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‎CHANGELOG.md

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@@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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## [1.9.0] - 2022-06-16
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### Added
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- Add new command: [`expand`] [#964]
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### Fixed
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- Fix OBOGraphs by updating `guava` [#1009]
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## [1.8.4] - 2022-06-10
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### Added
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First official release of ROBOT!
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[Unreleased]: https://github.com/ontodev/robot/compare/v1.8.4...HEAD
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[Unreleased]: https://github.com/ontodev/robot/compare/v1.9.0...HEAD
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[1.9.0]: https://github.com/ontodev/robot/compare/v1.8.4...v1.9.0
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[1.8.4]: https://github.com/ontodev/robot/compare/v1.8.3...v1.8.4
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[1.8.3]: https://github.com/ontodev/robot/compare/v1.8.2...v1.8.3
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[1.8.2]: https://github.com/ontodev/robot/compare/v1.8.1...v1.8.2
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[`template`]: http://robot.obolibrary.org/template
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[`validate`]: http://robot.obolibrary.org/validate
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[#1009]: https://github.com/ontodev/robot/issues/1009
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[#979]: https://github.com/ontodev/robot/pull/979
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[#978]: https://github.com/ontodev/robot/pull/978
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[#973]: https://github.com/ontodev/robot/pull/973
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[#971]: https://github.com/ontodev/robot/pull/971
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[#964]: https://github.com/ontodev/robot/pull/964
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[#960]: https://github.com/ontodev/robot/pull/960
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[#955]: https://github.com/ontodev/robot/pull/955
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[#953]: https://github.com/ontodev/robot/pull/953

‎README.md

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[![Maven Central](https://img.shields.io/maven-central/v/org.obolibrary.robot/robot.svg?label=Maven%20Central)](https://search.maven.org/search?q=g:%22org.obolibrary.robot%22%20AND%20a:%22robot%22)
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[![Javadocs](https://www.javadoc.io/badge/org.obolibrary.robot/robot-core.svg)](https://www.javadoc.io/doc/org.obolibrary.robot/robot-core)
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ROBOT is a tool for working with [Open Biomedical Ontologies](http://obofoundry.org).
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ROBOT is a command-line tool and library for automating ontology development tasks, with a focus on [Open Biological and Biomedical Ontologies (OBO)](http://obofoundry.org).
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### Cite ROBOT
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‎docs/_layouts/default.html

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<a href="/collapse">collapse</a><br>
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<a href="/convert">convert</a><br>
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<a href="/diff">diff</a><br>
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<a href="/expand">expand</a><br>
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<a href="/explain">explain</a><br>
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<a href="/export">export</a><br>
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<a href="/export-prefixes">export-prefixes</a><br>

‎docs/convert.md

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- owx - [OWL/XML](https://www.w3.org/TR/owl2-xml-serialization/)
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- ttl - [Turtle](https://www.w3.org/TR/turtle/)
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In the following example we convert an input ontology to OBOGraphs JSON, explicitly specifying the target format with `--format`:
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robot convert -i ro-base.owl --format json -o results/ro-base.json
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### Handling Compressed Files
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All ROBOT commands support [gzip](https://www.gzip.org/) format files ending with the extension `.gz`. Any of the above formats can be compressed as long as the output ends with `.gz` (format must be specified for a compressed output):

