Computational Material Sample Ontology (CMSO)
type: Ontology
Contributor: https://orcid.org/0000-0001-9560-4728
Contributor: 0000-0002-5149-603X
Contributor: https://orcid.org/0000-0002-6776-1213
Contributor: https://orcid.org/0000-0003-0698-4891
creator: https://orcid.org/0000-0001-7564-7990
description: CMSO is an ontology that aims to describe computational materials science samples (or structures), including crystalline defects.
License: https://creativecommons.org/licenses/by/4.0/
version info: 0.0.1
citation: Azocar Guzman, A., Menon, S., Hofmann, V., Hickel, T., Sandfeld. S. (2024), Computational Material Sample Ontology, https://purls.helmholtz-metadaten.de/cmso/
creative work status: Ontology Specification
funder: https://ror.org/05qj6w324

definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: IAO_0000122
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
IAO_0000116: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
IAO_0000117: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
IAO_0000111: definition source
IAO_0000114: IAO_0000122
definition: Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
IAO_0000117: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

mathematical formula
type: AnnotationProperty
IAO_0000112: A normal distribution probability density function has a formula of: f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2))
definition: An annotation property that represents a mathematical formula.
IAO_0000117: Asiyah Yu Lin, Jie Zheng, Yongqun He

Contributor
type: AnnotationProperty
comment: Examples of a Contributor include a person, an organization, or a service. Typically, the name of a Contributor should be used to indicate the entity.
definition: An entity responsible for making contributions to the resource.
sub property of: contributor

Creator
type: AnnotationProperty
comment: Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
definition: An entity primarily responsible for making the resource.
sub property of: creator
sub property of: Contributor
range: Agent

Description
type: AnnotationProperty
comment: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
definition: An account of the resource.
sub property of: description

License
type: AnnotationProperty
definition: A legal document giving official permission to do something with the resource.
range: LicenseDocument

Title
type: AnnotationProperty
definition: A name given to the resource.
note: In current practice, this term is used primarily with literal values; however, there are important uses with non-literal values as well. As of December 2007, the DCMI Usage Board is leaving this range unspecified pending an investigation of options.
sub property of: title

alternative label
type: AnnotationProperty
comment: The range of skos:altLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: An alternative lexical label for a resource.
example: Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
sub property of: label

example
type: AnnotationProperty
definition: An example of the use of a concept.
sub property of: note

note
type: AnnotationProperty
definition: A general note, for any purpose.

preferred label
type: AnnotationProperty
comment: A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag.
comment: The range of skos:prefLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: The preferred lexical label for a resource, in a given language.
sub property of: label

has crystallographic defect
type: ObjectProperty
domain: Crystalline Material
range: Crystallographic Defect
definition: A data property linking a crystalline material and a crystallographic defect, such as vacancies, interstitials, or dislocations.

has angle
type: ObjectProperty
domain: Class
  union of: Simulation Cell
  union of: Unit Cell
range: Angle
definition: The relation between a simulation or unit cell and its angle.

has attribute
type: ObjectProperty
domain: Atomic Scale Sample
range: Atom Attribute
definition: The relation between a sample and a type of atom attribute, which refers to a per atom quantity of the atomic scale sample.

has basis
type: ObjectProperty
domain: Unit Cell
range: Basis
definition: The relation between a unit cell and the basis of the crystal structure.

has element
type: ObjectProperty
domain: Chemical Species
range: Chemical Element
definition: The relation between an atom and its chemical element.

has lattice parameter
type: ObjectProperty
domain: Unit Cell
range: Lattice Parameter
definition: The relation between a unit cell and its lattice parameters.

has simulation cell length
type: ObjectProperty
domain: Simulation Cell
range: Simulation Cell Length
definition: The relation between a simulation cell and its length.

has material
type: ObjectProperty
inverse of: is material of
domain: Computational Sample
range: Material
definition: The relation between a computational sample and the material it represents.

has normal vector
type: ObjectProperty
sub property of: has vector
domain: Plane
range: Normal Vector
definition: The relation between a plane and a vector normal to it.

has simulation cell
type: ObjectProperty
domain: Atomic Scale Sample
range: Simulation Cell
definition: The relation between an atomic scale sample and the simulation cell.

