My response:

Materialize still produces an ontology that is in some sense non-redundant. It lacks the analog of --include-indirect in reason

However, we should clarify the intended semantics. the words "direct" and "redundant" are often used imprecisely

consider:

car SubclassOf has part some wheel
convertible SubclassOf car
wheel SubClassOf has part some hubcap
Transitive(has part)

visualized as:

Would you also expect to see convertible has-part hubcap?

This is in some sense the most straightforward scenario and is the output of relation-graph

If you want the most specific relationships materialized, currently this is only handled by OAK:

• https://github.com/INCATools/ontology-access-kit/releases/tag/v0.6.4
• Add option to relationships for walking up subclass hierarchy INCATools/ontology-access-kit#739

runoak -i car.db relationships .all --non-redundant-entailed

runoak -i car.db relationships .all --include-entailed

Note: it's OK to close this as out of scope, as robot doesn't have a very graphy view of the universe, but I wanted to capture the discussion where it won't be swallowed by the slack memory vortex

An alternative is the plain reason command with emr as the reasoner:

robot reason --include-indirect true --reasoner emr -i car.owl -o car2.owl

this includes things like 'car has-part hubcap`

I want to start a bit with robot development, so I decided to pick this issue.
However, it didn't work, the key is this:

Set<OWLClassExpression> sces = emr.getSuperClassExpressions(c, !includeIndirect);

@cmungall you know how better how emr works. Can you help me with that?

An alternative is the plain reason command with emr as the reasoner:

robot reason --include-indirect true --reasoner emr -i car.owl -o car2.owl

this includes things like 'car has-part hubcap`

Unfortunately, this adds also a lot of "noise" such as 'convertible subClassOf owl:thing'

One option would be to use relation-graph and then merge the output using ROBOT:

relation-graph --ontology-file input.owl --mode OWL --output-file relations.nt --property 'http://purl.obolibrary.org/obo/RO_0002162' --output-subclasses false

or leave off the property argument if you want all properties materialized.