Merge branch 'master' into elk05

.gitignore

@@ -3,6 +3,7 @@
 .project
 .settings
 .idea
+.vscode
 *.iml
 Gemfile*
 bin/original-robot.jar
@@ -14,3 +15,4 @@ docs/examples/out.owl
 docs/examples/results/
 junk/
 target/
+docs/examples/.gradle/

CHANGELOG.md

@@ -6,7 +6,37 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-- Downgrade SnakeYaml to 1.31 [#1070]
+
+## [1.9.4] - 2023-05-23
+
+### Changed
+- Speed up unsatisfiable object-property check on certain reasoners including HermiT [#1100]
+- Update HermiT from 1.3.8.413 to 1.4.5.456 [#1073]
+
+### Fixed
+- Preserve prefixes across ontology load and save [#1101]
+
+## [1.9.3] - 2023-02-16
+
+### Added
+- Subset method added to [`extract`] [#1000]
+
+### Changed
+- Upgrade OWLAPI to 4.5.25 [#1093]
+
+### Fixed
+- Restore logging details for CLI [#1091]
+- Fix OBO Serialiser bug where built in vocabulary was introduced as annotation properties [#1089]
+- Fix OBO Serialiser erroneous logging [#1088]
+
+## [1.9.2] - 2023-02-09
+
+### Changed
+- Upgrade OWLAPI to 4.5.24 [#1086]
+
+### Fixed
+- Downgrade SnakeYaml to 1.31 [#1071]
+- Don't check for disjoint annotation properties [#1084]
 
 ## [1.9.1] - 2022-10-28
 
@@ -287,7 +317,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 First official release of ROBOT!
 
-[Unreleased]: https://github.com/ontodev/robot/compare/v1.9.1...HEAD
+[Unreleased]: https://github.com/ontodev/robot/compare/v1.9.4...HEAD
+[1.9.4]: https://github.com/ontodev/robot/compare/v1.9.3...v1.9.4
+[1.9.3]: https://github.com/ontodev/robot/compare/v1.9.2...v1.9.3
+[1.9.2]: https://github.com/ontodev/robot/compare/v1.9.1...v1.9.2
 [1.9.1]: https://github.com/ontodev/robot/compare/v1.9.0...v1.9.1
 [1.9.0]: https://github.com/ontodev/robot/compare/v1.8.4...v1.9.0
 [1.8.4]: https://github.com/ontodev/robot/compare/v1.8.3...v1.8.4
@@ -332,12 +365,21 @@ First official release of ROBOT!
 [`template`]: http://robot.obolibrary.org/template
 [`validate`]: http://robot.obolibrary.org/validate
 
+[#1100]: https://github.com/ontodev/robot/pull/1100
+[#1091]: https://github.com/ontodev/robot/issues/1091
+[#1089]: https://github.com/ontodev/robot/issues/1089
+[#1088]: https://github.com/ontodev/robot/issues/1088
+[#1086]: https://github.com/ontodev/robot/pull/1086
+[#1084]: https://github.com/ontodev/robot/issues/1084
+[#1073]: https://github.com/ontodev/robot/pull/1073
+[#1071]: https://github.com/ontodev/robot/pull/1071
 [#1061]: https://github.com/ontodev/robot/issues/1061
 [#1030]: https://github.com/ontodev/robot/issues/1030
 [#1026]: https://github.com/ontodev/robot/issues/1026
 [#1017]: https://github.com/ontodev/robot/issues/1017
 [#1016]: https://github.com/ontodev/robot/issues/1016
 [#1009]: https://github.com/ontodev/robot/issues/1009
+[#1000]: https://github.com/ontodev/robot/pull/1000
 [#979]: https://github.com/ontodev/robot/pull/979
 [#978]: https://github.com/ontodev/robot/pull/978
 [#977]: https://github.com/ontodev/robot/pull/977

docs/annotate.md

@@ -10,7 +10,7 @@ General annotations can be added one-by-one with `--annotation`, and the IRIs ca
       --annotation rdfs:comment "Comment" \
       --annotation rdfs:label "Label" \
       --annotation-file annotations.ttl \
-      --output results/annotated.owl
+      --output results/edi-annotated.owl
 
 Or all at once from a turtle (.ttl) file with `--annotation-file`:
 <!-- DO NOT TEST -->

docs/examples/example2_defined_by.owl

@@ -31,7 +31,7 @@
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
+        <rdfs:label>definition</rdfs:label>
     </owl:AnnotationProperty>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
@@ -45,19 +45,19 @@
     <!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
-        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">editor note</rdfs:label>
+        <rdfs:label>editor note</rdfs:label>
     </owl:AnnotationProperty>
 
 
 
     <!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
-        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">uberon</oboInOwl:hasOBONamespace>
+        <oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">curator notes</rdfs:label>
+        <rdfs:label>curator notes</rdfs:label>
     </owl:AnnotationProperty>
 
 
@@ -121,6 +121,14 @@
 
 
 
+    <!-- http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral -->
+
+    <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral">
+        <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
+    </rdf:Description>
+
+
+
     <!-- http://www.w3.org/2001/XMLSchema#string -->
 
     <rdf:Description rdf:about="http://www.w3.org/2001/XMLSchema#string">
@@ -145,7 +153,7 @@
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
         <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part_of</rdfs:label>
+        <rdfs:label>part_of</rdfs:label>
     </owl:ObjectProperty>
 
 
@@ -166,7 +174,7 @@
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000061">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/some_other_ont.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">anatomical structure</rdfs:label>
+        <rdfs:label>anatomical structure</rdfs:label>
     </owl:Class>
 
 
@@ -182,7 +190,7 @@
             </owl:Restriction>
         </rdfs:subClassOf>
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">organ</rdfs:label>
+        <rdfs:label>organ</rdfs:label>
     </owl:Class>
 
 
@@ -226,7 +234,7 @@
 
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv1">
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 1</rdfs:label>
+        <rdfs:label>dummy individal 1</rdfs:label>
     </owl:NamedIndividual>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv1"/>
@@ -241,7 +249,7 @@
 
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv2">
         <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/pcl/some_other_ont.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 2</rdfs:label>
+        <rdfs:label>dummy individal 2</rdfs:label>
     </owl:NamedIndividual>
 
 
@@ -250,7 +258,7 @@
 
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv3">
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 3</rdfs:label>
+        <rdfs:label>dummy individal 3</rdfs:label>
     </owl:NamedIndividual>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/UBERON_0013702_indv3"/>
@@ -265,7 +273,7 @@
 
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv4">
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 4</rdfs:label>
+        <rdfs:label>dummy individal 4</rdfs:label>
     </owl:NamedIndividual>
 
 
@@ -274,10 +282,23 @@
 
     <owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/UBERON_0013702_indv5">
         <rdfs:isDefinedBy rdf:resource="https://github.com/ontodev/robot/examples/edit.owl"/>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dummy individal 5</rdfs:label>
+        <rdfs:label>dummy individal 5</rdfs:label>
     </owl:NamedIndividual>
+
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Annotations
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral"/>
 </rdf:RDF>
 
 
 
-<!-- Generated by the OWL API (version 4.5.6) https://github.com/owlcs/owlapi -->
+<!-- Generated by the OWL API (version 4.5.24) https://github.com/owlcs/owlapi -->
+