Crystal Structure Ontology
type: Ontology
contributor: Said Fathalla
contributor: Stefan Sandfeld
created: 17.08.2023
creator: Ahmad Zainul Ihsan
license: http://creativecommons.org/licenses/by/3.0/
preferred namespace prefix: CSO
version info: 1.1

has quantity kind
type: ObjectProperty
range: Quantity Kind

quantity value
type: ObjectProperty
range: Quantity value

unit
type: ObjectProperty
range: Unit
description: A reference to the unit of measure of a quantity (variable or constant) of interest.

has basis
type: ObjectProperty
inverse of: is basis of
domain: Class
  union of: Lattice
  union of: Vector Component of Basis
range: Basis
comment: hasBasis represents the relationship between a lattice or coordinate vector basis and basis.

has crystal system
type: ObjectProperty
domain: Lattice
range: Crystal System
comment: hasCrystalSystem represents the relationship between unit cell and crystal system.

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

has lattice
type: ObjectProperty
domain: Crystal Structure
range: Lattice
comment: hasLattice represents the relationship between a crystal structure and lattice.

has lattice parameter angle
type: ObjectProperty
domain: Unit Cell
range: Lattice Parameter Angle

has lattice parameter length
type: ObjectProperty
domain: Unit Cell
range: Lattice Parameter Length

has position vector
type: ObjectProperty
domain: Point
range: Position Vector
comment: hasPositionVector represents the relationship between entity and position vector.

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

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

has unit cell
type: ObjectProperty
domain: Lattice
range: Unit Cell
comment: hasUnitCell hasSpecies represents the relationship between a lattice and unit cells.

has vector component
type: ObjectProperty
domain: Vector
range: Vector Component of Basis
comment: hasVectorComponent relates the Vector with 'Vector Components of Basis'

is basis of
type: ObjectProperty
comment: Inverse property of hasBasis

is point group of
type: ObjectProperty
inverse of: has point group
domain: Point Group
range: Class
  union of: Crystal System
  union of: Space Group
comment: inverse property of hasPointGroup

is space group of
type: ObjectProperty
inverse of: has space group
domain: Space Group
range: Crystal Structure
comment: inverse property of hasSpaceGroup

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

has element
type: ObjectProperty
domain: Species
range: Atom
comment: hasElement represents the relationship between a species and atoms it has.

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

has occupancy
type: ObjectProperty
domain: Crystal Structure
range: Occupancy
comment: hasOccupancy represents the relationship between a structure and occupancies it has.

has point group
type: ObjectProperty
domain: Class
  union of: Crystal System
  union of: Space Group
range: Point Group
comment: hasPointGroup represents the relationship between a space group and point groups it corresponds to.

has site
type: ObjectProperty
domain: Occupancy
range: Site
comment: hasSite represents the relationship between an occupancy and sites it ties.

has space group
type: ObjectProperty
domain: Crystal Structure
range: Space Group
comment: hasSpaceGroup represents the relationship between a structure and a space group it corresponds to.

has species
type: ObjectProperty
domain: Occupancy
range: Species
comment: hasSpecies represents the relationship between an occupancy and species it ties.

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

first axis component
type: DatatypeProperty
domain: Vector Component of Basis
range: double
comment: A first vector component related to the first axis vector of a basis

lattice parameter angle alpha
type: DatatypeProperty
domain: Lattice Parameter Angle
range: double
comment: latticeParameterAngleAlpha represents lattice parameter angle alpha of lattice parameter angle in double.

lattice parameter angle beta
type: DatatypeProperty
domain: Lattice Parameter Angle
range: double
comment: latticeParameterAngleBeta represents lattice parameter angle beta of lattice parameter angle in double.

lattice parameter angle gamma
type: DatatypeProperty
domain: Lattice Parameter Angle
range: double
comment: latticeParameterAngleGamma represents lattice parameter angle gamma of lattice parameter angle in double.

lattice parameter length a
type: DatatypeProperty
domain: Lattice Parameter Length
range: double
comment: latticeParameterLengthA represents lattice parameter length a of lattice parameter length in double.

lattice parameter length b
type: DatatypeProperty
domain: Lattice Parameter Length
range: double
comment: latticeParameterLengthB represents lattice parameter length b of lattice parameter length in double.

