DL Query "refresh" problem

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DL Query "refresh" problem

samsontu
Hi,

I am finding that Protege 4 (build 62) does not refresh classification
after changes in the KB.

For example, initially I get no instances that satisfy the following query

is_studied_in_trial some (Study that scientific_title value
"Thrombolytic Therapy versus Primary Percutaneous Intervention")

I invoked the Reasoner, and saw that there is no instance satisfying the
DL query expression.

Next, I added an assertion that the study in question
has_health_condition_studied an instance of code that correspond to,
say, acute MI, where is_studied_in_trial is the inverse property of
is_studied_in_trial. I expect to get back an result indicating that the
acute MI code is  studied in the study.

It turns out that I don't get the correct results without restarting
Protege 4.

Samson

--
---------
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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Re: DL Query "refresh" problem

Rinke Hoekstra-4
Hi,

I'm having similar problems, though usually switching-off the reasoner  
(setting it to none), and switching it back on again is a sufficient  
reset.

-Rinke

On 7 mei 2008, at 19:23, Samson Tu wrote:

> Hi,
>
> I am finding that Protege 4 (build 62) does not refresh classification
> after changes in the KB.
>
> For example, initially I get no instances that satisfy the following  
> query
>
> is_studied_in_trial some (Study that scientific_title value
> "Thrombolytic Therapy versus Primary Percutaneous Intervention")
>
> I invoked the Reasoner, and saw that there is no instance satisfying  
> the
> DL query expression.
>
> Next, I added an assertion that the study in question
> has_health_condition_studied an instance of code that correspond to,
> say, acute MI, where is_studied_in_trial is the inverse property of
> is_studied_in_trial. I expect to get back an result indicating that  
> the
> acute MI code is  studied in the study.
>
> It turns out that I don't get the correct results without restarting
> Protege 4.
>
> Samson
>
> --
> ---------
> Samson Tu                                   email: [hidden email]
> Senior Research Scientist                   web: www.stanford.edu/
> ~swt/
> Center for Biomedical Informatics Research  phone: 1-650-725-3391
> Stanford University                         fax: 1-650-725-7944
>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

-----------------------------------------------
Drs. Rinke Hoekstra

Email: [hidden email]    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------



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Re: DL Query "refresh" problem

Nick Drummond
Hi,

I managed to reproduce this behaviour with pellet.
FaCT++ seems OK.
I'll have a look into it.

Nick

On 8 May 2008, at 07:34, Rinke Hoekstra wrote:

> Hi,
>
> I'm having similar problems, though usually switching-off the reasoner
> (setting it to none), and switching it back on again is a sufficient
> reset.
>
> -Rinke
>
> On 7 mei 2008, at 19:23, Samson Tu wrote:
>> Hi,
>>
>> I am finding that Protege 4 (build 62) does not refresh  
>> classification
>> after changes in the KB.
>>
>> For example, initially I get no instances that satisfy the following
>> query
>>
>> is_studied_in_trial some (Study that scientific_title value
>> "Thrombolytic Therapy versus Primary Percutaneous Intervention")
>>
>> I invoked the Reasoner, and saw that there is no instance satisfying
>> the
>> DL query expression.
>>
>> Next, I added an assertion that the study in question
>> has_health_condition_studied an instance of code that correspond to,
>> say, acute MI, where is_studied_in_trial is the inverse property of
>> is_studied_in_trial. I expect to get back an result indicating that
>> the
>> acute MI code is  studied in the study.
>>
>> It turns out that I don't get the correct results without restarting
>> Protege 4.
>>
>> Samson
>>
>> --
>> ---------
>> Samson Tu                                   email: [hidden email]
>> Senior Research Scientist                   web: www.stanford.edu/
>> ~swt/
>> Center for Biomedical Informatics Research  phone: 1-650-725-3391
>> Stanford University                         fax: 1-650-725-7944
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> -----------------------------------------------
> Drs. Rinke Hoekstra
>
> Email: [hidden email]    Skype:  rinkehoekstra
> Phone: +31-20-5253499     Fax:   +31-20-5253495
> Web:   http://www.leibnizcenter.org/users/rinke
>
> Leibniz Center for Law,          Faculty of Law
> University of Amsterdam,            PO Box 1030
> 1000 BA  Amsterdam,             The Netherlands
> -----------------------------------------------
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: DL Query "refresh" problem

Nick Drummond
This should be fixed in the next build.