‎docs/examples/expanded-annotated.ttl

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@prefix : <http://example.org/> .
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@prefix owl: <http://www.w3.org/2002/07/owl#> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix xml: <http://www.w3.org/XML/1998/namespace> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@base <http://example.org/> .
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<http://example.org/> rdf:type owl:Ontology .
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#################################################################
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# Annotation properties
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#################################################################
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### http://example.org/never_part_of
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:never_part_of rdf:type owl:AnnotationProperty ;
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<http://purl.obolibrary.org/obo/OMO_0002000> """PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX : <http://example.org/>
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CONSTRUCT {
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?a a owl:Class .
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?b a owl:Class .
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?a owl:disjointWith [
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a owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom ?b
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]
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}
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WHERE {
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?a :never_part_of ?b .
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}""" .
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### http://example.org/part_disjoint_with
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:part_disjoint_with rdf:type owl:AnnotationProperty ;
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<http://purl.obolibrary.org/obo/OMO_0002000> """PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX : <http://example.org/>
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CONSTRUCT {
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?a a owl:Class .
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?b a owl:Class .
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[
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a owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom ?a ;
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owl:disjointWith [
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a owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom ?b
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]
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]
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}
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WHERE {
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?a :part_disjoint_with ?b .
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}""" .
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### http://purl.obolibrary.org/obo/OMO_0002000
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<http://purl.obolibrary.org/obo/OMO_0002000> rdf:type owl:AnnotationProperty ;
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rdfs:label "defined by construct" .
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### http://purl.org/dc/terms/source
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<http://purl.org/dc/terms/source> rdf:type owl:AnnotationProperty .
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#################################################################
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# Object Properties
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#################################################################
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### http://example.org/part_of
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:part_of rdf:type owl:ObjectProperty .
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#################################################################
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# Classes
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#################################################################
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### http://example.org/A
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:A rdf:type owl:Class ;
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:part_disjoint_with :B .
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[ rdf:type owl:Axiom ;
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owl:annotatedSource :A ;
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owl:annotatedProperty rdf:type ;
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owl:annotatedTarget owl:Class ;
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<http://purl.org/dc/terms/source> :never_part_of
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] .
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[ rdf:type owl:Axiom ;
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owl:annotatedSource :A ;
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owl:annotatedProperty rdf:type ;
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owl:annotatedTarget owl:Class ;
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<http://purl.org/dc/terms/source> :part_disjoint_with
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] .
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### http://example.org/B
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:B rdf:type owl:Class ;
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owl:disjointWith [ rdf:type owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom :A
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] ;
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:never_part_of :A .
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[ rdf:type owl:Axiom ;
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owl:annotatedSource :B ;
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owl:annotatedProperty rdf:type ;
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owl:annotatedTarget owl:Class ;
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<http://purl.org/dc/terms/source> :never_part_of
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] .
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[ rdf:type owl:Axiom ;
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owl:annotatedSource :B ;
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owl:annotatedProperty rdf:type ;
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owl:annotatedTarget owl:Class ;
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<http://purl.org/dc/terms/source> :part_disjoint_with
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] .
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[ rdf:type owl:Axiom ;
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owl:annotatedSource :B ;
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owl:annotatedProperty owl:disjointWith ;
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owl:annotatedTarget [ rdf:type owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom :A
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] ;
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<http://purl.org/dc/terms/source> :never_part_of
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] .
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#################################################################
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# General axioms
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#################################################################
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[ rdf:type owl:Axiom ;
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owl:annotatedSource [ rdf:type owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom :A ;
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owl:disjointWith [ rdf:type owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom :B
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]
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] ;
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owl:annotatedProperty owl:disjointWith ;
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owl:annotatedTarget [ rdf:type owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom :B
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] ;
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<http://purl.org/dc/terms/source> :part_disjoint_with
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] .
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### Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi

‎docs/examples/expanded-terms.ttl

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@prefix : <http://example.org/> .
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@prefix owl: <http://www.w3.org/2002/07/owl#> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix xml: <http://www.w3.org/XML/1998/namespace> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@base <http://example.org/> .
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<http://example.org/> rdf:type owl:Ontology .
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#################################################################
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# Annotation properties
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#################################################################
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### http://example.org/never_part_of
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:never_part_of rdf:type owl:AnnotationProperty ;
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<http://purl.obolibrary.org/obo/OMO_0002000> """PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX : <http://example.org/>
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CONSTRUCT {
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?a a owl:Class .
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?b a owl:Class .
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?a owl:disjointWith [
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a owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom ?b
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]
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}
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WHERE {
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?a :never_part_of ?b .
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}""" .
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### http://example.org/part_disjoint_with
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:part_disjoint_with rdf:type owl:AnnotationProperty ;
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<http://purl.obolibrary.org/obo/OMO_0002000> """PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX : <http://example.org/>
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CONSTRUCT {
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?a a owl:Class .
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?b a owl:Class .
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[
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a owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom ?a ;
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owl:disjointWith [
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a owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom ?b
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]
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]
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}
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WHERE {
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?a :part_disjoint_with ?b .
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}""" .
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### http://purl.obolibrary.org/obo/OMO_0002000
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<http://purl.obolibrary.org/obo/OMO_0002000> rdf:type owl:AnnotationProperty ;
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rdfs:label "defined by construct" .
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#################################################################
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# Object Properties
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#################################################################
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### http://example.org/part_of
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:part_of rdf:type owl:ObjectProperty .
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#################################################################
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# Classes
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#################################################################
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### http://example.org/A
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:A rdf:type owl:Class ;
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:part_disjoint_with :B .
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### http://example.org/B
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:B rdf:type owl:Class ;
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owl:disjointWith [ rdf:type owl:Restriction ;
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owl:onProperty :part_of ;
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owl:someValuesFrom :A
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] ;
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:never_part_of :A .
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### Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi

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