieldingIsotropic | hasNormalMode | hasNuclearRepulsionEnergy | hasOccupancy | hasOccupiedOrbitalsIncluded | hasOpenShellTreatment | hasOrbital | hasOrbitalCount | hasOrbitalEnergy | hasOrbitalSymmetry | hasOscillatorStrength | hasOutput | hasParameterSet | hasRMSGradient | hasResidue | hasResult | hasSecondaryStructure | hasShielding | hasSourcePackage | hasSpinType | hasStatus | hasSystemCharge | hasSystemEnergiesResult | hasSystemMultiplicity | hasSystemTemperature | hasTechnology | hasTotalPotentialEnergy | hasTransitionCount | hasUnit | hasUnoccupiedOrbitalsIncluded | hasValue | hasVectorValue | hasVersion | hasVibrationCount | hasVisibility | hasWaveFunctionCoefficients | holds | isElement | relatedEntity |

Main Gainesville Core Ontology terms, grouped in broad categories.

Class Diagrams

Top Classes


Publication

publication


Molecular

molecular


Calculation

calculation


Auxiliary

auxiliary


Examples

A graphic of a simple example of an use case of the Gainesville Core Ontology

This section shows typical examples of using the ontology.

We assume the following prefix declarations for all examples:

# Prefix Declarations
@prefix	xsd:	<http://www.w3.org/2001/XMLSchema#>.
@prefix	rdf:	<http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix gc: 	<http://purl.org/gc/#>.
@prefix unit: 	<http://sweet.jpl.nasa.gov/ontology/units.owl#>.
@prefix foaf: 	<http://xmlns.com/foaf/0.1/#>.
@prefix dc: 	<http://purl.org/dc/terms/#>.
@prefix rdfs: 	<http://www.w3.org/2000/01/rdf-schema#>.
@prefix pt:     <http://www.daml.org/2003/01/periodictable/PeriodicTable#>.

Examples of publication plavix example with Vibrational & Electronic spectra.

Scenario: Simple publication on Chemical Semantic Portal
Part 1 - In the following, we define publication:
<http://purl.org/chem/pub/2013-09-01-hyperchem10_1#> 
  dc:abstract "Another plavix test with Vibrational & Electronic spectra";
  dc:creator [a dc:Agent ; 
    foaf:name "ms" ; 
    schema:worksFor "ms" ; 
    foaf:mbox "ms@ms"];
  dc:title "Plavix_Vib_Ele";
  gc:hasSourcePackage [ a gc:SourcePackage ;
    gc:hasName "HyperChem" ;
    gc:hasVersion "9.0.0"
  ] ;
  gc:hasStatus "Preliminary"@en ;
  gc:hasVisibility "Public" ;
  gc:hasCategory "Computational Chemistry" ;
  gc:hasPublisher <http://purl.org/chem/usr/mirek/#>;
  gc:hasTag "drug";
  a gc:ComputationalChemistryPublication;
  rdfs:comment "This is publication of computational chemistry result.";
  rdfs:label "Publication".
Part 2 - In the following, we define molecular system resource:
<http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/> 
  dc:isPartOf <http://purl.org/chem/pub/2013-09-01-hyperchem10_1>;
  gc:hasCalculationOn <http://purl.org/chem/pub/2013-09-01-hyperchem10_1mol-calc/>;
  gc:hasSystemCharge [a gc:FloatValue ; 
    rdfs:label "System Charge" ; 
    gc:hasFloatValue "0" ; 
    gc:hasUnit gc:atomicUnit];
  gc:hasSystemMultiplicity "1";
  gc:hasSystemTemperature [a gc:FloatValue ; 
    rdfs:label "Temperature" ; 
    gc:hasFloatValue "0" ; 
    gc:hasUnit unit:kelvin];
  gc:holds <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/>;
  a gc:MolecularSystem;
  rdfs:comment
    "This molecular system has been generated by HyperChem and converted by cml2rdf.";
  rdfs:label "Molecular System".
Part 3 - In the following, we define molecule
<http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/> 
  gc:hasInChIKey "GKTWGGQPFAXNFI-HNNXBMFYSA-N";
    gc:hasNumberOfAtoms "37";
    a gc:Molecule;
    rdfs:comment
      "An electrically neutral group of two or more atoms held together by covalent chemical bonds.";
    rdfs:label "Molecule: m1";
  gc:hasAtom <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a1/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a10/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a11/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a12/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a13/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a14/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a15/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a16/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a17/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a18/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a19/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a2/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a20/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a21/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a22/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a23/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a24/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a25/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a26/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a27/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a28/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a29/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a3/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a30/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a31/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a32/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a33/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a34/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a35/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a36/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a37/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a4/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a5/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a6/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a7/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a8/>,
     <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a9/>.
Part 4 - One of molecule "m1" atom description.
<http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a1/>  
  gc:hasBasisSet "None";
  gc:hasBond <http://purl.org/chem/pub/2013-09-01-hyperchem10_1molSys/m1/a1a16/>;
  gc:hasBondCount "1";
  gc:hasCalculatedAtomCharge [a gc:FloatValue ; 
    gc:hasFloatValue "0.08992456" ; 
    gc:hasUnit gc:atomicUnit];
  gc:hasCoordinates [a gc:VectorValue ; 
    gc:hasVectorValue "-0.6512369 0.01366634 -3.144512" ; 
    gc:hasUnit gc:angstrom];
  gc:hasFormalCharge [a gc:IntegerValue ; 
    gc:hasIntegerValue "0" ; 
    gc:hasUnit gc:atomicUnit];
  gc:hasMass [a gc:FloatValue ; 
    gc:hasFloatValue "35.45" ; 
    gc:hasUnit gc:atomicUnit];
  gc:hasShielding [a gc:FloatValue ; 
    gc:hasFloatValue "0" ; 
    gc:hasUnit gc:atomicUnit];
  gc:isElement pt:Cl;
  a gc:Atom;
  rdfs:label "Atom: Cl".
Part 5 - Calculation definition
<http://purl.org/chem/pub/2013-09-01-hyperchem10_1mol-calc/> 
  gc:hasBasisSet gc:DefaultBasis;
  gc:hasResult
    <http://purl.org/chem/pub/2013-09-01-hyperchem10_1electronicSpectra/>,
    <http://purl.org/chem/pub/2013-09-01-hyperchem10_1sys-energ/>,
    <http://purl.org/chem/pub/2013-09-01-hyperchem10_1waveFunction/>;
  gc:hasSpinType gc:RHF;
  a gc:SemiEmpiricalScf;
  rdfs:label "Molecular Calculation".
Part 6 - Electronic Spectra example
<http://purl.org/chem/pub/2013-09-01-hyperchem10_1electronicSpectra/> 
  gc:hasElectronicTransitions 
    <http://purl.org/chem/pub/2013-09-01-hyperchem10_1electronicSpectra/electronicTransitions/>;
  gc:hasExcitedStateMethod "CIS";
  gc:hasOccupiedOrbitalsIncluded "3";
  gc:hasOscillatorStrength
    <http://purl.org/chem/pub/2013-09-01-hyperchem10_1electronicSpectra/oscillatorStrength/>;
  gc:hasTransitionCount "18";
  gc:hasUnoccupiedOrbitalsIncluded "3";
  a gc:ElectronicSpectra;
  rdfs:comment "Electronic Spectra comment...";
  rdfs:label "Electronic Spectra".