has simulation cell volume
type: ObjectProperty
domain: Simulation Cell
range: Simulation Cell Volume
definition: The relation between a simulation cell and its volume.

has space group
type: ObjectProperty
domain: Crystal Structure
range: Space Group
definition: The relation between a crystal structure and the space group that describes the symmetry.

has species
type: ObjectProperty
domain: Computational Sample
range: Chemical Species
definition: The relation between a computational sample and the species that constitutes it.

has structure
type: ObjectProperty
domain: Material
range: Structure
definition: The relation between a material and its structure.

has unit
type: ObjectProperty
domain: Thing
range: Unit
definition: A relation indicating the unit.

has unit cell
type: ObjectProperty
domain: Crystal Structure
range: Unit Cell
definition: The relation between a crystal structure and its unit cell.

has vector
type: ObjectProperty
domain: Class
  union of: Simulation Cell
  union of: Unit Cell
range: Vector
definition: The relation between an entity and its vectors.

is calculated property of
type: ObjectProperty

is defect of
type: ObjectProperty

is material of
type: ObjectProperty

has alternative name
type: DatatypeProperty
sub property of: has name
domain: Thing
range: string
definition: A data property linking an entity with alternative names.

has angle alpha
type: DatatypeProperty
domain: Angle
range: float
definition: A data property linking the angle to the measurement in the x axis.

has angle beta
type: DatatypeProperty
domain: Angle
range: float
definition: A data property linking the angle to the measurement in the y axis.

has angle gamma
type: DatatypeProperty
domain: Angle
range: float
definition: A data property linking the angle to the measurement in the z axis.

has atomic percent
type: DatatypeProperty
domain: Chemical Element
range: float
definition: A data property linking a chemical element with atomic percentage present in the material.
comment: abbreviated at.%

has Bravais lattice
type: DatatypeProperty
domain: Unit Cell
range: string
definition: A data property linking the crystal structure and the corresponding Bravais lattice.
definition: In three-dimensional space there are 14 Bravais lattices. Indicated by the crystal family and the centering types (primitive or simple, base-centered, body-centered, face-centered).

has chemical symbol
type: DatatypeProperty
sub property of: has symbol
domain: Chemical Element
range: string
definition: A data property linking an element with its chemical symbol.

has component x
type: DatatypeProperty
domain: Vector
range: float
definition: A data property linking a vector with its component on the x axis.

has component y
type: DatatypeProperty
domain: Vector
range: float
definition: A data property linking a vector with its component on the y axis.

has component z
type: DatatypeProperty
domain: Vector
range: float
definition: A data property linking a vector with its component on the z axis.

has distance from origin
type: DatatypeProperty
domain: Plane
range: float
definition: A data property linking an plane with the value of distance from its origin.

has element ratio
type: DatatypeProperty
domain: Chemical Element
range: float
definition: A data property linking a chemical element with the ratio or fraction of it in the material.
comment: Indicated with a value from 0 to 1.

has grain size
type: DatatypeProperty
domain: Simulation Cell
range: float

has identifier
type: DatatypeProperty
domain: Thing
range: string
definition: A data property linking an entity with an identifier (internal or external) that represents the entity.

has length x
type: DatatypeProperty
domain: Simulation Cell Length
domain: Unit Cell
range: float
definition: A data property linking a length to the measurement in the x axis.

has length y
type: DatatypeProperty
domain: Simulation Cell Length
domain: Unit Cell
range: float
definition: A data property linking a length to the measurement in the y axis.

has length z
type: DatatypeProperty
domain: Simulation Cell Length
domain: Unit Cell
range: float
definition: A data property linking a length to the measurement in the z axis.

has name
type: DatatypeProperty
domain: Thing
range: string
definition: A data property linking an entity with its name.

has number of atoms
type: DatatypeProperty
domain: Atomic Scale Sample
range: integer
definition: A data property linking an atomic scale sample with the number of atoms it contains.

has number of grains
type: DatatypeProperty
domain: Simulation Cell
range: float

has path
type: DatatypeProperty
domain: Atom Attribute
range: string
definition: A data property linking an atom attribute (per atom quantity) with the path pointing to the file where the data is stored.

