Copyright © 2015 Chemical Semantics, Inc. |
Example Licencing Information
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.
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.
An a-z index of Gainesville Core Ontology terms, by class (categories or types) and by property.
Main Gainesville Core Ontology terms, grouped in broad categories.
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#>.
<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".
<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".
<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/>.
<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".
<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".
<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".
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,HPREFIX 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 introduces the following classes and properties.
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
[#] [back to top]
rdfs:comment
A class for bonds with aromatic character
rdfs:subClassOf gc:NormalBond
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A generic class representing Auxiliary concepts.
Subclasses gc:Value
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for generic concepts that describe calculations in computational chemistry.
Subclasses gc:MolecularMethodology gc:MethodologyFeature gc:MolecularComputation gc:CalculationResult
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for the complete active space perturbation theory methods.
rdfs:subClassOf gc:MultipleDeterminant
[#] [back to top]
rdfs:comment
A class for the coupled cluster method with double substitutions.
rdfs:subClassOf gc:MultipleDeterminant
[#] [back to top]
rdfs:comment
A class for the coupled cluster method with a full treatment singles and doubles.
rdfs:subClassOf gc:MultipleDeterminant
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for the configuration interaction (CI) method with single substitutions.
rdfs:subClassOf gc:MultipleDeterminant
[#] [back to top]
rdfs:comment
A class for the configuration interaction (CI) method with single and double substitutions.
rdfs:subClassOf gc:MultipleDeterminant
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for correlation functionals in Density Functional Theories.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasCorrelationFunctional
[#] [back to top]
rdfs:comment
A class for methods from the family of Density Functional Theories.
rdfs:subClassOf gc:SingleDeterminant
[#] [back to top]
rdfs:comment
A class for specific approximations to exchange-correlation functionals in the Density Functional Theory.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasDftFlavor
[#] [back to top]
rdfs:comment
A class for the exchange-correlation functionals in the Density Functional Theory.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasDftFunctional
[#] [back to top]
rdfs:subClassOf gc:CalculationResult
[#] [back to top]
rdfs:comment
A class for the dispersion correction in the Density Functional Theory.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasDispersionCorrection
[#] [back to top]
rdfs:comment
A class for double covalent bonds.
rdfs:subClassOf gc:NormalBond
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for exchange functionals in Density Functional Theories.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasExchangeFunctional
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for calculations in computational chemistry that aim to find molecular geometry of lowest energy.
rdfs:subClassOf gc:MolecularComputation
[#] [back to top]
rdfs:comment
A class for generic collection of atoms in molecules and residues
rdfs:subClassOf gc:MolecularStructureObject
[#] [back to top]
rdfs:comment
A class for hydrogen bond - the electrostatic interaction between polar molecules (strong dipole-dipole attraction).
rdfs:subClassOf gc:Bond
[#] [back to top]
rdfs:comment
A class that represents integer value, containing value and unit.
rdfs:subClassOf gc:Value
Domain of gc:hasIntegerValue
Range of gc:hasFormalCharge
[#] [back to top]
rdfs:comment
A class for the multi-configurational self-consistent field (MCSCF) method.
rdfs:subClassOf gc:MultipleDeterminant
[#] [back to top]
rdfs:comment
A class for the specific methodology used to conduct computational chemistry calculations.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasMethodology
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A generic class of various concepts related to molecular systems.
Subclasses gc:MolecularStructureObject
[#] [back to top]
rdfs:comment
A class for the classical methodologies of computational chemistry.
rdfs:subClassOf gc:MolecularMethodology
Domain of gc:hasParameterSet gc:hasForceField
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for objects related to molecular systems.
rdfs:subClassOf gc:MolecularStructureObject
Domain of gc:hasSystemTemperature gc:hasCalculationOn gc:hasSystemCharge gc:hasSystemMultiplicity
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for the second order Moller-Plesset perturbation theory method of quantum chemistry.
rdfs:subClassOf gc:SingleDeterminant
[#] [back to top]
rdfs:comment
A class for the third order Moller-Plesset perturbation theory method of quantum chemistry.
