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OWLAPI

======

OWL API main repository

The OWL API is a Java API for creating, manipulating and serialising OWL Ontologies.

The latest version of the API supports OWL 2.
OWLAPI 5.5.0 requires Java 11
It is available under Open Source licenses (LGPL and Apache).

The following components are included:

An API for OWL 2 and an in-memory reference implementation.
Read and write support for RDF/XML, OWL/XML, Functional syntax, Manchester syntax, Turtle, OBO.
Write support for KRSS, DL syntax, LaTeX.
Other formats via RIO integration (NTriples, JSON, etc.).
Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet, Racer, JFact and Chainsaw.
See documentation pages on the wiki for more details.

Release notes

5.5.1 7 September 2024

Bug fixes:

OBO serialisation illegal axiom annotation (#1093)
Add Trix to list of BANNED_PARSERS in OWLAPI 4.X #1088
Version5 OSGi fixes (#1098)
Fix violations in declarations not reported #1094 #1046
Fix Shared class expression causes extra triples in output #1109
Fix #1112 force use of oboInOwl ns translating OBO IDs.
Fix #1118 dependency updates
Fix forced use of oboInOwl namespace when translating OBO IDs.
Issue #1145: Upgrade to RDF4J 5.x
Fix case sensitive extensions in ZipIRIMapper #1140
Clarify "Entity not properly recognized" #1152
jaxb-ap dropped in OWLAPI 5.1 causes failure running on Java 11 #1150
Fix #1126 Handle exception when comparing integer literals.
Remove org.openrdf.rio.RDFParserFactory #1125

Features:

Allow arbitrary annotation properties as qualifier tags in OBO #1099
Provide a BOM for owlapi #1148

5.5.0 14 January 2023

Features:

Java 11 required to include dependencies that require Java 9 or newer
Added support for MS syntax to include all features from OWL2 DL

Bug fixes:

Memory leaks in semantic module extraction
Ensure pending annotations are cleared after handling triple
Only remove unannotated axiom if it received annotations.
Check for empty collections on AxiomSubjectProvder #1069
Allow forcing explicit xsd:xstrig type #1063
Bump rdf4j.version to 4.2.0, JDK to 11, version to 5.5.0
OBO serializer incorrectly quoting IRI property values (#1085)

5.1.20 19 February 2022

Features:

Upgraded to RDF4j 3.7.4 and fixed issues with OSGi bundles
Improve MAVEN build Performance
Extend messages for OWL exceptions #1020

Bug fixes:

Fix OWLDifferentIndividuals with two ops rendered with one triple #1031
Fix Abbreviated IRI as OntologyIRI in Manchester syntax #1041
Fix Individuals: anonymous individuals in Manchester syntax #1006
Fix UNPARSED TRIPLES ERROR for class assertions #1023

5.1.19 31 July 2021

Bug fixes:

vulnerable dependencies update

5.1.18 30 July 2021

Features:

Specify RioSetting values for Rio renderers #614

Bug fixes:

Fix sameAs failure when more than 2 entities included #994
Fix Trig and rdf/json should include a named graph. #1002
Fix ObjectHasSelf rendered wrongly in manchester syntax #1005

5.1.17 6 November 2020

Features:

Remove @Deprecated annotations for Set based methods in OWLAPI 5 #981
Support RDF4J Rio HDT parser #931
OWLLiteral for XSD:Long #970

Bug fixes:

Fix Performance of signature checks during ontology changes #968
Fix Error on RIO renderer when expression has 6000 elements #971
Fix OWLOntology#datatypesInSignature to include ontology header #965
Fix EntitySearcher.getSuperProperties fails when parent is inverse #964
Update guava and junit versions
Fix OWLParser not ensuring streams are closed on exit #973
Error with undeclared classes in domain axioms #962
Fix Ontology caches should use weak keys #984

5.1.16 28 July 2020

Bug fixes:

Fix follow multiple redirects across protocols #954
Javadoc fixes for deprecated stream methods #950

5.1.15 02 July 2020

Features:

Allow creation of tautologies for n-ary axioms #776
Configurable fast pruning window size

Bug fixes:

Fix javadoc for OWLObject::nestedClassExpressions #937
Fix classAssertionAxioms with OWLClassExpression fails #930
Fix Include ontology annotations in signature #928
Fix Unable to set base directive for turtle writers #938
Fix OWLAPI accepts IRIs with leading spaces #940
Fix SWRL body reordered when structure shared #936
Fix roundtrip through OBO changes IRI of owl:versionInfo #947

5.1.14 18 April 2020

Features:

General modularity classes contributed by Robn Nolte

Bug fixes:

Fix XSD datatypes are erroneously quoted in OBO writer #918
Fix referencingAxioms(OWLPrimitive) misses nested literals #912
Fix Empty line in META-INF/services/ files causes exceptions #924
Fix OWLOntologyWriterConfiguration does not disable banner comments #904

5.1.13 27 January 2020

Bug fixes:

Fix OWLEntityRenamer and anonymous individuals #892
Fix Builtin annotation properties lost during parsing #895
Deal with OWLAnnotationProperty entities in OWLEntityURIConverter class #896

5.1.12 20 October 2019

Bug fixes:

Implement Allow gzipped imports #887
Fix Race condition in Injector #883
Jackson update
Fix containsReference(OWLEntity) should be deprecated #864
Fix referencingAxioms(OWLPrimitive) misses IRI appearances #865
Fix Javadoc on applyChange/applyChanges and using the wrong manager #868
Fix OWLObjectPropertyExpression#getSimplified() used incorrectly #882
Fix Incomplete javadoc on OWLNaryAxiom#asPairwiseAxioms #884
Fix OWLNegative*AssertionAxiom#containsAnonymousIndividuals javadoc #885
Fix Annotated axiom with anon expression saved incorrectly #881
Fix Ontology with relative IRIs is serialized incorrectly #880
Fix Ann. annotation with anon individual saved in RDF incorrectly #877
Fix Annotations dropped if annotation property is undeclared #875
Fix SAXException from AutoIRIMapper at debug logging level #878
Ensure isAnonymous is implemented correctly #867
Fix Null pointers with imports and relation declarations #859
Amend base and escaped characters in Tutle parsing #857
Fix Exception when converting obi to obo #860

5.1.11 02 June 2019

Features:

Add support to load an ontology from classpath #837
Implement Allow annotations to be skipped in module extraction #838
Add support for custom tags in obo files.

Bug fixes:

Fix Unescaping characters: OBOFormatParser#handleNextChar() #822
Fix IRI PREFIX_CACHE instance uses too much memory #825
Fix roundtrip of escaped values #833
Fix MaximumNumberOfNamedSuperclasses should count super classes #836
Fix OWLDataPropertyAxiom not a subinterface of OWLPropertyAxiom #831
Fix HTTP 307 and HTTP 308 redirects are not followed (in 4.x) #821
Fix Missing escape character in OBO output #828
Fix 5.1.10 Regression in OwlStringTools#translate(..) #829
Fixed several incorrect XSD datatype matching patterns.
Fix OWLDataFactory::getLiteral error with empty string and integer #846
Fix Unnecessary dc prefix added by Manchester syntax parser #845
Fix Multiple Ontology Definitions should obey strict parsing #840
Fix OWLLogicalEntity is not an OWLAnnotationProperty #847
Security: Jackson to 2.9.9
Fix Manchester syntax parser crashes on class/property punning #851
Fix OBO parser does not support qualifier block #852

5.1.10 04 March 2019

Bug fixes:

Fix DLExpressivity checker never computes anything #810
Jackson version to 2.9.8
Fix ensure allValuesFrom axioms are not lost #808
Fix HTTP 307 and HTTP 308 redirects are not followed #821
Fix OBO renderer stuck with untranslatable axioms on concurrent managers
Fix Annotations on DifferentIndividualsAxioms lost #816
Fix No roundtrip for IRIs with colons in the fragment or path #817
Fix EOFException in CustomTokenizer #813
Fix Cyclic imports and missing declarations cause parsing error #798

5.1.9 12 December 2018

Bug fixes:

Refactor OWLProfile implementations #638
Fix Missing user defined datatype violation in literals #639
Fix RDFGraph getSubjectsForObjects caught in infinite loop #809

5.1.8 1 December 2018

Features:

Add OWLClassExpression.isNamed method #790
Fix injection problem under OSGi
Implement Allow Atomic Decomposition to skip assertions #796
Expressivity Checker for EL and FL #500

Bug fixes:

Fix ReadWriteLock should be injector singleton #785
Fix Cyclic import of versioned ontologies fails #788
Fix Annotate ontology annotations #791
Fix Incorrect documentation for OWLOntologyManager methods. #795
DisjointClasses with OWL:Thing produces incorrect axiom #747
Fix Concurrent managers with own lock shared with own ontologies #806

