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I have a "core" ontology (core.owl) in which I import a separated online ontology (imports.owl) using Protégé, ending up with a declaration in header

<Import>https://raw.githubusercontent.com/...../imports.owl</Import>

Some classes are found both in core.owl and in imports.owl, to structure the final hierarchy. Unfortunately in both ontologies they also include annotations (such as rdfs:label) resulting in the duplication of a number of annotations in the final ontology, which is no good (for example, violates the OBO profile) and is what I'd like to solve.

Could anyone suggest methods to:

  1. identify classes in both ontologies
  2. remove all annotations those classes have in the core.owl ontology
Svito
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  • Try manual import, as described [here](https://stackoverflow.com/a/44266590). Select "Axioms by type" on step 4, then _do not_ select "Annotation Axioms". – Stanislav Kralin Apr 09 '21 at 20:51
  • Thank you. I want to keep the importing method as it is in a separted owl file so the manual import would not do. I think that the process you pointed out would work, not in the importing or copying classes between ontologies, but rather by deleting axioms in `core.owl` *if* they are included in the `imports.owl`. The process form Refactor in Protégé is however all manual it seems (i.e. I need to manually select all classes for which deleting axioms); are there some ways to do it automatically (i.e. finding overlaps classes and then remove all annotation assertions for those classes)? – Svito Apr 10 '21 at 08:00
  • AFAIK, you do not need to select classes one-by-one after choosing "Axioms by Type". – Stanislav Kralin Apr 10 '21 at 09:19

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