Crystallographic Defect Core Ontology (CDCO)
type: Ontology
version IRI: http://purls.helmholtz-metadaten.de/cdos/cdco/1.0.0
creator: https://orcid.org/0000-0001-7564-7990
description: Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.
version info: 1.0.0
citation: Abril Azocar Guzman. (2025). Crystallographic Defect Core Ontology. http://purls.helmholtz-metadaten.de/cdos/cdco
creative work status: Pre-release
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>

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

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

definition
type: AnnotationProperty
definition: A statement or formal explanation of the meaning of a concept.
sub property of: note

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 defect complex
type: ObjectProperty
domain: Crystalline Material
range: Defect Complex
definition: A data property linking a crystalline material to a specific defect complex, which consists of two or more interacting defects.

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.

Defect Complex
type: Class
definition: A combination of two or more defects in close proximity that interact with each other, such as a vacancy-impurity pair or a grain boundary-impurity pair, often affecting the material’s properties.
alternative label: Defect Cluster

Material
type: Class
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

Line Defect
type: Class
subclass of: Crystallographic Defect
definition: Linear or one-dimensional defect around which some of the atoms are misaligned.

Planar Defect
type: Class
subclass of: Crystallographic Defect
definition: A planar defect is a defect of the crystal structure across a plane. It is considered to be a two-dimensional defect, such as an internal interface or the surface.
alternative label: Interface

Point Defect
type: Class
subclass of: Crystallographic Defect
definition: A point defect is a crystalline defect which is localized at or around a single lattice point. It is considered to be a zero-dimensional defect because it does not extend in any dimension in the lattice.