<http://purl.org/chem/pub/2013-09-01-hyperchem10_1electronicSpectra/electronicTransitions/> 
  gc:hasUnit unit:nano_meter;
  gc:hasVectorValue 
    "473.6777        367.0086        
    313.6338        274.0021        271.6655        262.6092        254.5908 
    243.263         214.3581        212.4229        197.9212        197.2178
    180.7098        179.9714        178.9294       
    178.8854        171.5141        171.4986        ";
  a gc:VectorValue;
  rdfs:label "Electronic Transitions".

<http://purl.org/chem/pub/2013-09-01-hyperchem10_1electronicSpectra/oscillatorStrength/> 
gc:hasUnit unit:nano_meter;
gc:hasVectorValue 
  "8.477688e-029   1.777297e-029   
  7.493906e-029   0.4066375       9.421863e-027   0.3774969       0.3787144      
  0.1360613       2.947013e-028   0.01811527      4.815454e-028   0.01084104
  2.574398e-028   0.01088483      1.027546e-028  
  0.0004991499    1.916689e-027   0.0002394384    ";
a gc:VectorValue;
rdfs:label "Oscillator Strength".

SPARQL Queries

This section shows typical examples of using the SPARQL. Each example can be performed on Chemical Semantic Portal SPARQL Endpoint

Scenario 1: Show all molecules that contain atoms other than C,O,N,H
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX gc: <http://purl.org/gc/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX pt: <http://www.daml.org/2003/01/periodictable/PeriodicTable#>

SELECT DISTINCT ?graph 
WHERE { 
	{GRAPH ?graph { ?mol gc:hasAtom ?atom}} 
	MINUS 
	{GRAPH ?graph { ?a gc:isElement pt:C }}
	MINUS
	{GRAPH ?graph { ?b gc:isElement pt:O }}
	MINUS
	{GRAPH ?graph { ?b gc:isElement pt:N }}
	MINUS
	{GRAPH ?graph { ?b gc:isElement pt:H }}
}
		
Scenario 2: Find all molecules that have any Halogen atom (and which it is). Halogen atoms are: fluorine (F), chlorine (Cl), bromine (Br), iodine (I), astatine (At)
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX gc: <http://purl.org/gc/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX pt: <http://www.daml.org/2003/01/periodictable/PeriodicTable#>

SELECT
	?something ?somethingType ?somethingLabel
WHERE {
	{
		?something gc:hasAtom ?atom1 ;
			rdf:type ?somethingType ;
			rdfs:label ?somethingLabel .
		?atom1 gc:isElement pt:F .
	}
	UNION 
	{
		?something gc:hasAtom ?atom2 ;
			rdf:type ?somethingType ;
			rdfs:label ?somethingLabel .
		?atom2 gc:isElement pt:Cl .
	}
	UNION
	{
		?something gc:hasAtom ?atom3 ;
			rdf:type ?somethingType ;
			rdfs:label ?somethingLabel .
		?atom3 gc:isElement pt:Br .
	}
	UNION
	{
		?something gc:hasAtom ?atom4 ;
			rdf:type ?somethingType ;
			rdfs:label ?somethingLabel .
		?atom4 gc:isElement pt:I .
	}
	UNION
	{
		?something gc:hasAtom ?atom4 ;
			rdf:type ?somethingType ;
			rdfs:label ?somethingLabel .
		?atom4 gc:isElement pt:At .
	}
}
		
Scenario 3: This example shows how to get InChIKey Identifier from CS2 database.
PREFIX gc: <http://purl.org/gc/>

SELECT
	?graph
	?molecule
	?inchikey
WHERE {
GRAPH ?graph {
	?molecule gc:hasInChIKey ?inchikey .
	}
}
ORDER BY ?graph ?molecule
		

The Gainesville Core Ontology cross-reference: Listing the Gainesville Core Ontology Classes and Properties

The Gainesville Core Ontology introduces the following classes and properties.

