After having some issues with extending an existing ontology using Python
as described in the docs, I had a look at the source code. What I found could be an issue, at least it should be mentioned in the docs:
The docs explicitly mention not to load an ontology before extending it ("Do not load the ontology here!"). When using the with-statement to "switch" to a certain ontology for extending it, the load flag of that ontology is set to True (line 873 in namepspace.py). This causes issues when subsequently loading an ontology using load(), as this has no effect, e.g. all individuals are not loaded. The workaround is to pass the reload=True flag.