5.1.7 2 September 2018

Features:

PROV and TIME vocabularies

Bug fixes:

Add representativeInstances() to OWLReasoner #772
SWRLRule hash code computed incorrectly
Fix OWLOntology with shared structure causes incorrect RDF/XML #780

5.1.6 24 July 2018

Features:

Remove Guice dependencies
Upgrade to jsonld-java version 0.12.0 (performance) #763
Allow building with Java 10

Bug fixes:

Move from Trove4j to HPPC-RT #774
Fix incorrect sorting of OBO header tags
Fix Line breaks in rdfs:label cause invalid FS output #758
Fix AutoIriMapper chooses wrong IRIs. #755

5.1.5 23 April 2018

Features:

Add an option to represent version build as strings
Implement #375 OWLZip reader and writer
Allow trimming to size after load to be disabled
do not register deprecated oboparser by default #729

Bug fixes:

Fix SWRL variable IRIs violate URN spec #732
default IRI for unnamed ontologies is not valid
doubling of # at the end of default namespace
IRI should return true for isIRI()
Fix OWL/XML writes langString unnecessarily #748
Fix importsDeclaration not returning imports for *.obo #727

5.1.4 4 January 2018

Features:

Support Authorization header in remote loading

Bug fixes:

Fix Problem saving ontologies in Turtle #719
Fix Null pointer in OWLObjectPropertyManager #723
Remove com.google.inject and add exclusion of javax.annotation. #720

5.1.3 4 November 2017

Features:

Performance improvements on parsing of large ontologies.

5.1.2 13 October 2017

Features:

Accept Headers to include all MIME types with supporting parsers #705
Add HasAnnotationValue interface with methods for mapping
Optional methods for OWLOntologyChange
Implement efficient way to test if an ontology refers entity type #698

Bug fixes:

Do not output xsd:string when unnecessary #640
OWL/XML should reject XML files that are not valid OWL/XML #657
getFragment advices an non existent replacement #684
OWLObject immutable collections sorted #702
Sort imports and imports closure #702
Sort namespace prefixes for XML serialization #702
OWLOntologyMerger fails with ConcurrentModificationException #673
Poor performance in OWLImmutableOntologyImpl.getImportsClosure #696
Fix AtomicDecomposition throws Nullpointer #695
Fix hashcode and equals on OWLOntology differ #694

5.1.1 25 July 2017

Features:

Add REPAIR_ILLEGAL_PUNNINGS property to disable fix of illegal punnings
Move punning log to warning

Bug fixes:

Fix Profiles.OWL2_FULL returns Profiles.OWL2_DL #667
Fix EntitySearcher.getEquivalentClasses incorrectly returns itself #663
OWLEntityRenamer should rename annotation props in ontology annotations
Fix blank node ids should be NCNames in the RDF/XML output #689

5.1.0 30 March 2017

Features:

Add stream support on reasoning interface.
Allow SyntacticLocalityModuleExtractor to exclude assertions. #462
Explanations: do not fail hard for profile violations
Latex formatting improvements
ensure ontology annotations are sorted
Implement HasApplyChanges.applyChanges returns ChangeApplied #544
recompile parsers with javacc 7
issue #612 : Add japicmp maven plugin to track API changes
Implement Zip with dependencies included for non Maven users #584
Dependencies update, move to rdf4j

Bug fixes:

Fix Relating to inferred axiom generators #646
Fix duplication and inverseOf properties in generators #646
Fix SimpleRenderer writes InverseOf instead of ObjectInverseOf #647
Fix nested annotation bug
Fix Turtle parser failure on some bioportal ontology #610
Fix Manchester expression parser bug with data cardinalities #609

5.0.5 4 January 2017

Bug fixes:

Allow supplier for null error messages
IsAnonymous, isIndividual, isAxiom, isAnonymousExpression on OWLObject
Performance improved in creating OWLOntologyManager
Ensure XXE vulnerability is prevented
Fix Structural sharing in GCIs causes errors #564
Fix Issue with serialization - OWLAPI version 3.5.5 #586
Fix Problems compiling version5 for Android v24 Nougat #585
Fix Order of RDF triples affects annotation parsing #574
Fix Property Axiom Generator should check set size #527
Fix Imports not properly loaded after all ontologies removed #580
Fix Incomplete Parsing of DifferentIndividuals with distinctMembers #569
Fix Apache Harmoony SAX parser not supported #581
Fix line separators in DLSyntaxHTMLStorer #583
Fix IRIs with query string cause OFN unparseable output #570
Fix Unqualified data restriction considered qualified #576

5.0.4 16 October 2016

Bug fixes:

Serializability issues

5.0.3 10 September 2016

Bug fixes:

Fix OMN Parser mistakes punned class for object property #548
Fix OWL/XML format does not support SWRL variable IRIs #535
Fix Explicit prefix ignored during serialization #529
Fix Saving to OFN loses namespaces due to double default prefix #537
Fix DL-Syntax HTML formatter issues #536
Fix ManchesterOWLSyntaxRenderer SubPropertyOf render inconsistent #534
Fix Slow inferred disjoint generator #542
Fix Relative Ontology IRI causes missing declaration #557
Fix Invalid Turtle ontologies when hash IRIs are used #543
Fix Calling setOntologyDocumentIRI reset imports closure cache #541
Fix OWLOntology::annotationPropertiesInSignature has duplicates #555
Fix Latex Renderer produces bad LaTeX for property inverses #526
Fix ManchesterOWLSyntaxParser doesn't handle the OWL 2 datatypes #556
Fix Turtle Renderer doesn't escape periods #525
Fix Import IRI not resolved correctly in OBO input #523

5.0.2 7 May 2016

Features:

Allow banning of parsers #510
Allow disabling banner comments
Move builders to api to be able to use them in parsers
Make AxiomType Comparable

Bug fixes:

Fix performance regression in String.intern() and improve memory footprint
Fix Default prefix overrides explicit prefixes #522
Fix Anonymous individuals parsing problems #494
Fix Noisy print messages from logging framework #516
Fix SWRL rules with incorrect equals() #512
Fix OWL 2 Full Profile #508
Fix Annotated entities not declared in RDF/XML #511
Fix XML literal is not self contained #509

5.0.1 19 March 2016

Bug fixes:

Fix Fixing punnings fails on dp subDataPropertyOf rdfs:label #505
"Dumping remaining triples" displayed when no triples left #502
Fix Annotations lost on entity renaming of SWRLRules #501
Fix Profile validation throws exception on ontology annotations #498
Fix RDF/XML parser failing to load ontology containing XMLLiteral #496
Fix #489 makeLoadImportRequest log should be a warning #489
Fix Anonymous individuals parsing problems #494
Fix Saving fails for ontologies containing XMLLiteral #495
Fix Anonymous individuals parsing problems #494

5.0.0 28 February 2015

Features:

Allow overridable and defaultable properties
FaCT++ AD implementation from OWLAPITOOLS
Add OWLObjectTransformer to replace any part of an ontology
Add HasOperands interface
Ad componentsWithoutAnnotations() to simplify equalsIgnoreAnnotations
Add componentsAnnotationsFirst() to OWLObject
Add component() to OWLObject to create a common interface for hashcode
Add rdf:langString data type
commons-rdf-api integration
Add InferenceDepth and convenience methods to OWLReasoner
OWLRDFConsumer fills guessed type declaration table with blank nodes
Marked methods returning sets where a stream is available as deprecated
Update guice version to beta 5
Replace Google Optional with Java 8 Optional (#250)
OWLProfileViolationVisitorEx returns Optional<T> rather than nulls
Add default methods to OWLOntology for direct add/remove of axioms
Added a getFormat method to OWLOntology
Merged visitor adapters into the interfaces with default methods
isAvailable/get pattern in OWLOntologyDocumentSource changed to Optional
OWLOntology.getReferencingAxioms() finds any of the OWLPrimitive objects
Enabled OWLOntologyManager to build and keep an OntologyConfigurator instance
Declaration of save methods on OWLOntology
OWLAPI 5 uses Java 8

4.5.23 14 January 2023

Features:

Allow forcing explicit xsd:xstrig type #1063

Bug fixes:

OBO serializer incorrectly quoting IRI property values #1085
Update dependencies for security issues
Check for empty collections on AxiomSubjectProvder #1069
Correct bad default args #1063
Fix OWLEntityRenamer and anonymous individuals #892

4.5.22 7 May 2022

Bug fixes:

Do not output xsd:string when unnecessary #640

4.5.21 19 February 2022

Features:

Improve MAVEN build Performance
Extend messages for OWL exceptions #1020

Bug fixes:

Fix OWLDifferentIndividuals with two ops rendered with one triple #1031
Fix Abbreviated IRI as OntologyIRI in Manchester syntax #1041
Fix Individuals: anonymous individuals in Manchester syntax #1006
Fix UNPARSED TRIPLES ERROR for class assertions #1023

4.5.20 31 July 2021

Features:

Specify RioSetting values for Rio renderers #614

Bug fixes:

Fix sameAs failure when more than 2 entities included #994
Ordering of literals to be consistent with OWLAPI 5
Fix Trig and rdf/json should include a named graph. #1002
Fix ObjectHasSelf rendered wrongly in manchester syntax #1005

4.5.19 7 November 2020

Bug fixes:

Fix OWLParser not ensuring streams are closed on exit #973
Error with undeclared classes in domain axioms #962
Fix Ontology caches should use weak keys #984

4.5.18 23 October 2020

Bug fixes:

Fix Performance of signature checks during ontology changes #968
Fix Error on RIO renderer when expression has 6000 elements #971
Fix OWLOntology#datatypesInSignature to include ontology header #965
Fix Ontology not loaded in case of multiple HTTP redirects #954

4.5.17 02 July 2020

Features:

Let OBO parser follow redirects
Allow creation of tautologies for n-ary axioms #776
Configurable fast pruning window size

Bug fixes:

Fix javadoc for OWLObject::nestedClassExpressions #937
Fix classAssertionAxioms with OWLClassExpression fails #930
Fix Include ontology annotations in signature #928
Fix Unable to set base directive for turtle writers #938
Fix OWLAPI accepts IRIs with leading spaces #940
Fix SWRL body reordered when structure shared #936
Fix roundtrip through OBO changes IRI of owl:versionInfo #947

4.5.16 18 April 2020

Bug fixes:

Fix XSD datatypes are erroneously quoted in OBO writer #918
Fix referencingAxioms(OWLPrimitive) misses nested literals #912
Fix Empty line in META-INF/services/ files causes exceptions #924

4.5.15 28 January 2020

Bug fixes:

Fix OWLEntityRenamer and anonymous individuals #892
Fix Builtin annotation properties lost during parsing #895
Deal with OWLAnnotationProperty entities in OWLEntityURIConverter class #896

4.5.14 19 October 2019

Bug fixes:

Implement Allow gzipped imports #887
Fix Race condition in Injector #883
Jackson update
Fix containsReference(OWLEntity) should be deprecated #864
Fix Javadoc on applyChange/applyChanges and using the wrong manager #868
Fix OWLObjectPropertyExpression#getSimplified() used incorrectly #882
Fix Incomplete javadoc on OWLNaryAxiom#asPairwiseAxioms #884
Fix OWLNegative*AssertionAxiom#containsAnonymousIndividuals javadoc #885
Fix Annotated axiom with anon expression saved incorrectly #881
Fix Ontology with relative IRIs is serialized incorrectly #880
Fix Ann. annotation with anon individual saved in RDF incorrectly #877
Fix Annotations dropped if annotation property is undeclared #875
Fix SAXException from AutoIRIMapper at debug logging level #878
Ensure isAnonymous is implemented correctly #867
Fix Null pointers with imports and relation declarations #859
Amend base and escaped characters in Tutle parsing #857

4.5.13 02 June 2019

Features:

Add support for custom tags in obo files. #848

Bug fixes:

Fix OWLLogicalEntity is not an OWLAnnotationProperty #847
Security: Jackson to 2.9.9
Fix Manchester syntax parser crashes on class/property punning #851
Fix OBO parser does not support qualifier block #852

4.5.12 06 May 2019

Features:

Add support to load an ontology from classpath #837
Implement Allow annotations to be skipped in module extraction #838

Bug fixes:

Fix Multiple Ontology Definitions should obey strict parsing #840
Fix Unnecessary dc prefix added by Manchester syntax parser #845
Fix OWLDataFactory::getLiteral error with empty string and integer #846
Fixed several incorrect XSD datatype matching patterns #844

4.5.11 17 April 2019

Bug fixes:

Fix HTTP 307 and HTTP 308 redirects are not followed (in 4.x) #821
Fix Missing escape character in OBO output #828
Fix OWLDataPropertyAxiom not a subinterface of OWLPropertyAxiom #831
Fix MaximumNumberOfNamedSuperclasses should count super classes #836
Fix OWLOntology::getGeneralClassAxioms slow #839
Fix roundtrip of escaped values #833

4.5.10 14 March 2019

Bug fixes:

Fix HTTP 307 and HTTP 308 redirects are not followed (in 4.x) #821
Fix Ensure allValuesFrom axioms are not lost #808
Fix EOFException in CustomTokenizer #813
Fix Cyclic imports and missing declarations cause parsing error #798
Fix Unescaping characters: OBOFormatParser#handleNextChar() #822
Fix IRI PREFIX_CACHE instance uses too much memory #825

4.5.9 1 February 2019

Bug fixes:

Jackson version to 2.9.8
Fix compatibility with Guava 27 #814
Fix OBO renderer stuck with untranslatable axioms on concurrent managers
Fix Annotations on DifferentIndividualsAxioms lost #816
Fix No roundtrip for IRIs with colons in the fragment or path #817

4.5.8 22 December 2018

Features:

Refactor OWLProfile implementations #638

Bug fixes:

Fix Missing user defined datatype violation in literals #639
Fix RDFGraph getSubjectsForObjects caught in infinite loop #809
Fix DLExpressivity checker never computes anything #810

4.5.7 1 December 2018

Features:

Add OWLClassExpression.isNamed method #790
Fix injection problem under OSGi
Expressivity Checker for EL and FL #500

Bug fixes:

Fix ReadWriteLock should be injector singleton #785
Fix Cyclic import of versioned ontologies fails #788
Fix Annotate ontology annotations #791
Fix Incorrect documentation for OWLOntologyManager methods. #795
DisjointClasses with OWL:Thing produces incorrect axiom #747
Fix Concurrent managers with own lock shared with own ontologies #806

4.5.6 6 September 2018

Bug fixes:

OSGi issues fixed

4.5.5 2 September 2018

Features:

PROV and TIME vocabularies

Bug fixes:

Prefix splitting at wrong place with percent encoded IRI #737
Fix OWLOntology with shared structure causes incorrect RDF/XML #780

4.5.4 26 July 2018

Features:

Remove Guice dependencies
Upgrade to jsonld-java version 0.12.0 (performance) #763
Build with Java 10

Bug fixes:

Move from Trove4j to HPPC-RT #774
Literals with no lang and string literals must equal each other
Fix OWLLiteral.parseDouble should throw NumberFormatException #764
No need for Guice and Guava version updates
Amend pom files to build vaild osgi distribution #768
Fix incorrect sorting of OBO header tags
Fix Line breaks in rdfs:label cause invalid FS output #758
Fix AutoIriMapper chooses wrong IRIs. #755

4.5.2 22 April 2018

Features:

Add an option to represent version build as strings
Implement #375 OWLZip reader and writer
Signature cache for ontologies
Allow trimming to size after load to be disabled
do not register deprecated oboparser by default #729

Bug fixes:

Fix SWRL variable IRIs violate URN spec #732
default IRI for unnamed ontologies is not valid
doubling of # at the end of default namespace
IRI should return true for isIRI()
Fix OWL/XML writes langString unnecessarily #748

4.5.1 7 December 2017

Features:

Support Authorization header in remote loading

4.5.0 13 October 2017

Features:

Accept Headers to include all MIME types with supporting parsers #705
Add HasAnnotationValue interface with methods for mapping
Optional methods for OWLOntologyChange
Implement efficient way to test if an ontology refers entity type #698

Bug fixes:

OWL/XML should reject XML files that are not valid OWL/XML #657
OWLObject immutable collections sorted #702
Sort imports and imports closure #702
Sort namespace prefixes for XML serialization #702
OWLOntologyMerger fails with ConcurrentModificationException #673
getFragment advices an non existent replacement #684
Fix Poor performance in OWLImmutableOntologyImpl.getImportsClosure #696

4.3.2 25 July 2017

Features:

Add REPAIR_ILLEGAL_PUNNINGS property to disable fix of illegal punnings
Move punning log to warning

Bug fixes:

Fix Profiles.OWL2_FULL returns Profiles.OWL2_DL #667
Fix EntitySearcher.getEquivalentClasses incorrectly returns itself #663
Fix blank node ids should be NCNames in the RDF/XML output #689
OWLEntityRenamer should rename annotation props in ontology annotations

4.3.1 27 March 2017

Features:

Allow SyntacticLocalityModuleExtractor to exclude assertions. #462
Explanations: do not fail hard for profile violations

Bug fixes:

Fix Relating to inferred axiom generators #646
Fix duplication and inverseOf properties in generators #646