Classes: | AbInitioScf | Aromatic | Atom | AuxiliaryConcept | BasisSet | Bond | CalculatedProperties | CalculationConcept | CalculationResult | Caspt2 | Ccd | Ccsd | Ccsd-t | Cis | Cisd | ComputationalChemistryPublication | CorrelationFunctional | Dft | DftFlavor | DftFunctional | DipoleMoment | DispersionCorrection | Double | ElectronicSpectra | ExchangeFunctional | FloatValue | ForceField | FrequencyPeak | GeometryOptimization | Group | HydrogenBond | IntegerValue | Mcscf | Methodology | MethodologyFeature | MolecularComputation | MolecularConcept | MolecularMechanics | MolecularMethodology | MolecularStructureObject | MolecularSystem | Molecule | Mp2 | Mp3 | Mp4 | MultipleDeterminant | MultipleReferenceState | Multiscale | NaturalValue | NormalBond | NumberBasisFunc | Orbital | ParameterSet | Publication | PublicationConcept | Quadruple | QuantumMechanics | Residue | Scf | SemiEmpiricalScf | Single | SingleDeterminant | SinglePoint | SingleReferenceState | SourcePackage | SpinType | SystemEnergies | Triple | Value | VectorValue | VibrationalAnalysis | VibrationalFrequencies | WaveFunction
Properties: | hasAtom | hasAtomCount | hasBasisSet | hasBindingEnergy | hasBond | hasBondCount | hasBondLength | hasCalculatedAtomCharge | hasCalculationOn | hasCategory | hasChainNumber | hasCoordinates | hasCorrelation | hasDipoleMoment | hasDipoleMomentAverage | hasDipoleResult | hasElectronicEnergy | hasElectronicSpectraResult | hasElectronicTransitions | hasElementSymbol | hasExchangeFunctional | hasExcitedStateMethod | hasFile | hasFloatValue | hasForceField | hasFormalCharge | hasFrequency | hasFrequencyPeak | hasHeatOfFormation | hasInChIKey | hasInChIString | hasIndex | hasInput | hasInsertion | hasIntegerValue | hasIntensity | hasKey | hasMethod | hasMethodology | hasMullikenCharges | hasName | hasNaturalValue | hasNmrShieldingAnisotropy | hasNmrShieldingIsotropic | hasNormalMode | hasNuclearRepulsionEnergy | hasOccupancy | hasOccupiedOrbitalsIncluded | hasOpenShellTreatment | hasOrbital | hasOrbitalCount | hasOrbitalEnergy | hasOrbitalSymmetry | hasOscillatorStrength | hasOutput | hasParameterSet | hasRMSGradient | hasResidue | hasResult | hasSecondaryStructure | hasShielding | hasSourcePackage | hasSpinType | hasStatus | hasSystemCharge | hasSystemEnergiesResult | hasSystemMultiplicity | hasSystemTemperature | hasTechnology | hasTotalPotentialEnergy | hasTransitionCount | hasUnit | hasUnoccupiedOrbitalsIncluded | hasValue | hasVectorValue | hasVersion | hasVibrationCount | hasVisibility | hasWaveFunctionCoefficients | holds | isElement | relatedEntity |

Classes

Class: gc:AbInitioScf

rdf:label Ab initio SCF

rdfs:comment

A class for Self Consistent Field methods (Hartree-Fock methods) for approximate solution of Schrodinger equation for quantum many body system.

rdfs:subClassOf gc:SingleDeterminant

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Class: gc:Aromatic

rdf:label Aromatic Bond

rdfs:comment

A class for bonds with aromatic character

rdfs:subClassOf gc:NormalBond

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Class: gc:Atom

rdf:label Atoms

rdfs:comment

A class for atoms, the basic unit of matter.

rdfs:subClassOf gc:MolecularStructureObject

Domain of gc:isElement gc:hasCalculatedAtomCharge gc:hasElementSymbol gc:hasBasisSet gc:hasCoordinates gc:hasFormalCharge gc:hasShielding gc:hasBond

Range of gc:hasAtom

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Class: gc:AuxiliaryConcept

rdf:label Auxiliary Concept

rdfs:comment

A generic class representing Auxiliary concepts.

Subclasses gc:Value

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Class: gc:BasisSet

rdf:label Basis Set

rdfs:comment

A class for the basis set. In computational chemistry basis set is a set of functions which are combined to create molecular orbitals.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasBasisSet

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Class: gc:Bond

rdf:label Bond

rdfs:comment

A class for generic chemical bond.

rdfs:subClassOf gc:MolecularStructureObject

Subclasses gc:NormalBond gc:HydrogenBond

Domain of gc:hasBondLength

Range of gc:hasBond

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Class: gc:CalculatedProperties

rdf:label Calculated Properties

rdfs:comment

A class for the properties of molecular system calculated in the course of computational chemistry procedure.

rdfs:subClassOf gc:CalculationResult

Domain of gc:hasRMSGradient gc:hasMullikenCharges gc:hasDipoleMoment gc:hasDipoleMomentAverage gc:hasNmrShieldingAnisotropy gc:hasNmrShieldingIsotropic

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Class: gc:CalculationConcept

rdf:label Calculation Concept

rdfs:comment

A class for generic concepts that describe calculations in computational chemistry.

Subclasses gc:MolecularMethodology gc:MethodologyFeature gc:MolecularComputation gc:CalculationResult

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Class: gc:CalculationResult

rdf:label Calculation Result

rdfs:comment

A class for specific concepts related to the results of computational chemistry procedures.

rdfs:subClassOf gc:CalculationConcept

Subclasses gc:Orbital gc:CalculatedProperties gc:ElectronicSpectra gc:WaveFunction gc:VibrationalFrequencies gc:DipoleMoment gc:SystemEnergies gc:FrequencyPeak

Range of gc:hasResult

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Class: gc:Caspt2

rdf:label Caspt2

rdfs:comment

A class for the complete active space perturbation theory methods.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:Ccd

rdf:label Ccd

rdfs:comment

A class for the coupled cluster method with double substitutions.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:Ccsd

rdf:label Ccsd

rdfs:comment

A class for the coupled cluster method with a full treatment singles and doubles.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:Ccsd-t

rdf:label Ccsd-t

rdfs:comment

A class for the coupled cluster method with a full treatment singles and doubles and approximate treatment of triple excitations.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:Cis

rdf:label Cis

rdfs:comment

A class for the configuration interaction (CI) method with single substitutions.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:Cisd

rdf:label Cisd

rdfs:comment

A class for the configuration interaction (CI) method with single and double substitutions.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:ComputationalChemistryPublication

rdf:label Computational Chemistry Publication

rdfs:comment

A class for publication of the results of the computional chemistry programs.

rdfs:subClassOf gc:Publication

Domain of gc:hasCategory gc:hasStatus gc:hasKey gc:hasFile gc:hasVisibility gc:hasSourcePackage

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Class: gc:CorrelationFunctional

rdf:label Correlation Functional

rdfs:comment

A class for correlation functionals in Density Functional Theories.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasCorrelationFunctional

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Class: gc:Dft

rdf:label Dft

rdfs:comment

A class for methods from the family of Density Functional Theories.

rdfs:subClassOf gc:SingleDeterminant

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Class: gc:DftFlavor

rdf:label Dft Flavor

rdfs:comment

A class for specific approximations to exchange-correlation functionals in the Density Functional Theory.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasDftFlavor

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Class: gc:DftFunctional

rdf:label Dft Functional

rdfs:comment

A class for the exchange-correlation functionals in the Density Functional Theory.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasDftFunctional

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Class: gc:DipoleMoment

rdf:label Dipole Moment

rdfs:subClassOf gc:CalculationResult

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Class: gc:DispersionCorrection

rdf:label Dispersion Correction

rdfs:comment

A class for the dispersion correction in the Density Functional Theory.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasDispersionCorrection

