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test.owl:
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/ro.owl#"
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://purl.obolibrary.org/obo/ro.owl"></owl:Ontology>
<!-- dodgy URI -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#http://www.w3.org/2000/01/rdf-schema#seeAlso"/>
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">part of</rdfs:label>
</owl:ObjectProperty>
</rdf:RDF>
robot convert -i test.owl -o z.owl && cat z.owl
WARN http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
WARN entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
INFO Notice: root element does not have an xml:base. Relative IRIs will be resolved against file:/Users/cjm/repos/porifera-ontology/src/ontology/test.owl
WARN http://www.oracle.com/xml/jaxp/properties/entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
WARN entityExpansionLimit not supported by parser type org.apache.xerces.jaxp.SAXParserImpl
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/ro.owl#"
xml:base="http://purl.obolibrary.org/obo/ro.owl"
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://purl.obolibrary.org/obo/ro.owl"/>
</rdf:RDF>
<!-- Generated by the OWL API (version 0.0.1-SNAPSHOT) https://github.com/owlcs/owlapi -->
Note the OP is silently lost.
The root cause is presumably the strange URI for the AP. However, if this is invalid an error should be thrown. If it is not invalid then the OP should pass through.
There is a hint in the OWLAPI version. Why does it say OWL API (version 0.0.1-SNAPSHOT). The pom says to get 4.2.6
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