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‎.gitignore‎

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*.DS_Store
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*.properties
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.vscode*
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*.ipynb

‎CDO/README.md‎

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### Crystallographic Defect Ontology
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Crystallographic Defect Ontology (CDO) is an ontology connecting the physical materials entity to the crystal structure and several defectsin crystalline materials, e.g., point defect, dislocation, and grain boundary. In CDO, the `EMMO:Material` class isreused to describe the physical entity of crystalline materials. The `CDO:CrystallineMaterialclass` is subsequently a subclass `ofEMMO:Material`.
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![CDO-classes](https://user-images.githubusercontent.com/71790028/164012431-a0d3db3c-488b-481c-887b-75f0b44f1659.png)

‎CDO/catalog-v001.xml‎

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
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<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
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<uri id="Automatically generated entry, Timestamp=1653487688618" name="https://purls.helmholtz-metadaten.de/cdo" uri="crystallographic-defect-ontology.owl"/>
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</group>
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</catalog>

‎CDO/crystallographic-defect-ontology.owl‎

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<?xml version="1.0"?>
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<rdf:RDF xmlns="https://purls.helmholtz-metadaten.de/cdo"
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xml:base="https://purls.helmholtz-metadaten.de/cdo"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:xml="http://www.w3.org/XML/1998/namespace"
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xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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xmlns:qudt="http://qudt.org/schema/qudt/"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
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xmlns:skos="http://www.w3.org/2004/02/skos/core#"
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xmlns:vann="http://purl.org/vocab/vann/"
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xmlns:terms="http://purl.org/dc/terms/">
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<owl:Ontology rdf:about="https://purls.helmholtz-metadaten.de/cdo">
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<owl:imports rdf:resource="https://purls.helmholtz-metadaten.de/cso"/>
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<owl:imports rdf:resource="https://purls.helmholtz-metadaten.de/diso"/>
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<terms:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Said Fathalla</terms:contributor>
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<terms:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Stefan Sandfeld</terms:contributor>
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<terms:created xml:lang="en">21.03.2022</terms:created>
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<terms:creator xml:lang="en">Ahmad Zainul Ihsan</terms:creator>
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<terms:license rdf:resource="http://creativecommons.org/licenses/by/3.0/"/>
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<terms:title xml:lang="en">Crystallographic Defect Ontology</terms:title>
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<vann:preferredNamespacePrefix rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CDO</vann:preferredNamespacePrefix>
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<rdfs:seeAlso>https://github.com/Materials-Data-Science-and-Informatics/dislocation-ontology</rdfs:seeAlso>
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</owl:Ontology>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Annotation properties
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<!-- http://purl.org/dc/terms/contributor -->
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<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/contributor"/>
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<!-- http://purl.org/dc/terms/created -->
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<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/created"/>
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<!-- http://purl.org/dc/terms/creator -->
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<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/creator"/>
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<!-- http://purl.org/dc/terms/title -->
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<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>
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<!-- http://purl.org/vocab/vann/preferredNamespacePrefix -->
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<owl:AnnotationProperty rdf:about="http://purl.org/vocab/vann/preferredNamespacePrefix"/>
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<!-- http://www.w3.org/2002/07/owl#qualifiedCardinality -->
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<owl:AnnotationProperty rdf:about="http://www.w3.org/2002/07/owl#qualifiedCardinality"/>
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<!-- http://www.w3.org/2004/02/skos/core#prefLabel -->
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<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#prefLabel">
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<rdfs:subPropertyOf rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
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</owl:AnnotationProperty>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Object Properties
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<!-- https://purls.helmholtz-metadaten.de/cdo#hasCrystalStructure -->
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<owl:ObjectProperty rdf:about="https://purls.helmholtz-metadaten.de/cdo#hasCrystalStructure">
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<rdfs:domain rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallineMaterial"/>
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<rdfs:range rdf:resource="https://purls.helmholtz-metadaten.de/cso#CrystalStructure"/>
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<rdfs:label xml:lang="en">has crystal structure</rdfs:label>
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</owl:ObjectProperty>
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<!-- https://purls.helmholtz-metadaten.de/cdo#hasCrystallographicDefect -->
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<owl:ObjectProperty rdf:about="https://purls.helmholtz-metadaten.de/cdo#hasCrystallographicDefect">
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<rdfs:domain rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallineMaterial"/>
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<rdfs:range rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect"/>
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<rdfs:label xml:lang="en">has crystallographic defect</rdfs:label>
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</owl:ObjectProperty>
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<!--
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///////////////////////////////////////////////////////////////////////////////////////
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//
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// Classes