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Class: gc:Double

rdf:label Double

rdfs:comment

A class for double covalent bonds.

rdfs:subClassOf gc:NormalBond

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Class: gc:ElectronicSpectra

rdf:label Electronic Spectra

rdfs:comment

A class for spectra resulting from the molecular electronic transitions.

rdfs:subClassOf gc:CalculationResult

Domain of gc:hasOscillatorStrength gc:hasOccupiedOrbitalsIncluded gc:hasExcitedStateMethod gc:hasElectronicTransitions gc:hasTransitionCount gc:hasUnoccupiedOrbitalsIncluded

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Class: gc:ExchangeFunctional

rdf:label Exchange Functional

rdfs:comment

A class for exchange functionals in Density Functional Theories.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasExchangeFunctional

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Class: gc:FloatValue

rdf:label Float Value

rdfs:comment

A class for float value, containing value and unit.

rdfs:subClassOf gc:Value

Domain of gc:hasFloatValue

Range of gc:hasElectronicEnergy gc:hasRMSGradient gc:hasSystemCharge gc:hasCalculatedAtomCharge gc:hasMullikenCharges gc:hasOrbitalEnergy gc:hasTotalPotentialEnergy gc:hasHeatOfFormation gc:hasIntensity gc:hasBondLength gc:hasDipoleMomentAverage gc:hasOccupancy gc:hasCorrelation gc:hasNmrShieldingAnisotropy gc:hasBindingEnergy gc:hasFrequency gc:hasShielding gc:hasSystemTemperature gc:hasNuclearRepulsionEnergy gc:hasNmrShieldingIsotropic

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Class: gc:ForceField

rdf:label Force Field

rdfs:comment

A class for the classical mechanical methods based on the concept of the Force Field.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasForceField

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Class: gc:FrequencyPeak

rdf:label Frequency Peak

rdfs:comment

A class representing frequency peak of the spectrum.

rdfs:subClassOf gc:CalculationResult

Domain of gc:hasFrequency gc:hasIntensity gc:hasNormalMode

Range of gc:hasFrequencyPeak

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Class: gc:GeometryOptimization

rdf:label Geometry optimization

rdfs:comment

A class for calculations in computational chemistry that aim to find molecular geometry of lowest energy.

rdfs:subClassOf gc:MolecularComputation

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Class: gc:Group

rdf:label Group

rdfs:comment

A class for generic collection of atoms in molecules and residues

rdfs:subClassOf gc:MolecularStructureObject

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Class: gc:HydrogenBond

rdf:label Hydrogen Bond

rdfs:comment

A class for hydrogen bond - the electrostatic interaction between polar molecules (strong dipole-dipole attraction).

rdfs:subClassOf gc:Bond

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Class: gc:IntegerValue

rdf:label Integer Value

rdfs:comment

A class that represents integer value, containing value and unit.

rdfs:subClassOf gc:Value

Domain of gc:hasIntegerValue

Range of gc:hasFormalCharge

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Class: gc:Mcscf

rdf:label Mcscf

rdfs:comment

A class for the multi-configurational self-consistent field (MCSCF) method.

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:Methodology

rdf:label Methodology

rdfs:comment

A class for the specific methodology used to conduct computational chemistry calculations.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasMethodology

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Class: gc:MethodologyFeature

rdf:label Methodology Feature

rdfs:comment

A class for specific features or properties of a given methodology.

rdfs:subClassOf gc:CalculationConcept

Subclasses gc:Methodology gc:BasisSet gc:NumberBasisFunc gc:CorrelationFunctional gc:DftFlavor gc:ParameterSet gc:ForceField gc:ExchangeFunctional gc:DispersionCorrection gc:SpinType gc:DftFunctional

Range of gc:hasFeature

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Class: gc:MolecularComputation

rdf:label Molecular Computation

rdfs:comment

A class for the specific type of calculation (like optimization, single point, etc) conducted by a computational chemistry program.

rdfs:subClassOf gc:CalculationConcept

Subclasses gc:SinglePoint gc:GeometryOptimization gc:VibrationalAnalysis

Domain of gc:hasResult

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Class: gc:MolecularConcept

rdf:label Molecular Concept

rdfs:comment

A generic class of various concepts related to molecular systems.

Subclasses gc:MolecularStructureObject

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Class: gc:MolecularMechanics

rdf:label Molecular Mechanics

rdfs:comment

A class for the classical methodologies of computational chemistry.

rdfs:subClassOf gc:MolecularMethodology

Domain of gc:hasParameterSet gc:hasForceField

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Class: gc:MolecularMethodology

rdf:label Molecular Methodology

rdfs:comment

A class for general methodologies of computational chemistry.

rdfs:subClassOf gc:CalculationConcept

Subclasses gc:MolecularMechanics gc:QuantumMechanics gc:Multiscale

Domain of gc:hasMethodology gc:hasBasisSet gc:hasSpinType gc:hasForceField gc:hasExchangeFunctional gc:hasParameterSet

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Class: gc:MolecularStructureObject

rdf:label Molecular Structure Object

rdfs:comment

A class that represents objects of molecular structure (atoms, molecules etc).

rdfs:subClassOf gc:MolecularConcept

Subclasses gc:Bond gc:Group gc:Atom gc:Molecule gc:MolecularSystem gc:Residue

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Class: gc:MolecularSystem

rdf:label Molecular System

rdfs:comment

A class for objects related to molecular systems.

rdfs:subClassOf gc:MolecularStructureObject

Domain of gc:hasSystemTemperature gc:hasCalculationOn gc:hasSystemCharge gc:hasSystemMultiplicity

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Class: gc:Molecule

rdf:label Molecule

rdfs:comment

A class for molecule - electrically neutral group (or polyatomic ion) of two or more atoms held together by chemical bonds.

rdfs:subClassOf gc:MolecularStructureObject

Domain of gc:hasInChIString gc:hasInChIKey gc:hasResidue

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Class: gc:Mp2

rdf:label Mp2

rdfs:comment

A class for the second order Moller-Plesset perturbation theory method of quantum chemistry.

rdfs:subClassOf gc:SingleDeterminant

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Class: gc:Mp3

rdf:label Mp3

rdfs:comment

A class for the third order Moller-Plesset perturbation theory method of quantum chemistry.

