Equivalent To logical defs. and asserted SubClass Of parents being stripped

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Equivalent To logical defs. and asserted SubClass Of parents being stripped

jbmunro
Hello,

I am experiencing issues with Protege 5.2 running the ELK 0.4.3 reasoner.  

Terms are somehow losing their asserted SubClass Of parents and Equivalent
To logical definitions and becoming orphaned.  I am working on both SubClass
Of assertions and Equivalent To logical definitions to improve relations
between terms and after syncing the reasoner, Equivalent To logical
definitions that I haven't touched are being stripped.

Additionally, I am finding that after saving, closing and committing changes
made in Protege, reopening the *-edit.owl file the next day in Protege shows
additional orphaned terms.

I'm curious to know if anyone else has seen this behaviour.  Whether this is
perhaps being caused by my choice in reasoner.  What I can do to prevent
this from happening.

Thank you.

James



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Re: Equivalent To logical defs. and asserted SubClass Of parents being stripped

samsontu
Occasionally I use the ELK reasoner too. I’ve never seen the behavior you described.

It would be best if you can provide a sample ontology and the precise steps needed to demonstrate this problem.

With best regards,
Samson


On Oct 8, 2018, at 6:53 AM, jbmunro <[hidden email]> wrote:

Hello,

I am experiencing issues with Protege 5.2 running the ELK 0.4.3 reasoner.  

Terms are somehow losing their asserted SubClass Of parents and Equivalent
To logical definitions and becoming orphaned.  I am working on both SubClass
Of assertions and Equivalent To logical definitions to improve relations
between terms and after syncing the reasoner, Equivalent To logical
definitions that I haven't touched are being stripped.

Additionally, I am finding that after saving, closing and committing changes
made in Protege, reopening the *-edit.owl file the next day in Protege shows
additional orphaned terms.

I'm curious to know if anyone else has seen this behaviour.  Whether this is
perhaps being caused by my choice in reasoner.  What I can do to prevent
this from happening.

Thank you.

James



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Re: Equivalent To logical defs. and asserted SubClass Of parents being stripped

jbmunro
Samson,

Thank you for letting me know that you too have seen this behavior.  I will
work on pulling together the sample ontology and precise steps.

James



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Re: Equivalent To logical defs. and asserted SubClass Of parents being stripped

jbmunro
Ooops!  In my excitement, I thought that you said that you *have* seen this
behavior.  Apologies.  

James



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Re: Equivalent To logical defs. and asserted SubClass Of parents being stripped

Yevgeny Kazakov
Hi James,

In which exactly place the asserted definitions disappear? In the class hierarchy view? Asserted or inferred? Could you provide a screenshot?

What do you mean by "orphaned" terms? Do they appear directly under owl:Thing in the class hierarchy?

In general, the reasoner (ELK or any other) should not make any difference in the asserted hierarchy view, except for adding additional inferred equivalence or subclass assertions (shown in the description frame in yellow). But there is another "structural reasoner", which computes asserted class hierarchy, and there could be a problem with that.

For a diagnostic purpose, next time if you experience the problem, can you try:

1. Restarting the reasoner:

Reasoner > Stop reasoner
Reasoner > Start reasoner

Are the missing asserted axioms restored?

2. Switching to another reasoner (e.g., HermiT).

If in both cases the asserted axioms are *not* restored, it is unlikely a problem with the reasoner.

3. If restarting ELK (point 1) fixes the problem, try to disable the incremental mode in ELK:

Preferences > Reasoner > ELK > Incremental reasoning => uncheck

If after that you do not observe the problem anymore, it is likely an ELK bug. Please file a bug report here:


It would be then helpful to provide a (small) ontology on which the issue can be reliably reproduced.

Best regards,

- Yevgeny



On Mon, Oct 8, 2018 at 8:34 PM jbmunro <[hidden email]> wrote:
Ooops!  In my excitement, I thought that you said that you *have* seen this
behavior.  Apologies. 

James



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Re: Equivalent To logical defs. and asserted SubClass Of parents being stripped

jbmunro
Hi Samson and Yevgeny,

First, to address Samson's suggestions - I will certainly provide the
requested details next time this happens.  Right now, all I can provide is a
general outline and I would like to be able to provide a more specific
example.

Second, to address Yevgeny's suggestions and questions.

Typically, I work in the class inferred view, however, in order to identify
terms with dual asserted parents, I have lately been working in the entities
asserted view.  The issue I am describing, i.e. the loss of Equivalent To
and SubClass Of definitions (they just disappear), seems to be happing in
both views but is more typically noticed in the former as that is the view I
typically use.

When I say "orphaned" I do indeed mean that the asserted parent term is lost
and the term appears as a subclass of owl:Thing.

Thank you for explaining the action of reasoners in the asserted hierarchy
view.  I have been working on correcting terms that have dual asserted
parents and improving inferred relationships in the ontology.

I will certainly try stopping and restarting the reasoner.  I sync it with
any modification I make to a logical definition to make sure that changes I
have made to an Equivalent To or SubClass Of definition results in the
desired behavior.

I will certainly try another reasoner and disabling the incremental mode.

Thanks both for your help.

James



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