loading instance definitions in Manchester syntax

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loading instance definitions in Manchester syntax

Derrick McCain
I am working with a group of uers that are not ontologists and do not have access to a a ont editor but need to provide some simple instance information based on my ontology. I woud like for them to use the Manchester syntax because of it's simplicy, but I don't know if there is a document reader availible to parse and add the instances to my ontology using the OWL/JENA API. Is ther support in a API to load information into a ontModel?
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Re: loading instance definitions in Manchester syntax

Timothy Redmond
On 04/14/2010 07:28 AM, Derrick McCain wrote:
> I am working with a group of uers that are not ontologists and do not have
> access to a a ont editor but need to provide some simple instance
> information based on my ontology. I woud like for them to use the Manchester
> syntax because of it's simplicy, but I don't know if there is a document
> reader availible to parse and add the instances to my ontology using the
> OWL/JENA API. Is ther support in a API to load information into a ontModel?
>    
So I am not sure how the Manchester Syntax will help with providing
instance information - I may need a simple example.  I am interpreting
this as meaning that you are adding OWL individuals to an OWL ontology
but this interpretation may be wrong.

If you don't want them to have to worry about installing a ontology
tool, then our best offering is probably Web Protege [1] which will
allow users to edit an ontology with just a browser.  This tool will
also be better at editing the definitions of individuals.  Unfortunately
in Protege 4.1 we do not yet have an ideal tab for editing individual
data but hopefully this will change soon.

-Timothy

[1] http://protegewiki.stanford.edu/wiki/WebProtege

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RE: loading instance definitions in Manchester syntax

Derrick McCain

Tim:

 

 

First, thanks for the quick reply. I apologize for the imprecise question. The users will be experienced software developers that will create some simple individuals based on a published ontology specification, so the simpler the better. The intent is to then to send the resulting text to a restful service for inclusion into a rdf store. My reading to date on loading is that the Manchester syntax is not supported as a format that can be automatically  parse the and insert the OWL individuals into a rdf store. I would like to conform that this can NOT be done or how could this be achieved using either the OWL or Protégé APIs.

 

 

Thanx

Derrick

 

From: Timothy Redmond [via Protege Ontology Editor & Knowledge Acquisition System] [mailto:[hidden email]]
Sent: Thursday, April 15, 2010 11:13 AM
To: McCain, Derrick (N-General Dynamics)
Subject: Re: loading instance definitions in Manchester syntax

 

On 04/14/2010 07:28 AM, Derrick McCain wrote:
> I am working with a group of uers that are not ontologists and do not have
> access to a a ont editor but need to provide some simple instance
> information based on my ontology. I woud like for them to use the Manchester
> syntax because of it's simplicy, but I don't know if there is a document
> reader availible to parse and add the instances to my ontology using the
> OWL/JENA API. Is ther support in a API to load information into a ontModel?
>    
So I am not sure how the Manchester Syntax will help with providing
instance information - I may need a simple example.  I am interpreting
this as meaning that you are adding OWL individuals to an OWL ontology
but this interpretation may be wrong.

If you don't want them to have to worry about installing a ontology
tool, then our best offering is probably Web Protege [1] which will
allow users to edit an ontology with just a browser.  This tool will
also be better at editing the definitions of individuals.  Unfortunately
in Protege 4.1 we do not yet have an ideal tab for editing individual
data but hopefully this will change soon.

-Timothy

[1] http://protegewiki.stanford.edu/wiki/WebProtege

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Re: loading instance definitions in Manchester syntax

Timothy Redmond

First, thanks for the quick reply. I apologize for the imprecise question. The users will be experienced software developers that will create some simple individuals based on a published ontology specification, so the simpler the better. The intent is to then to send the resulting text to a restful service for inclusion into a rdf store. My reading to date on loading is that the Manchester syntax is not supported as a format that can be automatically  parse the and insert the OWL individuals into a rdf store. I would like to conform that this can NOT be done or how could this be achieved using either the OWL or Protégé APIs.


There is no reason why the right combination of tools could work with the Manchester OWL syntax and a triple store.   To my knowledge the Manchester OWL api [1] is the best tool for working with the Manchester OWL syntax.  I am sure that this could be made to work with any triple store though depending on your architecture this may not be the simplest choice.

But we are getting into a tools discussion and your requirements are important.  It seems to me that these requirements should drive both the choice of tools and then the most natural data format.

Have you committed to a triple store on the server?  I think that there are may already be some restful services that operate at the RDF level.  In fact I believe that Sesame has such a set of services.   Is there a particular reason why the Manchester OWL syntax came up as a useful approach?  Will you be saying complex things about OWL individuals (e.g. giving an individual a type which is a class expression like

mypizza hasType hasTopping >= 5 Thing
  
?  More likely I would guess that your assertions would simply be property assertions like

mypizza hasTopping myTopping.
  
Is the focus going to be RDF or OWL?   Is the information that you are sending over the wire going to get more complicated (and OWL oriented) as your project develops?  Will you be using some sort of OWL tool/reasoner to validate your input on the server?

I tend to favor the Manchester OWL api in my work but that is partly because much of my work is being done at the OWL level of abstraction.  The manchester owl syntax will work well with the OWL api.  Though in my recent work on restful services I used OWL/XML with the OWL API.    If you are simply sending object and data property assertions and you have a triple store on the server then an RDF tool might be simpler.   If you use an RDF tool then it will probably play a role in what syntax you want to use to represent data (e.g. you might use rdf/xml syntax, turtle or n3).

-Timothy

[1] http://owlapi.sourceforge.net/


 

 

Thanx

Derrick

 

From: Timothy Redmond [via Protege Ontology Editor & Knowledge Acquisition System] [mailto:[hidden email]]
Sent: Thursday, April 15, 2010 11:13 AM
To: McCain, Derrick (N-General Dynamics)
Subject: Re: loading instance definitions in Manchester syntax

 

On 04/14/2010 07:28 AM, Derrick McCain wrote:
> I am working with a group of uers that are not ontologists and do not have
> access to a a ont editor but need to provide some simple instance
> information based on my ontology. I woud like for them to use the Manchester
> syntax because of it's simplicy, but I don't know if there is a document
> reader availible to parse and add the instances to my ontology using the
> OWL/JENA API. Is ther support in a API to load information into a ontModel?
>    
So I am not sure how the Manchester Syntax will help with providing
instance information - I may need a simple example.  I am interpreting
this as meaning that you are adding OWL individuals to an OWL ontology
but this interpretation may be wrong.

If you don't want them to have to worry about installing a ontology
tool, then our best offering is probably Web Protege [1] which will
allow users to edit an ontology with just a browser.  This tool will
also be better at editing the definitions of individuals.  Unfortunately
in Protege 4.1 we do not yet have an ideal tab for editing individual
data but hopefully this will change soon.