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//
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///////////////////////////////////////////////////////////////////////////////////////
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-->
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<!-- http://emmo.info/emmo/middle/physicalistic#EMMO_4207e895_8b83_4318_996a_72cfb32acd94 -->
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<owl:Class rdf:about="http://emmo.info/emmo/middle/physicalistic#EMMO_4207e895_8b83_4318_996a_72cfb32acd94">
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<rdfs:comment xml:lang="en">A instance of a material (e.g. nitrogen) can represent different states of matter. The fact that the individual also belongs to other classes (e.g. Gas) would reveal the actual form in which the material is found.</rdfs:comment>
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<rdfs:comment xml:lang="en">Material usually means some definite kind, quality, or quantity of matter, especially as intended for use.</rdfs:comment>
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<skos:prefLabel xml:lang="en">Material</skos:prefLabel>
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</owl:Class>
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<!-- https://purls.helmholtz-metadaten.de/cdo#CrystallineMaterial -->
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<owl:Class rdf:about="https://purls.helmholtz-metadaten.de/cdo#CrystallineMaterial">
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<rdfs:subClassOf rdf:resource="http://emmo.info/emmo/middle/physicalistic#EMMO_4207e895_8b83_4318_996a_72cfb32acd94"/>
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<rdfs:subClassOf>
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<owl:Class>
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<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
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<owl:onProperty rdf:resource="https://purls.helmholtz-metadaten.de/cdo#hasCrystalStructure"/>
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<owl:someValuesFrom rdf:resource="https://purls.helmholtz-metadaten.de/cso#CrystalStructure"/>
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</owl:Restriction>
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<owl:Restriction>
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<owl:onProperty rdf:resource="https://purls.helmholtz-metadaten.de/cdo#hasCrystalStructure"/>
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<owl:allValuesFrom rdf:resource="https://purls.helmholtz-metadaten.de/cso#CrystalStructure"/>
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</owl:Restriction>
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</owl:intersectionOf>
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</owl:Class>
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</rdfs:subClassOf>
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<rdfs:subClassOf>
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<owl:Class>
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<owl:intersectionOf rdf:parseType="Collection">
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<owl:Restriction>
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<owl:onProperty rdf:resource="https://purls.helmholtz-metadaten.de/cdo#hasCrystallographicDefect"/>
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<owl:someValuesFrom rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect"/>
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</owl:Restriction>
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<owl:Restriction>
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<owl:onProperty rdf:resource="https://purls.helmholtz-metadaten.de/cdo#hasCrystallographicDefect"/>
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<owl:allValuesFrom rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect"/>
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</owl:Restriction>
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</owl:intersectionOf>
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</owl:Class>
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</rdfs:subClassOf>
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<rdfs:comment xml:lang="en">Crystalline material is material characterized by a periodic arrangement of the constituent atoms. The arrangement could be described its crystal structure.</rdfs:comment>
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<rdfs:label xml:lang="en">Crystalline Material</rdfs:label>
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</owl:Class>
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<!-- https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect -->
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<owl:Class rdf:about="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect">
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<rdfs:comment xml:lang="en">Lattice irregularity having one or more of its dimensions on the order of an atomic diameter.</rdfs:comment>
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<rdfs:label xml:lang="en">Crystallographic Defect</rdfs:label>
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</owl:Class>
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<!-- https://purls.helmholtz-metadaten.de/cdo#GrainBoundary -->
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<owl:Class rdf:about="https://purls.helmholtz-metadaten.de/cdo#GrainBoundary">
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<rdfs:subClassOf rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect"/>
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</owl:Class>
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<!-- https://purls.helmholtz-metadaten.de/cdo#PointDefect -->
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<owl:Class rdf:about="https://purls.helmholtz-metadaten.de/cdo#PointDefect">
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<rdfs:subClassOf rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect"/>
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</owl:Class>
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<!-- https://purls.helmholtz-metadaten.de/cso#CrystalStructure -->
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<owl:Class rdf:about="https://purls.helmholtz-metadaten.de/cso#CrystalStructure"/>
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<!-- https://purls.helmholtz-metadaten.de/diso#Dislocation -->
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<owl:Class rdf:about="https://purls.helmholtz-metadaten.de/diso#Dislocation">
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<rdfs:subClassOf rdf:resource="https://purls.helmholtz-metadaten.de/cdo#CrystallographicDefect"/>
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</owl:Class>
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<rdf:Description>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
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</rdf:Description>
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<rdf:Description>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
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</rdf:Description>
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<rdf:Description>
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<owl:qualifiedCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:qualifiedCardinality>
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</rdf:Description>
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</rdf:RDF>
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<!-- Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi -->
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‎CSO/CQs.md‎

