Planar Defect Ontology (PLDO)
type: Ontology
version IRI: http://purls.helmholtz-metadaten.de/cdos/pldo/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: PLDO focuses on the description of planar defects in crystalline materials.
version info: 1.0.0
citation: Abril Azocar Guzman. (2025). Planar 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 grain boundary energy
type: ObjectProperty
domain: Computational Sample
domain: Grain Boundary
range: Grain Boundary Energy
definition: The relation between a grain boundary and the corresponding energy.

has stacking fault energy
type: ObjectProperty
domain: Computational Sample
domain: Stacking Fault
range: Stacking Fault Energy
definition: The relation between a stacking fault and the corresponding energy.

has surface energy
type: ObjectProperty
domain: Computational Sample
domain: Surface
range: Surface Energy
definition: The relation between a surface structure and the corresponding energy.

has tilt component
type: ObjectProperty
domain: Mixed Grain Boundary
range: Tilt Grain Boundary
definition: The relation between a mixed grain boundary and the tilt grain boundary component.

has twist component
type: ObjectProperty
domain: Mixed Grain Boundary
range: Twist Grain Boundary
definition: The relation between a mixed grain boundary and the twist grain boundary component.

geometrical degrees of freedom
type: DatatypeProperty
domain: Grain Boundary
definition: The geometrical degrees of freedom are the parameters that are necessary to characterize a grain boundary.

has displacement vector
type: DatatypeProperty
sub property of: has SF plane
domain: Stacking Fault
range: string
definition: A data property indicating the displacement vector associated with the stacking fault.

has GB plane
type: DatatypeProperty
sub property of: macroscopic degrees of freedom
domain: Grain Boundary
range: string
definition: A data property indicating the grain boundary (GB) plane using Miller indices.

has misorientation angle
type: DatatypeProperty
sub property of: macroscopic degrees of freedom
domain: Grain Boundary
range: float
definition: A data property indicating the misorientation angle (θ) of the grains with respect to each other.
definition source: https://doi.org/10.1016/j.actamat.2022.118006
comment: A disorientation angle can also be used to describe the grain boundary and is defined by the minimum misorientation angle when the misorientation axis is found in the standard stereographic triangle.

has rotation axis
type: DatatypeProperty
sub property of: macroscopic degrees of freedom
domain: Grain Boundary
range: string
definition: A data property indicating the rotation axis [uvw].

has SF plane
type: DatatypeProperty
domain: Stacking Fault
range: string
definition: A data property indicating the stacking fault (SF) plane using Miller indices.
comment: The SF plane defines the crystallographic plane along which a stacking fault occurs, disrupting the ideal stacking sequence of the crystal structure.

has sigma value
type: DatatypeProperty
domain: Grain Boundary
range: integer
definition: A data property linking a GB with its sigma value.
comment: Sigma value of a GB is the coincidence index, calculated as the ratio of the coincidence unit cell volume by the crystal primitive unit cell volume. The coincidence index refers to the Coincidence Site Lattice (CSL).

has stacking sequence
type: DatatypeProperty
domain: Stacking Fault
range: string
definition: A data property indicating the stacking sequence in a crystal structure. For the ideal hcp structure, this sequence is •••ABABAB••• and for fcc •••ABCABC•••.

macroscopic degrees of freedom
type: DatatypeProperty
sub property of: geometrical degrees of freedom
domain: Grain Boundary
definition: There are five macroscopic degrees of freedom (DOFs) that are sufficient to describe the thermodynamic description of the grain boundary.
comment: In simulations of grain boundaries, the macroscopic DOFs are imposed on the structure.

microscopic degrees of freedom
type: DatatypeProperty
sub property of: geometrical degrees of freedom
domain: Grain Boundary
definition: The microscopic degrees of freedom (DOFs) refer to the translation of one crystal with respect to the other at the microscopic scale. The microscopic parameters result from the relaxation process and are not independent of the macroscopic parameters.
comment: In simulations of grain boundaries, the microscopic DOFs are obtained after the grain boundary energy minimization.

Antiphase Boundary
type: Class
subclass of: Planar Defect
definition: An antiphase boundary is a planar defect that occurs in ordered alloys. The boundary separates two domains of the same ordered phase.
alternative label: APB

Calculated Property
type: Class
definition: A calculated property is a property of a material resulting from a calculation or simulation.

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.

Energy
type: Class
subclass of: PhysicalQuantity
definition: Energy is a physical quantity characterizing the ability of a system to do work.
definition source: https://doi.org/10.1351/goldbook.E02101
alternative label: E

Extrinsic Stacking Fault
type: Class
subclass of: Stacking Fault
definition: An extrinsic stacking fault is a stacking fault produced by the change in sequence resulting from the introduction of an extra layer.