rdfs:subClassOf gc:SingleDeterminant

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Class: gc:Mp4

rdf:label Mp4

rdfs:comment

A class for the fourth order Moller-Plesset perturbation theory method of quantum chemistry.

rdfs:subClassOf gc:SingleDeterminant

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Class: gc:MultipleDeterminant

rdf:label Multiple Determinant

rdfs:comment

A class for the methods of quantum chemistry using multiple Slater determinants.

rdfs:subClassOf gc:QuantumMechanics

Subclasses gc:Cisd gc:Ccsd gc:Cis gc:Caspt2 gc:Ccd gc:Ccsd-t gc:Scf gc:Mcscf

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Class: gc:MultipleReferenceState

rdf:label Multiple Reference State

rdfs:comment

A class representing methods of quantum chemistry using multiple reference state determinants.

rdfs:subClassOf gc:QuantumMechanics

Subclasses gc:Mcscf gc:Caspt2

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Class: gc:Multiscale

rdf:label Multiscale Methods

rdfs:comment

A class for methods of computational chemistry combining different methodologies (e.g. quantum and classical) for large molecular systems.

rdfs:subClassOf gc:MolecularMethodology

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Class: gc:NaturalValue

rdf:label Natural Value

rdfs:comment

A class for natural values, containing value and unit.

rdfs:subClassOf gc:Value

Domain of gc:hasNaturalValue

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Class: gc:NormalBond

rdf:label Normal Bond

rdfs:comment

A class for covalent bond in molecules.

rdfs:subClassOf gc:Bond

Subclasses gc:Quadruple gc:Triple gc:Double gc:Aromatic gc:Single

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Class: gc:NumberBasisFunc

rdf:label Number Basis Func

rdfs:comment

A class representing the number of basis set functions used in calculations.

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasNumberBasisFunc

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Class: gc:Orbital

rdf:label Orbital

rdfs:comment

A class for molecular orbital (MO) - a mathematical function describing an electron in a molecule.

rdfs:subClassOf gc:CalculationResult

Domain of gc:hasOrbitalSymmetry gc:hasOccupancy gc:hasWaveFunctionCoefficients gc:hasOrbitalEnergy

Range of gc:hasOrbital

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Class: gc:ParameterSet

rdf:label Parameter Set

rdfs:comment

A class representing a specific set of parameters used by the Force Field calculations (Molecular Mechanics).

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasParameterSet

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Class: gc:Publication

rdf:label Publication

rdfs:comment

A generic class for objects related to the publication of results of computational chemistry calculations.

rdfs:subClassOf gc:PublicationConcept

Subclasses gc:ComputationalChemistryPublication

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Class: gc:PublicationConcept

rdf:label Publication Concept

rdfs:comment

A generic class representing concepts related to publications.

Subclasses gc:Publication gc:SourcePackage

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Class: gc:Quadruple

rdf:label Quadruple

rdfs:comment

??? !!!

rdfs:subClassOf gc:NormalBond

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Class: gc:QuantumMechanics

rdf:label Quantum Mechanics

rdfs:comment

A class for Quantum Mechanical methods.

rdfs:subClassOf gc:MolecularMethodology

Subclasses gc:MultipleReferenceState gc:SingleReferenceState gc:MultipleDeterminant

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Class: gc:Residue

rdf:label Residue

rdfs:comment

A class for residues - monomers of polysaccharide, protein, nucleic acid or polymer

rdfs:subClassOf gc:MolecularStructureObject

Domain of gc:hasSecondaryStructure gc:hasInsertion gc:hasChainNumber

Range of gc:hasResidue

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Class: gc:Scf

rdf:label Scf

rdfs:comment

A class for self-consisted field methods (SCF) of Quantum Chemistry

rdfs:subClassOf gc:MultipleDeterminant

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Class: gc:SemiEmpiricalScf

rdf:label Semi-empirical Scf

rdfs:comment

A class for SemiEmpirical Methods of Quantum Chemistry

rdfs:subClassOf gc:SingleDeterminant

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Class: gc:Single

rdf:label Single

rdfs:comment

A class for single covalent bonds.

rdfs:subClassOf gc:NormalBond

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Class: gc:SingleDeterminant

rdf:label Single Determinant

rdfs:comment

A class for Single Determinant methods of Quantum Chemistry.

rdfs:subClassOf gc:SingleReferenceState

Subclasses gc:Mp4 gc:SemiEmpiricalScf gc:Dft gc:AbInitioScf gc:Mp3 gc:Mp2

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Class: gc:SinglePoint

rdf:label Single Point

rdfs:comment

A class for Single Point calculations - computation of the energy of molecular system for given geometry.

rdfs:subClassOf gc:MolecularComputation

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Class: gc:SingleReferenceState

rdf:label Single Reference State

rdfs:comment

A class for Single Reference (SR) coupled-cluster methods.

rdfs:subClassOf gc:QuantumMechanics

Subclasses gc:Cisd gc:Ccsd gc:Cis gc:Ccd gc:SingleDeterminant gc:Ccsd-t gc:Scf

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Class: gc:SourcePackage

rdf:label Source Package

rdfs:comment

A class for quantum chemistry packages used to peform computations.

rdfs:subClassOf gc:PublicationConcept

Domain of gc:hasInput gc:hasOutput

Range of gc:hasSourcePackage

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Class: gc:SpinType

rdf:label Spin Type

rdfs:comment

A class for method for spin treatment in quantum chemical calculations (rhf,uhf,rohf).

rdfs:subClassOf gc:MethodologyFeature

Range of gc:hasSpinType

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Class: gc:SystemEnergies

rdf:label System Energies

rdfs:comment

A class for various types of energies associated with molecular system.

rdfs:subClassOf gc:CalculationResult

Domain of gc:hasElectronicEnergy gc:hasTotalPotentialEnergy gc:hasHeatOfFormation gc:hasCorrelation gc:hasBindingEnergy gc:hasNuclearRepulsionEnergy

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Class: gc:Triple

rdf:label Triple

rdfs:comment

A class for triple covalent bond.

rdfs:subClassOf gc:NormalBond

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Class: gc:Value

rdf:label Value

rdfs:comment

This is super class for the expression of various types of values.