rdfs:subClassOf gc:SingleDeterminant
[#] [back to top]
rdfs:comment
A class for the fourth order Moller-Plesset perturbation theory method of quantum chemistry.
rdfs:subClassOf gc:SingleDeterminant
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class representing methods of quantum chemistry using multiple reference state determinants.
rdfs:subClassOf gc:QuantumMechanics
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A class for natural values, containing value and unit.
rdfs:subClassOf gc:Value
Domain of gc:hasNaturalValue
[#] [back to top]
rdfs:comment
A class for covalent bond in molecules.
rdfs:subClassOf gc:Bond
Subclasses gc:Quadruple gc:Triple gc:Double gc:Aromatic gc:Single
[#] [back to top]
rdfs:comment
A class representing the number of basis set functions used in calculations.
rdfs:subClassOf gc:MethodologyFeature
Range of gc:hasNumberBasisFunc
[#] [back to top]
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
[#] [back to top]
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
[#] [back to top]
rdfs:comment
A generic class for objects related to the publication of results of computational chemistry calculations.
rdfs:subClassOf gc:PublicationConcept
Subclasses gc:ComputationalChemistryPublication
[#] [back to top]
rdfs:comment
A generic class representing concepts related to publications.
Subclasses gc:Publication gc:SourcePackage
[#] [back to top]
rdfs:comment
??? !!!
rdfs:subClassOf gc:NormalBond
[#] [back to top]
rdfs:comment
A class for Quantum Mechanical methods.
rdfs:subClassOf gc:MolecularMethodology
Subclasses gc:MultipleReferenceState gc:SingleReferenceState gc:MultipleDeterminant
[#] [back to top]
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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rdfs:comment
A class for self-consisted field methods (SCF) of Quantum Chemistry
rdfs:subClassOf gc:MultipleDeterminant
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rdfs:comment
A class for SemiEmpirical Methods of Quantum Chemistry
rdfs:subClassOf gc:SingleDeterminant
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rdfs:comment
A class for single covalent bonds.
rdfs:subClassOf gc:NormalBond
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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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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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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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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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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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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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rdfs:comment
A class for triple covalent bond.
rdfs:subClassOf gc:NormalBond
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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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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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rdfs:comment
A class for the computations of vibrational spectrum of molecules.
rdfs:subClassOf gc:MolecularComputation
Domain of gc:hasFrequencyPeak
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rdfs:comment
A class for the vibrational frequences of molecules.
rdfs:subClassOf gc:CalculationResult
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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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rdfs:comment
A property that describes atoms comprised by a molecule or residue
rdfs:range gc:Atom
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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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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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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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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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rdfs:comment
A property that determinates the count of bonds into Molecule, Residue or Atom.
rdfs:range xsd:nonNegativeInteger
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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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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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rdfs:comment
A property that tells whether the molecular system has calculations done.
rdfs:domain gc:MolecularSystem
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rdfs:comment
A property that determines a category of the publication.
rdfs:domain gc:ComputationalChemistryPublication
rdfs:range xsd:string
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rdfs:comment
A property that defines chain number in the molecule.
rdfs:domain gc:Residue
rdfs:range xsd:int
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rdfs:comment
A property that describes atom coordinates.
rdfs:domain gc:Atom
rdfs:range gc:VectorValue
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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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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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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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rdfs:comment
A property that describes molecular dipol moment.
Has sub properties gc:hasDipoleMomentAverage gc:hasDipoleMoment
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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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rdfs:comment
A property that describes the electronic spectra.