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## Competence Questions(CQs)
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1. Which crystal structure share the same crystal system(e.g. Cubic, hexagonal, etc)?
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2. What are the lattice parameters of length given a crystal structure?
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3. What are the lattice parameters of angle given a crystal structure?
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4. Given the space group of a crystal structure, what is the bravais lattice centering?
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5. Given the crystal structure, what are the corresponding space group and point group?
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6. Given the point group of a crystal structure, what is the corresponding crystal system?
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## Answer to CQs via SPARQL
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CQ1.1: Which crystal structure share the same cubic crystal system?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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SELECT ?crystalstructure ?crystal_system WHERE{
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?crystalstructure a cso:CrystalStructure ; cso:hasLattice ?lattice .
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?lattice cso:hasCrystalSystem ?crystal_system.
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?crystal_system a cso:Cubic .
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}
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```
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CQ1.2: Which crystal structure share the same hexagonal crystal system?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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SELECT ?crystalstructure ?crystal_system WHERE{
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?crystalstructure a cso:CrystalStructure ; cso:hasLattice ?lattice .
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?lattice cso:hasCrystalSystem ?crystal_system.
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?crystal_system a cso:Hexagonal .
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}
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```
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CQs. 2: What are the lattice parameters of length given a crystal structure?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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SELECT ?crystalstructure ?length_a ?length_b ?length_c WHERE{
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?crystalstructure a cso:CrystalStructure ; cso:hasLattice ?lattice .
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?lattice cso:hasUnitCell ?unitcell .
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?unitcell cso:hasLatticeParameterLength ?latticeParameterLength.
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?latticeParameterLength cso:latticeParameterLengthA ?length_a;
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cso:latticeParameterLengthB ?length_b;
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cso:latticeParameterLengthC ?length_c.
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}
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```
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CQs. 3: What are the lattice parameters of angle given a crystal structure?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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SELECT ?crystalstructure ?angle_alpha ?angle_beta ?angle_gamma WHERE{
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?crystalstructure a cso:CrystalStructure ; cso:hasLattice ?lattice .
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?lattice cso:hasUnitCell ?unitcell .
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?unitcell cso:hasLatticeParameterAngle ?latticeParameterAngle.
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?latticeParameterAngle cso:latticeParameterAngleAlpha ?angle_alpha;
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cso:latticeParameterAngleBeta ?angle_beta;
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cso:latticeParameterAngleGamma ?angle_gamma.
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}
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```
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CQs 4: Given the space group of a crystal structure, what is the bravais lattice centering?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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SELECT ?crystal_structure ?centering WHERE{
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?crystal_structure a cso:CrystalStructure;
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cso:hasLattice ?bravais_lattice .
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?bravais_lattice cso:centering ?centering .
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}
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```
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CQs 5: Given the crystal structure, what are the corresponding space group and point group?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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PREFIX mdo: <https://w3id.org/mdo/structure/>
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SELECT ?crystal_structure ?space_group ?point_group WHERE{
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?crystal_structure a cso:CrystalStructure;
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mdo:hasSpaceGroup ?sg.
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?sg mdo:hasPointGroup ?pg ;
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mdo:SpaceGroupSymbol ?space_group .
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?pg mdo:PointGroupHMName ?point_group .
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}
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```
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CQs 6a : Given the point group of a crystal structure, what is the corresponding crystal system, e.g. Cubic?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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PREFIX mdo: <https://w3id.org/mdo/structure/>
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SELECT ?point_group ?crystal_system WHERE{
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?pg a mdo:PointGroup;
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mdo:PointGroupHMName ?point_group ;
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cso:isPointGroupOf ?crystal_system.
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?crystal_system rdf:type cso:Cubic.
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}
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```
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CQs 6b : Given the point group of a crystal structure, what is the corresponding crystal system, e.g. Hexagonal?
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```
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PREFIX cso: <https://purls.helmholtz-metadaten.de/cso#>
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PREFIX mdo: <https://w3id.org/mdo/structure/>
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SELECT ?point_group ?crystal_system WHERE{
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?pg a mdo:PointGroup;
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mdo:PointGroupHMName ?point_group ;
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cso:isPointGroupOf ?crystal_system.
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?crystal_system rdf:type cso:Hexagonal.
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}
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```