-Timothy

[1] http://protegewiki.stanford.edu/wiki/WebProtege

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Webprotege

Madani,Sina

Hi,

What is the latest version of Collaborative Protégé that is compatible with current Web protégé?

 

Thanks

Sina


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Re: Webprotege

Tania Tudorache
Sina,

I've just published on the wiki a version of WebProtege that works with Protege 3.4.4:

http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide

If you are developing something for WebProtege, then you should be aware that we are in a transitory phase in which all the development takes place in the who branch, not on trunk. This is a transitory state, and we will fix it soon. So, if you want the latest code, please use the who branch:

http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who

Tania

On 05/12/2010 06:56 AM, Madani,Sina wrote:

Hi,

What is the latest version of Collaborative Protégé that is compatible with current Web protégé?

 

Thanks

Sina

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Re: Webprotege

Madani,Sina

Thank you Tania,

Web Protégé works but Tomcat complains about not finding “plugins” directory while it deploys Web Protégé.

Also, during the sign in process when I enter myusername I get an error that “webprotege” user does not have enough privileges to access metaproject. Any hint?

 

Thanks

Sina

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Tania Tudorache
Sent: Wednesday, May 12, 2010 5:02 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege

 

Sina,

I've just published on the wiki a version of WebProtege that works with Protege 3.4.4:

http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide

If you are developing something for WebProtege, then you should be aware that we are in a transitory phase in which all the development takes place in the who branch, not on trunk. This is a transitory state, and we will fix it soon. So, if you want the latest code, please use the who branch:

http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who

Tania

On 05/12/2010 06:56 AM, Madani,Sina wrote:

Hi,

What is the latest version of Collaborative Protégé that is compatible with current Web protégé?

 

Thanks

Sina

 
 
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Re: Webprotege

Thomas Russ

On May 17, 2010, at 12:57 PM, Madani,Sina wrote:

> Thank you Tania,
> Web Protégé works but Tomcat complains about not finding “plugins”  
> directory while it deploys Web Protégé.

This sounds like Protege is not finding the protege directory.

You will need to set the protege.dir Java variable to the proper  
value, but I'm not 100% sure where you would do this for Tomcat.  In a  
stand-alone java you can do it by passing -Dprotege.dir=... to the  
JVM.  Maybe the CATALINA_OPTS or JAVA_OPTS environment variable?

> Also, during the sign in process when I enter myusername I get an  
> error that “webprotege” user does not have enough privileges to  
> access metaproject. Any hint?
>
> Thanks
> Sina
>
> From: [hidden email] [mailto:[hidden email]
> ] On Behalf Of Tania Tudorache
> Sent: Wednesday, May 12, 2010 5:02 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] Webprotege
>
> Sina,
>
> I've just published on the wiki a version of WebProtege that works  
> with Protege 3.4.4:
>
> http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide
>
> If you are developing something for WebProtege, then you should be  
> aware that we are in a transitory phase in which all the development  
> takes place in the who branch, not on trunk. This is a transitory  
> state, and we will fix it soon. So, if you want the latest code,  
> please use the who branch:
>
> http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who
>
> Tania
>
> On 05/12/2010 06:56 AM, Madani,Sina wrote:
> Hi,
> What is the latest version of Collaborative Protégé that is  
> compatible with current Web protégé?
>
> Thanks
> Sina
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

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Re: Webprotege

Tania Tudorache
Thomas is right. However, the plugins folder is not important for
webprotege. If you are using the ant script to build webprotege, it will
gather all the needed jars (also from plugins) and will copy them to
WEB-INF/lib as a flat list. I know this has disadvantages (e.g.
conflicting jars), but it works fine. Protege has its own plugin load
mechanism and I am not sure how that would work with Tomcat's loader.

You need to give to webprotege the right to delegate on the server. If
you are using the example metaproject that comes with Protege 3.4.4 this
should already be set up. If you still have problems, please send me the
exact error. Also make sure that the user name and password from
war/protege.properties match the ones in the metaproject. (These are
used when webprotege tries to open the metaproject).

Tania

On 05/17/2010 01:43 PM, Thomas Russ wrote:

>
> On May 17, 2010, at 12:57 PM, Madani,Sina wrote:
>
>> Thank you Tania,
>> Web Protégé works but Tomcat complains about not finding “plugins”
>> directory while it deploys Web Protégé.
>
> This sounds like Protege is not finding the protege directory.
>
> You will need to set the protege.dir Java variable to the proper
> value, but I'm not 100% sure where you would do this for Tomcat.  In a
> stand-alone java you can do it by passing -Dprotege.dir=... to the
> JVM.  Maybe the CATALINA_OPTS or JAVA_OPTS environment variable?
>
>> Also, during the sign in process when I enter myusername I get an
>> error that “webprotege” user does not have enough privileges to
>> access metaproject. Any hint?
>>
>> Thanks
>> Sina
>>
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Tania
>> Tudorache
>> Sent: Wednesday, May 12, 2010 5:02 PM
>> To: User support for the Protege-OWL editor
>> Subject: Re: [protege-owl] Webprotege
>>
>> Sina,
>>
>> I've just published on the wiki a version of WebProtege that works
>> with Protege 3.4.4:
>>
>> http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide
>>
>> If you are developing something for WebProtege, then you should be
>> aware that we are in a transitory phase in which all the development
>> takes place in the who branch, not on trunk. This is a transitory
>> state, and we will fix it soon. So, if you want the latest code,
>> please use the who branch:
>>
>> http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who
>>
>> Tania
>>
>> On 05/12/2010 06:56 AM, Madani,Sina wrote:
>> Hi,
>> What is the latest version of Collaborative Protégé that is
>> compatible with current Web protégé?
>>
>> Thanks
>> Sina
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>

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Re: Webprotege

Madani,Sina
Adding Webportege user to admin group solved the problem.
In my collaborative project I mapped some of my classes to external reference terminologies through bioportal. I can add Bioportal search portlet to my tab in webprotege and do new search but it doesn't show the mappings that has already been done in the fat client. Also, for new mappings in webprotge biportal, it seems "import" is not functioning.
 

Thanks
Sina



-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Tania Tudorache
Sent: Monday, May 17, 2010 4:01 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege

Thomas is right. However, the plugins folder is not important for
webprotege. If you are using the ant script to build webprotege, it will
gather all the needed jars (also from plugins) and will copy them to
WEB-INF/lib as a flat list. I know this has disadvantages (e.g.
conflicting jars), but it works fine. Protege has its own plugin load
mechanism and I am not sure how that would work with Tomcat's loader.

