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Add tautologies & structural-tautologies axiom selectors #579

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merged 23 commits into from
Nov 20, 2019
Merged

Add tautologies & structural-tautologies axiom selectors #579

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67ca5dd
Add 'foreign' selector and '--exclude' option for remove/filter, add …
Sep 23, 2019
db7266e
Fix extra header
Sep 23, 2019
2aa738f
Fix if statements
Sep 23, 2019
1d79cc8
Add test files
Sep 23, 2019
1c55f88
Add internal/external axiom selectors and bases
Sep 30, 2019
67219c2
Fix uberon_annotated example (too many annotated classes)
Sep 30, 2019
a6c2099
Remove extra test file
Oct 1, 2019
6694d6e
Fix queries to exclude nary only axioms?
Oct 2, 2019
0149863
Remove comment lines
Oct 3, 2019
3a5e655
Fix some prefixes, ignore duplicated obsolete labels
Oct 3, 2019
53bc2f1
Add doc comments
Oct 14, 2019
5406a25
Add tautologies and structural-tautologies axiom selectors to remove …
Oct 14, 2019
3881040
Update javadocs, rename methods to be more clear
Oct 15, 2019
125fa15
Merge branch 'master' into 562-feature
Oct 15, 2019
30d94fe
ignore annotation assertions for tautology checker
Oct 15, 2019
840dd8d
Only look at logical axioms for tautology checker
Oct 17, 2019
22f053d
Add Jenkinsfile
jamesaoverton Oct 29, 2019
2e75603
Merge remote-tracking branch 'upstream/master' into foreign-ax
Oct 31, 2019
53e76ef
Merge branch 'foreign-ax' of http://github.com/ontodev/robot into for…
Oct 31, 2019
57ba109
Merge remote-tracking branch 'upstream/foreign-ax' into 562-feature
Oct 31, 2019
3c312cb
Merge branch 'master' into foreign-ax
Nov 19, 2019
5b2cee0
Merge branch 'foreign-ax' into 562-feature
Nov 19, 2019
cbd55b7
Fix remove no-tautologies output path
jamesaoverton Nov 20, 2019
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317 changes: 50 additions & 267 deletions docs/examples/mitochondrion-full.owl
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51 changes: 51 additions & 0 deletions docs/examples/no-tautologies.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995#"
xml:base="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"
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#">
<owl:Ontology rdf:about="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"/>



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




<!-- http://robot.obolibrary.org/example/A -->

<owl:Class rdf:about="http://robot.obolibrary.org/example/A">
<rdfs:label>A</rdfs:label>
</owl:Class>



<!-- http://robot.obolibrary.org/example/B -->

<owl:Class rdf:about="http://robot.obolibrary.org/example/B">
<rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/A"/>
<rdfs:label>B</rdfs:label>
</owl:Class>



<!-- http://robot.obolibrary.org/example/C -->

<owl:Class rdf:about="http://robot.obolibrary.org/example/C">
<rdfs:label>C</rdfs:label>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->

67 changes: 67 additions & 0 deletions docs/examples/tautologies.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995#"
xml:base="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
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#">
<owl:Ontology rdf:about="http://www.semanticweb.org/tauber/ontologies/2019/9/untitled-ontology-995"/>



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




<!-- http://robot.obolibrary.org/example/A -->

<owl:Class rdf:about="http://robot.obolibrary.org/example/A">
<rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/A"/>
<rdfs:label>A</rdfs:label>
</owl:Class>



<!-- http://robot.obolibrary.org/example/B -->

<owl:Class rdf:about="http://robot.obolibrary.org/example/B">
<rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/A"/>
<rdfs:label>B</rdfs:label>
</owl:Class>



<!-- http://robot.obolibrary.org/example/C -->

<owl:Class rdf:about="http://robot.obolibrary.org/example/C">
<rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
<rdfs:label>C</rdfs:label>
</owl:Class>



<!-- http://www.w3.org/2002/07/owl#Nothing -->

<owl:Class rdf:about="http://www.w3.org/2002/07/owl#Nothing">
<rdfs:subClassOf rdf:resource="http://robot.obolibrary.org/example/B"/>
</owl:Class>



<!-- http://www.w3.org/2002/07/owl#Thing -->

<owl:Class rdf:about="http://www.w3.org/2002/07/owl#Thing"/>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->

154 changes: 154 additions & 0 deletions docs/examples/template-base.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="https://github.com/ontodev/robot/examples/template.owl#"
xml:base="https://github.com/ontodev/robot/examples/template.owl"
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:example="http://example.com/">
<owl:Ontology rdf:about="https://github.com/ontodev/robot/examples/template.owl"/>



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




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

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>



<!-- 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"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Data properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://example.com/propery-1 -->

<owl:DatatypeProperty rdf:about="http://example.com/propery-1">
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">weight in kilograms</rdfs:label>
</owl:DatatypeProperty>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/propery-1"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Weight of a mouse or rat in kilograms (kg).</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Rebecca C Jackson</obo:IAO_0000119>
</owl:Axiom>



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




<!-- http://example.com/B6C3F1 -->

<owl:Class rdf:about="http://example.com/B6C3F1">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>
<owl:disjointWith rdf:resource="http://example.com/F344N"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">B6C3F1</rdfs:label>
<rdfs:seeAlso rdf:resource="http://jaxmice.jax.org/strain/100010.html"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/B6C3F1"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of mouse used in many scientific investigations.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
</owl:Axiom>



<!-- http://example.com/F344N -->

<owl:Class rdf:about="http://example.com/F344N">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000117>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">F 344/N</rdfs:label>
<rdfs:seeAlso rdf:resource="http://www.informatics.jax.org/external/festing/rat/docs/F344.shtml"/>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://example.com/F344N"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An inbred strain of rat used in many scientific investigations.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">James A. Overton</obo:IAO_0000119>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_10090 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10090"/>



<!-- http://purl.obolibrary.org/obo/NCBITaxon_10116 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/NCBITaxon_10116"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Individuals
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://example.com/rat-1234 -->

<owl:NamedIndividual rdf:about="http://example.com/rat-1234">
<rdf:type rdf:resource="http://example.com/F344N"/>
<example:propery-1 rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">0.2</example:propery-1>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">rat 1234</rdfs:label>
</owl:NamedIndividual>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->

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