has reference
type: DatatypeProperty
domain: Thing
range: anyURI
definition: A data property linking an entity with a reference (e.g. bibliographic) to another resource.
comment: The expected usage is to provide a Uniform Resource Identifier Reference (URI), which should point the referenced resource (e.g. a DOI for a publication)

has repetition x
type: DatatypeProperty
domain: Simulation Cell
range: integer
definition: A data property linking a simulation cell with its number of repetitions in the x direction.

has repetition y
type: DatatypeProperty
domain: Simulation Cell
range: integer
definition: A data property linking a simulation cell with its number of repetitions in the y direction.

has repetition z
type: DatatypeProperty
domain: Simulation Cell
range: integer
definition: A data property linking a simulation cell with its number of repetitions in the z direction.

has space group number
type: DatatypeProperty
domain: Crystal Structure
range: integer
definition: A data property linking a crystal structure with its space group number.

has space group symbol
type: DatatypeProperty
sub property of: has symbol
domain: Crystal Structure
range: string
definition: A data property linking a crystal structure with its space group symbol.

has symbol
type: DatatypeProperty
domain: Thing
range: string
definition: A data property linking an entity with its symbol.

has vacuum direction
type: DatatypeProperty
domain: Simulation Cell
range: string
definition: A data property defining the parameter that indicates the specific direction(s) in which vacuum space is added in a simulation cell

has vacuum length
type: DatatypeProperty
domain: Simulation Cell
range: float
definition: A data property defining the distance or thickness of vacuum space included in a simulation cell, often used to separate periodic images of a system to prevent interactions between them, especially in slab or surface simulations.

has value
type: DatatypeProperty
domain: Thing
range: float
definition: A data property linking an entity to its value.

has volume
type: DatatypeProperty
domain: Simulation Cell
range: float
definition: A data property linking a simulation cell with its volume. Comment: the unit of the volume is indicated by the unit of the simulation cell length.

has weight percent
type: DatatypeProperty
domain: Chemical Element
range: float
definition: A data property linking a chemical element with percentage by mass present in the material.
comment: abbreviated wt.%

Crystalline Material
type: Class
subclass of: Material
definition: Crystalline material is material characterized by a periodic arrangement of the constituent atoms. The arrangement could be described its crystal structure.

Crystallographic Defect
type: Class
definition: Lattice irregularity having one or more of its dimensions on the order of an atomic diameter.

Material
type: Class
equivalent class: Material
definition: Materials are substances in the condensed states (liquid, solid, colloidal) designed or manipulated for technological ends.
definition source: https://web.archive.org/web/20100801234616/http://www.nature.com/nmat/authors/index.html

Amorphous Material
type: Class
subclass of: Material
definition: An amorphous material or solid is a material which has no defined long-range order.
alternative label: Amorphous Solid
alternative label: Non-crystalline Solid

Angle
type: Class
definition: An angle is a measure of the the space (usually in degrees) between two intersecting lines at the point where they meet or vertex.

Atom
type: Class
subclass of: Chemical Species
definition: Smallest particle still characterizing a chemical element. It consists of a nucleus of a positive charge (Z is the proton number and e the elementary charge) carrying almost all its mass (more than 99.9%) and Z electrons determining its size.
definition source: https://goldbook.iupac.org/terms/view/A00493

Atom Attribute
type: Class
definition: Atom attribute refers to the features or quantities per atom of an atomic scale sample.

Atomic Force
type: Class
subclass of: Atom Attribute
definition: Atomic force refers to the vector that represents the force of each atom.

Atomic Position
type: Class
subclass of: Atom Attribute
definition: Atomic position refers to the vector that represents the position of each atom.
comment: Cartesian coordinates are preferred over direct (or fractional) coordinates.

Atomic Scale Sample
type: Class
subclass of: Computational Sample
definition: Atomic scale sample is a computational sample in the atomic length scale.

Atomic Velocity
type: Class
subclass of: Atom Attribute
definition: Atomic velocity refers to the vector that represents the velocity of each atom.