Has sub properties gc:hasElectronicTransitions gc:hasOscillatorStrength
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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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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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rdfs:comment
A property that describes the exchange functionals.
rdfs:domain gc:MolecularMethodology
rdfs:range gc:ExchangeFunctional
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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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rdfs:comment
A property that describes the reference to the attachment file.
rdfs:domain gc:ComputationalChemistryPublication
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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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rdfs:comment
A property that describes Force Field.
rdfs:domain gc:MolecularMechanics gc:MolecularMethodology
rdfs:range gc:ForceField xsd:string
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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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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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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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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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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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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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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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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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rdfs:comment
A property that defines the insertion code for residue numbering.
rdfs:domain gc:Residue
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rdfs:comment
A property that describes Integer Value.
rdfs:domain gc:IntegerValue
rdfs:range xsd:integer
rdfs:subPropertyOf gc:hasValue
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rdfs:comment
A property that describes the intensity of a frequency peak
rdfs:domain gc:FrequencyPeak
rdfs:range gc:FloatValue
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rdfs:comment
A property that defines the security key of the publication.
rdfs:domain gc:ComputationalChemistryPublication
rdfs:range xsd:string
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rdfs:comment
A property that defines the calculation method for given technology.
rdfs:range rdfs:Literal
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rdfs:comment
A property that describes a methodology of computations.
rdfs:domain gc:MolecularMethodology
rdfs:range gc:Methodology xsd:string
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rdfs:comment
A property that describes computed Mulliken Charges.
rdfs:domain gc:CalculatedProperties
rdfs:range gc:FloatValue
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rdfs:comment
The name of an entity.
rdfs:range rdfs:Literal xsd:string
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rdfs:comment
A property that defines natural value.
rdfs:domain gc:NaturalValue
rdfs:range xsd:nonNegativeInteger
rdfs:subPropertyOf gc:hasValue
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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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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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rdfs:comment
A property that describes the normal mode of a vibration
rdfs:domain gc:FrequencyPeak
rdfs:range gc:VectorValue
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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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rdfs:comment
A property that describes the occupancy of the orbital
rdfs:domain gc:Orbital
rdfs:range gc:FloatValue
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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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rdfs:comment
A property that describes the treatment of open shell systems.
rdfs:range rdfs:Literal
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rdfs:comment
A property that describes the orbital.
rdfs:domain gc:WaveFunction
rdfs:range gc:Orbital
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rdfs:comment
A property that defines the number of electron orbitals
rdfs:range xsd:int
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rdfs:comment
A property that describes the orbital energy.
rdfs:domain gc:Orbital
rdfs:range gc:FloatValue
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rdfs:comment
A property that defines Orbital symmetry
rdfs:domain gc:Orbital
rdfs:range xsd:string
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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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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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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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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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rdfs:comment
A property that describes the residue in a molecule.
rdfs:domain gc:Molecule
rdfs:range gc:Residue
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rdfs:comment
A property that describes generic results of the computations.
rdfs:domain gc:MolecularComputation
rdfs:range gc:CalculationResult
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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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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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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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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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rdfs:comment
A property that describes the status of the publication.
rdfs:domain gc:ComputationalChemistryPublication
rdfs:range xsd:string
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rdfs:comment
A property that describes molecular system charge.
rdfs:domain gc:MolecularSystem
rdfs:range gc:FloatValue
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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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rdfs:comment
A property that describes the system spin multiplicity.
rdfs:domain gc:MolecularSystem
rdfs:range xsd:positiveInteger
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rdfs:comment
A property that describes system temperature.
rdfs:domain gc:MolecularSystem
rdfs:range gc:FloatValue
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rdfs:comment
A property that describes the calculation's technology for molecular system.
rdfs:range rdfs:Literal
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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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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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rdfs:comment
A property that describes a unit of the value.
rdfs:domain gc:Value
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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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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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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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rdfs:comment
A property that describes the version of the software package used.
rdfs:range xsd:string
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rdfs:comment
A property that describes the number of vibrational frequencies.
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rdfs:comment
A property that defines the allowed visibility of the publication.
rdfs:domain gc:ComputationalChemistryPublication
rdfs:range xsd:string
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rdfs:comment
A property that describes Wave Function Coefficients.
rdfs:domain gc:Orbital
rdfs:range gc:VectorValue
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rdfs:comment
A property that defines objects held by a container.
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rdfs:comment
A property that describes what element the given atom is.
rdfs:domain gc:Atom
rdfs:range pt:Element
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