lattice parameter length c
type: DatatypeProperty
domain: Lattice Parameter Length
range: double
comment: latticeParameterLengthA represents lattice parameter length c of lattice parameter length in double.

second axis component
type: DatatypeProperty
domain: Vector Component of Basis
range: double
comment: A second vector component related to the second axis vector of a basis

third axis component
type: DatatypeProperty
domain: Vector Component of Basis
range: double
comment: A third vector component related to the third axis vector of a basis

vector magnitude
type: DatatypeProperty
domain: Vector
range: double

element ratio
type: DatatypeProperty
domain: Species
range: double
comment: ElementRatio represents that a species has the ratio in a double.

point group Hermann-Mauguin name
type: DatatypeProperty
domain: Point Group
range: string
comment: PointGroupHMName represents that a point group has the Hermann-Mauguin in a string.

space group ID
type: DatatypeProperty
domain: Space Group
range: integer
comment: SpaceGroupID represents that a space group has the unique ID in an integer.

space group symbol
type: DatatypeProperty
domain: Space Group
range: string
comment: SpaceGroupSymbol represents that a space group has the symbol in a string.

X_axis coordinate
type: DatatypeProperty
domain: Coordinate Vector
range: double
comment: X_axisCoordinate represents that a coordinate vector has the value of a coordinate in a double in X axis.

Y_axis coordinate
type: DatatypeProperty
domain: Coordinate Vector
range: double
comment: Y_axisCoordinate represents that a coordinate vector has the value of a coordinate in a double in Y axis.

Z_axis coordinate
type: DatatypeProperty
domain: Coordinate Vector
range: double
comment: Z_axisCoordinate represents that a coordinate vector has the value of a coordinate in a double in Z axis.

Atom
type: Class
subclass of: Restriction
  on property: formula
  qualified cardinality: 1
  on data range: string
defintion: A chemical entity constituting the smallest component of an element having the chemical properties of the element.

Quantity
type: Class
subclass of: Restriction
  on property: has quantity kind
  all values from: Quantity Kind
subclass of: Restriction
  on property: quantity value
  all values from: Quantity value
description: A quantity is the measurement of an observable property of a particular object, event, or physical system. A quantity is always associated with the context of measurement (i.e. the thing measured, the measured value, the accuracy of measurement, etc.) whereas the underlying quantity kind is independent of any particular measurement. Thus, length is a quantity kind while the height of a rocket is a specific quantity of length; its magnitude that may be expressed in meters, feet, inches, etc. Examples of physical quantities include physical constants, such as the speed of light in a vacuum, Planck's constant, the electric permittivity of free space, and the fine structure constant. In other words, quantities are quantifiable aspects of the world, such as time, distance, velocity, mass, momentum, energy, and weight, and units are used to describe their measure. Many of which are related to each other by various physical laws, and as a result the units of some of the quantities can be expressed as products (or ratios) of powers of other units (e.g., momentum is mass times velocity and velocity is measured in distance divided by time). These relationships are discussed in dimensional analysis. Those that cannot be so expressed can be regarded as "fundamental" in this sense. A quantity is distinguished from a "quantity kind" in that the former carries a value and the latter is a type specifier.

Quantity Kind
type: Class
description: A Quantity Kind is any observable property that can be measured and quantified numerically. Familiar examples include physical properties such as length, mass, time, force, energy, power, electric charge, etc. Less familiar examples include currency, interest rate, price to earning ratio, and information capacity.

Quantity value
type: Class
subclass of: Restriction
  on property: unit
  all values from: Unit
description: A Quantity Value expresses the magnitude and kind of a quantity and is given by the product of a numerical value n and a unit of measure U. The number multiplying the unit is referred to as the numerical value of the quantity expressed in that unit. Refer to NIST SP 811 section 7 for more on quantity values.

Unit
type: Class
description: A unit of measure, or unit, is a particular quantity value that has been chosen as a scale for measuring other quantities the same kind (more generally of equivalent dimension). For example, the meter is a quantity of length that has been rigorously defined and standardized by the BIPM (International Board of Weights and Measures). Any measurement of the length can be expressed as a number multiplied by the unit meter. More formally, the value of a physical quantity Q with respect to a unit (U) is expressed as the scalar multiple of a real number (n) and U, as \(Q = nU\).