You need to give to webprotege the right to delegate on the server. If
you are using the example metaproject that comes with Protege 3.4.4 this
should already be set up. If you still have problems, please send me the
exact error. Also make sure that the user name and password from
war/protege.properties match the ones in the metaproject. (These are
used when webprotege tries to open the metaproject).

Tania

On 05/17/2010 01:43 PM, Thomas Russ wrote:

>
> On May 17, 2010, at 12:57 PM, Madani,Sina wrote:
>
>> Thank you Tania,
>> Web Protégé works but Tomcat complains about not finding "plugins"
>> directory while it deploys Web Protégé.
>
> This sounds like Protege is not finding the protege directory.
>
> You will need to set the protege.dir Java variable to the proper
> value, but I'm not 100% sure where you would do this for Tomcat.  In a
> stand-alone java you can do it by passing -Dprotege.dir=... to the
> JVM.  Maybe the CATALINA_OPTS or JAVA_OPTS environment variable?
>
>> Also, during the sign in process when I enter myusername I get an
>> error that "webprotege" user does not have enough privileges to
>> access metaproject. Any hint?
>>
>> Thanks
>> Sina
>>
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Tania
>> Tudorache
>> Sent: Wednesday, May 12, 2010 5:02 PM
>> To: User support for the Protege-OWL editor
>> Subject: Re: [protege-owl] Webprotege
>>
>> Sina,
>>
>> I've just published on the wiki a version of WebProtege that works
>> with Protege 3.4.4:
>>
>> http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide
>>
>> If you are developing something for WebProtege, then you should be
>> aware that we are in a transitory phase in which all the development
>> takes place in the who branch, not on trunk. This is a transitory
>> state, and we will fix it soon. So, if you want the latest code,
>> please use the who branch:
>>
>> http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who
>>
>> Tania
>>
>> On 05/12/2010 06:56 AM, Madani,Sina wrote:
>> Hi,
>> What is the latest version of Collaborative Protégé that is
>> compatible with current Web protégé?
>>
>> Thanks
>> Sina
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>

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Re: Webprotege

Csongor Nyulas
Administrator
Hi Sina,

WebProtege should be able to both
 - show the existing mappings that you have created in the thick client (supposed that you used the same configuration of the BioPortalReferenceWidget in Protege as for the externalreference widget in WebProtege), and
 - to create new references (if you have configured the externalreference widget in your WebProtege correctly)

Here is an example complete configuration of the BioPortal reference widget in WebProtege:


    <entry>
        <string>http://who.int/icd#bodySystem</string>
        <map>
            <entry>
                <string>name</string>
                <string>Body_System</string>
            </entry>
            <entry>
                <string>ont_type</string>
                <string>http://who.int/icd#BodySystemTerm</string>
            </entry>
            <entry>
                <string>label</string>
                <string>Body System</string>
            </entry>
            <entry>
                <string>tooltip</string>
                <string>Traditional divisions of body systems used to organize codes taken from list of body systems currently used in the ICD-10</string>
            </entry>
            <entry>
                <string>help</string>
                <string>http://apps.who.int/classifications/apps/icd/icatfiles/iCAT_Glossary.html#body_system</string>
            </entry>
            <entry>
                <string>component_type</string>
                <string>externalreference</string>
            </entry>
            <entry>
                <string>bp_search_properties</string>
                <map>
                    <entry>
                        <string>create_reference_as_class</string>
                        <boolean>false</boolean>
                    </entry>
                    <entry>
                        <string>reference_class</string>
                        <!-- string>ExternalReference
(default value, if not specified)</string-->
                        <string>http://who.int/icd#BodySystemTerm</string>
                    </entry>
                    <entry>
                        <string>reference_property</string>
                        <string>http://who.int/icd#bodySystem</string>
                    </entry>
                    <entry>
                        <string>bioportal_base_url</string>
                        <string>http://bioportal.bioontology.org/</string>
                    </entry>
                    <entry>
                        <string>bioportal_rest_base_url</string>
                        <string>http://rest.bioontology.org/bioportal/</string>
                    </entry>
                    <entry>
                        <string>bioportal_search_url</string>
                        <string>http://rest.bioontology.org/bioportal/search/</string>
                    </entry>
                    <entry>
                        <string>search_ontology_ids</string>
                        <string>1487</string>
                    </entry>
                    <entry>
                        <string>search_options</string>
                        <string>includeproperties=1</string>
                    </entry>
                    <entry>
                        <string>search_one_page_option</string>
                        <string>pagesize=10&amp;pagenum=1</string>
                    </entry>
                    <entry>
                        <string>default_search_string</string>
                        <string>@none@</string>
                    </entry>
                    <entry>
                        <string>import_from_original_ontology</string>
                        <!-- boolean>by default: true</boolean-->
                        <boolean>true</boolean>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>index</string>
                <string>0</string>
            </entry>
            <entry>
                <string>height</string>
                <string>150</string>
            </entry>
            <entry>
                <string>Column1</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>label</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>all</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://who.int/icd#label</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>0</string>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>Column2</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>Term ID</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>150</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://bioportal.bioontology.org#shortTermId</string>
                    </entry>
                    <entry>
                        <string>field_type</string>
                        <string>nolink</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>1</string>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>Column3</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>Link</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>30</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://who.int/icd#url</string>
                    </entry>
                    <entry>
                        <string>field_type</string>
                        <string>linkicon</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>2</string>
                    </entry>
                </map>
            </entry>
        </map>
    </entry>

Here are some details about the meaning of some of the most important configuration options:
- in the first line:
        <string>http://who.int/icd#bodySystem</string>
must specify to the full URI of the property being displayed. This is supposed to be the same object property that you used in the thick client.
- The XML property-value pair:
                <string>name</string>
                <string>Body_System</string>

can specify and arbitrary string that is a valid HTML id: must be unique in the configuration file, should start with an alphanumeric character and should only contain numbers, letters and or underscore (no spaces or other special characters are allowed)
- The XML property-value pair:
                <string>ont_type</string>
                <string>http://who.int/icd#BodySystemTerm</string>
must specify the full URI of the class that is used as the range of the property (i.e. the instances that are values of the property must be of this type)
- The XML property-value pair:
                <string>label</string>
                <string>Body System</string>

can be any valid HTML text that you would like to be used as the label of the property in the UI. Please be aware that if you want to use special characters, like <, &, ", etc., you must encode them appropriately (as &lt; &amp; &quot; etc). This rule is to be applied for most of the XML property values that are to be used in WebProtege.
- Component type must be "externalreference"
                <string>component_type</string>
                <string>externalreference</string>

