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ROBOT is an OBO Tool
I have two ontologies O and U and need to produce an ontology X as follows: 1) take all axioms from diff(O, U) and add to X 2) take all...
Some ontologies contain axioms that will not properly convert to OBO, and the OBO writer sometimes fails with no good information on how to fix the issue - see https://github.com/OBOFoundry/COB/issues/168...
Dear All, I am trying to develop an ontology where some classes make reference to specific external uris, like for instance: http://purl.obolibrary.org/obo/BFO_0000019. The class with this URI is successfully created,...
see #887 Please do not even look at this, just needed a place to stache it for safety. I may still withdraw this PR.
when using `robot reason --annotate-inferred-axioms true`, we end up with this axiom `oboInOwl:is_inferred "true"^^xsd:string` Should it be `^^xsd:boolean` instead?
Robot annotate `--axiom-annotation` parameter is always giving the below error: ``` java.lang.UnsupportedOperationException: errors#AXIOM TYPE ERROR cannot annotate axioms of type: class uk.ac.manchester.cs.owl.owlapi.OWLAnnotationAssertionAxiomImpl at org.obolibrary.robot.OntologyHelper.addAxiomAnnotation(OntologyHelper.java:95) at org.obolibrary.robot.OntologyHelper.addAxiomAnnotation(OntologyHelper.java:71) at org.obolibrary.robot.OntologyHelper.addAxiomAnnotations(OntologyHelper.java:112) at org.obolibrary.robot.AnnotateCommand.execute(AnnotateCommand.java:254)...
robot extract --annotate-with-source currently annotates extracted terms with the IRI of the source ontology. It would be more useful if the version-iri was used for this (or this could be...
On the OBO Slack a user pointed out that we handle ".json" extension differently for input and output. We are interpreting input JSON as JSON-LD https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java#L392 while the output JSON...
I tried the following test (on the way to trying to figure out how to extract from this ontology): ``` $ robot validate-profile --profile DL -I http://identifiers.org/so OWL 2 DL...
I have tabular instance data with linkml related info, such as linkml:required, a true / false boolean shown below.  Is there a way of just controlling the datatype of...
