Fact++ not showing up in p4 build 64 on redhat 64bit machine

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Fact++ not showing up in p4 build 64 on redhat 64bit machine

David Osumi-Sutherland
Hi all,

I've just installed p4 build 64 on a 64 bit linux machine. There's no
sign of the Fact++ reasoner in the Reasoner menu.  Haven't seen this
problem with build 64 on my laptop, so was wondering if this was a java
version issue.

Here's the machine details:
java -version
java version "1.5.0_13"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_13-b05)
Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_13-b05, mixed mode)
Linux 2.6.18-92.1.1.el5 x86_64

Cheers,

David




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Inconsistency in "Render entities using annotation values"

helen.chen

Dear Protege 4 team

I use "Render entities using annotation values" to look at the drug ontology made by Samson and colleagues.

In protege, some entities (i.e 'Warfarin Potassium') are displayed with a single quote and some without ('Warfarin"), see the screen shot below.  This cause problems when searching a term and related terms because I can not tell if a term is rendered with (') or without in advance.



I checked the owl file, all terms are annotated in the same way using rdfs:label, for example:

For "Warfarin Potassium"
[

  <owl:Class rdf:ID="C0282378">
    <rdfs:subClassOf>
      <owl:Class rdf:ID="C0043031"/>
    </rdfs:subClassOf>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >Warfarin Potassium</rdfs:label>
  </owl:Class>
]

For Warfarin
[
  <owl:Class rdf:about="#C0043031">
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0032787"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0027051"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0042487"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="#has_mechanism_of_action"/>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C1373065"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0151744"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0032787"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0034065"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#DB_11106"/>
        <owl:onProperty rdf:resource="#has_drug_target"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0038454"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0004238"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0038454"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0040038"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf rdf:resource="#C0035805"/>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0007787"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0010072"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0042487"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0040038"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0040046"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >Warfarin</rdfs:label>
    <rdfs:subClassOf rdf:resource="#C0360596"/>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0034065"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
  </owl:Class>
]

Kind Regards,

Helen Chen |
Agfa HealthCare
Senior Researcher | HE/Advanced Clinical Applications Research
T  +1 519 746 6210 Ext.3186 | M  +1 519 498 6244

Agfa HealthCare Inc., 455 Phillip Street, Waterloo, ON N2L 3X2, Canada

http://www.agfa.com/healthcare/

Click on link to read important disclaimer: http://www.agfa.com/healthcare/maildisclaimer
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Re: Fact++ not showing up in p4 build 64 on redhat 64bit machine

Nick Drummond
In reply to this post by David Osumi-Sutherland
We haven't currently got a 64bit linux build of the FaCT++ binaries in the distribution (we've been waiting for someone to ask because this adds to the time doing new FaCT++ builds).

I'll see if we have a machine available to build it on. If not, might you be interested in helping here?

Cheers

Nick

On Tue, Jul 1, 2008 at 5:24 PM, David Sutherland <[hidden email]> wrote:
Hi all,

I've just installed p4 build 64 on a 64 bit linux machine. There's no
sign of the Fact++ reasoner in the Reasoner menu.  Haven't seen this
problem with build 64 on my laptop, so was wondering if this was a java
version issue.

Here's the machine details:
java -version
java version "1.5.0_13"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_13-b05)
Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_13-b05, mixed mode)
Linux 2.6.18-92.1.1.el5 x86_64

Cheers,

David




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p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback


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Re: Fact++ not showing up in p4 build 64 on redhat 64bit machine

David Osumi-Sutherland
On Fri, 2008-07-04 at 17:28 +0100, Nick Drummond wrote:
> We haven't currently got a 64bit linux build of the FaCT++ binaries in
> the distribution (we've been waiting for someone to ask because this
> adds to the time doing new FaCT++ builds).
>
> I'll see if we have a machine available to build it on. If not, might
> you be interested in helping here?
>
Sure,

David

> Cheers
>
> Nick
>
> On Tue, Jul 1, 2008 at 5:24 PM, David Sutherland <[hidden email]>
> wrote:
>         Hi all,
>        
>         I've just installed p4 build 64 on a 64 bit linux machine.
>         There's no
>         sign of the Fact++ reasoner in the Reasoner menu.  Haven't
>         seen this
>         problem with build 64 on my laptop, so was wondering if this
>         was a java
>         version issue.
>        
>         Here's the machine details:
>         java -version
>         java version "1.5.0_13"
>         Java(TM) 2 Runtime Environment, Standard Edition (build
>         1.5.0_13-b05)
>         Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_13-b05, mixed
>         mode)
>         Linux 2.6.18-92.1.1.el5 x86_64
>        
>         Cheers,
>        
>         David
>        
>        
>        
>        
>         _______________________________________________
>         p4-feedback mailing list
>         [hidden email]
>         https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: Inconsistency in "Render entities using annotation values"

Nick Drummond
In reply to this post by helen.chen
Helen,

This has also been requested recently by others. Now fixed.

Nick

On Wed, Jul 2, 2008 at 9:54 AM, <[hidden email]> wrote:

Dear Protege 4 team

I use "Render entities using annotation values" to look at the drug ontology made by Samson and colleagues.

In protege, some entities (i.e 'Warfarin Potassium') are displayed with a single quote and some without ('Warfarin"), see the screen shot below.  This cause problems when searching a term and related terms because I can not tell if a term is rendered with (') or without in advance.



I checked the owl file, all terms are annotated in the same way using rdfs:label, for example:

For "Warfarin Potassium"
[

  <owl:Class rdf:ID="C0282378">
    <rdfs:subClassOf>
      <owl:Class rdf:ID="C0043031"/>
    </rdfs:subClassOf>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >Warfarin Potassium</rdfs:label>
  </owl:Class>
]

For Warfarin
[
  <owl:Class rdf:about="#C0043031">
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0032787"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0027051"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0042487"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty rdf:resource="#has_mechanism_of_action"/>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C1373065"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0151744"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0032787"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0034065"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#DB_11106"/>
        <owl:onProperty rdf:resource="#has_drug_target"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0038454"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0004238"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0038454"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom rdf:resource="#C0040038"/>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf rdf:resource="#C0035805"/>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0007787"/>
        </owl:someValuesFrom>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0010072"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0042487"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_prevent"/>
        </owl:onProperty>
        <owl:someValuesFrom rdf:resource="#C0040038"/>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0040046"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >Warfarin</rdfs:label>
    <rdfs:subClassOf rdf:resource="#C0360596"/>
    <rdfs:subClassOf>
      <owl:Restriction>
        <owl:someValuesFrom>
          <owl:Class rdf:about="#C0034065"/>
        </owl:someValuesFrom>
        <owl:onProperty>
          <owl:ObjectProperty rdf:about="#may_treat"/>
        </owl:onProperty>
      </owl:Restriction>
    </rdfs:subClassOf>
  </owl:Class>
]

Kind Regards,

Helen Chen |
Agfa HealthCare
Senior Researcher | HE/Advanced Clinical Applications Research
T  +1 519 746 6210 Ext.3186 | M  +1 519 498 6244

Agfa HealthCare Inc., 455 Phillip Street, Waterloo, ON N2L 3X2, Canada

http://www.agfa.com/healthcare/

Click on link to read important disclaimer: http://www.agfa.com/healthcare/maildisclaimer
_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback



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[hidden email]
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