- The value of the "create_reference_as_class" XML property should be "false":
                        <string>create_reference_as_class</string>
                        <boolean>false</boolean>
This corresponds to the "Create new BioPortal reference as: instance" option in the BioPortalReferenceWidget.
- The XML property-value
                        <string>reference_class</string>
                        <string>http://who.int/icd#BodySystemTerm</string>
specifies the URI of the class which will be used as the type of the imported external reference instances. It should be the name of the class that is specified as the range of the property. If this XML property is not specified the class used by default would be ExternalReference (which is probably not what you want in most of the cases).
- The XML property-value
                        <string>reference_property</string>
                        <string>http://who.int/icd#bodySystem</string>
specifies the URI of the property which will be the property used to refer to the imported external reference instances. It should always be the name of the property that is specified in the first line.
- The XML properties within the bp_search_properties map:
    bioportal_base_url
   
bioportal_rest_base_url
   
bioportal_search_url
   
search_ontology_ids
   
import_from_original_ontology
have the same meaning as in the BioPortalReferenceWidget configuration.
- with the XML property search_options one can specify additional BioPortal search options
- with the XML property search_one_page_option one can specify the BioPortal search options that would be used to present the search result on the first page
- with the XML property default_search_string one can specify a string that will be searched automatically whenever the user clicks on the "Find Term" button. There are a few specially interpreted values for this propery: @none@ - leaves the search box empty, @entity@ - searches for the name of the selected entity (for example the selected class in the class tree).
- The "tooltip" and "help" XML properties are to specify different ways for informing user about the meaning and usage of a particular property.
- The entries named Column1, Column2, etc. configure the displayed columns in the ExternalReference widget.

I hope this little overview would prove to be useful and not too confusing.
Best,
Csongor

On 5/18/2010 6:42 AM, Madani,Sina wrote:
Adding Webportege user to admin group solved the problem. 
In my collaborative project I mapped some of my classes to external reference terminologies through bioportal. I can add Bioportal search portlet to my tab in webprotege and do new search but it doesn't show the mappings that has already been done in the fat client. Also, for new mappings in webprotge biportal, it seems "import" is not functioning. 
 

Thanks
Sina



-----Original Message-----
From: [hidden email] [[hidden email]] On Behalf Of Tania Tudorache
Sent: Monday, May 17, 2010 4:01 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege

Thomas is right. However, the plugins folder is not important for 
webprotege. If you are using the ant script to build webprotege, it will 
gather all the needed jars (also from plugins) and will copy them to 
WEB-INF/lib as a flat list. I know this has disadvantages (e.g. 
conflicting jars), but it works fine. Protege has its own plugin load 
mechanism and I am not sure how that would work with Tomcat's loader.

You need to give to webprotege the right to delegate on the server. If 
you are using the example metaproject that comes with Protege 3.4.4 this 
should already be set up. If you still have problems, please send me the 
exact error. Also make sure that the user name and password from 
war/protege.properties match the ones in the metaproject. (These are 
used when webprotege tries to open the metaproject).

Tania

On 05/17/2010 01:43 PM, Thomas Russ wrote:
  
On May 17, 2010, at 12:57 PM, Madani,Sina wrote:

    
Thank you Tania,
Web Protégé works but Tomcat complains about not finding "plugins" 
directory while it deploys Web Protégé.
      
This sounds like Protege is not finding the protege directory.

You will need to set the protege.dir Java variable to the proper 
value, but I'm not 100% sure where you would do this for Tomcat.  In a 
stand-alone java you can do it by passing -Dprotege.dir=... to the 
JVM.  Maybe the CATALINA_OPTS or JAVA_OPTS environment variable?

    
Also, during the sign in process when I enter myusername I get an 
error that "webprotege" user does not have enough privileges to 
access metaproject. Any hint?

Thanks
Sina

From: [hidden email] 
[[hidden email]] On Behalf Of Tania 
Tudorache
Sent: Wednesday, May 12, 2010 5:02 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege

Sina,

I've just published on the wiki a version of WebProtege that works 
with Protege 3.4.4:

http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide

If you are developing something for WebProtege, then you should be 
aware that we are in a transitory phase in which all the development 
takes place in the who branch, not on trunk. This is a transitory 
state, and we will fix it soon. So, if you want the latest code, 
please use the who branch:

http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who

Tania

On 05/12/2010 06:56 AM, Madani,Sina wrote:
Hi,
What is the latest version of Collaborative Protégé that is 
compatible with current Web protégé?

Thanks
Sina


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Re: Webprotege

Madani,Sina

Thank you Csongor,

How can I configure externalReference property in Web Protégé to be linked to BioportalWidget? I tried “configure” button in the Bioportal content in WebProtege but it shows “no configuration option”

Same message when I tried to configure externalReference property. Maybe I need to be able to visualize rdfs:Class and owl:Class in webprotege first. I tried metatab but it comes empty

I signed is as admin user if it makes a difference.

 

Shouldn’t all configurations be transferable/interchangeable between thin and thick clients? I can see all properties related to Bioportal Widget in Webportge but not sure how to associate them to the widget.

 

Thanks for the help

Sina

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Csongor Nyulas
Sent: Wednesday, May 19, 2010 1:29 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege

 

Hi Sina,

WebProtege should be able to both
 - show the existing mappings that you have created in the thick client (supposed that you used the same configuration of the BioPortalReferenceWidget in Protege as for the externalreference widget in WebProtege), and
 - to create new references (if you have configured the externalreference widget in your WebProtege correctly)

Here is an example complete configuration of the BioPortal reference widget in WebProtege:


