Point Defects Ontology (PODO)
type: Ontology
version IRI: http://purls.helmholtz-metadaten.de/cdos/podo/1.0.0
Contributor: https://orcid.org/0000-0001-9560-4728
Contributor: https://orcid.org/0000-0002-6776-1213
creator: https://orcid.org/0000-0001-7564-7990
description: PODO focuses on the description of point defects in crystalline materials.
version info: 1.0.0
citation: Abril Azocar Guzman. (2025). Line Defect Ontology.
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
range: Agent

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

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 impurity concentration
type: DatatypeProperty
domain: Material
domain: Computational Sample
range: float
definition: A data property indicating the impurity concentration.
comment: The domain of this property should correspond to a material sample (either computational or experimental).

has number of impurity atoms
type: DatatypeProperty
domain: Material
domain: Computational Sample
range: integer
definition: A data property indicating the total number of impurity atoms in the crystal structure.
comment: The domain of this property should correspond to a material sample (either computational or experimental).

has number of vacancies
type: DatatypeProperty
domain: Material
domain: Computational Sample
range: integer
definition: A data property indicating the total number of vacancies in the crystal structure.
comment: The domain of this property should correspond to a material sample (either computational or experimental).

has vacancy concentration
type: DatatypeProperty
domain: Material
domain: Computational Sample
range: float
definition: A data property indicating the vacancy concentration.
comment: Note that the vacancy concentration is given as a fraction, with a value from 0 to 1.
comment: The domain of this property should correspond to a material sample (either computational or experimental).

occupies interstitial site
type: DatatypeProperty
domain: Interstitial
range: string

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

Antisite Defect
type: Class
subclass of: Point Defect
definition: Antisite Defect is a point defect which occurs in ordered alloys or compounds when two atoms of different type switch positions.
definition source: ISBN 978-1-119-45416-8

Frenkel Defect
type: Class
subclass of: Point Defect
definition: A Frenkel defect is a point defect which occurs in ionic crystals when an ion is removed to an interstitial position, leaving a vacancy behind.
definition source: ISBN 978-1-119-45416-8
alternative label: Frenkel Pair

Impurity
type: Class
subclass of: Point Defect
definition: An impurity is a point defect where foreign atoms (of different type as the host atom) enter the crystal lattice.

Interstitial
type: Class
subclass of: Point Defect
definition: An interstitial is a point defect where an atom occupies an interstitial site. In crystallography, interstitial sites are the empty space between the atoms (assuming a hard-sphere model).

Interstitial Impurity
type: Class
subclass of: Impurity
subclass of: Interstitial
definition: A interstitial impurity is a point defect where the atom occupying the interstitial site is of a different type as the matrix.

Point Defect
type: Class
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.

Schottky Defect
type: Class
subclass of: Point Defect
definition: A Schottky defect is a point defect which occurs in ionic crystals when oppositely charged ions create a vacancy in the interior of the lattice and go to the surface.

Self-interstitial
type: Class
subclass of: Interstitial
definition: A self-interstitial is an insterstitial defect where the atom occupying the interstitial site is of the same type as the matrix.

Substitutional Impurity
type: Class
subclass of: Impurity
definition: A substitutional impurity is an impurity where an atom of different type replaces a host or matrix atom.

Vacancy
type: Class
subclass of: Point Defect
definition: A vacancy is a point defect in which an atom is missing from its original lattice site.

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.

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.