blank nodes re-used in files in the same directory

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blank nodes re-used in files in the same directory

Eric Prud'hommeaux
I have a dir structure like:
core.ttl
  <...core:hasMedicationFrequency cardinality 1...>

subjects.ttl
  <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subjects> a owl:Ontology ;
     owl:imports <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy> ,
                 <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob> ,
                 <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue> .

subject-amy.ttl
  :subjectOnImmunosuppressantB
      core:hasDosagePlan [
          core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
      ] .

subject-sue.ttl
  :subjectOnImmunosuppressantB
      core:hasDosagePlan [
          core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
      ] .

subject-bob.ttl
  <more of the same>


When I run the reasoner, I get cardinality conflicts because e.g.
_:file/tmp/FDA-TA/tests/RenalTransplatation/genid3 has more then one
core:hasMedicationFrequency. This implies to me that bnodes aren't
effectively scoped to files but instead directories. If I push the
data down into distinct directories, the error goes away.


= to reproduce =

Untar the attached file and load RenalTransplantation/subjects.ttl.
Running the reasoner should reveal the conflict.

= compare against =

Edit catalog-v001.xml to comment out the subject-*.ttl in the first
directory and uncomment the <uri.../> directives referncing the
files that are in their own directories:
<!--
    <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy" uri="amy/subject-amy.ttl"/>
    <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue" uri="sue/subject-sue.ttl"/>
    <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob" uri="bob/subject-bob.ttl"/>
 -->
If you freshly start Protege, and load subjects.ttl, the error should
be gone.


I'm using Protege for a highly modular (and high-profile) FDA task and
I'd like to not screw stuff up because everything in the same
directory shares bnodes. Can you suggest a test I can use to see if
the same thing is happening in T-box?

V 4.3.0 (Build 304)
OWL API 3.4.2 2012_12_05
Factplusplus Plug-in 1.6.2 (also fails with Hermit).

--
-ericP

office: +1.617.599.3509
mobile: +33.6.80.80.35.59

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Re: blank nodes re-used in files in the same directory

Eric Prud'hommeaux
* Eric Prud'hommeaux <[hidden email]> [2014-02-28 14:43-0500]

> I have a dir structure like:
> core.ttl
>   <...core:hasMedicationFrequency cardinality 1...>
>
> subjects.ttl
>   <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subjects> a owl:Ontology ;
>      owl:imports <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy> ,
>                  <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob> ,
>                  <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue> .
>
> subject-amy.ttl
>   :subjectOnImmunosuppressantB
>       core:hasDosagePlan [
>           core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
>       ] .
>
> subject-sue.ttl
>   :subjectOnImmunosuppressantB
>       core:hasDosagePlan [
>           core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
>       ] .
>
> subject-bob.ttl
>   <more of the same>
>
>
> When I run the reasoner, I get cardinality conflicts because e.g.
> _:file/tmp/FDA-TA/tests/RenalTransplatation/genid3 has more then one
> core:hasMedicationFrequency. This implies to me that bnodes aren't
> effectively scoped to files but instead directories. If I push the
> data down into distinct directories, the error goes away.
>
>
> = to reproduce =
>
> Untar the attached file and load RenalTransplantation/subjects.ttl.
sigh, now attached

> Running the reasoner should reveal the conflict.
>
> = compare against =
>
> Edit catalog-v001.xml to comment out the subject-*.ttl in the first
> directory and uncomment the <uri.../> directives referncing the
> files that are in their own directories:
> <!--
>     <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy" uri="amy/subject-amy.ttl"/>
>     <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue" uri="sue/subject-sue.ttl"/>
>     <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob" uri="bob/subject-bob.ttl"/>
>  -->
> If you freshly start Protege, and load subjects.ttl, the error should
> be gone.
>
>
> I'm using Protege for a highly modular (and high-profile) FDA task and
> I'd like to not screw stuff up because everything in the same
> directory shares bnodes. Can you suggest a test I can use to see if
> the same thing is happening in T-box?
>
> V 4.3.0 (Build 304)
> OWL API 3.4.2 2012_12_05
> Factplusplus Plug-in 1.6.2 (also fails with Hermit).
>
> --
> -ericP
>
> office: +1.617.599.3509
> mobile: +33.6.80.80.35.59
>
> ([hidden email])
> Feel free to forward this message to any list for any purpose other than
> email address distribution.
>
> There are subtle nuances encoded in font variation and clever layout
> which can only be seen by printing this message on high-clay paper.
--
-ericP