    <entry>
        <string>http://who.int/icd#bodySystem</string>
        <map>
            <entry>
                <string>name</string>
                <string>Body_System</string>
            </entry>
            <entry>
                <string>ont_type</string>
                <string>http://who.int/icd#BodySystemTerm</string>
            </entry>
            <entry>
                <string>label</string>
                <string>Body System</string>
            </entry>
            <entry>
                <string>tooltip</string>
                <string>Traditional divisions of body systems used to organize codes taken from list of body systems currently used in the ICD-10</string>
            </entry>
            <entry>
                <string>help</string>
                <string>http://apps.who.int/classifications/apps/icd/icatfiles/iCAT_Glossary.html#body_system</string>
            </entry>
            <entry>
                <string>component_type</string>
                <string>externalreference</string>
            </entry>
            <entry>
                <string>bp_search_properties</string>
                <map>
                    <entry>
                        <string>create_reference_as_class</string>
                        <boolean>false</boolean>
                    </entry>
                    <entry>
                        <string>reference_class</string>
                        <!-- string>ExternalReference (default value, if not specified)</string-->
                        <string>http://who.int/icd#BodySystemTerm</string>
                    </entry>
                    <entry>
                        <string>reference_property</string>
                        <string>http://who.int/icd#bodySystem</string>
                    </entry>
                    <entry>
                        <string>bioportal_base_url</string>
                        <string>http://bioportal.bioontology.org/</string>
                    </entry>
                    <entry>
                        <string>bioportal_rest_base_url</string>
                        <string>http://rest.bioontology.org/bioportal/</string>
                    </entry>
                    <entry>
                        <string>bioportal_search_url</string>
                        <string>http://rest.bioontology.org/bioportal/search/</string>
                    </entry>
                    <entry>
                        <string>search_ontology_ids</string>
                        <string>1487</string>
                    </entry>
                    <entry>
                        <string>search_options</string>
                        <string>includeproperties=1</string>
                    </entry>
                    <entry>
                        <string>search_one_page_option</string>
                        <string>pagesize=10&amp;pagenum=1</string>
                    </entry>
                    <entry>
                        <string>default_search_string</string>
                        <string>@none@</string>
                    </entry>
                    <entry>
                        <string>import_from_original_ontology</string>
                        <!-- boolean>by default: true</boolean-->
                        <boolean>true</boolean>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>index</string>
                <string>0</string>
            </entry>
            <entry>
                <string>height</string>
                <string>150</string>
            </entry>
            <entry>
                <string>Column1</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>label</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>all</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://who.int/icd#label</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>0</string>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>Column2</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>Term ID</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>150</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://bioportal.bioontology.org#shortTermId</string>
                    </entry>
                    <entry>
                        <string>field_type</string>
                        <string>nolink</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>1</string>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>Column3</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>Link</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>30</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://who.int/icd#url</string>
                    </entry>
                    <entry>
                        <string>field_type</string>
                        <string>linkicon</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>2</string>
                    </entry>
                </map>
            </entry>
        </map>
    </entry>

Here are some details about the meaning of some of the most important configuration options:
- in the first line:
        <string>http://who.int/icd#bodySystem</string>
must specify to the full URI of the property being displayed. This is supposed to be the same object property that you used in the thick client.
- The XML property-value pair:
                <string>name</string>
                <string>Body_System</string>

can specify and arbitrary string that is a valid HTML id: must be unique in the configuration file, should start with an alphanumeric character and should only contain numbers, letters and or underscore (no spaces or other special characters are allowed)
- The XML property-value pair:
                <string>ont_type</string>
                <string>http://who.int/icd#BodySystemTerm</string>
must specify the full URI of the class that is used as the range of the property (i.e. the instances that are values of the property must be of this type)
- The XML property-value pair:
                <string>label</string>
                <string>Body System</string>

can be any valid HTML text that you would like to be used as the label of the property in the UI. Please be aware that if you want to use special characters, like <, &, ", etc., you must encode them appropriately (as &lt; &amp; &quot; etc). This rule is to be applied for most of the XML property values that are to be used in WebProtege.
- Component type must be "externalreference"
                <string>component_type</string>
                <string>externalreference</string>

- The value of the "create_reference_as_class" XML property should be "false":
                        <string>create_reference_as_class</string>
                        <boolean>false</boolean>
This corresponds to the "Create new BioPortal reference as: instance" option in the BioPortalReferenceWidget.
- The XML property-value
                        <string>reference_class</string>
                        <string>http://who.int/icd#BodySystemTerm</string>
specifies the URI of the class which will be used as the type of the imported external reference instances. It should be the name of the class that is specified as the range of the property. If this XML property is not specified the class used by default would be ExternalReference (which is probably not what you want in most of the cases).
- The XML property-value
                        <string>reference_property</string>
                        <string>http://who.int/icd#bodySystem</string>
specifies the URI of the property which will be the property used to refer to the imported external reference instances. It should always be the name of the property that is specified in the first line.
- The XML properties within the bp_search_properties map:
    bioportal_base_url
    bioportal_rest_base_url
    bioportal_search_url
    search_ontology_ids
    import_from_original_ontology
have the same meaning as in the BioPortalReferenceWidget configuration.
- with the XML property search_options one can specify additional BioPortal search options
- with the XML property search_one_page_option one can specify the BioPortal search options that would be used to present the search result on the first page
- with the XML property default_search_string one can specify a string that will be searched automatically whenever the user clicks on the "Find Term" button. There are a few specially interpreted values for this propery: @none@ - leaves the search box empty, @entity@ - searches for the name of the selected entity (for example the selected class in the class tree).
- The "tooltip" and "help" XML properties are to specify different ways for informing user about the meaning and usage of a particular property.
- The entries named Column1, Column2, etc. configure the displayed columns in the ExternalReference widget.

I hope this little overview would prove to be useful and not too confusing.
Best,
Csongor

On 5/18/2010 6:42 AM, Madani,Sina wrote:

Adding Webportege user to admin group solved the problem. 
In my collaborative project I mapped some of my classes to external reference terminologies through bioportal. I can add Bioportal search portlet to my tab in webprotege and do new search but it doesn't show the mappings that has already been done in the fat client. Also, for new mappings in webprotge biportal, it seems "import" is not functioning. 
 
 
Thanks
Sina
 
 
 
-----Original Message-----
From: [hidden email] [[hidden email]] On Behalf Of Tania Tudorache
Sent: Monday, May 17, 2010 4:01 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege
 
Thomas is right. However, the plugins folder is not important for 
webprotege. If you are using the ant script to build webprotege, it will 
gather all the needed jars (also from plugins) and will copy them to 
WEB-INF/lib as a flat list. I know this has disadvantages (e.g. 
conflicting jars), but it works fine. Protege has its own plugin load 
mechanism and I am not sure how that would work with Tomcat's loader.
 
You need to give to webprotege the right to delegate on the server. If 
you are using the example metaproject that comes with Protege 3.4.4 this 
should already be set up. If you still have problems, please send me the 
exact error. Also make sure that the user name and password from 
war/protege.properties match the ones in the metaproject. (These are 
used when webprotege tries to open the metaproject).
 
Tania
 
On 05/17/2010 01:43 PM, Thomas Russ wrote:
  
 
On May 17, 2010, at 12:57 PM, Madani,Sina wrote:
 
    
Thank you Tania,
Web Protégé works but Tomcat complains about not finding "plugins" 
directory while it deploys Web Protégé.
      
 
This sounds like Protege is not finding the protege directory.
 
You will need to set the protege.dir Java variable to the proper 
value, but I'm not 100% sure where you would do this for Tomcat.  In a 
stand-alone java you can do it by passing -Dprotege.dir=... to the 
JVM.  Maybe the CATALINA_OPTS or JAVA_OPTS environment variable?
 
    
Also, during the sign in process when I enter myusername I get an 
error that "webprotege" user does not have enough privileges to 
access metaproject. Any hint?
 