Basis
type: Class
definition: The basis of a crystal indicates the arrangement or position of atoms in the crystal lattice.

Bicrystal
type: Class
subclass of: Crystalline Material

Chemical Composition
type: Class
definition: Chemical composition refers to the type, arrangement and ratio of the chemical elements of a compound (or material).

Chemical Element
type: Class
definition: A species of atoms; all atoms with the same number of protons in the atomic nucleus.
definition source: https://goldbook.iupac.org/terms/view/C01022

Chemical Species
type: Class
definition: A chemical species is an ensemble of chemically identical atomic or molecular structural units in a solid array. Comment: In this context, it refers to either an atom, ion or molecule.
definition source: https://goldbook.iupac.org/terms/view/CT01038
comment: In this context, it refers to either an atom, ion or molecule.

Computational Sample
type: Class
definition: A computational sample is a representative system of a material for analysis through computational methods in the context of materials science.

Coordination Number
type: Class
subclass of: Atom Attribute
definition: Coordination number refers to the number of neighbors of each atom.
comment: In the case of molecules, it refers to the number of atoms, molecules or ions bonded to a central atom of the molecule. Also known as ligancy.

Crystal Defect
type: Class
definition: A crystal defect is an imperfection or irregularity in the atomic arrangement of a crystalline solid.
alternative label: Crystallographic Defect

Crystal Structure
type: Class
subclass of: Structure
definition: Crystal structure is the arrangement of atoms or molecules in the solid state. Crystal structure also involves consideration of defects, or abnormalities, in the idealized atomic/molecular arrangements.
comment: In this context, the crystal structure refers to the idealized state, while the defect information is represented elsewhere (see Crystal Defect).

Lattice Angle
type: Class
subclass of: Angle
definition: The lattice angle refers to the angles between the crystallographic axes.

Lattice Parameter
type: Class
definition: The lattice parameter is the measurement of length of the unit cell of the crystal lattice.
comment: The lattice angles can also be considered lattice parameters (see Lattice Angle)
alternative label: Lattice Constant

Lattice Plane
type: Class
subclass of: Plane
definition: In crystallography, lattice planes are sets of parallel mathematical planes, where each lattice point is on a lattice plane. The lattice plane of a crystal is represented by three integers —h,k,l— which are referred to as the Miller indices.

Lattice Vector
type: Class
subclass of: Vector
definition: A lattice vector is a vector that defines the lattice of the crystal structure.
comment: Note that it differs from the simulation cell vector.

Macroscale Sample
type: Class
subclass of: Computational Sample
definition: Macroscale sample is a computational sample in the macroscale.
alternative label: Macro Scale Sample

Material
type: Class
definition: Materials are substances in the condensed states (liquid, solid, colloidal) designed or manipulated for technological ends.
comment: In the CMSO context, 'Material' refers to a theoretical entity and not necessarily a tangible object.

Mesoscale Sample
type: Class
subclass of: Computational Sample
definition: Mesoscale sample is a computational sample in the mesoscale.
alternative label: Meso Scale Sample

Microscale Sample
type: Class
subclass of: Computational Sample
definition: Microscale sample is a computational sample in the microscale.
alternative label: Micro Scale Sample

Microstructure
type: Class
subclass of: Structure
definition: The microstructure is the structure or arrangement of all components (atomic arrangement, defects, phases, etc.) of the material at the microscale.

Molecule
type: Class
subclass of: Chemical Species
definition: An electrically neutral entity consisting of more than one atom (n>1). Rigorously, a molecule, in which n>1 must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state.
definition source: https://goldbook.iupac.org/terms/view/M04002

Nanoscale Sample
type: Class
subclass of: Computational Sample
definition: Nanoscale sample is a computational sample in the nanoscale.

Normal Vector
type: Class
subclass of: Vector
definition: The normal vector is a vector perpendicular to a given object.

