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Crystal Structure Ontology

Release 17.08.2023

Latest version:
https://purls.helmholtz-metadaten.de/disos/cso
Revision:
1.1
Authors:
Ahmad Zainul Ihsan
Contributors:
Said Fathalla
Stefan Sandfeld
Download serialization:
RDF/XML
License:
http://creativecommons.org/licenses/by/3.0/
Visualization:
Visualize with WebVowl
GitHub:
Repository
Ontology Specification Draft

Introduction back to ToC

Crystal Structure Ontology (CSO) is an ontology developed to represent crystallographic information needed to describe the dislocation. In CSO, several MDO classes are reused to describe the crystal coordinate system, motif/base in a crystal structure, point groups, and space groups. The standard coordinate system is defined by MDO:Basis and MDO:CoordinateVector classes that CSO reuses. The motif/base is an arrangement of chemical species in the crystal structure reuses MDO:Occupancy, MDO:Site, and MDO:Species. Subsequently, to define the point groups and space groups of a crystal structure, MDO:PointGroup and MDO:SpaceGroup are reused. Lastly, to define the unit quantity of a property in CSO, the QUDT:Quantity, QUDT:QuantityKind, and QUDT:QuantityValue classes are reused.

Namespace declarations

Table 1: Namespaces used in the document
CSO<https://purls.helmholtz-metadaten.de/disos/cso>
qudt<http://qudt.org/schema/qudt>
chebi<http://purl.obolibrary.org/obo/chebi>
owl<http://www.w3.org/2002/07/owl>
xsd<http://www.w3.org/2001/XMLSchema>
skos<http://www.w3.org/2004/02/skos/core>
rdfs<http://www.w3.org/2000/01/rdf-schema>
structure<https://w3id.org/mdo/structure>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns>
terms<http://purl.org/dc/terms>
xml<http://www.w3.org/XML/1998/namespace>
vann<http://purl.org/vocab/vann>
obo<http://purl.obolibrary.org/obo>

Crystal Structure Ontology: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Annotation Properties

Cross-reference for Crystal Structure Ontology classes, object properties and data properties back to ToC

This section provides details for each class and property defined by Crystal Structure Ontology.

Classes

Atomc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_33250

has super-classes
is in domain of
formula dp
is in range of
has element op

Basisc back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/Basis

A basis defines a spatial unit used to express fractional coordinates.
has super-classes
is in domain of
has first axis vector op, has second axis vector op, has third axis vector op
is in range of
has basis op

Bravais Latticec back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#BravaisLattice

Lattice types that has seven primitive lattices and seven non-primitive lattices.
has super-classes
Lattice c
is in domain of
centering dp

Coordinate Vectorc back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/CoordinateVector

has super-classes
is in domain of
X_axis coordinate dp, Y_axis coordinate dp, Z_axis coordinate dp
is in range of
has cartesian coordinates op, has first axis vector op, has fractional coordinates op, has second axis vector op, has third axis vector op

Crystal Structurec back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#CrystalStructure

has super-classes
is in domain of
has lattice op, has occupancy op, has space group op
is in range of
is space group of op

Crystal Systemc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#CrystalSystem

has super-classes
has sub-classes
Cubic c, Hexagonal c, Monoclinic c, Orthorhombic c, Tetragonal c, Triclinic c, Trigonal c
is in range of
has crystal system op

Cubicc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Cubic

has super-classes
Crystal System c

Hexagonalc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Hexagonal

has super-classes
Crystal System c

Latticec back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Lattice

has super-classes
has sub-classes
Bravais Lattice c
is in domain of
has crystal system op, has unit cell op
is in range of
has lattice op

Lattice Parameter Anglec back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#LatticeParameterAngle

has super-classes
is in domain of
lattice parameter angle alpha dp, lattice parameter angle beta dp, lattice parameter angle gamma dp
is in range of
has lattice parameter angle op
is disjoint with
Lattice Parameter Length c

Lattice Parameter Lengthc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#LatticeParameterLength

has super-classes
is in domain of
lattice parameter length a dp, lattice parameter length b dp, lattice parameter length c dp
is in range of
has lattice parameter length op
is disjoint with
Lattice Parameter Angle c

Monoclinicc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Monoclinic

has super-classes
Crystal System c

Occupancyc back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/Occupancy

has super-classes
is in domain of
has site op, has species op
is in range of
has occupancy op

Orthorhombicc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Orthorhombic

has super-classes
Crystal System c

Pointc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Point

In classical Euclidean geometry, a point is a primitive notion that models an exact location in the space, and has no length, width, or thickness.
has super-classes
is in domain of
has position vector op

Point Groupc back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/PointGroup

A group of linear mappings of vector space, which is corresonpond to the group of motions in point space determining the symmetry of the macroscopic crystal, is called the point group of the crystal, furthermore of the crystal structure, and is also called the point group of its space group.
has super-classes
is in domain of
is point group of op, point group Hermann-Mauguin name dp
is in range of
has point group op