Thanks
Sina
 
From: [hidden email] 
[[hidden email]] On Behalf Of Tania 
Tudorache
Sent: Wednesday, May 12, 2010 5:02 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege
 
Sina,
 
I've just published on the wiki a version of WebProtege that works 
with Protege 3.4.4:
 
http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide
 
If you are developing something for WebProtege, then you should be 
aware that we are in a transitory phase in which all the development 
takes place in the who branch, not on trunk. This is a transitory 
state, and we will fix it soon. So, if you want the latest code, 
please use the who branch:
 
http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who
 
Tania
 
On 05/12/2010 06:56 AM, Madani,Sina wrote:
Hi,
What is the latest version of Collaborative Protégé that is 
compatible with current Web protégé?
 
Thanks
Sina
 
 
_______________________________________________
protege-owl mailing list
[hidden email]
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Instructions for unsubscribing: 
http://protege.stanford.edu/doc/faq.html#01a.03
 
 
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Re: Webprotege

Patrick Cornic
Hello,
I have this message when i try to launch Protege 4. This arrives when i
want to create a new OWL ontology and just after the choice of the
ontologie Format (RDF/XML).

This message occurs also when i want to load an 3.4.1 ontology.

I want to use the version 4 just to try the SKOS plugin.

thanks for helping


Best regards
Patick Cornic




Error 1 Logged at Wed May 19 17:52:17 CEST 2010
NoClassDefFoundError: org/protege/editor/owl/ui/action/ProtegeOWLAction
     java.lang.ClassLoader.defineClass1(Native Method)
     java.lang.ClassLoader.defineClass(Unknown Source)
     
org.apache.felix.framework.ModuleImpl$ModuleClassLoader.findClass(ModuleImpl.java:1787)
     
org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:682)
     org.apache.felix.framework.ModuleImpl.access$100(ModuleImpl.java:60)
     
org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1650)
     java.lang.ClassLoader.loadClass(Unknown Source)
     
org.apache.felix.framework.ModuleImpl.getClassByDelegation(ModuleImpl.java:598)
     org.apache.felix.framework.Felix.loadBundleClass(Felix.java:1487)
     org.apache.felix.framework.BundleImpl.loadClass(BundleImpl.java:897)
     
org.protege.editor.core.plugin.PluginUtilities.getExtensionObject(PluginUtilities.java:131)
     
org.protege.editor.core.plugin.ExtensionInstantiator.instantiate(ExtensionInstantiator.java:74)
     
org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:152)
     
org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:31)
     org.protege.editor.core.ui.menu.MenuBuilder.add(MenuBuilder.java:164)
     org.protege.editor.core.ui.menu.MenuBuilder.add(MenuBuilder.java:125)
     
org.protege.editor.core.ui.menu.MenuBuilder.buildMenu(MenuBuilder.java:88)
     
org.protege.editor.core.ui.workspace.WorkspaceFrame.createMenuBar(WorkspaceFrame.java:171)
     
org.protege.editor.core.ui.workspace.WorkspaceFrame.createUI(WorkspaceFrame.java:141)
     
org.protege.editor.core.ui.workspace.WorkspaceFrame.<init>(WorkspaceFrame.java:59)
     
org.protege.editor.core.ui.workspace.WorkspaceManager.addWorkspace(WorkspaceManager.java:37)
     
org.protege.editor.core.editorkit.EditorKitManager.addEditorKit(EditorKitManager.java:45)
     
org.protege.editor.core.ProtegeManager.createAndSetupNewEditorKit(ProtegeManager.java:128)
     
org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$1.actionPerformed(ProtegeWelcomeFrame.java:114)
     
org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:102)
     org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
     
org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:68)
     java.awt.Component.processMouseEvent(Unknown Source)
     javax.swing.JComponent.processMouseEvent(Unknown Source)
     java.awt.Component.processEvent(Unknown Source)
     java.awt.Container.processEvent(Unknown Source)
     java.awt.Component.dispatchEventImpl(Unknown Source)
     java.awt.Container.dispatchEventImpl(Unknown Source)
     java.awt.Component.dispatchEvent(Unknown Source)
     java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
     java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
     java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
     java.awt.Container.dispatchEventImpl(Unknown Source)
     java.awt.Window.dispatchEventImpl(Unknown Source)
     java.awt.Component.dispatchEvent(Unknown Source)
     java.awt.EventQueue.dispatchEvent(Unknown Source)
     java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
     java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
     java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
     java.awt.EventDispatchThread.pumpEvents(Unknown Source)
     java.awt.EventDispatchThread.pumpEvents(Unknown Source)
     java.awt.EventDispatchThread.run(Unknown Source)
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Re: Webprotege

Tania Tudorache
In reply to this post by Madani,Sina
Hi Sina,

The configuration of the BioPortal reference portlet for WebProtege is made in the configuration_YourProjectName.xml from war/projectConfigurations folder. This is an XML file that defines how the user interface of WebProtege should look like, and other configuration properties for the portlets. You can think of this configuration file as a correspondent of the pprj file for the rich client.

Just like in the rich client, you need to associate to a property (e.g. externalReference property) a porltet for editing in the configuration file. Csongor explained with details how to associate the bioportal external reference porltet to a property. This is a one time configuration that you need to do for your project.

The rich and web Protege clients do not share the layout and widget configurations, because they have different components. We are working on making the layout configuration more user friendly, but right now, you need to edit the configuration xml file.

We also have some example configuration files that you can look at:
http://smi-protege.stanford.edu/svn/web-protege/branches/who/war/projectConfigurations/configuration_example_property_field_portlet.xml?view=markup
http://smi-protege.stanford.edu/svn/web-protege/branches/who/war/projectConfigurations/configuration_ICD.xml?view=markup

Tania


On 05/19/2010 08:30 AM, Madani,Sina wrote:

Thank you Csongor,

How can I configure externalReference property in Web Protégé to be linked to BioportalWidget? I tried “configure” button in the Bioportal content in WebProtege but it shows “no configuration option”

Same message when I tried to configure externalReference property. Maybe I need to be able to visualize rdfs:Class and owl:Class in webprotege first. I tried metatab but it comes empty

I signed is as admin user if it makes a difference.

 

Shouldn’t all configurations be transferable/interchangeable between thin and thick clients? I can see all properties related to Bioportal Widget in Webportge but not sure how to associate them to the widget.

