Warnings from owlready on make all

[netfl0]

We think it might have something to do with our puns when you make all

#12 40.85 build/d3fend-architecture.owl done 
#12 41.39 build/d3fend-prefixes.json done 
#12 45.68 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2102
#12 45.68 
#12 45.68 * Owlready2 * Warning: ignoring cyclic type of, involving storid 843
#12 45.68 
#12 45.68 * Owlready2 * Warning: ignoring cyclic type of, involving storid 416
#12 45.68 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2511
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 722
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 723
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2531
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2385
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2154
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 842
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 855
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2109
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 889
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 753
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2123
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2319
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 907
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2697
#12 45.69 
#12 45.69 * Owlready2 * Warning: ignoring cyclic type of, involving storid 3776
#12 45.69 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2812
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2135
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2937
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2138
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2186
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 903
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2936
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2180
#12 45.70 
#12 45.70 * Owlready2 * Warning: ignoring cyclic type of, involving storid 2157
#12 45.70 ```

We wanted to migrate our puns from instances of their parent classes to instances of themselves. 

Any thoughts on this @hack-sentinel @aamedina ?

[aamedina]

I think it has to do with asserting owl:Class, owl:NamedIndividual and the class itself ie

:SomeClass a owl:Class, owl:NamedIndividual, :SomeClass .

I think :SomeClass a :SomeClass can be removed and you can still use "punning". Not sure about how the GUI tools work though (eg protege et al).

My naive perspective is I think I'd prefer it to be unasserted just so I can query an ontology of individuals that transitively owl:imports d3fend for instances of a particular artifact class and not have it match the class itself without including that exception in the filter/query.

[netfl0]

To pun or not to pun...

We use the puns for the kb, and queries against the knowledge itself. Otherwise we had previously queries against restrictions.

[aamedina]

I definitely see the utility for metamodeling and appreciate the flexibility... If the tool knows how to deal with the semantics of punning, it seems powerful, I guess the "tricks" just need to be documented.

[netfl0]

Agree. Need to flesh out the Design.md

I forgot to note, the only tool having any issues with it is owlready2.

I believe our API and all the rest are handling puns correctly. I do believe the "instance of itself" is correct.

[aamedina]

Re: readmes I like the way FIBO documents their ontology conventions https://github.com/edmcouncil/fibo/blob/master/ONTOLOGY_GUIDE.md