Position Vectorc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#PositionVector

has super-classes
Vector c
is in range of
has position vector op

Quantityc back to ToC or Class ToC

IRI: http://qudt.org/schema/qudt/Quantity

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
has super-classes
has sub-classes
Vector Component of Basis c

Quantity Kindc back to ToC or Class ToC

IRI: http://qudt.org/schema/qudt/QuantityKind

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
is in range of
has quantity kind op

Quantity valuec back to ToC or Class ToC

IRI: http://qudt.org/schema/qudt/QuantityValue

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
has super-classes
is in range of
quantity value op

Sitec back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/Site

has super-classes
is in domain of
has cartesian coordinates op, has fractional coordinates op
is in range of
has site op

Space Groupc back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/SpaceGroup

A space group is the symmetry group of a three-dimensional crystal pattern is called its space group.
has super-classes
is in domain of
is space group of op, space group ID dp, space group symbol dp
is in range of
has space group op

Speciesc back to ToC or Class ToC

IRI: https://w3id.org/mdo/structure/Species

has super-classes
is in domain of
element ratio dp, has element op
is in range of
has species op

Tetragonalc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Tetragonal

has super-classes
Crystal System c

Triclinicc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Triclinic

has super-classes
Crystal System c

Trigonalc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Trigonal

has super-classes
Crystal System c

Unitc back to ToC or Class ToC

IRI: http://qudt.org/schema/qudt/Unit

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
is in range of
unit op

Unit Cellc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#UnitCell

has super-classes
is in domain of
has lattice parameter angle op, has lattice parameter length op
is in range of
has unit cell op

Vectorc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#Vector

has super-classes
has sub-classes
Position Vector c
is in domain of
has vector component op, vector magnitude dp

Vector Component of Basisc back to ToC or Class ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#VectorComponentOfBasis

Vector components/vector coordinates of particular basis. It has relation to a specific basis.
has super-classes
Quantity c
is in domain of
first axis component dp, second axis component dp, third axis component dp
is in range of
has vector component op

Object Properties

has basisop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasBasis

hasBasis represents the relationship between a lattice or coordinate vector basis and basis.
has domain
Lattice c or Vector Component of Basis c
has range
Basis c
is inverse of
is basis of op

has cartesian coordinatesop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasCartesianCoordinates

hasCartesianCoordinates represents the relationship between a site and coordinates in cartesian format it has.
has domain
Site c
has range
Coordinate Vector c

has crystal systemop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasCrystalSystem

hasCrystalSystem represents the relationship between unit cell and crystal system.
has domain
Lattice c
has range
Crystal System c

has elementop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasElement

hasElement represents the relationship between a species and atoms it has.
has domain
Species c
has range
Atom c

has first axis vectorop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasFirstAxisVector

hasFirstAxisVector represents the relationship between a basis and a coordinate vector to define the coordianates of the axis vector the first basis
has domain
Basis c
has range
Coordinate Vector c

has fractional coordinatesop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasFractionalCoordinates

hasFractionalCoordinates represents the relationship between a site and coordinates in fractional format it has.
has domain
Site c
has range
Coordinate Vector c

has latticeop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasLattice

hasLattice represents the relationship between a crystal structure and lattice.
has domain
Crystal Structure c
has range
Lattice c

has lattice parameter angleop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasLatticeParameterAngle

has domain
Unit Cell c
has range
Lattice Parameter Angle c

has lattice parameter lengthop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasLatticeParameterLength

has domain
Unit Cell c
has range
Lattice Parameter Length c

has occupancyop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasOccupancy

hasOccupancy represents the relationship between a structure and occupancies it has.
has domain
Crystal Structure c
has range
Occupancy c

has point groupop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasPointGroup

hasPointGroup represents the relationship between a space group and point groups it corresponds to.
has domain
Crystal System c or Space Group c
has range
Point Group c
is inverse of
is point group of op

has position vectorop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasPositionVector

hasPositionVector represents the relationship between entity and position vector.
has domain
Point c
has range
Position Vector c

has quantity kindop back to ToC or Object Property ToC

IRI: http://qudt.org/schema/qudt/hasQuantityKind

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
has range
Quantity Kind c

has second axis vectorop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasSecondAxisVector

hasSexondAxisVector represents the relationship between a basis and a coordinate vector to define the coordianates of the axis vector the second basis
has domain
Basis c
has range
Coordinate Vector c

has siteop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasSite

hasSite represents the relationship between an occupancy and sites it ties.
has domain
Occupancy c
has range
Site c

has space groupop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasSpaceGroup

hasSpaceGroup represents the relationship between a structure and a space group it corresponds to.
has domain
Crystal Structure c
has range
Space Group c
is inverse of
is space group of op

has speciesop back to ToC or Object Property ToC

IRI: https://w3id.org/mdo/structure/hasSpecies

hasSpecies represents the relationship between an occupancy and species it ties.
has domain
Occupancy c
has range
Species c

has third axis vectorop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasThirdAxisVector

hasThirdAxisVector represents the relationship between a basis and a coordinate vector to define the coordianates of the axis vector the third basis
has domain
Basis c
has range
Coordinate Vector c