office: +1.617.599.3509
mobile: +33.6.80.80.35.59

([hidden email])
Feel free to forward this message to any list for any purpose other than
email address distribution.

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which can only be seen by printing this message on high-clay paper.
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RenalTransplantation.tar (27K) Download Attachment
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Re: blank nodes re-used in files in the same directory

Timothy Redmond

At first glance it looks like you are correct. I will see if I can convert this into an OWL api bug report.

-Timothy


On 02/28/2014 11:48 AM, Eric Prud'hommeaux wrote:
* Eric Prud'hommeaux [hidden email] [2014-02-28 14:43-0500]
I have a dir structure like:
core.ttl
  <...core:hasMedicationFrequency cardinality 1...>

subjects.ttl
  <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subjects> a owl:Ontology ;
     owl:imports <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy> ,
                 <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob> ,
                 <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue> .

subject-amy.ttl
  :subjectOnImmunosuppressantB 
      core:hasDosagePlan [ 
          core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
      ] .

subject-sue.ttl
  :subjectOnImmunosuppressantB 
      core:hasDosagePlan [ 
          core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ] 
      ] .

subject-bob.ttl
  <more of the same>


When I run the reasoner, I get cardinality conflicts because e.g.
_:file/tmp/FDA-TA/tests/RenalTransplatation/genid3 has more then one
core:hasMedicationFrequency. This implies to me that bnodes aren't
effectively scoped to files but instead directories. If I push the
data down into distinct directories, the error goes away.


= to reproduce =

Untar the attached file and load RenalTransplantation/subjects.ttl.
sigh, now attached

Running the reasoner should reveal the conflict.

= compare against =

Edit catalog-v001.xml to comment out the subject-*.ttl in the first
directory and uncomment the <uri.../> directives referncing the
files that are in their own directories:
<!-- 
    <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy" uri="amy/subject-amy.ttl"/>
    <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue" uri="sue/subject-sue.ttl"/>
    <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob" uri="bob/subject-bob.ttl"/>
 -->
If you freshly start Protege, and load subjects.ttl, the error should
be gone.


I'm using Protege for a highly modular (and high-profile) FDA task and
I'd like to not screw stuff up because everything in the same
directory shares bnodes. Can you suggest a test I can use to see if
the same thing is happening in T-box?

V 4.3.0 (Build 304)
OWL API 3.4.2 2012_12_05
Factplusplus Plug-in 1.6.2 (also fails with Hermit).

-- 
-ericP

office: +1.617.599.3509
mobile: +33.6.80.80.35.59

([hidden email])
Feel free to forward this message to any list for any purpose other than
email address distribution.

There are subtle nuances encoded in font variation and clever layout
which can only be seen by printing this message on high-clay paper.

      

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Re: blank nodes re-used in files in the same directory

Eric Prud'hommeaux
* Timothy Redmond <[hidden email]> [2014-02-28 15:03-0800]
>
> At first glance it looks like you are correct. I will see if I can
> convert this into an OWL api bug report.

I tested Protege 4.2beta and it did NOT emit the reasoner error caused
by this BNode scoping bug. This appears to be new.