4.3.0 22 March 2017

Features:

Implement HasApplyChanges.applyChanges returns ChangeApplied #544
Implement Zip with dependencies included for non Maven users #584
issue #612 : Add japicmp maven plugin to track API changes
dependencies update

Bug fixes:

Fix OWLLiteral produce different hash codes in version 4 #645
Multiple nested annotations fail in RDF/XML #470
Parsing of nested anonymous nodes broken in 4.1.1 #478
ensure ontology annotations are sorted
Fix Turtle parser failure on some bioportal ontology #610
Fix Manchester expression parser bug with data cardinalities #609

4.2.8 4 January 2017

Bug fixes:

Fix Structural sharing in GCIs causes errors #564
Fix Issue with serialization - OWLAPI version 3.5.5 #586
Fix Order of RDF triples affects annotation parsing #574
Fix Property Axiom Generator should check set size #527
Fix Imports not properly loaded after all ontologies removed #580
Performance improved in creating OWLOntologyManager
Fix Incomplete Parsing of DifferentIndividuals with distinctMembers #569
Fix Apache Harmoony SAX parser not supported #581
Ensure XXE vulnerability does not exist
Fix line separators in DLSyntaxHTMLStorer #583
Fix IRIs with query string cause OFN unparseable output #570
Fix Unqualified data restriction considered qualified #576
Fix OWLOntologyManager in OWLImmutableOntologyImpl should be @Nullable #568

4.2.7 16 October 2016

Bug fixes:

Serialization issues

4.2.6 10 September 2016

Bug fixes:

Fix OMN Parser mistakes punned class for object property #548
Fix OWL/XML format does not support SWRL variable IRIs #535
Fix Explicit prefix ignored during serialization #529
Fix Saving to OFN loses namespaces due to double default prefix #537
Fix DL-Syntax HTML formatter issues #536
Fix ManchesterOWLSyntaxRenderer SubPropertyOf render inconsistent #534
Fix Slow inferred disjoint generator #542
Fix Relative Ontology IRI causes missing declaration #557
Fix Invalid Turtle ontologies when hash IRIs are used #543
Fix Calling setOntologyDocumentIRI reset imports closure cache #541
Fix Latex Renderer produces bad LaTeX for property inverses #526
Fix ManchesterOWLSyntaxParser doesn't handle the OWL 2 datatypes #556

4.2.5 17 May 2016

Bug fixes:

Fix Turtle Renderer doesn't escape periods #525
Fix Import IRI not resolved correctly in OBO input #523

4.2.4 7 May 2016

Bug fixes:

Fix Default prefix overrides explicit prefixes #522
Fix Anonymous individuals parsing problems #494
Fix OWL 2 Full Profile #508
Fix Annotated entities not declared in RDF/XML #511
Fix XML literal is not self contained #509

Features:

Allow banning of parsers #510
Allow disabling banner comments
Fix Noisy print messages from logging framework #516

4.2.3 19 March 2016

Bug fixes:

Fix Fixing punnings fails on dp subDataPropertyOf rdfs:label #505

4.2.2 15 March 2016

Bug fixes:

Fix RDF/XML parser failing to load ontology containing XMLLiteral #496
Fix Profile validation throws exception on ontology annotations #498
Fix Annotations lost on entity renaming of SWRLRules #501
Fix "Dumping remaining triples" displayed when no triples left #502

4.2.1 5 March 2016

Bug fixes:

Fix Anonymous individuals parsing problems #494
Fix makeLoadImportRequest log should be a warning #489
Fix Saving fails for ontologies containing XMLLiteral #495

4.2.0 28 February 2016

Features:

Allow overridable and defaultable properties

Bug fixes:

Fix EntitySearcher.getDomains(OWLAnnotationProperty, OWLOntology) returns the range axioms instead of the domain axioms #492

4.1.4 3 February 2016

Features:

Add OWLObjectTransformer to replace any part of an ontology #487
Add OWLLiteralReplacer to replace literals with different values #487
Throw error on malformed ontologies when parsing is strict (avoid Error1 classes) #444

Bug fixes:

Fix RBox axiom types #479
Fix Parsing of nested anonymous nodes broken in 4.1.1 #478
Fix Error in rdf handling of deep nested annotations
Fix EntitySearcher.subPropertiesFilter is broken #486
Fix Cyclic imports cause illegal punning #483
Fix OWLOntologyManager.copyOntology does not copy imports #480
Fix Changes not successfully applied broadcasted as applied #476
Add restriction on aduna packages #471
Fix BOM removal wrapper is applied to all input streams #212
Fix Serialization into incorrect OWL syntax #468
Fix Constraint Sesame Versions in OSGi Imports #471
Fix ExplanationOrdererImpl.SeedExtractor throws exception #469
Fix for Multiple nested annotations fail in RDF/XML #470

4.1.0 25 October 2015

Features:

Port protege-owlapi concurrency support to the OWL API
Enabled the creation of a concurrent manager
Part of Add transactional support to OWLOntology #382 : ability to rollback the application of a set of changes if one fails. Added a ChangeApplied.NO_OPERATION to track those changes that did not have any effect (e.g., adding an axiom that is already present or removing an axiom that is not present).
ManchesterOWLSyntaxParser could use a convenience method parseClassExpression(String s) #384
Add setting to use labels as banner comment or use IRIs as before
Add config to switch saving all anon individuals
Enforce correct argument types for OWLObjectInverseProperty in default impl
Add control flag to structure walking to allow annotations to be walked
Reduce space used by OBO Parser
update jackson dependency to 2.5.1

Bug fixes:

OWLImmutableOntologyImpl.asSet() assumes input iterable is coming from a duplicate free collection #404
OWLOntologyManagerImpl.getVersions() calls get() on Optional without checking if the contained value is present #401
OWLOntologyManagerImpl tests storers with keys rather than canStoreOntology #400
setOntologyLoaderConfigurationProvider should accept a javax.inject.Provider #399
Cleaned distribution jar
Losing Annotations on Annotation Assertion Axioms #406
Return types of RemoveAxiom(s) vs. AddAxiom(s) #408
Examples file needs review #407
BFO fails to load in API version 4.0.X #405
Fix RDF/XML renderer does not like properties using urns (or almost urns) #301
All anonymous individuals are remapped consistently upon loading. #443
Only output node id for anonymous individuals if needed
Anon individuals appearing more than once as objects #443
Sort annotation assertions on output for manchester syntax #332
OWL 2 profile validation mistakes #435
[Typedef] created_by don't support space #419
ttl namespace abbreviations not preserved on serialization #421
Use EntitySearcher.getAnnotationObjects() when interested only in the object of annotation assertion axioms on an entity rather than the annotations on the annotation assertion axioms.
convincing owlapi-distribution to export rio dependencies
RDF issues testing 4.1.0 RC 1 #412
Annotation subproperty/domain/range disappear after save/load cycle (punning enhancement) #351

4.0.2 17 April 2015

Features:

Simple OWL/FSS IRI sniffing for AutoIRIMapper.
Fix #373 Individuals in SWRL rules get extra type
XZ compression support
Sorting of FunctionalSyntaxObjectRenderer
Sort untyped IRI Annotation Assertions, general axioms.
Sort axiom Annotations, if they are output using the translateAnnotations method. Negative property assertions not yet ordered; neither are nary axioms and class expressions.
Add legacy files to the OSGI distribution for version 3.5 backwards compatibility.
Some reasoners may not support certain types of reasoning. They may also not support OWLReasoner::isEntailed, and hence may return false for all calls to OWLReasoner::isEntailmentCheckingSupported.
Support preserving, transferring, and adding annotations during OBO Macro expansion
Add Extensions to link document formats and common file extensions
Optimise annotation lookup for module extraction enrichment
Change strategy for MapPointer storage: do all initial insertions in a list, and turn it into a THashSet upon first call to trimToSize or any get/size calls
Add benchmarking util to load ontology then dump to an hprof file for use with MAT
Improve conversion from OWL to OBO, add test case

Bug fixes:

Fix PriorityCollectionSorting should be fixed at manager creation time #395
Fix OWLOntologyManagerImpl.getVersions() calls get() on Optional without checking if the contained value is present #401
Fix XMLLiterals should be output as XML, not quoted XML #333
Fix Should RDF/XML Renderer include annotation assertions from the entire closure? #371
Fix Using a PriorityCollection for IRI mappers (and perhaps other things) is confusing #386
Fix THashSets got left using default load factor (0.50) after construction is finished. #380
Fix RDF Consumer failing to guess property types #322
Fix NonMappingOntologyIRIMapper confuses extra OWLOntologyIRIMapper implementations #383
Fix Data property with xsd:integer range parsed as Object property (RDF/XML source) #378
Fix imports in OWL Manchester Notation fail #347
Fix ELProfile incorrectly rejects DisjointClasses axioms. #343
Fix OWLRDFConsumer fills guessed type declaration table with blank nodes #336
Fix #338 OWL-API: DOCTYPE declaration missing in XML serialization
Fix #337 Axiom Equality short-circuits are in the wrong place
Fixed bug when rendering anonymous individual in Manchester OWL syntax.
Reverted incorrect setting of all packaging types to bundle