Bravais Lattice
type: Class
subclass of: Lattice
subclass of: Restriction
  on property: centering
  qualified cardinality: 1
  on data range: string
comment: Lattice types that has seven primitive lattices and seven non-primitive lattices.

Crystal Structure
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has occupancy
    some values from: Occupancy
  intersection of: Restriction
    on property: has occupancy
    all values from: Occupancy
subclass of: Class
  intersection of: Restriction
    on property: has space group
    all values from: Space Group
  intersection of: Restriction
    on property: has space group
    qualified cardinality: 1
    on class: Space Group
subclass of: Restriction
  on property: has lattice
  all values from: Lattice
defintion: A crystal structure is described by both of the lattice geometry and atomic arrangements within the unit cell.

Crystal System
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has point group
    all values from: Point Group
  intersection of: Restriction
    on property: has point group
    qualified cardinality: 1
    on class: Point Group
defintion: A classification scheme for crystal structures on the basis of unit cell geometry.

Cubic
type: Class
subclass of: Crystal System

Hexagonal
type: Class
subclass of: Crystal System

Lattice
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has basis
    some values from: Basis
  intersection of: Restriction
    on property: has basis
    all values from: Basis
subclass of: Class
  intersection of: Restriction
    on property: has crystal system
    some values from: Crystal System
  intersection of: Restriction
    on property: has crystal system
    all values from: Crystal System
subclass of: Class
  intersection of: Restriction
    on property: has unit cell
    some values from: Unit Cell
  intersection of: Restriction
    on property: has unit cell
    all values from: Unit Cell
defintion: A lattice defines a periodic arrangement of one or more atoms.

Lattice Parameter Angle
type: Class
subclass of: Class
  intersection of: Restriction
    on property: lattice parameter angle alpha
    qualified cardinality: 1
    on data range: double
  intersection of: Restriction
    on property: lattice parameter angle beta
    qualified cardinality: 1
    on data range: double
  intersection of: Restriction
    on property: lattice parameter angle gamma
    qualified cardinality: 1
    on data range: double
disjoint with: Lattice Parameter Length
defintion: The three angles of edges in lattice parameter lengths characterizing the unit cell.

Lattice Parameter Length
type: Class
subclass of: Class
  intersection of: Restriction
    on property: lattice parameter length a
    qualified cardinality: 1
    on data range: double
  intersection of: Restriction
    on property: lattice parameter length b
    qualified cardinality: 1
    on data range: double
  intersection of: Restriction
    on property: lattice parameter length c
    qualified cardinality: 1
    on data range: double
defintion: The three edges characterize the unit cell that parallelepiped.

Monoclinic
type: Class
subclass of: Crystal System

Orthorhombic
type: Class
subclass of: Crystal System

Point
type: Class
subclass of: Restriction
  on property: has position vector
  all values from: Position Vector
comment: 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.

Position Vector
type: Class
subclass of: Vector
defintion: Position vector is a Euclidean vector that represents the position of a point P in space in relation to an arbitrary reference origin O.

Tetragonal
type: Class
subclass of: Crystal System

Triclinic
type: Class
subclass of: Crystal System

Trigonal
type: Class
subclass of: Crystal System

Unit Cell
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has lattice parameter angle
    some values from: Lattice Parameter Angle
  intersection of: Restriction
    on property: has lattice parameter angle
    all values from: Lattice Parameter Angle
subclass of: Class
  intersection of: Restriction
    on property: has lattice parameter length
    some values from: Lattice Parameter Length
  intersection of: Restriction
    on property: has lattice parameter length
    all values from: Lattice Parameter Length
defintion: Basic structural unit or building block of the crystal structure and defines the crystal structure by virtue of its geometry and the atom positions within.

Vector
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has vector component
    some values from: Vector Component of Basis
  intersection of: Restriction
    on property: has vector component
    all values from: Vector Component of Basis
subclass of: Restriction
  on property: vector magnitude
  qualified cardinality: 1
  on data range: double
defintion: (Euclidean) vector used to represent quantities that both magnitude and direction.