Thanks Rinke for the workaround.

Nick

On 8 May 2008, at 12:06, Nick Drummond wrote:

> Hi,
>
> I managed to reproduce this behaviour with pellet.
> FaCT++ seems OK.
> I'll have a look into it.
>
> Nick
>
> On 8 May 2008, at 07:34, Rinke Hoekstra wrote:
>
>> Hi,
>>
>> I'm having similar problems, though usually switching-off the  
>> reasoner
>> (setting it to none), and switching it back on again is a sufficient
>> reset.
>>
>> -Rinke
>>
>> On 7 mei 2008, at 19:23, Samson Tu wrote:
>>> Hi,
>>>
>>> I am finding that Protege 4 (build 62) does not refresh
>>> classification
>>> after changes in the KB.
>>>
>>> For example, initially I get no instances that satisfy the following
>>> query
>>>
>>> is_studied_in_trial some (Study that scientific_title value
>>> "Thrombolytic Therapy versus Primary Percutaneous Intervention")
>>>
>>> I invoked the Reasoner, and saw that there is no instance satisfying
>>> the
>>> DL query expression.
>>>
>>> Next, I added an assertion that the study in question
>>> has_health_condition_studied an instance of code that correspond to,
>>> say, acute MI, where is_studied_in_trial is the inverse property of
>>> is_studied_in_trial. I expect to get back an result indicating that
>>> the
>>> acute MI code is  studied in the study.
>>>
>>> It turns out that I don't get the correct results without restarting
>>> Protege 4.
>>>
>>> Samson
>>>
>>> --
>>> ---------
>>> Samson Tu                                   email: [hidden email]
>>> Senior Research Scientist                   web: www.stanford.edu/
>>> ~swt/
>>> Center for Biomedical Informatics Research  phone: 1-650-725-3391
>>> Stanford University                         fax: 1-650-725-7944
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> -----------------------------------------------
>> Drs. Rinke Hoekstra
>>
>> Email: [hidden email]    Skype:  rinkehoekstra
>> Phone: +31-20-5253499     Fax:   +31-20-5253495
>> Web:   http://www.leibnizcenter.org/users/rinke
>>
>> Leibniz Center for Law,          Faculty of Law
>> University of Amsterdam,            PO Box 1030
>> 1000 BA  Amsterdam,             The Netherlands
>> -----------------------------------------------
>>
>>
>>
>> _______________________________________________
>> 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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FaCT++

samsontu
In reply to this post by Nick Drummond
FaCT++  is not available under Reasoner tab in my Protege 4 (build 62). Can it be that FaCT does not work in Windows XP 64-bit OS?

Samson

Nick Drummond wrote:
Hi,

I managed to reproduce this behaviour with pellet.
FaCT++ seems OK.
I'll have a look into it.

Nick

On 8 May 2008, at 07:34, Rinke Hoekstra wrote:

  
Hi,

I'm having similar problems, though usually switching-off the reasoner
(setting it to none), and switching it back on again is a sufficient
reset.

-Rinke

On 7 mei 2008, at 19:23, Samson Tu wrote:
    
Hi,

I am finding that Protege 4 (build 62) does not refresh  
classification
after changes in the KB.

For example, initially I get no instances that satisfy the following
query

is_studied_in_trial some (Study that scientific_title value
"Thrombolytic Therapy versus Primary Percutaneous Intervention")

I invoked the Reasoner, and saw that there is no instance satisfying
the
DL query expression.

Next, I added an assertion that the study in question
has_health_condition_studied an instance of code that correspond to,
say, acute MI, where is_studied_in_trial is the inverse property of
is_studied_in_trial. I expect to get back an result indicating that
the
acute MI code is  studied in the study.

It turns out that I don't get the correct results without restarting
Protege 4.

Samson

-- 
---------
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/
~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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

Email: [hidden email]    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------



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

-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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Re: FaCT++

Nick Drummond
Did you get any warnings about not finding the libraries (I think we'd need a separate binary for this).

I have no machine to verify this but if someone else could try it quickly it would rule out other nasties.

Nick


On 8 May 2008, at 17:20, Samson Tu wrote:

FaCT++  is not available under Reasoner tab in my Protege 4 (build 62). Can it be that FaCT does not work in Windows XP 64-bit OS?