4.0.1 22 November 2014

Features:

trimToSize available to cut ontology internals collections to minimal size after loading (Simon Spero)
various memory optimizations and caching of rarely used values removed (Simon Spero)
use of Trove collections for ontology internals
OBOFormat: Configuration option to skip validation before writing OBO file #290

Bug fixes:

fix a multithread bug revealed by owlapitools tests
fix #299 roundtrip errors on TriX and various other syntaxes
fix #292 SWRL rules saved by older versions of OWLAPI/Protege lose annotations
fix #288 Errors with object property assertions with inverseOf properties
fix #289 Manchester syntax errors: inverse() not recognized, SWRL rules rendered twice
fix #287 Error parsing RDF/Turtle with triple quoted literals - mismatching single and double quotes
fix #281 OntologyIRIShortFormProvider does wrong shortform generation

4.0.0 10 September 2014

Supported Java versions: Java 7, Java 8

Features:

added HasAnnotationPropertiesInSignature to uniform treatment of annotation properties
added missing EntitySearcher methods for negative property assertions
Use Trove collections for ontology internals
improved performance of OWLAxiomImpl.equals
Transform functions from Collection<OWLOntoloy> and Collection<OWLOntologyID> to Collection<IRI>
PMD critical violations addressed
fix ServiceLoader use to be OSGi compatible
create osgidistribution: osgidistribution is a jar with embedded dependencies and including the compatibility module. It addresses the issues due to the OWLAPI dependencies not being wrapped in OSGi bundles separately.
enabled OWLOntologyManager to build and keep a loader configuration
OBO 1.2 ontologies cannot be parsed by the 1.4 parser. Added 1.2 parser from OWLAPITOOLS to compatibility package.
added saveOntology() methods to OWLMutableOntology
Add a copy/move ontology method to OWLOntologyManager #12
Search introduced to replace forSuperPosition, forSubPosition, ignoreAnnotations booleans
Imports.INCLUDED, Imports.EXCLUDED introduced instead of boolean arguments #156
introduced ChangeApplied to simplify code around applying changes and remove null warnings
Introduction of Searcher with transform functions
OWLOntology now exposes a new method for searching for axioms referring an entity, abstracting all various getAxiomsBy... methods.
Refactor OWLSignature for uniform imports closure use
Refactored OWLAxiomCollection for uniform use of import closure
Added targeted parsing to allow one and only one parser to be tried on a document input source. Takes into account MIME type as well.
Use MultiMap from Guava throughout V4.0.0 #153
OBO parser updated and replaced with oboformat 5.5 release
@Nonnull annotations and warnings
Centralised and uniformed sax parser factories
OWLOntologyID to use Optional #160
Refactored property hierarchy to remove generics.
Added an OWLParser implementation to enable actual use of DL parser
Added a pairwise visitor, changed storage strategy for nary axioms. The pairwise visitor interface is a functional interface that is applied to all distinct pairs in a collection of objects.
Added asPairwiseAxioms to all nary axiom types
Added HasPriority annotation and comparator for prioritizable objects
Added PriorityCollection for managing injected collections
Added ServiceLoader adapter for Guice injection
Added ManchesterOWLSyntaxParser interface to api
OWLAPITOOLS profiles and fixers included
Added Profiles enumeration and supported OWL profile for known reasoners.
Dependency injection enabled for fixers.
Added Guice module for creating OWLOntologyManager and OWLDataFactory
Introduced OWLOntologyBuilder to allow swapping OWLOntology implementations via Guice
Service loader module in api to be used independently of the owlapi-impl module
Add RDFa parser and use static META-INF/services files for owlapi-rio
Add JSON-LD support
Add rdf:langString from RDF 1.1 to OWL/RDF vocabulary.
Better BOM treatment through Apache BOMInputStream
Use SLFJ for logging
Guava 17
Guice 4.0-beta
Added jsr305 for Nonnull and Nullable annotations
Fix build and javadoc for Java 8
Do not raise violations from entities used only in declarations.
Do not add declarations for illegal punnings when saving ontologies #112
Do not cache any literals in OWLDataFactoryInternalsImpl. Overall improvement of about 9% when parsing Gene Ontology in FSS.
Implement Default prefix manager in prefix ontology format objects cannot be overriden #9
Implement automatic retries when loading from URLs, managed through OWLOntologyLoaderConfiguration #66
Switched OWLDataFactory IllegalArgumentExceptions to NullPointerExceptions #131
Handle annotations on punned types when rendering RDF #183
Add OWLOntologyManagerFactory and code to allow use of RioOWLRDFParser through an injector
Convert RioParserImpl to stream statements through wherever possible
Default datatype in RDFLiteral to PLAIN_LITERAL.
Made generated classes package protected
Rename OWLObjectRenderer to FunctionalSyntaxObjectRenderer
OWLReasoner change lists generic
Moved OWLOntologyFormat implementation to formats package
Performance improvement for rdf/xml rendering
Optimised functional renderer and prefix manager
feature: OBO parser replaced with oboformat.
OWL2Datatype implements HasIRI
Add XSD IRIs simple parsing support #56
GZip read/write ability
Manchester OWL syntax cleanup

Bug fixes:

Fix #278 AutoIRIMapper is not namespace aware
Direct imports result not updated correctly after manual load #277
fix #275 DL Syntax rendering of disjoint classes missing comma
fix #271 OWLOntology.getXXXInSignature(boolean) and similar methods
fix #270 Add OWLOntology.getReferencingAxioms(OWLPrimitive)
fix #268 Add documentation to OWLOntologyID to clarify the relationship between isAnonymous() and getOntologyIRI()
fix #267 Consider adding containsXInSignature methods that do not have an imports flag to OWLOntology.
fix #254 OWLAsymmetricObjectPropertyAxiom not rendered in DL Syntax
fix OWLDocumentFormat as interface #258 #259
fix #260 and fix #261 data and object cardinality are quantified restricitons
fix #255 PrefixOWLOntologyFormat is missing from the compatibility module
fix #253 StructuralReasoner.getSameIndividuals does not behave as advertised
Fixed #198 A SubClassOf B will not parse
Fixed IRI with a space: %20 escape #146
Old OWLEntityCollector brought forward as DeprecatedOWLEntityCollector
Fixed serialization warnings reported in #163
Use AtomicLong for concurrency support in gzip document sources
Moved transitive object property type to rbox
Set turtle default prefix slash aware #121
Fixed #116 import statement erroneously names anonymous ontology
Added test for roundtripping annotated SWRL rules and datatype definitions
Fixed annotations on datatype definition axioms fixed in OWL/XML
Fixed #20 and #60 use zipped buffer for StreamDocumentBase
Fixed #71 Misleading message on resolving illegal IRI
Fixed variable rendering in Manchester OWL Syntax to preserve ns.
Fixed #46 Round tripping error in functional syntax
Fixed #40 RDFGraph.getSortedTriplesForSubject throws exception in Java7
Fixed infinite recursion on cyclic import structures when declaration does not match location.

3.4.10 18 January 2014

Features:

Improved feature 32 implementation (simple SWRL variables rendering)
javadoc warnings and errors removed to allow building with Java 8
refactored OWLAxiomVisitorExAdapter for general use
performance improvement for rdf/xml
Renamed variables, added explicit flush. Fixes #67 slow functional sytnax renderer on Java 6
default, final and abstract classes changed to allow interface verification
add oraclejdk8 early access build to travis
update oboformat class names to sync with oboformat project
make OBOFormatException extend OWLParserException

Bug fixes:

Fixes #72 Manchester syntax roundtrip of doubles and SWRL rules fails
Fixes #24 Manchester Syntax writer generates unparsable file
simple renderer writes duplicate annotations
Optimised functional renderer and prefix manager
Fix #63 null pointer exception loading an ontology and fix #64 empty ontology returned
Fixes #63 OBO Ontology Parsing throws NullPointer
updated OSGi settings for oboformat, module name, dependencies
fix bundle configuration for oboformat

3.4.9 25 November 2013

Features:

Added default methods and return values for a few visitor adapters
#57 Reimplement NodeID so that it doesn't use an inner class
#56 parse things like xsd:string easily
OBO parser replaced with oboformat. Original code at: https://code.google.com/p/oboformat/

Bug fixes:

Fixed wrong naming of gzip file source and target and added stream only versions.
Restore UnparseableOntologyException interface
Added back deprecated parseConstant for compatibility with Pellet CLI code. Warning: it has bugs.