> -Timothy
>
>
> On 02/28/2014 11:48 AM, Eric Prud'hommeaux wrote:
> >* Eric Prud'hommeaux <[hidden email]> [2014-02-28 14:43-0500]
> >>I have a dir structure like:
> >>core.ttl
> >>   <...core:hasMedicationFrequency cardinality 1...>
> >>
> >>subjects.ttl
> >>   <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subjects> a owl:Ontology ;
> >>      owl:imports <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy> ,
> >>                  <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob> ,
> >>                  <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue> .
> >>
> >>subject-amy.ttl
> >>   :subjectOnImmunosuppressantB
> >>       core:hasDosagePlan [
> >>           core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
> >>       ] .
> >>
> >>subject-sue.ttl
> >>   :subjectOnImmunosuppressantB
> >>       core:hasDosagePlan [
> >>           core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
> >>       ] .
> >>
> >>subject-bob.ttl
> >>   <more of the same>
> >>
> >>
> >>When I run the reasoner, I get cardinality conflicts because e.g.
> >>_:file/tmp/FDA-TA/tests/RenalTransplatation/genid3 has more then one
> >>core:hasMedicationFrequency. This implies to me that bnodes aren't
> >>effectively scoped to files but instead directories. If I push the
> >>data down into distinct directories, the error goes away.
> >>
> >>
> >>= to reproduce =
> >>
> >>Untar the attached file and load RenalTransplantation/subjects.ttl.
> >sigh, now attached
> >
> >>Running the reasoner should reveal the conflict.
> >>
> >>= compare against =
> >>
> >>Edit catalog-v001.xml to comment out the subject-*.ttl in the first
> >>directory and uncomment the <uri.../> directives referncing the
> >>files that are in their own directories:
> >><!--
> >>     <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy" uri="amy/subject-amy.ttl"/>
> >>     <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue" uri="sue/subject-sue.ttl"/>
> >>     <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob" uri="bob/subject-bob.ttl"/>
> >>  -->
> >>If you freshly start Protege, and load subjects.ttl, the error should
> >>be gone.
> >>
> >>
> >>I'm using Protege for a highly modular (and high-profile) FDA task and
> >>I'd like to not screw stuff up because everything in the same
> >>directory shares bnodes. Can you suggest a test I can use to see if
> >>the same thing is happening in T-box?
> >>
> >>V 4.3.0 (Build 304)
> >>OWL API 3.4.2 2012_12_05
> >>Factplusplus Plug-in 1.6.2 (also fails with Hermit).
> >>
> >>--
> >>-ericP
> >>
> >>office: +1.617.599.3509
> >>mobile: +33.6.80.80.35.59
> >>
> >>([hidden email])
> >>Feel free to forward this message to any list for any purpose other than
> >>email address distribution.
> >>
> >>There are subtle nuances encoded in font variation and clever layout
> >>which can only be seen by printing this message on high-clay paper.
> >
> >
> >_______________________________________________
> >protege-user mailing list
> >[hidden email]
> >https://mailman.stanford.edu/mailman/listinfo/protege-user
>

> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


--
-ericP

office: +1.617.599.3509
mobile: +33.6.80.80.35.59

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Re: blank nodes re-used in files in the same directory

Timothy Redmond

It appears that this bug is fixed in the latest development version of
the owlapi.  I put a copy of that development version here:

         http://mousey.synology.me/2014-03-02-owlapi-issue/org.semanticweb.owl.owlapi.jar


If you want to experiment with the bleeding edge you can try this in one
of your protege installations.  Just replace the
org.semanticweb.owl.owlapi.jar file in the plugins directory of the
installation with the one above.