Samson

Nick Drummond wrote:
Hi,

I managed to reproduce this behaviour with pellet.
FaCT++ seems OK.
I'll have a look into it.

Nick

On 8 May 2008, at 07:34, Rinke Hoekstra wrote:

  
Hi,

I'm having similar problems, though usually switching-off the reasoner
(setting it to none), and switching it back on again is a sufficient
reset.

-Rinke

On 7 mei 2008, at 19:23, Samson Tu wrote:
    
Hi,

I am finding that Protege 4 (build 62) does not refresh  
classification
after changes in the KB.

For example, initially I get no instances that satisfy the following
query

is_studied_in_trial some (Study that scientific_title value
"Thrombolytic Therapy versus Primary Percutaneous Intervention")

I invoked the Reasoner, and saw that there is no instance satisfying
the
DL query expression.

Next, I added an assertion that the study in question
has_health_condition_studied an instance of code that correspond to,
say, acute MI, where is_studied_in_trial is the inverse property of
is_studied_in_trial. I expect to get back an result indicating that
the
acute MI code is  studied in the study.

It turns out that I don't get the correct results without restarting
Protege 4.

Samson

-- 
---------
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/
~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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

Email: [hidden email]    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------



_______________________________________________
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
  

-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944



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[hidden email]
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Re: FaCT++

Simon Jupp
On my 64bit mac, I needed to get a binary compiled by Dimitry. It also needs a line added to the MANIFEST.MF so the plugin picks up the correct binary.

Simon

On 8 May 2008, at 18:27, Nick Drummond wrote:

Did you get any warnings about not finding the libraries (I think we'd need a separate binary for this).

I have no machine to verify this but if someone else could try it quickly it would rule out other nasties.

Nick


On 8 May 2008, at 17:20, Samson Tu wrote:

FaCT++  is not available under Reasoner tab in my Protege 4 (build 62). Can it be that FaCT does not work in Windows XP 64-bit OS?

Samson

Nick Drummond wrote:
Hi,

I managed to reproduce this behaviour with pellet.
FaCT++ seems OK.
I'll have a look into it.

Nick

On 8 May 2008, at 07:34, Rinke Hoekstra wrote:

  
Hi,

I'm having similar problems, though usually switching-off the reasoner
(setting it to none), and switching it back on again is a sufficient
reset.

-Rinke

On 7 mei 2008, at 19:23, Samson Tu wrote:
    
Hi,

I am finding that Protege 4 (build 62) does not refresh  
classification
after changes in the KB.

For example, initially I get no instances that satisfy the following
query

is_studied_in_trial some (Study that scientific_title value
"Thrombolytic Therapy versus Primary Percutaneous Intervention")

I invoked the Reasoner, and saw that there is no instance satisfying
the
DL query expression.

Next, I added an assertion that the study in question
has_health_condition_studied an instance of code that correspond to,
say, acute MI, where is_studied_in_trial is the inverse property of
is_studied_in_trial. I expect to get back an result indicating that
the
acute MI code is  studied in the study.

It turns out that I don't get the correct results without restarting
Protege 4.

Samson

-- 
---------
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/
~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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

Email: [hidden email]    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------



_______________________________________________
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
  

-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944



_______________________________________________
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[hidden email]
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[hidden email]
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Re: FaCT++

samsontu
In reply to this post by Nick Drummond
right, I got the following:

C:\apps\rklauncher>set P4="C:\Program Files\Protege_4.0"

C:\apps\rklauncher>cd "C:\Program Files\Protege_4.0"

...
Starting Protege 4 OWL Editor
Platform:
    Framework: Eclipse (1.4.0)
    OS: Windows2003 (5.2)
    Processor: amd64
Could not install plugin in file/directory named plugins\uk.ac.manchester.cs.owl
.factplusplus.jar: org.osgi.framework.BundleException: No Bundle-NativeCode match

Samson

Nick Drummond wrote:
Did you get any warnings about not finding the libraries (I think we'd need a separate binary for this).

I have no machine to verify this but if someone else could try it quickly it would rule out other nasties.

Nick


On 8 May 2008, at 17:20, Samson Tu wrote:

FaCT++  is not available under Reasoner tab in my Protege 4 (build 62). Can it be that FaCT does not work in Windows XP 64-bit OS?

