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getAnnotation() currently returns a string. When there are multiple annotations using the same annotationProperty, this string consists of one of the annotationProperty chosen seemingly at random. Given that it is always possible for an OWLEntity to be annotated with multiple annotationProperty axioms using the same annotationProperty, getAnnotation() should return an array.
A new method was created to retrieve the value of all annotations: getAnnotations("entity", "annotationProperty"). The feature is part of the release 1.5.1. More info in the documentation.
Request to be able to retrieve the array of annotations
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