Unfortunately this version of the OWL api does not do a good job of
loading your ontologies as they are currently stated.  To load your
ontologies in the development version of the OWL api you have to give
the core ontology a name (which might be a good idea anyway).  I have
reported this problem with anonymous ontologies on the OWL api mailing
list here:

           https://github.com/owlcs/owlapi/issues/88



-Timothy


On 03/01/2014 04:26 AM, Eric Prud'hommeaux wrote:

> * Timothy Redmond <[hidden email]> [2014-02-28 15:03-0800]
>> At first glance it looks like you are correct. I will see if I can
>> convert this into an OWL api bug report.
> I tested Protege 4.2beta and it did NOT emit the reasoner error caused
> by this BNode scoping bug. This appears to be new.
>
>
>> -Timothy
>>
>>
>> On 02/28/2014 11:48 AM, Eric Prud'hommeaux wrote:
>>> * Eric Prud'hommeaux <[hidden email]> [2014-02-28 14:43-0500]
>>>> I have a dir structure like:
>>>> core.ttl
>>>>    <...core:hasMedicationFrequency cardinality 1...>
>>>>
>>>> subjects.ttl
>>>>    <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subjects> a owl:Ontology ;
>>>>       owl:imports <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy> ,
>>>>                   <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob> ,
>>>>                   <http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue> .
>>>>
>>>> subject-amy.ttl
>>>>    :subjectOnImmunosuppressantB
>>>>        core:hasDosagePlan [
>>>>            core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
>>>>        ] .
>>>>
>>>> subject-sue.ttl
>>>>    :subjectOnImmunosuppressantB
>>>>        core:hasDosagePlan [
>>>>            core:hasMedicationSchedule [ core:hasMedicationFrequency 6 ; core:hasMedicationDuration 1.0 ]
>>>>        ] .
>>>>
>>>> subject-bob.ttl
>>>>    <more of the same>
>>>>
>>>>
>>>> When I run the reasoner, I get cardinality conflicts because e.g.
>>>> _:file/tmp/FDA-TA/tests/RenalTransplatation/genid3 has more then one
>>>> core:hasMedicationFrequency. This implies to me that bnodes aren't
>>>> effectively scoped to files but instead directories. If I push the
>>>> data down into distinct directories, the error goes away.
>>>>
>>>>
>>>> = to reproduce =
>>>>
>>>> Untar the attached file and load RenalTransplantation/subjects.ttl.
>>> sigh, now attached
>>>
>>>> Running the reasoner should reveal the conflict.
>>>>
>>>> = compare against =
>>>>
>>>> Edit catalog-v001.xml to comment out the subject-*.ttl in the first
>>>> directory and uncomment the <uri.../> directives referncing the
>>>> files that are in their own directories:
>>>> <!--
>>>>      <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-amy" uri="amy/subject-amy.ttl"/>
>>>>      <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-sue" uri="sue/subject-sue.ttl"/>
>>>>      <uri id="User Entered Import Resolution" name="http://www.w3.org/2013/12/FDA-TA/tests/RenalTransplantation/subject-bob" uri="bob/subject-bob.ttl"/>
>>>>   -->
>>>> If you freshly start Protege, and load subjects.ttl, the error should
>>>> be gone.
>>>>
>>>>
>>>> I'm using Protege for a highly modular (and high-profile) FDA task and
>>>> I'd like to not screw stuff up because everything in the same
>>>> directory shares bnodes. Can you suggest a test I can use to see if
>>>> the same thing is happening in T-box?
>>>>
>>>> V 4.3.0 (Build 304)
>>>> OWL API 3.4.2 2012_12_05
>>>> Factplusplus Plug-in 1.6.2 (also fails with Hermit).
>>>>
>>>> --
>>>> -ericP
>>>>
>>>> office: +1.617.599.3509
>>>> mobile: +33.6.80.80.35.59
>>>>
>>>> ([hidden email])
>>>> Feel free to forward this message to any list for any purpose other than
>>>> email address distribution.
>>>>
>>>> There are subtle nuances encoded in font variation and clever layout
>>>> which can only be seen by printing this message on high-clay paper.
>>>
>>> _______________________________________________
>>> protege-user mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-user
>> _______________________________________________
>> protege-user mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-user
>

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