has unit cellop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasUnitCell

hasUnitCell hasSpecies represents the relationship between a lattice and unit cells.
has domain
Lattice c
has range
Unit Cell c

has vector componentop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#hasVectorComponent

hasVectorComponent relates the Vector with 'Vector Components of Basis'
has domain
Vector c
has range
Vector Component of Basis c

is basis ofop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#isBasisOf

Inverse property of hasBasis
is inverse of
has basis op

is point group ofop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#isPointGroupOf

inverse property of hasPointGroup
has domain
Point Group c
has range
Crystal System c or Space Group c
is inverse of
has point group op

is space group ofop back to ToC or Object Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#isSpaceGroupOf

inverse property of hasSpaceGroup
has domain
Space Group c
has range
Crystal Structure c
is inverse of
has space group op

quantity valueop back to ToC or Object Property ToC

IRI: http://qudt.org/schema/qudt/quantityValue

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
has range
Quantity value c

unitop back to ToC or Object Property ToC

IRI: http://qudt.org/schema/qudt/unit

Is defined by
http://qudt.org/2.0/schema/qudt
http://qudt.org/schema/qudt
has range
Unit c

Data Properties

centeringdp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#centering

Centering type of a Bravais lattice, e.g., primitive (P), base-centered (S), face-centered (F), and body-centered (I).
has domain
Bravais Lattice c
has range
string

element ratiodp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/ElementRatio

ElementRatio represents that a species has the ratio in a double.
has domain
Species c
has range
double

first axis componentdp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#firstAxisComponent

A first vector component related to the first axis vector of a basis
has domain
Vector Component of Basis c
has range
double

formuladp back to ToC or Data Property ToC

IRI: http://purl.obolibrary.org/obo/chebi/formula

has domain
Atom c
has range
string

lattice parameter angle alphadp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#latticeParameterAngleAlpha

latticeParameterAngleAlpha represents lattice parameter angle alpha of lattice parameter angle in double.
has domain
Lattice Parameter Angle c
has range
double

lattice parameter angle betadp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#latticeParameterAngleBeta

latticeParameterAngleBeta represents lattice parameter angle beta of lattice parameter angle in double.
has domain
Lattice Parameter Angle c
has range
double

lattice parameter angle gammadp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#latticeParameterAngleGamma

latticeParameterAngleGamma represents lattice parameter angle gamma of lattice parameter angle in double.
has domain
Lattice Parameter Angle c
has range
double

lattice parameter length adp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#latticeParameterLengthA

latticeParameterLengthA represents lattice parameter length a of lattice parameter length in double.
has domain
Lattice Parameter Length c
has range
double

lattice parameter length bdp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#latticeParameterLengthB

latticeParameterLengthB represents lattice parameter length b of lattice parameter length in double.
has domain
Lattice Parameter Length c
has range
double

lattice parameter length cdp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#latticeParameterLengthC

latticeParameterLengthA represents lattice parameter length c of lattice parameter length in double.
has domain
Lattice Parameter Length c
has range
double

point group Hermann-Mauguin namedp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/PointGroupHMName

PointGroupHMName represents that a point group has the Hermann-Mauguin in a string.
has domain
Point Group c
has range
string

second axis componentdp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#secondAxisComponent

A second vector component related to the second axis vector of a basis
has domain
Vector Component of Basis c
has range
double

space group IDdp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/SpaceGroupID

SpaceGroupID represents that a space group has the unique ID in an integer.
has domain
Space Group c
has range
integer

space group symboldp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/SpaceGroupSymbol

SpaceGroupSymbol represents that a space group has the symbol in a string.
has domain
Space Group c
has range
string

third axis componentdp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#thirdAxisComponent

A third vector component related to the third axis vector of a basis
has domain
Vector Component of Basis c
has range
double

vector magnitudedp back to ToC or Data Property ToC

IRI: https://purls.helmholtz-metadaten.de/disos/cso#vectorMagnitude

has domain
Vector c
has range
double

X_axis coordinatedp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/X_axisCoordinate

X_axisCoordinate represents that a coordinate vector has the value of a coordinate in a double in X axis.
has domain
Coordinate Vector c
has range
double

Y_axis coordinatedp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/Y_axisCoordinate

Y_axisCoordinate represents that a coordinate vector has the value of a coordinate in a double in Y axis.
has domain
Coordinate Vector c
has range
double

Z_axis coordinatedp back to ToC or Data Property ToC

IRI: https://w3id.org/mdo/structure/Z_axisCoordinate

Z_axisCoordinate represents that a coordinate vector has the value of a coordinate in a double in Z axis.
has domain
Coordinate Vector c
has range
double

Annotation Properties

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/contributor

createdap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/created

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/creator

defintionap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#defintion

descriptionap back to ToC or Annotation Property ToC

IRI: http://qudt.org/schema/qudt/description

equivalent classap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#equivalentClass

licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

preferred namespace prefixap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespacePrefix

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/title

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.