rdfs:subClassOf gc:AuxiliaryConcept

Subclasses gc:NaturalValue gc:VectorValue gc:IntegerValue gc:FloatValue

Domain of gc:hasUnit gc:relatedEntity gc:hasValue

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Class: gc:VectorValue

rdf:label Vector Value

rdfs:comment

A class for vector type of data, containing value and unit.

rdfs:subClassOf gc:Value

Domain of gc:hasVectorValue

Range of gc:hasOscillatorStrength gc:hasDipoleMoment gc:hasCoordinates gc:hasNormalMode gc:hasElectronicTransitions gc:hasWaveFunctionCoefficients

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Class: gc:VibrationalAnalysis

rdf:label Vibrational Analysis

rdfs:comment

A class for the computations of vibrational spectrum of molecules.

rdfs:subClassOf gc:MolecularComputation

Domain of gc:hasFrequencyPeak

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Class: gc:VibrationalFrequencies

rdf:label Vibrational Frequencies

rdfs:comment

A class for the vibrational frequences of molecules.

rdfs:subClassOf gc:CalculationResult

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Class: gc:WaveFunction

rdf:label Wave Function

rdfs:comment

A class for the mathematical description of a quantum particle, in most practical cases of the electron.

rdfs:subClassOf gc:CalculationResult

Domain of gc:hasOrbital

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Properties

Property: gc:hasAtom

rdf:label has atom

rdfs:comment

A property that describes atoms comprised by a molecule or residue

rdfs:range gc:Atom

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Property: gc:hasAtomCount

rdf:label has number of atoms

rdfs:comment

A property that allows to declare total count of atoms in a given structure - Molecular System or Molecule or Residue.

rdfs:range xsd:nonNegativeInteger

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Property: gc:hasBasisSet

rdf:label has basis set

rdfs:comment

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.

rdfs:domain gc:MolecularMethodology gc:Atom

rdfs:range gc:BasisSet rdfs:Literal

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Property: gc:hasBindingEnergy

rdf:label has binding energy

rdfs:comment

A property that allows to assign the Binding Energy to the molecular system

rdfs:domain gc:SystemEnergies

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasBond

rdf:label has bond

rdfs:comment

A property that allows the bond to be assigned to atoms.

rdfs:domain gc:Atom

rdfs:range gc:Bond

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Property: gc:hasBondCount

rdf:label has bond count

rdfs:comment

A property that determinates the count of bonds into Molecule, Residue or Atom.

rdfs:range xsd:nonNegativeInteger

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Property: gc:hasBondLength

rdf:label has bond length

rdfs:comment

A property that allows bond length to be assigned the a bond.

rdfs:domain gc:Bond

rdfs:range gc:FloatValue

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Property: gc:hasCalculatedAtomCharge

rdf:label has calculated atom charge

rdfs:comment

A property that describes the atom charge calculated by a specific methodology.

rdfs:domain gc:Atom

rdfs:range gc:FloatValue

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Property: gc:hasCalculationOn

rdf:label has calculation on

rdfs:comment

A property that tells whether the molecular system has calculations done.

rdfs:domain gc:MolecularSystem

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Property: gc:hasCategory

rdf:label has category

rdfs:comment

A property that determines a category of the publication.

rdfs:domain gc:ComputationalChemistryPublication

rdfs:range xsd:string

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Property: gc:hasChainNumber

rdf:label has chain number

rdfs:comment

A property that defines chain number in the molecule.

rdfs:domain gc:Residue

rdfs:range xsd:int

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Property: gc:hasCoordinates

rdf:label has coordinates

rdfs:comment

A property that describes atom coordinates.

rdfs:domain gc:Atom

rdfs:range gc:VectorValue

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Property: gc:hasCorrelation

rdf:label has correlation

rdfs:comment

A property that describes system correlation energy.

rdfs:domain gc:SystemEnergies

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasDipoleMoment

rdf:label has dipole moment

rdfs:comment

A property that describes molecular dipol moment.

rdfs:domain gc:CalculatedProperties

rdfs:range gc:VectorValue

rdfs:subPropertyOf gc:hasDipoleResult

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Property: gc:hasDipoleMomentAverage

rdf:label has dipole moment average

rdfs:comment

A property that describes the average molecular dipol moment.

rdfs:domain gc:CalculatedProperties

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasDipoleResult

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Property: gc:hasDipoleResult

rdf:label has dipole result

rdfs:comment

A property that describes molecular dipol moment.

Has sub properties gc:hasDipoleMomentAverage gc:hasDipoleMoment

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Property: gc:hasElectronicEnergy

rdf:label has electronic energy

rdfs:comment

A property that describes the electronic energy.

rdfs:domain gc:SystemEnergies

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasElectronicSpectraResult

rdf:label has electronic spectra result

rdfs:comment

A property that describes the electronic spectra.

Has sub properties gc:hasElectronicTransitions gc:hasOscillatorStrength

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Property: gc:hasElectronicTransitions

rdf:label has electronic transitions

rdfs:comment

A property that describes electronic transition energies.

rdfs:domain gc:ElectronicSpectra

rdfs:range gc:VectorValue

rdfs:subPropertyOf gc:hasElectronicSpectraResult

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Property: gc:hasElementSymbol

rdf:label has element symbol

rdfs:comment

A property that defines the Symbol of the element of an atom.

rdfs:domain gc:Atom

rdfs:range xsd:string

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Property: gc:hasExchangeFunctional

rdf:label has exchange functional

rdfs:comment

A property that describes the exchange functionals.

rdfs:domain gc:MolecularMethodology

rdfs:range gc:ExchangeFunctional

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Property: gc:hasExcitedStateMethod

rdf:label has excited state method

rdfs:comment

A property that defines the method for the calculation of the excited states of molecules.

rdfs:domain gc:ElectronicSpectra

rdfs:range rdfs:Literal

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Property: gc:hasFile

rdf:label has file

rdfs:comment

A property that describes the reference to the attachment file.

rdfs:domain gc:ComputationalChemistryPublication

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Property: gc:hasFloatValue

rdf:label has float value

rdfs:comment

A property that describes floating point value.

rdfs:domain gc:FloatValue

rdfs:range xsd:float

rdfs:subPropertyOf gc:hasValue

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Property: gc:hasForceField

rdf:label has force field

rdfs:comment

A property that describes Force Field.

rdfs:domain gc:MolecularMechanics gc:MolecularMethodology

rdfs:range gc:ForceField xsd:string

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Property: gc:hasFormalCharge

rdf:label has formal charge

rdfs:comment

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.