3.4.8 02 November 2013

Features:

GZip read/write ability. Compressed gzip input and output streams, but make sure to close the stream in the calling code.
OSGI dependency removed
Added Namespaces.inNamespace
Made ParserException to extend OWLParserException, and OWLParserException a runtime exception.
Tidying up Manchester OWL Syntax parser code
Added to the documentation on getOWLDatatype(OWLDataFactory)
Added a convenience method to convert an OWL2Datatype object to an OWLDatatype.
mvn install and mvn deploy now make aggregate sources available.
Added more well known namespaces, removed non-explanatory comments
Added RDFa Core Initial Context prefixes and other well known prefixes and prefix names.
GITHUB-10 : Add RDFa Core Initial Context prefixes
Extend Namespaces enum with common prefixes

Bug fixes:

Fixes #40 Fixes #7 RDFGraph.getSortedTriplesForSubject throws exception in Java7 Refactored TripleComparator into RDFTriple and RDFNode as Comparable
DLQueryExample did not print the StringBuilder with the answers
Fixes #50 Null anonymous individual parsing ObjectHasValue from OWL/XML
Fixes SF 313 Man Syntax Parser gives facets unexpected datatype
Fixes SF 101 Manchester OWL Syntax Parser doesn't do precedence correctly
Fixes #43 Functional Syntax Parser does not support comments
Fixes #41 Parsing error of SWRL atom.
Fixes #46 Round tripping error in functional syntax
Fixes #37 setAddMissingTypes logging if disabled
Missed serialization transients and tests, serialization bug fixes
Patch IRI.create(String,String) to match IRI.create(String)

3.4.5 25 July 2013

Features:

Refactored DefaultPrefixManager to expose addPrefixes
Updated pom files for OSGI compatible artifacts.
Allow override of DefaultPrefixManager in PrefixOWLOntologyFormat
Add CollectionFactory.getExpectedThreads
Reduce expected threads from 16 to 8 to improve general performance

Bug fixes:

literal parsing error was stopping HermiT builds with 3.4.4.
errors in OSGI support were stopping Protege from using the feature.
Fix #370 Typo in website/htdocs/reasoners.html.
Fixed a bug with large integer values being parsed as negative ints.
Fix infinite recursion on cyclic import structures.
Reverted the use of ThreadLocal as this causes memory leaks in webapps.
Bug #343 SWRL roundtrip in manchester syntax

3.4.4 19 May 2013

Features and updates implemented:

feature 103 - Add methods to get EntityType names.
Updated IRI prefix caching to use thread local caches rather than synchronized caches.
added test for annotation retrieval for anonymous individuals.
WeakIndexCache vulnerability fixed.
Improved redirect following.
Added method to OWLOntologyLoaderConfiguration to disable cross protocol redirects on URLConnections.
Added parameter to OWLOntologyFormat for temp files, default disabled.
Update all JavaCharStream versions to fix the UTF BOM issue.
Travis Integration (on github).
Update KE interface with getBlocker method.
OSGI compatible build.
Removed IRI.toString() call when checking blank nodes.
Change logging of remaining triples to use less memory.
updates for javadoc.
Update Mockito to 1.9.5.

Bug fixes:

Bug #369 IRI.create(String) uses / and # to look for namespace and fragments.
Bug #348 ManchesterOWLSyntax round trip problem with disjoint classes.
Bug #269 single anonymous individual split in two on save to RDF.
Bug #319 redirects from http to https are not followed.
Bug #367 Serving ontologies from github as well.
Bug 4 (github) Missing method in OWLIndividual.
Bug 359 Incorrect Javadoc in OWL2DatatypeImpl and redundant javadoc.
Bug 360 - Axiom annotations are not parsed correctly.
Bug 364 Null pointer checking for containment of anonymous ontologies.
Bug #363 Turtle parser fails when loading valid Turtle document.
Bug 362 - owlapi files in temp folder.
Bug 357 duplicate axioms saving in OWL functional syntax.
Bug 355 - added assertions. Ability to parse 1+e7 as 10000000.
Bug 355 - Turtle Parser + Integer format Problem.
OntologyAlreadyExist bug when calls are made too fast.

3.4.3 26 Jan 2013

Features implemented:

Updated OWLFunctionalSyntaxFactory with more methods.
Removed deprecated method calls.
Test package broken up in smaller packages.
Web site updated and added to version management.

Bug fixes:

Changed VersionInfo message default to provide more information.
Bug 354 fixed: There is AnnotationChange, but no AnnotationChangeData
Bug 353 fixed: SimpleRenderer renders SubDataPropertyOfAxiom wrong.
Bug 351 fixed: QNameShortFormProvider swapped prefix and iri.
Bug 352 fixed: SimpleRenderer does not escape double quotes in literals.

3.4.2 4 December 2012

Features implemented:

Repository migrated to Git.
Fixed memory leak with OWLObject signatures never being released once cached.
Improved Serializable implementation.
Made timeout property functional.
3585007 Make OWLAxiomChange.isAdd().
3579488 Clean documentation page.
3578004 Javadoc OWLRDFVocabulary.
3578003 Add OWLOntologyManager.removeOntology(OntologyID).
3578002 Add new constructor for SetOntologyID.
3576182 Bump minimum java version to 1.6.
3575834 Improvements to OWLOntologyManager and related contrib.
3566810 Lack of support in OWLOntologyManager for version IRIs.
3521809 KRSS parser throws Error instead of RuntimeException.

Bug fixes:

Some OWLLiterals cannot be optimised: -0.0^^xsd:float, 01^^xsd:int (optimisation with primitive types makes reasoners queasy in combination with W3C tests).
3590243 hashCode for literals inconsistent.
3590084 misuse of XMLUtils.getNCNameSuffix().
3581575 OWLOntologyDocumentAlreadyExistsException in OWL API 3.4.1.
3580114 IRI isAbsolute method.
3579862 OWLDataFactory.getRDFPlainLiteral creates new objects.
3579861 rdf:PlainLiteral is not in the allowed OWL2EL datatypes.

3.4.1 16 September 2012

Features:

3578004 OWLRDFVocabulary Javadoc
3575834 Improvements to OWLOntologyManager and related contrib

Bug fixes:

3463200 rdf/functional round trip problem (anonymous individuals)
3341637 round trip problem with owl functional or rdf/xml syntax
3576182 Bump minimum java version to 1.6 (Fixed the bugs, moved the request to feature requests)
3497161 Manchester syntax imports
3403855 Imports of multiple ont docs containing the same ont fails
3491516 unhelpful Manchester parse exception
3536150 TypeOntologyHandler/TPVersionIRIHandler overwrite ontologyID
3314432 Manchester OWL parser does not handle data ranges in rules
3186250 annotation assertion lost when annotation prop undeclared
3309666 [Turtle] Parsing turtle files containing relative IRIs
3562296 Switch version 3.4.1 to 3.4.1-SNAPSHOT
3560287 Is QNameShortFormProvider deprecated?
3566820 Missing Imports are not reported
3306980 file in Manchester OWL Syntax with BOM doesn't parse
3559116 Wrong VersionInfo in OWL-API 3.4 release
2887890 Parsing hasValue restrictions with punned properties fails
3178902 RDF/XML round trip problem with 3-way equivalent classes
3174734 ManSyntax fails to read ontology with single data property
3440117 Turtle parser doesn't handle qnames with empty name part

3.4 12 August 2012

This version restructures the Maven modules into six modules: api, impl, parsers, tools, apibinding and contract. Code is unchanged, only its organization in the SVN is changed.

To split the dependencies accordingly, DefaultExplanationOrderer is in contract and is only a shell for ExplanationOrdererImpl, which does not depend on OWLManager directly. This enables the tools module to be used with a different apibinfing without recompilation.

Bug fixes:

3554073 Manchester Syntax Parser won't parse DisjointUnionOf
3552028 DataFactory returns integer instead of double restrictions
3550607 property cycle detection does not work
3545194 OWLEquivalentObjectProperties as SubObjectPropertyOfAxioms
3541476 OWLRDFConsumer.getErrorEntity counter is not thread safe
3541475 Remove shared static in OWLOntologyXMLNamespaceManager
3535046 Use ArrayList instead of TreeSet in TurtleRenderer
3532600 Use AtomicInteger in OWLOntologyID for counter

3.3 15 May 2012

This version wraps together some minor bug fixes and some performance improvements for loading time and memory footprint for large ontologies. Maven support has been much improved, thanks to Thomas Scharrenbach's efforts and Peter Ansell's feedback and suggestions.