 

Thanks for the help

Sina

 

From: [hidden email] [[hidden email]] On Behalf Of Csongor Nyulas
Sent: Wednesday, May 19, 2010 1:29 AM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege

 

Hi Sina,

WebProtege should be able to both
 - show the existing mappings that you have created in the thick client (supposed that you used the same configuration of the BioPortalReferenceWidget in Protege as for the externalreference widget in WebProtege), and
 - to create new references (if you have configured the externalreference widget in your WebProtege correctly)

Here is an example complete configuration of the BioPortal reference widget in WebProtege:


    <entry>
        <string>http://who.int/icd#bodySystem</string>
        <map>
            <entry>
                <string>name</string>
                <string>Body_System</string>
            </entry>
            <entry>
                <string>ont_type</string>
                <string>http://who.int/icd#BodySystemTerm</string>
            </entry>
            <entry>
                <string>label</string>
                <string>Body System</string>
            </entry>
            <entry>
                <string>tooltip</string>
                <string>Traditional divisions of body systems used to organize codes taken from list of body systems currently used in the ICD-10</string>
            </entry>
            <entry>
                <string>help</string>
                <string>http://apps.who.int/classifications/apps/icd/icatfiles/iCAT_Glossary.html#body_system</string>
            </entry>
            <entry>
                <string>component_type</string>
                <string>externalreference</string>
            </entry>
            <entry>
                <string>bp_search_properties</string>
                <map>
                    <entry>
                        <string>create_reference_as_class</string>
                        <boolean>false</boolean>
                    </entry>
                    <entry>
                        <string>reference_class</string>
                        <!-- string>ExternalReference (default value, if not specified)</string-->
                        <string>http://who.int/icd#BodySystemTerm</string>
                    </entry>
                    <entry>
                        <string>reference_property</string>
                        <string>http://who.int/icd#bodySystem</string>
                    </entry>
                    <entry>
                        <string>bioportal_base_url</string>
                        <string>http://bioportal.bioontology.org/</string>
                    </entry>
                    <entry>
                        <string>bioportal_rest_base_url</string>
                        <string>http://rest.bioontology.org/bioportal/</string>
                    </entry>
                    <entry>
                        <string>bioportal_search_url</string>
                        <string>http://rest.bioontology.org/bioportal/search/</string>
                    </entry>
                    <entry>
                        <string>search_ontology_ids</string>
                        <string>1487</string>
                    </entry>
                    <entry>
                        <string>search_options</string>
                        <string>includeproperties=1</string>
                    </entry>
                    <entry>
                        <string>search_one_page_option</string>
                        <string>pagesize=10&amp;pagenum=1</string>
                    </entry>
                    <entry>
                        <string>default_search_string</string>
                        <string>@none@</string>
                    </entry>
                    <entry>
                        <string>import_from_original_ontology</string>
                        <!-- boolean>by default: true</boolean-->
                        <boolean>true</boolean>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>index</string>
                <string>0</string>
            </entry>
            <entry>
                <string>height</string>
                <string>150</string>
            </entry>
            <entry>
                <string>Column1</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>label</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>all</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://who.int/icd#label</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>0</string>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>Column2</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>Term ID</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>150</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://bioportal.bioontology.org#shortTermId</string>
                    </entry>
                    <entry>
                        <string>field_type</string>
                        <string>nolink</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>1</string>
                    </entry>
                </map>
            </entry>
            <entry>
                <string>Column3</string>
                <map>
                    <entry>
                        <string>header</string>
                        <string>Link</string>
                    </entry>
                    <entry>
                        <string>width</string>
                        <string>30</string>
                    </entry>
                    <entry>
                        <string>property</string>
                        <string>http://who.int/icd#url</string>
                    </entry>
                    <entry>
                        <string>field_type</string>
                        <string>linkicon</string>
                    </entry>
                    <entry>
                        <string>index</string>
                        <string>2</string>
                    </entry>
                </map>
            </entry>
        </map>
    </entry>

Here are some details about the meaning of some of the most important configuration options:
- in the first line:
        <string>http://who.int/icd#bodySystem</string>
must specify to the full URI of the property being displayed. This is supposed to be the same object property that you used in the thick client.
- The XML property-value pair:
                <string>name</string>
                <string>Body_System</string>

can specify and arbitrary string that is a valid HTML id: must be unique in the configuration file, should start with an alphanumeric character and should only contain numbers, letters and or underscore (no spaces or other special characters are allowed)
- The XML property-value pair:
                <string>ont_type</string>
                <string>http://who.int/icd#BodySystemTerm</string>
must specify the full URI of the class that is used as the range of the property (i.e. the instances that are values of the property must be of this type)
- The XML property-value pair:
                <string>label</string>
                <string>Body System</string>

can be any valid HTML text that you would like to be used as the label of the property in the UI. Please be aware that if you want to use special characters, like <, &, ", etc., you must encode them appropriately (as &lt; &amp; &quot; etc). This rule is to be applied for most of the XML property values that are to be used in WebProtege.
- Component type must be "externalreference"
                <string>component_type</string>
                <string>externalreference</string>

- The value of the "create_reference_as_class" XML property should be "false":
                        <string>create_reference_as_class</string>
                        <boolean>false</boolean>
This corresponds to the "Create new BioPortal reference as: instance" option in the BioPortalReferenceWidget.
- The XML property-value
                        <string>reference_class</string>
                        <string>http://who.int/icd#BodySystemTerm</string>
specifies the URI of the class which will be used as the type of the imported external reference instances. It should be the name of the class that is specified as the range of the property. If this XML property is not specified the class used by default would be ExternalReference (which is probably not what you want in most of the cases).
- The XML property-value
                        <string>reference_property</string>
                        <string>http://who.int/icd#bodySystem</string>
specifies the URI of the property which will be the property used to refer to the imported external reference instances. It should always be the name of the property that is specified in the first line.
- The XML properties within the bp_search_properties map:
    bioportal_base_url
    bioportal_rest_base_url
    bioportal_search_url
    search_ontology_ids
    import_from_original_ontology
have the same meaning as in the BioPortalReferenceWidget configuration.
- with the XML property search_options one can specify additional BioPortal search options
- with the XML property search_one_page_option one can specify the BioPortal search options that would be used to present the search result on the first page
- with the XML property default_search_string one can specify a string that will be searched automatically whenever the user clicks on the "Find Term" button. There are a few specially interpreted values for this propery: @none@ - leaves the search box empty, @entity@ - searches for the name of the selected entity (for example the selected class in the class tree).
- The "tooltip" and "help" XML properties are to specify different ways for informing user about the meaning and usage of a particular property.
- The entries named Column1, Column2, etc. configure the displayed columns in the ExternalReference widget.

I hope this little overview would prove to be useful and not too confusing.
Best,
Csongor

On 5/18/2010 6:42 AM, Madani,Sina wrote:

Adding Webportege user to admin group solved the problem. 
In my collaborative project I mapped some of my classes to external reference terminologies through bioportal. I can add Bioportal search portlet to my tab in webprotege and do new search but it doesn't show the mappings that has already been done in the fat client. Also, for new mappings in webprotge biportal, it seems "import" is not functioning. 
 