Vector Component of Basis
type: Class
subclass of: Quantity
subclass of: Class
  intersection of: Restriction
    on property: has basis
    some values from: Basis
  intersection of: Restriction
    on property: has basis
    all values from: Basis
subclass of: Class
  intersection of: Restriction
    on property: first axis component
    qualified cardinality: 1
    on data range: double
  intersection of: Restriction
    on property: second axis component
    qualified cardinality: 1
    on data range: double
  intersection of: Restriction
    on property: third axis component
    qualified cardinality: 1
    on data range: double
comment: Vector components/vector coordinates of particular basis. It has relation to a specific basis.

Basis
type: Class
subclass of: Restriction
  on property: has first axis vector
  qualified cardinality: 1
  on class: Coordinate Vector
subclass of: Restriction
  on property: has second axis vector
  qualified cardinality: 1
  on class: Coordinate Vector
subclass of: Restriction
  on property: has third axis vector
  qualified cardinality: 1
  on class: Coordinate Vector
comment: A basis defines a spatial unit used to express fractional coordinates.
defintion: Set of vector(in 2-D two vectors and in 3-D three vectors) that linearly independent.

Coordinate Vector
type: Class
subclass of: Restriction
  on property: X_axis coordinate
  qualified cardinality: 1
  on data range: double
subclass of: Restriction
  on property: Y_axis coordinate
  qualified cardinality: 1
  on data range: double
subclass of: Restriction
  on property: Z_axis coordinate
  qualified cardinality: 1
  on data range: double
defintion: A coordinate vector according to standard basis, i.e., e_x (1, 0, 0), e_y(0, 1, 0), and e_z (0, 0, 1).

Occupancy
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has site
    some values from: Site
  intersection of: Restriction
    on property: has site
    all values from: Site
subclass of: Class
  intersection of: Restriction
    on property: has species
    some values from: Species
  intersection of: Restriction
    on property: has species
    all values from: Species
defintion: An occupancy ties a specific species to a site.

Point Group
type: Class
subclass of: Restriction
  on property: is point group of
  some values from: Crystal System
subclass of: Restriction
  on property: is point group of
  some values from: Space Group
subclass of: Restriction
  on property: point group Hermann-Mauguin name
  qualified cardinality: 1
  on data range: string
comment: 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.
comment: In the symmetry point of view, a set of point groups (32 point groups) is classified into the crystal system. Note that the point group describes the symmetry of macroscopic or finite object, thus the Bravais lattice (translation symmetry) is negligible.
see also: International Tables for Crystallography, Volume A, Fourth, revised edition, Section 8.1.5.

Site
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has cartesian coordinates
    all values from: Coordinate Vector
  intersection of: Restriction
    on property: has cartesian coordinates
    max qualified cardinality: 1
    on class: Coordinate Vector
subclass of: Class
  intersection of: Restriction
    on property: has fractional coordinates
    all values from: Coordinate Vector
  intersection of: Restriction
    on property: has fractional coordinates
    max qualified cardinality: 1
    on class: Coordinate Vector
defintion: A site is a point in a lattice.

Space Group
type: Class
subclass of: Class
  intersection of: Restriction
    on property: has point group
    some values from: Point Group
  intersection of: Restriction
    on property: has point group
    all values from: Point Group
subclass of: Restriction
  on property: is space group of
  some values from: Crystal Structure
subclass of: Restriction
  on property: space group ID
  qualified cardinality: 1
  on data range: integer
subclass of: Restriction
  on property: space group symbol
  qualified cardinality: 1
  on data range: string
comment: A space group is the symmetry group of a three-dimensional crystal pattern is called its space group.
comment: Combination of Bravais lattice, point groups, two symmetry operations (screw rotation and glide reflection) results in space groups
comment: The nomenclature consists of a maximum of four symbols for each space group, e.g., Fm-3m(Cubic) First symbol defines the Bravais lattice centering, here is the cubic centering, C. The next three symbols defines symmetry elements with respect to viewing directions, which are different from crystal system to crystal system.
see also: International Tables for Crystallography, Volume !, Fourth, revised edition, Section 8.1.5.

Species
type: Class
subclass of: Restriction
  on property: has element
  qualified cardinality: 1
  on class: Atom
defintion: A species is the combination of atoms on each site.