cdco/cdco.owl

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purls.helmholtz-metadaten.de/cdos/cdco#"
     xml:base="http://purls.helmholtz-metadaten.de/cdos/cdco"
     xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:obo="http://purl.obolibrary.org/obo/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:skos="http://www.w3.org/2004/02/skos/core#"
     xmlns:terms="http://purl.org/dc/terms/"
     xmlns:schema="https://schema.org/">
    <owl:Ontology rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco">
        <owl:versionIRI rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/1.0.0"/>
        <terms:creator rdf:resource="https://orcid.org/0000-0001-7564-7990"/>
        <terms:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</terms:description>
        <terms:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Crystallographic Defect Core Ontology (CDCO)</terms:title>
        <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/OCDO/cdco</rdfs:seeAlso>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.0.0</owl:versionInfo>
        <schema:citation rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Abril Azocar Guzman. (2025). Crystallographic Defect Core Ontology. http://purls.helmholtz-metadaten.de/cdos/cdco</schema:citation>
        <schema:creativeWorkStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pre-release</schema:creativeWorkStatus>
        <schema:funder rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://ror.org/05qj6w324</schema:funder>
        <schema:logo rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://raw.githubusercontent.com/OCDO/.github/refs/heads/main/profile/ocdo_logo.png</schema:logo>
    </owl:Ontology>
    


    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Annotation properties
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->

    


    <!-- http://purl.obolibrary.org/obo/IAO_0000111 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
    


    <!-- http://purl.obolibrary.org/obo/IAO_0000114 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
    


    <!-- http://purl.obolibrary.org/obo/IAO_0000115 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
        <obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
        <obo:IAO_0000115 xml:lang="en">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
        <obo:IAO_0000116 xml:lang="en">2012-04-05: 
Barry Smith

The official OBI definition, explaining the meaning of a class or property: &apos;Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions&apos;  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&apos;t be evaluated by those criteria. 

On the specifics of the proposed definition:

We don&apos;t have definitions of &apos;meaning&apos; or &apos;expression&apos; or &apos;property&apos;. For &apos;reference&apos; in the intended sense I think we use the term &apos;denotation&apos;. For &apos;expression&apos;, I think we you mean symbol, or identifier. For &apos;meaning&apos; it differs for class and property. For class we want documentation that let&apos;s the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let&apos;s the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The &apos;intended reader&apos; 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.  </obo:IAO_0000116>
        <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
        <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
        <rdfs:label xml:lang="en">definition</rdfs:label>
    </owl:AnnotationProperty>
    


    <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
    


    <!-- http://purl.obolibrary.org/obo/IAO_0000117 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
    


    <!-- http://purl.obolibrary.org/obo/IAO_0000119 -->

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
        <obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
        <obo:IAO_0000115 xml:lang="en">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</obo:IAO_0000115>
        <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
        <obo:IAO_0000119 xml:lang="en">Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
        <obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
        <rdfs:label xml:lang="en">definition source</rdfs:label>
    </owl:AnnotationProperty>
    


    <!-- http://purl.org/dc/elements/1.1/contributor -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
    


    <!-- http://purl.org/dc/elements/1.1/creator -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>
    


    <!-- http://purl.org/dc/elements/1.1/description -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
    


    <!-- http://purl.org/dc/elements/1.1/title -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
    


    <!-- http://purl.org/dc/terms/contributor -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/contributor">
        <rdfs:comment xml:lang="en-us">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.</rdfs:comment>
        <rdfs:label xml:lang="en-us">Contributor</rdfs:label>
        <skos:definition xml:lang="en-us">An entity responsible for making contributions to the resource.</skos:definition>
        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/contributor"/>
    </owl:AnnotationProperty>
    


    <!-- http://purl.org/dc/terms/creator -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator">
        <rdfs:comment xml:lang="en-us">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.</rdfs:comment>
        <rdfs:label xml:lang="en-us">Creator</rdfs:label>
        <skos:definition xml:lang="en-us">An entity primarily responsible for making the resource.</skos:definition>
        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/creator"/>
        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/contributor"/>
        <rdfs:range rdf:resource="http://purl.org/dc/terms/Agent"/>
    </owl:AnnotationProperty>
    


    <!-- http://purl.org/dc/terms/description -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description">
        <rdfs:comment xml:lang="en-us">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.</rdfs:comment>
        <rdfs:label xml:lang="en-us">Description</rdfs:label>
        <skos:definition xml:lang="en-us">An account of the resource.</skos:definition>
        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/description"/>
    </owl:AnnotationProperty>
    


    <!-- http://purl.org/dc/terms/title -->

    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title">
        <rdfs:label xml:lang="en-us">Title</rdfs:label>
        <skos:definition xml:lang="en-us">A name given to the resource.</skos:definition>
        <skos:note xml:lang="en-us">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.</skos:note>
        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/title"/>
    </owl:AnnotationProperty>
    


    <!-- http://www.w3.org/2004/02/skos/core#altLabel -->

    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel">
        <rdfs:comment xml:lang="en">The range of skos:altLabel is the class of RDF plain literals.</rdfs:comment>
        <rdfs:comment xml:lang="en">skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.</rdfs:comment>
        <rdfs:isDefinedBy rdf:resource="http://www.w3.org/2004/02/skos/core"/>
        <rdfs:label xml:lang="en">alternative label</rdfs:label>
        <skos:definition xml:lang="en">An alternative lexical label for a resource.</skos:definition>
        <skos:example xml:lang="en">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).</skos:example>
        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
    </owl:AnnotationProperty>
    