rdfs:domain gc:Atom

rdfs:range gc:IntegerValue

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Property: gc:hasFrequency

rdf:label has frequency

rdfs:comment

A property that describes the value of a frequency at the peak of the spectrum.

rdfs:domain gc:FrequencyPeak

rdfs:range gc:FloatValue

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Property: gc:hasFrequencyPeak

rdf:label has frequency peak

rdfs:comment

A property that describes the value of a frequency peak of the vibrational spectrum.

rdfs:domain gc:VibrationalAnalysis

rdfs:range gc:FrequencyPeak

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Property: gc:hasHeatOfFormation

rdf:label has heat of formation

rdfs:comment

A property that describes the value of a the Heat of Formation.

rdfs:domain gc:SystemEnergies

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasInChIKey

rdf:label has InChI key

rdfs:comment

A property that describes the InChI Key - the condensed, 27 character hashed version of the InChI String.

rdfs:domain gc:Molecule

rdfs:range xsd:string

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Property: gc:hasInChIString

rdf:label has InChI string

rdfs:comment

A property that describes the InChI String - International Chemical Identifier - a textual identifier for chemical substances.

rdfs:domain gc:Molecule

rdfs:range xsd:string

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Property: gc:hasIndex

rdf:label has index

rdfs:comment

A property that defines a sequential arrangement of material in numerical order, i.e. Frequency Peak, Orbital or a sequence number in residue.

rdfs:range xsd:nonNegativeInteger

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Property: gc:hasInput

rdf:label has input

rdfs:comment

A property that defines the contents of the input file of the calculation.

rdfs:domain gc:SourcePackage

rdfs:range xsd:string

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Property: gc:hasInsertion

rdf:label has insertion code

rdfs:comment

A property that defines the insertion code for residue numbering.

rdfs:domain gc:Residue

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Property: gc:hasIntegerValue

rdf:label has integer value

rdfs:comment

A property that describes Integer Value.

rdfs:domain gc:IntegerValue

rdfs:range xsd:integer

rdfs:subPropertyOf gc:hasValue

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Property: gc:hasIntensity

rdf:label has intensity

rdfs:comment

A property that describes the intensity of a frequency peak

rdfs:domain gc:FrequencyPeak

rdfs:range gc:FloatValue

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Property: gc:hasKey

rdf:label has key

rdfs:comment

A property that defines the security key of the publication.

rdfs:domain gc:ComputationalChemistryPublication

rdfs:range xsd:string

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Property: gc:hasMethod

rdf:label has method

rdfs:comment

A property that defines the calculation method for given technology.

rdfs:range rdfs:Literal

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Property: gc:hasMethodology

rdf:label has methodology

rdfs:comment

A property that describes a methodology of computations.

rdfs:domain gc:MolecularMethodology

rdfs:range gc:Methodology xsd:string

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Property: gc:hasMullikenCharges

rdf:label has Mulliken charges

rdfs:comment

A property that describes computed Mulliken Charges.

rdfs:domain gc:CalculatedProperties

rdfs:range gc:FloatValue

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Property: gc:hasName

rdf:label has name

rdfs:comment

The name of an entity.

rdfs:range rdfs:Literal xsd:string

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Property: gc:hasNaturalValue

rdf:label has natural value

rdfs:comment

A property that defines natural value.

rdfs:domain gc:NaturalValue

rdfs:range xsd:nonNegativeInteger

rdfs:subPropertyOf gc:hasValue

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Property: gc:hasNmrShieldingAnisotropy

rdf:label has nmr shielding anisotropy

rdfs:comment

A property that describes computed NMR Shielding Anisotropic component.

rdfs:domain gc:CalculatedProperties

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasShielding

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Property: gc:hasNmrShieldingIsotropic

rdf:label has nmr shielding isotropic

rdfs:comment

A property that describes computed NMR Shielding Isotropic component

rdfs:domain gc:CalculatedProperties

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasShielding

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Property: gc:hasNormalMode

rdf:label has normal mode

rdfs:comment

A property that describes the normal mode of a vibration

rdfs:domain gc:FrequencyPeak

rdfs:range gc:VectorValue

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Property: gc:hasNuclearRepulsionEnergy

rdf:label has nuclear repulsion energy

rdfs:comment

A property that describes the potential energy arising from Coulombic nuclei-nuclei repulsions

rdfs:domain gc:SystemEnergies

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasOccupancy

rdf:label has occupancy

rdfs:comment

A property that describes the occupancy of the orbital

rdfs:domain gc:Orbital

rdfs:range gc:FloatValue

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Property: gc:hasOccupiedOrbitalsIncluded

rdf:label has occupied orbitals included

rdfs:comment

A property that describes the inclusion of occupied orbitals in electronic spectra calculations.

rdfs:domain gc:ElectronicSpectra

rdfs:range xsd:int

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Property: gc:hasOpenShellTreatment

rdf:label has open shell treatment

rdfs:comment

A property that describes the treatment of open shell systems.

rdfs:range rdfs:Literal

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Property: gc:hasOrbital

rdf:label has orbital

rdfs:comment

A property that describes the orbital.

rdfs:domain gc:WaveFunction

rdfs:range gc:Orbital

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Property: gc:hasOrbitalCount

rdf:label has orbital count

rdfs:comment

A property that defines the number of electron orbitals

rdfs:range xsd:int

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Property: gc:hasOrbitalEnergy

rdf:label has orbital energy

rdfs:comment

A property that describes the orbital energy.

rdfs:domain gc:Orbital

rdfs:range gc:FloatValue

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Property: gc:hasOrbitalSymmetry

rdf:label has orbital symmetry

rdfs:comment

A property that defines Orbital symmetry

rdfs:domain gc:Orbital

rdfs:range xsd:string

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Property: gc:hasOscillatorStrength

rdf:label has oscillator strength

rdfs:comment

A property that defines oscillator strengths of electronic spectra.

rdfs:domain gc:ElectronicSpectra

rdfs:range gc:VectorValue

rdfs:subPropertyOf gc:hasElectronicSpectraResult

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Property: gc:hasOutput

rdf:label has output

rdfs:comment

The property that defines the contents of the output file of the calculation.

rdfs:domain gc:SourcePackage

rdfs:range xsd:string

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Property: gc:hasParameterSet

rdf:label has parameter set

rdfs:comment

A property that defines the parametr set for calculations.

