https://orcid.org/0000-0001-9560-4728 https://orcid.org/0000-0002-5149-603X https://orcid.org/0000-0002-6776-1213 https://orcid.org/0000-0003-0698-4891 https://orcid.org/0000-0001-7564-7990 CMSO is an ontology that aims to describe computational materials science samples (or structures), including crystalline defects. Computational Material Sample Ontology (CMSO) 0.0.1 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. 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). definition A statement or formal explanation of the meaning of a concept. 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. skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties. preferred label The preferred lexical label for a resource, in a given language. has angle The relation between a simulation or unit cell and its angle. has basis The relation between a unit cell and the basis of the crystal structure. has calculated property The relation between a computational sample and the calculated property. has defect The relation between a crystalline material and the crystal defects it contains. has element The relation between an atom and its chemical element. has lattice parameter The relation between a unit cell and its lattice parameters. has length The relation between a simulation cell and its length. has material The relation between a computational sample and the material it represents. has simulation cell The relation between an atomic scale sample and the simulation cell. has space group The relation between a crystal structure and the space group that describes the symmetry. has species The relation between a computational sample and the species that constitutes it. has structure The relation between a material and its structure. has unit A relation indicating the unit. has unit cell The relation between a crystal structure and its unit cell. has vector The relation between a simulation or unit cell and its vectors. is calculated property of is defect of is material of has alternative name A data property linking an entity with alternative names. has angle alpha A data property linking the angle to the measurement in the x axis. has angle beta A data property linking the angle to the measurement in the y axis. has angle gamma A data property linking the angle to the measurement in the z axis. abbreviated at.% has atomic percent A data property linking a chemical element with atomic percentage present in the material. has chemical symbol A data property linking an element with its chemical symbol. has component x A data property linking a vector with its component on the x axis. has component y A data property linking a vector with its component on the y axis. has component z A data property linking a vector with its component on the z axis. Indicated with a value from 0 to 1. has element ratio A data property linking a chemical element with the ratio or fraction of it in the material. has identifier A data property linking an entity with an identifier (internal or external) that represents the entity. has length x A data property linking a length to the measurement in the x axis. has length y A data property linking a length to the measurement in the y axis. has length z A data property linking a length to the measurement in the z axis. has name A data property linking an entity with its name. has number of atoms A data property linking an atomic scale sample with the number of atoms it contains. has path A data property linking an atom attribute (per atom quantity) with the path pointing to the file where the data is stored. has reference A data property linking an entity with a reference (e.g. bibliographic) to another resource. has repetition x A data property linking a simulation cell with its number of repetitions in the x direction. has repetition y A data property linking a simulation cell with its number of repetitions in the y direction. has repetition z A data property linking a simulation cell with its number of repetitions in the z direction. has space group number A data property linking a crystal structure with its space group number. has space group symbol A data property linking a crystal structure with its space group symbol. has symbol A data property linking an entity with its symbol. has value A data property linking a calculated property to its value. has volume 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. abbreviated wt.% has weight percent A data property linking a chemical element with percentage by mass present in the material. Amorphous Material Amorphous Solid Non-crystalline Solid An amorphous material or solid is a material which has no defined long-range order. Angle An angle is a measure of the the space (usually in degrees) between two intersecting lines at the point where they meet or vertex. Reference: https://goldbook.iupac.org/terms/view/A00493 Atom 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 Atom attribute refers to the features or quantities per atom of an atomic scale sample. Atomic Force Atomic force refers to the vector that represents the force of each atom. Cartesian coordinates are preferred over direct (or fractional) coordinates. Atomic Position Atomic position refers to the vector that represents the position of each atom. Atomic Scale Sample Atomic scale sample is a computational sample in the atomic length scale. Atomic Velocity Atomic velocity refers to the vector that represents the velocity of each atom. Basis The basis of a crystal indicates the arrangement or position of atoms in the crystal lattice. Calculated Property A calculated property is a property of a material resulting from a calculation or simulation. Chemical Composition Chemical composition refers to the type, arrangement and ratio of the chemical elements of a compound (or material). Reference: https://goldbook.iupac.org/terms/view/C01022 Chemical Element A species of atoms; all atoms with the same number of protons in the atomic nucleus. In this context, it refers to either an atom, ion or molecule. Reference: https://goldbook.iupac.org/terms/view/CT01038 Chemical Species 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. Computational Sample A computational sample is a representative system of a material for analysis through computational methods in the context of materials science. 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. Coordination Number Coordination number refers to the number of neighbors of each atom. Crystal Defect Crystallographic Defect A crystal defect is an imperfection or irregularity in the atomic arrangement of a crystalline solid. In this context, the crystal structure refers to the idealized state, while the defect information is represented elsewhere (see Crystal Defect). Crystal Structure 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. Crystalline Material Crystal Crystalline Solid A crystalline material or solid is a material in which atoms or molecules are arranged in a highly ordered and repeating pattern, forming a three-dimensional crystal lattice. Lattice Angle The lattice angle refers to the angles between the crystallographic axes. The lattice angles can also be considered lattice parameters (see Lattice Angles) Lattice Parameter Lattice Constant The lattice parameter is the measurement of length of the unit cell of the crystal lattice. Note that it differs from the simulation cell vector. Lattice Vector A lattice vector is a vector that defines the lattice of the crystal structure. Length Length is a measure of distance. Macroscale Sample Macro Scale Sample Macroscale sample is a computational sample in the macroscale. Reference: https://web.archive.org/web/20100801234616/http://www.nature.com/nmat/authors/index.html Material Materials are substances in the condensed states (liquid, solid, colloidal) designed or manipulated for technological ends. Mesoscale Sample Meso Scale Sample Mesoscale sample is a computational sample in the mesoscale. Microscale Sample Micro Scale Sample Microscale sample is a computational sample in the microscale. Microstructure The microstructure is the structure or arrangement of all components (atomic arrangement, defects, phases, etc.) of the material at the microscale. Reference: https://goldbook.iupac.org/terms/view/M04002 Molecule 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 Nanoscale sample is a computational sample in the nanoscale. Note the difference from a total ratio or percentage of the occupancy of a site in the crystal structure (as defined in CIF) Occupancy Occupancy refers to the atom type at each lattice site. Simulation Cell Box Supercell 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. Simulation Cell Angle The simulation cell angle refers to the angles of the simulation cell in each direction. Simulation Cell Length Box length The simulation cell length refers to the length (dimension) of the simulation cell or box. Note that it differs from the lattice vector. Simulation Cell Vector The simulation cell vector is a vector that defines the simulation cell or box. Space Group The space group represents the symmetry properties of the crystal. In three-dimensions, space groups are classified in 230 distinct groups. Reference: https://www.merriam-webster.com/dictionary/structure Structure Structure is the the arrangement of particles or parts in a substance or body. Unit Cell 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 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 \(Q = nU\). Unit 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.