Extrinsic Stacking Fault Energy
type: Class
subclass of: Stacking Fault Energy

Gamma-Surface
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: The gamma-surface is the excess interlayer energy, γ, as a function of an imposed rigid-body translation, t, parallel to the interface.
definition source: https://doi.org/10.1080/14786436808227500

Generalized Stacking Fault Energy
type: Class
subclass of: Stacking Fault Energy
definition: The generalized stacking fault (GSF) energy is a measure of the energy penalty between two adjacent planes during shear deformation in a specific slip direction on a given slip plane, representing the nature of slip and involving the stable and unstable stacking and twin fault energies.
definition source: https://doi.org/10.1016/j.actamat.2013.12.019

Grain Boundary
type: Class
subclass of: Planar Defect
definition: A grain boundary is a planar defect that separates two crystals (or grains) of the same material.
alternative label: GB

Grain Boundary Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: Grain boundary energy is the excess energy due to the presence of a grain boundary, with the perfect lattice (bulk) as the reference.
comment: Usually expressed in units of energy per area.

I1 Stacking Fault Energy
type: Class
subclass of: Stacking Fault Energy
definition: The I1 stacking fault, or growth fault, is a type of intrinsic stacking fault in hcp systems due to the removal of a plane above the B plane, and then shearing of the remaining planes above the B plane by the displacement 1/3[-1-100].
definition source: https://doi.org/10.1103/PhysRevB.56.10844

I2 Stacking Fault Energy
type: Class
subclass of: Stacking Fault Energy
definition: The I2 stacking fault, or deformation fault, is a type of intrinsic stacking fault in hcp systems due to directly shearing the hcp lattice by the displacement 1/3[-1-100].
definition source: https://doi.org/10.1103/PhysRevB.56.10844

Intrinsic Stacking Fault
type: Class
subclass of: Stacking Fault
definition: An intrinsic stacking fault is a stacking fault produced by the change in sequence resulting from the removal of an extra layer.

Low Angle Grain Boundary
type: Class
subclass of: Grain Boundary
definition: A low angle grain boundary is a grain boundary with a misorientation angle lower than 15 degrees.
definition source: ISBN 978-94-007-4968-9
alternative label: Low-Angle Grain Boundary

Mixed Grain Boundary
type: Class
subclass of: Grain Boundary
definition: A mixed grain boundary is a grain boundary where the [uvw] rotation axis has perpendicular and parallel components with respect to the boundary plane.
definition source: ISBN 978-94-007-4968-9

Planar Defect
type: Class
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

Stacking Fault
type: Class
subclass of: Planar Defect
definition: A stacking fault is a planar defect created by an error (fault) in the order of the sequential layering of crystallographic planes.

Stacking Fault Energy
type: Class
subclass of: Calculated Property
subclass of: Energy
definition: Stacking fault energy is the excess energy due to the presence of a stacking fault, with the perfect lattice (bulk) as the reference.
comment: Usually expressed in units of energy per area.

Surface
type: Class
subclass of: Planar Defect
definition: The free surface (or external surface) of the material is a planar defect where the surface atoms have no neighbors or cohesive bonds on the external side.

Surface Energy
type: Class
subclass of: Calculated Property
subclass of: Energy

Symmetrical Tilt Grain Boundary
type: Class
subclass of: Tilt Grain Boundary
definition: A symmetrical tilt grain boundary is a tilt grain boundary where the two grains are symmetric. The boundary plane has the same Miller indices in crystals I and II: {hkl}_1 = {hkl}_2.
definition source: ISBN 978-94-007-4968-9

Tilt Grain Boundary
type: Class
subclass of: Grain Boundary
definition: A tilt boundary is a grain boundary with a [uvw] rotation axis perpendicular to the boundary plane.
definition source: ISBN 978-94-007-4968-9
alternative label: Tilt Boundary

Twin-like Stacking Fault
type: Class
subclass of: Stacking Fault
definition: A twin-like stacking fault is a type of stacking fault that possesses mirror symmetry about the fault plane.

Twin Boundary
type: Class
subclass of: Planar Defect
definition: A twin boundary is a planar defect that occurs between two separate crystals which are mirror images of each other. Both crystals have the same crystal structure.

Twist Grain Boundary
type: Class
subclass of: Grain Boundary
definition: A twist boundary is a grain boundary with a [uvw] rotation axis contained within the boundary plane.
definition source: ISBN 978-94-007-4968-9
alternative label: Twist Boundary

Work of Separation
type: Class
subclass of: Calculated Property
subclass of: Energy

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.