Samson

Nick Drummond wrote:
Hi,

I managed to reproduce this behaviour with pellet.
FaCT++ seems OK.
I'll have a look into it.

Nick

On 8 May 2008, at 07:34, Rinke Hoekstra wrote:

  
Hi,

I'm having similar problems, though usually switching-off the reasoner
(setting it to none), and switching it back on again is a sufficient
reset.

-Rinke

On 7 mei 2008, at 19:23, Samson Tu wrote:
    
Hi,

I am finding that Protege 4 (build 62) does not refresh  
classification
after changes in the KB.

For example, initially I get no instances that satisfy the following
query

is_studied_in_trial some (Study that scientific_title value
"Thrombolytic Therapy versus Primary Percutaneous Intervention")

I invoked the Reasoner, and saw that there is no instance satisfying
the
DL query expression.

Next, I added an assertion that the study in question
has_health_condition_studied an instance of code that correspond to,
say, acute MI, where is_studied_in_trial is the inverse property of
is_studied_in_trial. I expect to get back an result indicating that
the
acute MI code is  studied in the study.

It turns out that I don't get the correct results without restarting
Protege 4.

Samson

-- 
---------
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/
~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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

Email: [hidden email]    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------



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

-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944



    
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-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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Re: FaCT++

Nick Drummond
Looks like we'll need to compile up a native library for 64bit machines.

Nick

On 8 May 2008, at 20:08, Samson Tu wrote:

right, I got the following:

C:\apps\rklauncher>set P4="C:\Program Files\Protege_4.0"

C:\apps\rklauncher>cd "C:\Program Files\Protege_4.0"

...
Starting Protege 4 OWL Editor
Platform:
    Framework: Eclipse (1.4.0)
    OS: Windows2003 (5.2)
    Processor: amd64
Could not install plugin in file/directory named plugins\uk.ac.manchester.cs.owl
.factplusplus.jar: org.osgi.framework.BundleException: No Bundle-NativeCode match

Samson

Nick Drummond wrote:
Did you get any warnings about not finding the libraries (I think we'd need a separate binary for this).

I have no machine to verify this but if someone else could try it quickly it would rule out other nasties.

Nick


On 8 May 2008, at 17:20, Samson Tu wrote:

FaCT++  is not available under Reasoner tab in my Protege 4 (build 62). Can it be that FaCT does not work in Windows XP 64-bit OS?

Samson

Nick Drummond wrote:
Hi,

I managed to reproduce this behaviour with pellet.
FaCT++ seems OK.
I'll have a look into it.

Nick

On 8 May 2008, at 07:34, Rinke Hoekstra wrote:

  
Hi,

I'm having similar problems, though usually switching-off the reasoner
(setting it to none), and switching it back on again is a sufficient
reset.

-Rinke

On 7 mei 2008, at 19:23, Samson Tu wrote:
    
Hi,

I am finding that Protege 4 (build 62) does not refresh  
classification
after changes in the KB.

For example, initially I get no instances that satisfy the following
query

is_studied_in_trial some (Study that scientific_title value
"Thrombolytic Therapy versus Primary Percutaneous Intervention")

I invoked the Reasoner, and saw that there is no instance satisfying
the
DL query expression.

Next, I added an assertion that the study in question
has_health_condition_studied an instance of code that correspond to,
say, acute MI, where is_studied_in_trial is the inverse property of
is_studied_in_trial. I expect to get back an result indicating that
the
acute MI code is  studied in the study.

It turns out that I don't get the correct results without restarting
Protege 4.

Samson

-- 
---------
Samson Tu                                   email: [hidden email]
Senior Research Scientist                   web: www.stanford.edu/
~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944




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

Email: [hidden email]    Skype:  rinkehoekstra
Phone: +31-20-5253499     Fax:   +31-20-5253495
Web:   http://www.leibnizcenter.org/users/rinke

Leibniz Center for Law,          Faculty of Law
University of Amsterdam,            PO Box 1030
1000 BA  Amsterdam,             The Netherlands
-----------------------------------------------



_______________________________________________
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-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944



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

-- 
---------
Samson Tu                                   email: [hidden email] 
Senior Research Scientist                   web: www.stanford.edu/~swt/
Center for Biomedical Informatics Research  phone: 1-650-725-3391
Stanford University                         fax: 1-650-725-7944



_______________________________________________
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