Features:

Performance improvements at loading time

Bug fixes:

OBO Parser updated to be more compliant with the latest draft of the OBO syntax and semantics spec.
OBO Parser doesn't expand XREF values (3515525)
Integrating with OpenRDF (3512217)
maven should use snapshot versions during development (3511755)
junit should be in maven test scope (3511754)
mvn clean install requires gpg key (3511732)
OWLOntologyManager.contains(IRI) bug (3497086)
Functional and Manchester syntax writers prefix problem (3479677)
SyntacticLocalityModuleExtractor and SubAnnotationPropertyOf (3477470)
Ignored Imports List uses the wrong IRIs (3472712)
OWLLiteralImpl corrupts non-ascii unicode (3452932)
OWLOntologyXMLNamespaceManager QName problem (3449316)
MultiImportsTestCase assumes incorrect working directory (3448125)
Mismatch between HasKeyTestCase and corresponding resource (3447280)
functional Renderer: OWLObjectRenderer swaps SWRL variables (3442060)
maven build fails because of dependency issue (3440757)
manchester owl syntax doesn't handle rules with anon classes (3421317)
RDFTurtleFormatter doesn't escape '' (3415108)
RDF consumer does not check for all annotated axiom triples (3405822)
mis-parsing/mis-serialization of haskey (3403359)
Literal not a builtin (3305113)
OWL API throws NullPointerException loading ontology (3302982)

3.2.1 22 July 2011

This version of the API is released under both LGPL v3 and Apache license v2; developers are therefore free to choose which one to use.

Features:

Tutorial code has been added following the OWLED 2011 tutorial (subpackage tutorialowled2011);
A visitor to determine whether a set of axioms is a Horn-SHIQ ontology has been added (HornAxiomVisitorEx.java).

Bug fixes:

Some test files and extra modules had not had their copyright notices updated to the new license; this has now been fixed.

3.2.3 27 May 2011

This version of the API is released under both LGPL v3 and Apache license v2; developers are therefore free to choose which one to use.

Bug fixes:

MAVEN support has been fixed (3296393).
Some minor problems with rdfs:Literal have been fixed (3305113).
Parsers and renderers for various languages have had some corner case errors fixed (3302982, 3300090, 3207844, 3235181, 3277496, 3294069, 3293620, 3235198).
An error in OWLOntologyManager.removeAxioms() which was throwing ConcurrentModificationExceptions when called on a specific axiom type has been fixed (3290632).
OWLOntologyLoaderConfiguration has been introduced to provide ontology wise parsing configuration (strict and lax parsing modes now enabled) (3203646) More options coming up.
Parsers no longer leave streams open when a parsing error is detected (3189947).

3.2.2 17 February 2011

Bug fixes:

In RDF based serialisations, type triples for entities that don't have "defining axioms" don't get added even if the renderer is instructed to type undeclared entities (related to 3184131). Fixed.
The RDF parser would not recognise XSD datatypes that aren't OWL 2 Datatypes even in lax parsing mode (related to 3184131). Fixed.
OWLOntologyManager.createOntology() methods don't set the document IRI of the created ontologies as adverstised if there aren't any ontology IRI mappers installed (3184878). Fixed.

3.2.1 4 February 2011

Bug fixes:

Issues with -INF as serialisation for -infinity for floating point literals. Fixed.
Null pointer exception can be thrown by OBO parser (3162800). Fixed.
OWLOntologyManager.loadOntology() can throw unchecked exceptions (IllegalArgumentException) (3158293). Fixed.
OWLOntologyAlreadyExistsException get wrapped as as a parse exception by the OBO parser. (3165446). Fixed.
OWLRDFConsumer (OWL RDFParser) used owl:Datatype instead of rdfs:Datatype. Fixed.
OWLOntology.getDisjointUnionAxioms() does not work as expected. (3165000). Fixed.
Anonymous ontologies do not get typed as owl:Ontology during saving in RDF. (3158177). Fixed.
OWLOntology hashCode is not implemented properly. (3165583). Fixed.

3.2.0 14 January 2011

This version of the API includes various bug fixes and performance enhancements since version 3.1.0

Bug fixes:

Various round tripping problems for various syntaxes (3155509, 3154524, 3149789, 3141366, 3140693, 3137303, 3121903)
Plain Literals are rendered incorrectly. Fixed.
Cyclic imports cause an OntologyAlreadyExistsException to be thrown. Fixed.
OWLAxiom.getAnnotatedAxiom() does not merge annotations. Fixed.
OWLObject.getSignature() returns an unmodifiable collection. Fixed.
Various problems with character encodings (3068076, 3077637, 3096546, 3140693). Fixed.
IRI.create resulted in a memory leak. Fixed.
Imports by location does not work. Fixed.
Various problems with anonymous individuals (2998616, 2943908, 3073742). Fixed.
Dublin Core Vocabulary is built into OWL API parsers. Fixed.
Files are left open on parse errors. Fixed.

3.1.0 20 August 2010

This version of the API includes various bug fixes and enhancements since version 3.0.0.

Features:

Changes to the representation of literals:

Please note that there is a slight incompatibility between version 3.1.0 and version 3.0.0. This is due to some changes in the way that literals are represented and handled in the API. There was a disparity between how they are described in the OWL 2 specification and how they are represented in version 3.0.0 of the API. The changes bring 3.1.0 inline with the OWL 2 specification. The changes are as follows: OWLStringLiteral and OWLTypedLiteral have been removed and replaced OWLLiteral. In version 3.0.0 OWLLiteral was a super-interface of OWLStringLiteral and OWLTypedLiteral. Clients therefore need to replace occurrences of OWLStringLiteral and OWLTypedLiteral with OWLLiteral. Method calls need not be changed - methods on OWLStringLiteral and OWLTypedLiteral have corresponding methods on OWLLiteral. Note that all literals are now typed. What used to be regarded as OWLStringLiterals are now OWLLiterals with the datatype rdf:PlainLiteral. Although this change introduces a slight backward incompatibility with the previous version of the API we believe that the handling of literals in 3.1.0 is much cleaner and follows the specification more closely.

Changes to the OWLReasoner interface:

The OWLReasoner interface has been updated. There are now methods which allow for fine-grained control over reasoning tasks. For example, it is now possible to request that a reasoner just classifies the class hierarchy, when in version 3.0.0 the prepare reasoner method caused realisation to occur as well. The prepareReasoner method has been removed from the interface due to the huge amount of confusion it caused (it was not necessary to call this method to get correct results, but the name suggested that it was necessary). Clients should update their code to replace any calls to prepareReasoner with appropriate calls to precomputeInferences.

JavaDoc for various methods has been cleaned up.

Bug fixes:

Annotations on Declaration axioms were not save. Fixed.
OWLObjectMaxCardinality restrictions incorrectly resulted in a profile violation of the OWL2RL profile. Fixed.
OWLOntology.containsAxiom() failed various round trip tests. Fixed.
OWLObjectPropertyExpression.getInverses() did not include properties that were asserted to be inverses of themselves. Fixed.
Writing large rdf:Lists can cause a stack overflow on saving. Fixed.
System.out is closed when using SystemOutDocumentTarget. Fixed.
An OWLOntologyAlreadyExists exception is thrown when an imports graph contains multiple imports of the same ontology. Fixed.
OWLReasoner.getSubclasses() is missing declarations in the throws list for runtime exceptions that get thrown. Fixed.
Parsing RDF graphs containing blank nodes with NodeIDs is broken. Fixed.
Some methods on OWLOntology return sets of object that change with ontology changes. Fixed.
Double dashes (--) are not escaped in XML comments output by the XMLWriter. Fixed.
The API sometimes prints to System.err. Fixed.
The functional syntax writer writes out annotation assertions twice. Fixed.
Ontologies with DataSomeValuesFrom restrictions are incorrectly considered non-OWL2QL. Fixed.
Ontologies with Functional data properties are incorrectly considered non-OWL2RL. Fixed.
OWL2Datatype.XSD_NAME has the wrong regex pattern. Fixed.
RDF rendering of GCIs with multiple elements is broken. Fixed.
SubObjectPropertyOf axioms with annotations and property chains don't get parsed correctly from RDF. Fixed.
StructuralReasoner sometimes crashes when determining superclasses. Fixed.
SimpleRenderer renders declarations incorrectly. Fixed.
Object property characteristics are not answered correctly. Fixed.
OWLOntology.getReferencingAxioms gives mutable and incorrect results. Fixed.
StructuralReasoner call OWLClassExpression.asOWLClass() on anonymous classes. Fixed.
SKOSVocabulary is not up to date. Fixed.
Regular expression for xsd:double has extra white space. Fixed.
Structural reasoner sometimes misses subclasses of owl:Thing. Fixed.
OWLOntologyManager.getImportsClosure() fails on reload. Fixed.
PrefixOWLOntologyFormat has not methods to remove prefixes. Fixed.
RDF/XML rendering of unicode characters is ugly. Fixed.
Turtle parser does parse shared blank nodes correctly. Fixed.