‎CSO/README.md‎

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### Crystal Structure Ontology
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Crystal Structure Ontology (CSO) is an ontology developed to represent crystallographic information needed to describe the dislocation. In CSO, several MDO classes are reused to describe the crystal coordinate system, motif/base in a crystal structure, point groups, and space groups.
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The standard coordinate system is defined by `MDO:Basis` and `MDO:CoordinateVector` classes that CSO reuses.
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The motif/base is an arrangement of chemical species in the crystal structure reuses `MDO:Occupancy`, `MDO:Site`, and `MDO:Species`.
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Subsequently, to define the point groups and space groups of a crystal structure, `MDO:PointGroup` and `MDO:SpaceGroup` are reused. Lastly, to define the unit quantity of a property in CSO, the `QUDT:Quantity`, `QUDT:QuantityKind`, and `QUDT:QuantityValue` classes are reused.
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![CSO-classes-2](https://user-images.githubusercontent.com/71790028/165483629-0f66d3a9-cde7-4a35-a7b5-17d35429df02.png)
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### Project Structure
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* [data](/crystal-structure-ontology/data/)
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* [Nickel crystal structure](/crystal-structure-ontology/data/MaterialProject/Nickel/overall.ttl)
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The Nickel data is collected from [Materials Project](https://materialsproject.org)
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* [CQs](/crystal-structure-ontology/CQs.md) is a collection of the competence questions.
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* [RDF genererator](/crystal-structure-ontology/python-script/)
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* For generating the RDF graph from the given [data](/crystal-structure-ontology/data/), we use the [RDFLib](https://github.com/RDFLib/rdflib) python library.
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* To generate the nickel crystal structure, the script is in [here](/crystal-structure-ontology/python-script/) and execute with `python map_data.py`
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### Acknowledgments
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* European Research Council through the ERC Grant Agreement No. 759419 MuDiLingo (”A Multiscale Dislocation Language for Data-Driven Materials Science”)
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* Helmholtz Metadata Collaboration (HMC) within the Hub Information at the Forschungszentrum Jülich.
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### Citation
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please cite the following paper if you used any part of this work.
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`@inproceedings{ihsan2021steps,
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title={Steps towards a Dislocation Ontology for Crystalline Materials},
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author={Ahmad Zainul Ihsan and Danilo Dessì and Mehwish Alam and Harald Sack and Stefan Sandfeld},
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booktitle={Second International Workshop on Semantic Digital Twins },
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year={2021},
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url={http://ceur-ws.org/Vol-2887/paper4.pdf}}`

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