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adding reflexivity to part_of causes unsatisfiable classes #1159

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balhoff opened this Issue Oct 8, 2015 · 5 comments

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balhoff commented Oct 8, 2015

The part_of property used in Uberon is not marked as reflexive, nor is it in the current RO. However my recollection is that it used to be considered reflexive by RO, and I have been relying on that behavior in queries for a long time. When part_of is marked reflexive in http://purl.obolibrary.org/obo/uberon/releases/2015-09-27/ext.owl, it results in 17 unsatisfiable classes. Is part_of intentionally non-reflexive?

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cmungall Oct 8, 2015

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Intentionally non-gloabally-reflexive:
https://github.com/oborel/obo-relations/wiki/ROGuideDraft#local-reflexivity

We can add local reflexivity… but that would help you neither with
your queries nor with replicating your error, assuming Elk.

Any suggestions? Local axioms for phenoscape? part-of is the one OP it
is probably safe to do global reflexivity on, as it applies to pretty
much any upper category in my view (BFO may be undercommitted here, need
to check)

On 7 Oct 2015, at 19:39, Jim Balhoff wrote:

The part_of property used in Uberon is not marked as reflexive, nor
is it in the current RO. However my recollection is that it used to be
considered reflexive by RO, and I have been relying on that behavior
in queries for a long time. When part_of is marked reflexive in
http://purl.obolibrary.org/obo/uberon/releases/2015-09-27/ext.owl, it
results in 17 unsatisfiable classes. Is part_of intentionally
non-reflexive?


Reply to this email directly or view it on GitHub:
#1159

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cmungall commented Oct 8, 2015

Intentionally non-gloabally-reflexive:
https://github.com/oborel/obo-relations/wiki/ROGuideDraft#local-reflexivity

We can add local reflexivity… but that would help you neither with
your queries nor with replicating your error, assuming Elk.

Any suggestions? Local axioms for phenoscape? part-of is the one OP it
is probably safe to do global reflexivity on, as it applies to pretty
much any upper category in my view (BFO may be undercommitted here, need
to check)

On 7 Oct 2015, at 19:39, Jim Balhoff wrote:

The part_of property used in Uberon is not marked as reflexive, nor
is it in the current RO. However my recollection is that it used to be
considered reflexive by RO, and I have been relying on that behavior
in queries for a long time. When part_of is marked reflexive in
http://purl.obolibrary.org/obo/uberon/releases/2015-09-27/ext.owl, it
results in 17 unsatisfiable classes. Is part_of intentionally
non-reflexive?


Reply to this email directly or view it on GitHub:
#1159

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balhoff Oct 8, 2015

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Thanks, I missed that. Yes, I should have said the results were with Elk. I currently have a file used in the Phenoscape KB that makes sure the object properties have expected characteristics, but I should take out reflexive part_of if there are going to be Uberon axioms that conflict with that. I think mostly it's just a matter of making sure I have "A or part_of some A" everywhere I am currently just using "part_of some A".

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balhoff commented Oct 8, 2015

Thanks, I missed that. Yes, I should have said the results were with Elk. I currently have a file used in the Phenoscape KB that makes sure the object properties have expected characteristics, but I should take out reflexive part_of if there are going to be Uberon axioms that conflict with that. I think mostly it's just a matter of making sure I have "A or part_of some A" everywhere I am currently just using "part_of some A".

@balhoff balhoff closed this Oct 8, 2015

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uberon Oct 8, 2015

I'd still like to investigate… if the logical incoherencies are
biological ones we can at least retain this as a test

On 8 Oct 2015, at 6:16, Jim Balhoff wrote:

Closed #1159.


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#1159 (comment)

uberon commented Oct 8, 2015

I'd still like to investigate… if the logical incoherencies are
biological ones we can at least retain this as a test

On 8 Oct 2015, at 6:16, Jim Balhoff wrote:

Closed #1159.


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#1159 (comment)

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cmungall Oct 9, 2015

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Unsats:

screen shot 2015-10-09 at 1 06 09 pm

Feather issue:

screen shot 2015-10-09 at 1 12 27 pm

VT nucleus:

screen shot 2015-10-09 at 1 08 10 pm

Thymoid:

screen shot 2015-10-09 at 1 08 54 pm

Another nucleus:

screen shot 2015-10-09 at 1 09 32 pm

These are bona-fide ontology issues, looks like some axioms are too strong. Thanks!

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cmungall commented Oct 9, 2015

Unsats:

screen shot 2015-10-09 at 1 06 09 pm

Feather issue:

screen shot 2015-10-09 at 1 12 27 pm

VT nucleus:

screen shot 2015-10-09 at 1 08 10 pm

Thymoid:

screen shot 2015-10-09 at 1 08 54 pm

Another nucleus:

screen shot 2015-10-09 at 1 09 32 pm

These are bona-fide ontology issues, looks like some axioms are too strong. Thanks!

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cmungall Feb 6, 2017

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See also #1305

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cmungall commented Feb 6, 2017

See also #1305

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