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ROBOT annotate with provencance duplicates annotations. #1098

@areleu

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@areleu

Related to this issue OpenEnergyPlatform/ontology#1474

Other general problem is that some annotations are being duplicated. This meets particularly the label axioms. It is very annoying that I can't really find the root cause.

Edit: This is definitively a problem with ROBOT, when using the annotate command with --annotate-derived-from or the --annotate-defined-by I don't think the axioms should be duplicated but replaced. The output file has both:

<rdfs:label xml:lang="en">preceded by</rdfs:label>

and

<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000062"/>
    <owl:annotatedProperty rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
    <owl:annotatedTarget xml:lang="en">preceded by</owl:annotatedTarget>
    <prov:wasDerivedFrom rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2023-02-22/ro.owl"/>
</owl:Axiom>

While it should only have the latter.

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