Question about remove

[srobb1]

Hello All,
I have two relationship terms that are causing me issues from imports when I use reasoning. If I delete these two terms using protege (highlight term and click the delete button) then "start reasoner", all is good.

I am trying to do this atomically with robot. Below is my command. When I run this the terms are indeed removed from my ontology but when I open the simr-clean and try to reason I get crazy errors.

robot remove  --input simr.owl -t CLO:0000015 -t OBI:0000293 --select "self descendants" --signature true --output simr-clean.owl

I have also tried

robot remove  --input simr.owl -t CLO:0000015 -t OBI:0000293   --output simr-clean.owl

as well as variety of other variations.

What robot command can I use to replicate the protege delete?

Thank you,
Sofia

[beckyjackson]

Would you mind sharing the file that you're using so I can recreate this issue? Thanks!

[srobb1]

Thank you for helping with this. Here is my owl file:

simr.owl

Thanks!
Sofia

[beckyjackson]

Hi again - it looks like there's something weird going on with --preserve-structure true and the object properties. I'm going to look into this, but for now, you should be able to get a clean output by adding --preserve-structure false (or -p false). Since you're just removing those two object properties, it shouldn't make a difference for the hierarchy.

[srobb1]

Hi @beckyjackson Thanks!! It seems like it is working, but any idea why I get
owl:Nothing is_a owl:Nothing after I reason? By the way, I am using elk-0.5.0.snapshot.

[balhoff]

@srobb1 if you are using the latest ROBOT, try adding --exclude-tautologies structural to get rid of that.

[srobb1]

Hi @balhoff. I have ROBOT version 1.4.3 when I run robot remove -h I do not see that argument in the list.

[balhoff]

Sorry—this is an option for reason.

[srobb1]

@balhoff I tried using my owl with the ObjProps removed by robot remove as input to robot reason with --exclude-tautologies structural and I still get the double nothing. It isn't pretty, but does it hurt anything to have this weirdness?

[jamesaoverton]

The extra Nothing sounds like this: #562 (comment)

[beckyjackson]

This issue was resolved by #575 and the owl:Nothing issue was resolved in #579. You can remove owl:Nothing with:

robot remove --input input.owl \
  --axioms structural-tautologies \
  --output output.owl