    <!-- http://www.w3.org/2004/02/skos/core#definition -->

    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition">
        <rdfs:isDefinedBy rdf:resource="http://www.w3.org/2004/02/skos/core"/>
        <rdfs:label xml:lang="en">definition</rdfs:label>
        <skos:definition xml:lang="en">A statement or formal explanation of the meaning of a concept.</skos:definition>
        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#note"/>
    </owl:AnnotationProperty>
    


    <!-- http://www.w3.org/2004/02/skos/core#example -->

    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#example">
        <rdfs:isDefinedBy rdf:resource="http://www.w3.org/2004/02/skos/core"/>
        <rdfs:label xml:lang="en">example</rdfs:label>
        <skos:definition xml:lang="en">An example of the use of a concept.</skos:definition>
        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2004/02/skos/core#note"/>
    </owl:AnnotationProperty>
    


    <!-- http://www.w3.org/2004/02/skos/core#note -->

    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#note">
        <skos:definition xml:lang="en">A general note, for any purpose.</skos:definition>
    </owl:AnnotationProperty>
    


    <!-- http://www.w3.org/2004/02/skos/core#prefLabel -->

    <owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel">
        <rdfs:comment xml:lang="en">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.</rdfs:comment>
        <rdfs:comment xml:lang="en">The range of skos:prefLabel is the class of RDF plain literals.</rdfs:comment>
        <rdfs:comment xml:lang="en">skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise
      disjoint properties.</rdfs:comment>
        <rdfs:isDefinedBy rdf:resource="http://www.w3.org/2004/02/skos/core"/>
        <rdfs:label xml:lang="en">preferred label</rdfs:label>
        <skos:definition xml:lang="en">The preferred lexical label for a resource, in a given language.</skos:definition>
        <rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
    </owl:AnnotationProperty>
    


    <!-- https://schema.org/citation -->

    <owl:AnnotationProperty rdf:about="https://schema.org/citation"/>
    


    <!-- https://schema.org/creativeWorkStatus -->

    <owl:AnnotationProperty rdf:about="https://schema.org/creativeWorkStatus"/>
    


    <!-- https://schema.org/funder -->

    <owl:AnnotationProperty rdf:about="https://schema.org/funder"/>
    


    <!-- https://schema.org/logo -->

    <owl:AnnotationProperty rdf:about="https://schema.org/logo"/>
    


    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Object Properties
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->

    


    <!-- http://purls.helmholtz-metadaten.de/cdos/cdco/hasCrystallographicDefect -->

    <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco/hasCrystallographicDefect">
        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial"/>
        <rdfs:range rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect"/>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data property linking a crystalline material and a crystallographic defect, such as vacancies, interstitials, or dislocations.</obo:IAO_0000115>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has crystallographic defect</rdfs:label>
    </owl:ObjectProperty>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/cdco/hasDefectComplex -->

    <owl:ObjectProperty rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco/hasDefectComplex">
        <rdfs:domain rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial"/>
        <rdfs:range rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/DefectComplex"/>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A data property linking a crystalline material to a specific defect complex, which consists of two or more interacting defects.</obo:IAO_0000115>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has defect complex</rdfs:label>
    </owl:ObjectProperty>
    


    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Classes
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->

    


    <!-- http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial">
        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/Material"/>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Crystalline material is material characterized by a periodic arrangement of the constituent atoms. The arrangement could be described its crystal structure.</obo:IAO_0000115>
        <rdfs:label>Crystalline Material</rdfs:label>
    </owl:Class>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect">
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Lattice irregularity having one or more of its dimensions on the order of an atomic diameter.</obo:IAO_0000115>
        <rdfs:label>Crystallographic Defect</rdfs:label>
    </owl:Class>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/cdco/DefectComplex -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco/DefectComplex">
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</obo:IAO_0000115>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Defect Complex</rdfs:label>
        <skos:altLabel rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Defect Cluster</skos:altLabel>
    </owl:Class>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/cdco/Material -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/cdco/Material">
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Materials are substances in the condensed states (liquid, solid, colloidal) designed or manipulated for technological ends.</obo:IAO_0000115>
        <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://web.archive.org/web/20100801234616/http://www.nature.com/nmat/authors/index.html</obo:IAO_0000119>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Material</rdfs:label>
    </owl:Class>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/ldo/LineDefect -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/ldo/LineDefect">
        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect"/>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Linear or one-dimensional defect around which some of the atoms are misaligned.</obo:IAO_0000115>
        <rdfs:label>Line Defect</rdfs:label>
    </owl:Class>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/pldo/PlanarDefect -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/pldo/PlanarDefect">
        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect"/>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</obo:IAO_0000115>
        <rdfs:label>Planar Defect</rdfs:label>
        <skos:altLabel>Interface</skos:altLabel>
    </owl:Class>
    


    <!-- http://purls.helmholtz-metadaten.de/cdos/podo/PointDefect -->

    <owl:Class rdf:about="http://purls.helmholtz-metadaten.de/cdos/podo/PointDefect">
        <rdfs:subClassOf rdf:resource="http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect"/>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</obo:IAO_0000115>
        <rdfs:label>Point Defect</rdfs:label>
    </owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->