CMSO is an ontology that aims to describe computational materials science samples (or structures), including crystalline defects.
Computational Material Sample Ontology (CMSO)
Azocar Guzman, A., Menon, S., Hofmann, V., Hickel, T., Sandfeld. S. (2024), Computational Material Sample Ontology, https://purls.helmholtz-metadaten.de/cmso/
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
PERSON:Daniel Schober
definition source
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
A normal distribution probability density function has a formula of: f(x) = 1/(√(2 π) σ) e^-((x - μ)^2/(2 σ^2))
An annotation property that represents a mathematical formula.
mathematical formula
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.
Contributor
An entity responsible for making contributions to the resource.
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.
Creator
An entity primarily responsible for making the resource.
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.
Description
An account of the resource.
License
A legal document giving official permission to do something with the resource.
Title
A name given to the resource.
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.
The range of skos:altLabel is the class of RDF plain literals.
skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
alternative label
An alternative lexical label for a resource.
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).
example
An example of the use of a concept.
A general note, for any purpose.
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.
The range of skos:prefLabel is the class of RDF plain literals.
preferred label
The preferred lexical label for a resource, in a given language.
A data property linking a crystalline material and a crystallographic defect, such as vacancies, interstitials, or dislocations.
The relation between a simulation or unit cell and its angle.
The relation between a sample and a type of atom attribute, which refers to a per atom quantity of the atomic scale sample.
The relation between a unit cell and the basis of the crystal structure.
The relation between an atom and its chemical element.
The relation between a unit cell and its lattice parameters.
The relation between a simulation cell and its length.
The relation between a computational sample and the material it represents.
The relation between a plane and a vector normal to it.
The relation between an atomic scale sample and the simulation cell.
The relation between a simulation cell and its volume.
The relation between a crystal structure and the space group that describes the symmetry.
The relation between a computational sample and the species that constitutes it.
The relation between a material and its structure.
The relation between a crystal structure and its unit cell.
The relation between an entity and its vectors.
A data property linking an entity with alternative names.
A data property linking the angle to the measurement in the x axis.
A data property linking the angle to the measurement in the y axis.
A data property linking the angle to the measurement in the z axis.
A data property linking a chemical element with atomic percentage present in the material.
A data property linking the crystal structure and the corresponding Bravais lattice.
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).
A data property linking an element with its chemical symbol.
A data property linking a vector with its component on the x axis.
A data property linking a vector with its component on the y axis.
A data property linking a vector with its component on the z axis.
A data property linking an plane with the value of distance from its origin.
A data property linking a chemical element with the ratio or fraction of it in the material.
A data property linking an entity with an identifier (internal or external) that represents the entity.
A data property linking a length to the measurement in the x axis.
A data property linking a length to the measurement in the y axis.
A data property linking a length to the measurement in the z axis.
A data property linking an entity with its name.
A data property linking an atomic scale sample with the number of atoms it contains.
A data property linking an atom attribute (per atom quantity) with the path pointing to the file where the data is stored.
A data property linking an entity with a reference (e.g. bibliographic) to another resource.
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)
A data property linking a simulation cell with its number of repetitions in the x direction.
A data property linking a simulation cell with its number of repetitions in the y direction.
A data property linking a simulation cell with its number of repetitions in the z direction.
A data property linking a crystal structure with its space group number.
A data property linking a crystal structure with its space group symbol.
A data property linking an entity with its symbol.
A data property defining the parameter that indicates the specific direction(s) in which vacuum space is added in a simulation cell
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.
A data property linking an entity to its value.
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.
A data property linking a chemical element with percentage by mass present in the material.
Crystalline material is material characterized by a periodic arrangement of the constituent atoms. The arrangement could be described its crystal structure.
Lattice irregularity having one or more of its dimensions on the order of an atomic diameter.
Materials are substances in the condensed states (liquid, solid, colloidal) designed or manipulated for technological ends.