rdfs:domain gc:MolecularMechanics gc:MolecularMethodology

rdfs:range gc:ParameterSet xsd:string

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Property: gc:hasRMSGradient

rdf:label has RMS Gradient

rdfs:comment

A property that describes RMS gradient of the computations.

rdfs:domain gc:CalculatedProperties

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasResidue

rdf:label has residue

rdfs:comment

A property that describes the residue in a molecule.

rdfs:domain gc:Molecule

rdfs:range gc:Residue

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Property: gc:hasResult

rdf:label has result

rdfs:comment

A property that describes generic results of the computations.

rdfs:domain gc:MolecularComputation

rdfs:range gc:CalculationResult

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Property: gc:hasSecondaryStructure

rdf:label has secondary structure

rdfs:comment

A property that defines the three-dimensional form of local segments of biopolymers.

rdfs:domain gc:Residue

rdfs:range rdfs:Literal

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Property: gc:hasShielding

rdf:label has shielding

rdfs:comment

A property that describes an NMR shielding of an atom.

rdfs:domain gc:Atom

rdfs:range gc:FloatValue

Has sub properties gc:hasNmrShieldingIsotropic gc:hasNmrShieldingAnisotropy

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Property: gc:hasSourcePackage

rdf:label has source package

rdfs:comment

A property that defines relations that allows to describe Source Package for Publication.

rdfs:domain gc:ComputationalChemistryPublication

rdfs:range gc:SourcePackage

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Property: gc:hasSpinType

rdf:label has spin type

rdfs:comment

A property that describes handling of spins by the methodology (RHF,UHF,ROHF).

rdfs:domain gc:MolecularMethodology

rdfs:range rdfs:Literal gc:SpinType

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Property: gc:hasStatus

rdf:label has status

rdfs:comment

A property that describes the status of the publication.

rdfs:domain gc:ComputationalChemistryPublication

rdfs:range xsd:string

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Property: gc:hasSystemCharge

rdf:label has system charge

rdfs:comment

A property that describes molecular system charge.

rdfs:domain gc:MolecularSystem

rdfs:range gc:FloatValue

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Property: gc:hasSystemEnergiesResult

rdf:label has system energies result

rdfs:comment

A property that describes system energies.

Has sub properties gc:hasElectronicEnergy gc:hasRMSGradient gc:hasTotalPotentialEnergy gc:hasHeatOfFormation gc:hasCorrelation gc:hasBindingEnergy gc:hasNuclearRepulsionEnergy

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Property: gc:hasSystemMultiplicity

rdf:label has system multiplicity

rdfs:comment

A property that describes the system spin multiplicity.

rdfs:domain gc:MolecularSystem

rdfs:range xsd:positiveInteger

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Property: gc:hasSystemTemperature

rdf:label has system temperature

rdfs:comment

A property that describes system temperature.

rdfs:domain gc:MolecularSystem

rdfs:range gc:FloatValue

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Property: gc:hasTechnology

rdf:label has technology

rdfs:comment

A property that describes the calculation's technology for molecular system.

rdfs:range rdfs:Literal

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Property: gc:hasTotalPotentialEnergy

rdf:label has total potential energy

rdfs:comment

A property that describes Total Potential Energy.

rdfs:domain gc:SystemEnergies

rdfs:range gc:FloatValue

rdfs:subPropertyOf gc:hasSystemEnergiesResult

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Property: gc:hasTransitionCount

rdf:label has transition count

rdfs:comment

A property that describes the number of the electronic transitions in spectral calculations.

rdfs:domain gc:ElectronicSpectra

rdfs:range xsd:int

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Property: gc:hasUnit

rdf:label has unit

rdfs:comment

A property that describes a unit of the value.

rdfs:domain gc:Value

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Property: gc:hasUnoccupiedOrbitalsIncluded

rdf:label has unoccupied orbitals included

rdfs:comment

A property that describes the inclusion of occupied orbitals in electronic spectra calculations.

rdfs:domain gc:ElectronicSpectra

rdfs:range xsd:int

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Property: gc:hasValue

rdf:label has value

rdfs:comment

A Superproperty of typed numerical values.

rdfs:domain gc:Value

rdfs:range rdfs:Literal

Has sub properties gc:hasNaturalValue gc:hasVectorValue gc:hasIntegerValue gc:hasFloatValue

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Property: gc:hasVectorValue

rdf:label has vector value

rdfs:comment

A property that describes the vector values.

rdfs:domain gc:VectorValue

rdfs:range rdfs:Literal

rdfs:subPropertyOf gc:hasValue

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Property: gc:hasVersion

rdf:label has version

rdfs:comment

A property that describes the version of the software package used.

rdfs:range xsd:string

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Property: gc:hasVibrationCount

rdf:label has vibration count

rdfs:comment

A property that describes the number of vibrational frequencies.

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Property: gc:hasVisibility

rdf:label has visibility

rdfs:comment

A property that defines the allowed visibility of the publication.

rdfs:domain gc:ComputationalChemistryPublication

rdfs:range xsd:string

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Property: gc:hasWaveFunctionCoefficients

rdf:label has wave function coefficients

rdfs:comment

A property that describes Wave Function Coefficients.

rdfs:domain gc:Orbital

rdfs:range gc:VectorValue

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Property: gc:holds

rdf:label holds

rdfs:comment

A property that defines objects held by a container.

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Property: gc:isElement

rdf:label is element

rdfs:comment

A property that describes what element the given atom is.

rdfs:domain gc:Atom

rdfs:range pt:Element

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Property: gc:relatedEntity

rdf:label related entity

rdfs:comment

A property that describes related entity.

rdfs:domain gc:Value

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External Vocabulary References

dc
http://purl.org/dc/elements/1.1/
foaf
http://xmlns.com/foaf/0.1/
gc
http://purl.org/gc/0.2/
owl
http://www.w3.org/2002/07/owl#
pt
http://www.daml.org/2003/01/periodictable/PeriodicTable#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
schema
http://schema.org/
unit
http://sweet.jpl.nasa.gov/ontology/units.owl#
xsd
http://www.w3.org/2001/XMLSchema#

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Chemical Semantics, Inc.
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Telephone: +48 (42) 6837467
eMail: info@chemicalsemantics.com
Web: http://chemicalsemantics.com