 
Thanks
Sina
 
 
 
-----Original Message-----
From: [hidden email] [[hidden email]] On Behalf Of Tania Tudorache
Sent: Monday, May 17, 2010 4:01 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege
 
Thomas is right. However, the plugins folder is not important for 
webprotege. If you are using the ant script to build webprotege, it will 
gather all the needed jars (also from plugins) and will copy them to 
WEB-INF/lib as a flat list. I know this has disadvantages (e.g. 
conflicting jars), but it works fine. Protege has its own plugin load 
mechanism and I am not sure how that would work with Tomcat's loader.
 
You need to give to webprotege the right to delegate on the server. If 
you are using the example metaproject that comes with Protege 3.4.4 this 
should already be set up. If you still have problems, please send me the 
exact error. Also make sure that the user name and password from 
war/protege.properties match the ones in the metaproject. (These are 
used when webprotege tries to open the metaproject).
 
Tania
 
On 05/17/2010 01:43 PM, Thomas Russ wrote:
  
 
On May 17, 2010, at 12:57 PM, Madani,Sina wrote:
 
    
Thank you Tania,
Web Protégé works but Tomcat complains about not finding "plugins" 
directory while it deploys Web Protégé.
      
 
This sounds like Protege is not finding the protege directory.
 
You will need to set the protege.dir Java variable to the proper 
value, but I'm not 100% sure where you would do this for Tomcat.  In a 
stand-alone java you can do it by passing -Dprotege.dir=... to the 
JVM.  Maybe the CATALINA_OPTS or JAVA_OPTS environment variable?
 
    
Also, during the sign in process when I enter myusername I get an 
error that "webprotege" user does not have enough privileges to 
access metaproject. Any hint?
 
Thanks
Sina
 
From: [hidden email] 
[[hidden email]] On Behalf Of Tania 
Tudorache
Sent: Wednesday, May 12, 2010 5:02 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Webprotege
 
Sina,
 
I've just published on the wiki a version of WebProtege that works 
with Protege 3.4.4:
 
http://protegewiki.stanford.edu/wiki/WebProtegeAdminGuide
 
If you are developing something for WebProtege, then you should be 
aware that we are in a transitory phase in which all the development 
takes place in the who branch, not on trunk. This is a transitory 
state, and we will fix it soon. So, if you want the latest code, 
please use the who branch:
 
http://smi-protege.stanford.edu/repos/protege/web-protege/branches/who
 
Tania
 
On 05/12/2010 06:56 AM, Madani,Sina wrote:
Hi,
What is the latest version of Collaborative Protégé that is 
compatible with current Web protégé?
 
Thanks
Sina
 
 
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Re: Protege-4 question - was [Webprotege]

Tania Tudorache
In reply to this post by Patrick Cornic
Patrick,

Please start a new thread when the topic is different.

It looks like your Protege 4 installation is corrupted. I suggest that you remove the old installation, and make a clean install from the website.

There is also a separate mailing list for Protege 4 related questions (p4-feedback), this one is for Protege-OWL 3.x:
http://protege.stanford.edu/community/lists.html

Tania

On 05/19/2010 09:02 AM, Patrick Cornic wrote:
Hello,
I have this message when i try to launch Protege 4. This arrives when i want to create a new OWL ontology and just after the choice of the ontologie Format (RDF/XML).

This message occurs also when i want to load an 3.4.1 ontology.

I want to use the version 4 just to try the SKOS plugin.

thanks for helping


Best regards
Patick Cornic




Error 1 Logged at Wed May 19 17:52:17 CEST 2010
NoClassDefFoundError: org/protege/editor/owl/ui/action/ProtegeOWLAction
    java.lang.ClassLoader.defineClass1(Native Method)
    java.lang.ClassLoader.defineClass(Unknown Source)
    org.apache.felix.framework.ModuleImpl$ModuleClassLoader.findClass(ModuleImpl.java:1787)
    org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:682)
    org.apache.felix.framework.ModuleImpl.access$100(ModuleImpl.java:60)
    org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1650)
    java.lang.ClassLoader.loadClass(Unknown Source)
    org.apache.felix.framework.ModuleImpl.getClassByDelegation(ModuleImpl.java:598)
    org.apache.felix.framework.Felix.loadBundleClass(Felix.java:1487)
    org.apache.felix.framework.BundleImpl.loadClass(BundleImpl.java:897)
    org.protege.editor.core.plugin.PluginUtilities.getExtensionObject(PluginUtilities.java:131)
    org.protege.editor.core.plugin.ExtensionInstantiator.instantiate(ExtensionInstantiator.java:74)
    org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:152)
    org.protege.editor.core.ui.menu.MenuActionPluginJPFImpl.newInstance(MenuActionPluginJPFImpl.java:31)
    org.protege.editor.core.ui.menu.MenuBuilder.add(MenuBuilder.java:164)
    org.protege.editor.core.ui.menu.MenuBuilder.add(MenuBuilder.java:125)
    org.protege.editor.core.ui.menu.MenuBuilder.buildMenu(MenuBuilder.java:88)
    org.protege.editor.core.ui.workspace.WorkspaceFrame.createMenuBar(WorkspaceFrame.java:171)
    org.protege.editor.core.ui.workspace.WorkspaceFrame.createUI(WorkspaceFrame.java:141)
    org.protege.editor.core.ui.workspace.WorkspaceFrame.<init>(WorkspaceFrame.java:59)
    org.protege.editor.core.ui.workspace.WorkspaceManager.addWorkspace(WorkspaceManager.java:37)
    org.protege.editor.core.editorkit.EditorKitManager.addEditorKit(EditorKitManager.java:45)
    org.protege.editor.core.ProtegeManager.createAndSetupNewEditorKit(ProtegeManager.java:128)
    org.protege.editor.core.ProtegeWelcomeFrame$ProtegeWelcomePanel$1.actionPerformed(ProtegeWelcomeFrame.java:114)
    org.protege.editor.core.ui.util.LinkLabel.activateLink(LinkLabel.java:102)
    org.protege.editor.core.ui.util.LinkLabel.access$100(LinkLabel.java:30)
    org.protege.editor.core.ui.util.LinkLabel$1.mouseReleased(LinkLabel.java:68)
    java.awt.Component.processMouseEvent(Unknown Source)
    javax.swing.JComponent.processMouseEvent(Unknown Source)
    java.awt.Component.processEvent(Unknown Source)
    java.awt.Container.processEvent(Unknown Source)
    java.awt.Component.dispatchEventImpl(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    java.awt.Container.dispatchEventImpl(Unknown Source)
    java.awt.Window.dispatchEventImpl(Unknown Source)
    java.awt.Component.dispatchEvent(Unknown Source)
    java.awt.EventQueue.dispatchEvent(Unknown Source)
    java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    java.awt.EventDispatchThread.run(Unknown Source)
---------------------------------------------------------------------------------------------------



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