An amorphous material or solid is a material which has no defined long-range order.
An angle is a measure of the the space (usually in degrees) between two intersecting lines at the point where they meet or vertex.
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.
Atom attribute refers to the features or quantities per atom of an atomic scale sample.
Atomic force refers to the vector that represents the force of each atom.
Atomic position refers to the vector that represents the position of each atom.
Cartesian coordinates are preferred over direct (or fractional) coordinates.
Atomic scale sample is a computational sample in the atomic length scale.
Atomic velocity refers to the vector that represents the velocity of each atom.
The basis of a crystal indicates the arrangement or position of atoms in the crystal lattice.
Chemical composition refers to the type, arrangement and ratio of the chemical elements of a compound (or material).
A species of atoms; all atoms with the same number of protons in the atomic nucleus.
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.
In this context, it refers to either an atom, ion or molecule.
A computational sample is a representative system of a material for analysis through computational methods in the context of materials science.
Coordination number refers to the number of neighbors of each atom.
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.
A crystal defect is an imperfection or irregularity in the atomic arrangement of a crystalline solid.
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.
In this context, the crystal structure refers to the idealized state, while the defect information is represented elsewhere (see Crystal Defect).
The lattice angle refers to the angles between the crystallographic axes.
The lattice parameter is the measurement of length of the unit cell of the crystal lattice.
The lattice angles can also be considered lattice parameters (see Lattice Angle)
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.
A lattice vector is a vector that defines the lattice of the crystal structure.
Note that it differs from the simulation cell vector.
Macroscale sample is a computational sample in the macroscale.
In the CMSO context, 'Material' refers to a theoretical entity and not necessarily a tangible object.
Mesoscale sample is a computational sample in the mesoscale.
Microscale sample is a computational sample in the microscale.
The microstructure is the structure or arrangement of all components (atomic arrangement, defects, phases, etc.) of the material at the microscale.
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.
Nanoscale sample is a computational sample in the nanoscale.
The normal vector is a vector perpendicular to a given object.
Occupancy refers to the atom type at each lattice site.
Note the difference from a total ratio or percentage of the occupancy of a site in the crystal structure (as defined in CIF)
In mathematics, a plane is a two-dimensional space or flat surface that extends indefinitely.
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.
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.
The simulation cell angle refers to the angles of the simulation cell in each direction.
The simulation cell length refers to the length (dimension) of the simulation cell or box.
The simulation cell vector is a vector that defines the simulation cell or box.
Note that it differs from the lattice vector.
The simulation cell volume refers to the volume of the simulation cell or box.
The space group represents the symmetry properties of the crystal. In three-dimensions, space groups are classified in 230 distinct groups.
Structure is the the arrangement of particles or parts in a substance or body.
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 is a quantity that has a magnitude and direction.
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 \(Q = nU\).
A meaningful collection of concepts.
An idea or notion; a unit of thought.
A set of concepts, optionally including statements about semantic relationships between those concepts.
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.
An ordered collection of concepts, where both the grouping and the ordering are meaningful.
skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.
Relates a concept to a concept that is more general in meaning.
skos:broaderTransitive is a transitive superproperty of skos:broader.
A note about a modification to a concept.
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.
A note for an editor, translator or maintainer of the vocabulary.
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.
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.
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.
A note about the past state/use/meaning of a concept.
Relates a resource (for example a concept) to a concept scheme in which it is included.
Relates two concepts coming, by convention, from different schemes, and that have comparable meanings
Relates a collection to one of its members.
Relates an ordered collection to the RDF list containing its members.
skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.
Relates a concept to a concept that is more specific in meaning.
skos:narrowerTransitive is a transitive superproperty of skos:narrower.
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.
Relates a concept to a concept with which there is an associative semantic relationship.
skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes.
A note that helps to clarify the meaning and/or the use of a concept.
Links a concept to a concept related by meaning.
Relates a concept to the concept scheme that it is a top level concept of.