Occupancy
type: Class
subclass of: Atom Attribute
definition: Occupancy refers to the atom type at each lattice site.
comment: Note the difference from a total ratio or percentage of the occupancy of a site in the crystal structure (as defined in CIF)

Plane
type: Class
definition: In mathematics, a plane is a two-dimensional space or flat surface that extends indefinitely.
mathematical formula: 𝑎 𝑥 + 𝑏 𝑦 + 𝑐 𝑧 + 𝑑 = 0
comment: The equation of a plane is 𝑎 𝑥 + 𝑏 𝑦 + 𝑐 𝑧 + 𝑑 = 0 , where 𝑎 , 𝑏 , and 𝑐 are the components of the normal vector ⃑ 𝑛 = ( 𝑎 , 𝑏 , 𝑐 ) , which is perpendicular to the plane or any vector parallel to the plane.

Polycrystal
type: Class
subclass of: Crystalline Material

Simulation Cell
type: Class
definition: A simulation cell is a representation of the structure or system to be simulated. It is often a three-dimensional box (although not necessarily), where information about the crystal structure and material is contained.
alternative label: Box
alternative label: Supercell

Simulation Cell Angle
type: Class
subclass of: Angle
definition: The simulation cell angle refers to the angles of the simulation cell in each direction.

Simulation Cell Length
type: Class
definition: The simulation cell length refers to the length (dimension) of the simulation cell or box.
alternative label: Box length

Simulation Cell Vector
type: Class
subclass of: Vector
definition: The simulation cell vector is a vector that defines the simulation cell or box.
comment: Note that it differs from the lattice vector.

Simulation Cell Volume
type: Class
definition: The simulation cell volume refers to the volume of the simulation cell or box.

Space Group
type: Class
definition: The space group represents the symmetry properties of the crystal. In three-dimensions, space groups are classified in 230 distinct groups.

Structure
type: Class
definition: Structure is the the arrangement of particles or parts in a substance or body.
definition source: https://www.merriam-webster.com/dictionary/structure

Unit Cell
type: Class
definition: The unit cell is the smallest repeating unit of the crystal structure which contains the overal symmetry of the crystal. The entire crystal lattice can be generated by repeating the unit cell in three dimensions.

Vector
type: Class
definition: Vector is a quantity that has a magnitude and direction.

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 \(Q = nU\).

Collection
definition: A meaningful collection of concepts.

Concept
definition: An idea or notion; a unit of thought.

ConceptScheme
definition: A set of concepts, optionally including statements about semantic relationships between those concepts.
example: Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies.

OrderedCollection
definition: An ordered collection of concepts, where both the grouping and the ordering are meaningful.

broadMatch
definition: skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.

broader
definition: Relates a concept to a concept that is more general in meaning.

broaderTransitive
definition: skos:broaderTransitive is a transitive superproperty of skos:broader.

changeNote
definition: A note about a modification to a concept.

closeMatch
definition: skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property.

editorialNote
definition: A note for an editor, translator or maintainer of the vocabulary.

exactMatch
definition: skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.

hasTopConcept
definition: Relates, by convention, a concept scheme to a concept which is topmost in the broader/narrower concept hierarchies for that scheme, providing an entry point to these hierarchies.

hiddenLabel
definition: A lexical label for a resource that should be hidden when generating visual displays of the resource, but should still be accessible to free text search operations.

historyNote
definition: A note about the past state/use/meaning of a concept.

inScheme
definition: Relates a resource (for example a concept) to a concept scheme in which it is included.

mappingRelation
definition: Relates two concepts coming, by convention, from different schemes, and that have comparable meanings

member
definition: Relates a collection to one of its members.

memberList
definition: Relates an ordered collection to the RDF list containing its members.

narrowMatch
definition: skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.

narrower
definition: Relates a concept to a concept that is more specific in meaning.

narrowerTransitive
definition: skos:narrowerTransitive is a transitive superproperty of skos:narrower.

notation
definition: A notation, also known as classification code, is a string of characters such as "T58.5" or "303.4833" used to uniquely identify a concept within the scope of a given concept scheme.

related
definition: Relates a concept to a concept with which there is an associative semantic relationship.

relatedMatch
definition: skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes.

scopeNote
definition: A note that helps to clarify the meaning and/or the use of a concept.

semanticRelation
definition: Links a concept to a concept related by meaning.

topConceptOf
definition: Relates a concept to the concept scheme that it is a top level concept of.