3.0.0 28 January 2010

Version 3.0.0 is incompatible with previous releases. Many interface names have been changed in order to acheive a close alignment with the names used in the OWL 2 Structural Specification and Functional Style Syntax. (See http://www.w3.org/TR/2009/REC-owl2-syntax-20091027/)

The opportunity to clean up method names was also taken.

2.2.0 17 April 2008

Features:

Added support for building using ANT
OWL 1.1 namespaces changed to OWL 2. Old ontologies that are written using the owl11 namespace will still load, but will be converted to use the owl2 namespace.
Updated the RDF parser and RDF rendere to support AllDisjointClasses and AllDisjointProperties
Added the ability to save ontologies in Turtle.
Added the ability to load ontologies that are written in Turtle
Added explanation code contributed by Clark & Parsia
Added a KRSS renderer (contributed by Olaf Noppens)
Added a new, more comprehensive KRSS parser (contributed by Olaf Noppens). This parser can parser the version of the KRSS syntax that is used by Racer.
Added the ability to specify a connection timeout for URL connections via a system property (owlapi.connectionTimeOut) - the default value for the timeout is 20 seconds.
Added a method to OWLOntologyManager to clear all registered URI mappers
Added a method to OWLOntologyManager so that imports can be obtained by an imports declaration.
Added a convenience method to OWLOntologyManager to add a set of axioms to an ontology without having to create the AddAxiom changes
Added a makeLoadImportsRequest method on OWLOntologyManager which should be used by parsers and other loaders in order to load imports
Added the ability to set an option for silent missing imports handling on OWLOntologyManager. When this option is set, exceptions are not thrown when imports cannot be found or cannot be loaded. It is possible to set a listeners that gets informed when an import cannot be found, so that the exception doesn't get lost entirely.
Added the ability to add a ontology loader listener to OWLOntologyManager. The listener gets informed when the loading process for an ontology starts and finishes (which ontology is being loaded, from where and whether it was successfully loaded etc.).
Added a method to OWLReasonerFactory to obtain the human readable name of the reasoner that a factory creates.
Added a convenience method to OWLOntology to obtain all referenced entities
Added convenience methods to OWLEntity that check whether the entity is an OWLClass, OWLObjectProperty, OWLDataProperty, OWLIndividual or OWLDatatype. Also added asXXX to obtain an entity in its more specific form.
Added convenience methods to OWLDataFactory for creating disjoint class axioms and equivalent classes axioms.
Added a general purpose renderer interface for OWLObjects
Added an OWLInconsistentOntologyException to the inference module.
Added SKOS core to the list of well known namespaces
Added a SKOS vocabulary enum
Added methods to the OWLOntologyManager interface, so that ontologies can be saved to an output target as well as a URI. Added implementations of OWLOntologyOutputTarget to enable writing directly to OutputStreams and Writers.
Added a StringOutputTarget for writing ontologies into a buffer that can be obtained as a string.
Added some new input sources: StreamInputSource, ReaderInputSource, FileInputSource
RDF Parser. Made the classExpression translator selector more intelligent so that when properties aren't typed as either object or data properties, other triples are examined to make the appropriate choice.
OWLRestrictedDataRangeFacetVocabulary. Added methods to obtain facets by their symbolic name (e.g. >=)
BidirectionalShortFormProvider. Added a method to obtain all short forms cached by the provider.
Added an option to turn tabbing on/off when rendering Manchester Syntax
Added more documentation for the method which adds ontology URI mappers
Improved error handling when loading ontologies: For errors that have nothing to do with parse errors e.g. unknown host exceptions, the factory will rethrow the error at the earliest opportunity rather than trying all parsers.
Updated parser to throw ManchesterOWLSyntaxOntologyParserException which is a more specific type of OWLParserException
Updated the BidirectionalShortFormProviderAdapter with functionality to track ontology changes and update the rendering cache depending on whether entities are referenced or not.
Added a latex renderer for rendering ontology axioms in a latex format
Added the ability to parse ontologies written in ManchesterOWLSyntax
Added URIShortFormProvider as a general purpose interface for providing short forms for URIs. Changed SimpleShortFormProvider to use the SimpleURIShortFormProvider as a base
Made the toString rendering of the default implementation pluggable via the ToStringRenderer singleton class.
Added some convenience methods to the OWLDataFactory to make creating certain types of objects less tedious. Specifically: ObjectIntersectionOf, ObjectUnionOf, ObjectOneOf and DataOneOf can now be created using methods that take a variable number of arguments (OWLDescriptions, OWLIndividuals or OWLConstants as appropriate). Also, added convenience methods that create typed literals directly from Java Strings, ints, doubles, floats and booleans. For example, createOWLTypedConstant(3) will create a typed literal with a lexical value of "3" and a datatype of xsd:integer. Added convenice methods for creating entity annotations without manually having to create OWLAnnotation objects.
Added a getAxiomType method on to the OWLAxiom interface for convenience.
Added functionality to the debugging module for ordering explanations
Added generics to the inferred axiom generator API
Added a new constructor to OWLOntologyNamespaceManager so that it is possible to override the ontology format that is used as a hint when generating namespaces.
Added a dlsyntax renderer module that can renderer axioms etc. in the traditional dlsyntax using unicode for the dlsyntax symbols.
Modified the RDFXMLNamespaceManager to select the minimal amount of entities for which namespaces need to be generated. Namespaces are only generated for classes in OWLClassAssertionAxioms, and properties in OWLObjectPropertyAssertionAxioms and OWLDataPropertyAssertionAxioms. This basically corresponds to the places where valid QNames are needed for entities.
Added code to add declarations for "dangling entities". If an RDF graph contains <ClsA> rdfs:type owl:Class and ClsA has not been referenced by any other axioms then this would have been dropped by the parser - this has been changed so that declaration axioms are added to the ontology in such cases. (Hopefully, the OWL 1.1 spec will be updated to do something like this in the mapping to RDF graphs).
Added a utility class, AxiomSubjectProvider, which given an axiom returns an object which is regarded to be the "subject" of the axioms. For example given SubClassOf(ClsA ClsB), ClsA is regarded as being the subject.
Modified the ontology URI short form provider to provide nicer looking short forms.
Added a convenience method to get the individuals that have been asserted to be an instance of an OWLClass.
Commons lang is no longer used in the API because it had been replaced with a lightweight utility class in order to escape strings.
Removed the fragments module and replaced it with the profiles module. The EL++ profile is currently implemented.
Added support for extended visitors that can return objects in the visit method.
Turned off logging in the RDF parser classes by default.

Bug fixes:

The getOntologyURIs method on AutoURIMapper would return physical rather than logic URIs. Fixed.
Namespaces for annotation URIs weren't generated. Fixed.
Removing a subclass axiom from an ontology cause the axiom to be added to the ontology as a GCI. Fixed.
When parsing an ontology, the accept types has been set to include RDF/XML. This means that ontologies can be parsed correctly from servers that are configured to return RDF or HTML depending on the request type.
OWL/XML writer has been modified to write the datatype URI attribute name correctly. Previously the name was written as "Datatype", however it should be "datatypeURI".
OWL/XML parser. Modified the literal handler to parse literals using the correct datatype URI attribute name (was "Datatype" and should have been "datatypeURI").
The constructor that required a manager in BidirectionalShortFormProviderAdapter did not rebuild the cache. Fixed.
Unqualified cardinality restrictions were rendered out as qualified cardinality restrictions. Fixed.
Saving an ontology would fail if the necessary directories did not exist. Fixed.
Rendering anonymous property inverses in OWL/XML was incorrect. Fixed.
Label and Comment annotations in the functional syntax weren't parsed properly, they were parsed as regular annotations. Fixed.
In the OWLXMLParserHandler, no handler for negative data property assertions was registered. Fixed.
Annotations that have anonymous individuals as values weren't rendered correctly. Fixed.
RDFXMLOntologyStorer and RDFXMLRenderer always used the ontology format that is obtainable from the manager, regardless of whether or not a custom ontology format was specified - fixed.
Rules that contained individual or data value objects couldn't be rendered. Fixed.
Declaration axioms were automatically added for data properties whether an ontology contained declaredAs triples or not. Fixed.
Anonymous properties weren't rendered correcty. Fixed.
RDF rendering for sub property axioms whose sub property is a property chain used an old rendering. The rendering now complies with the latest OWL 2 specification. Ontologies that use the old rendering can still be parsed.
RDF lists were reordered on rendering. Fixed.