RadLex Owl in Protege 4.3

classic Classic list List threaded Threaded
8 messages Options
Reply | Threaded
Open this post in threaded view
|

RadLex Owl in Protege 4.3

pwoodwar

When I load the RadLex owl ontology into Protege,  I get the RadLex identifiers rather than the domain terms.

 

The Protege 3.5 download notes for RadLex states:

 

"The Protege version of RadLex available from the web has been pre-processed to make it suitable for display on the Bioportal web site.  This process sets the display value to the RadLex ID (RID), rather than the English preferred name.  In order to set your version to display English in the left-hand box that displays the hierarchy, go to the Forms tab and click  through the hierarchy on the left (Form Browser) to get to radlex_metaclass.  Then on the right (Form Editor), select Preferred_name as the value for Display Slot"

 

Can anyone advise how I can do this in V4.3 as ‘forms tab’ interface component is not present/visible in this version of Protege.

 

thanks,

Peter Woodward

 

 

Peter Woodward. Research Associate.

Simulation and Modelling in Medicine and Surgery (SiMMS group)

Faculty of Medicine (Department of Surgery and Cancer)

Imperial College London.

St. Mary's Hospital. Room 46, 2nd Floor, Paterson Centre

South Wharf Road. London W2 1BL

(t) +44 (0)203 312 6379

http://www.imperial.ac.uk/medicine/people/peter.woodward/


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: RadLex Owl in Protege 4.3

Tania Tudorache
If Preferred_name is an annotation property (probably it is), then go to View menu -> Render by annotation property -> and select Preferred_name.

Tania


On 03/24/2014 10:19 AM, Woodward, Peter J wrote:

When I load the RadLex owl ontology into Protege,  I get the RadLex identifiers rather than the domain terms.

 

The Protege 3.5 download notes for RadLex states:

 

"The Protege version of RadLex available from the web has been pre-processed to make it suitable for display on the Bioportal web site.  This process sets the display value to the RadLex ID (RID), rather than the English preferred name.  In order to set your version to display English in the left-hand box that displays the hierarchy, go to the Forms tab and click  through the hierarchy on the left (Form Browser) to get to radlex_metaclass.  Then on the right (Form Editor), select Preferred_name as the value for Display Slot"

 

Can anyone advise how I can do this in V4.3 as ‘forms tab’ interface component is not present/visible in this version of Protege.

 

thanks,

Peter Woodward

 

 

Peter Woodward. Research Associate.

Simulation and Modelling in Medicine and Surgery (SiMMS group)

Faculty of Medicine (Department of Surgery and Cancer)

Imperial College London.

St. Mary's Hospital. Room 46, 2nd Floor, Paterson Centre

South Wharf Road. London W2 1BL

(t) +44 (0)203 312 6379

http://www.imperial.ac.uk/medicine/people/peter.woodward/



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


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: RadLex Owl in Protege 4.3

pwoodwar

Tania,

 

Unfortunately the Preferred_name is offered as an annotation property I’ve tried 4 view options -> (i) render by name (rdf:id) / (ii) by label (rdf:label) and render by annotation property -> (iii) comment  / (iv) label and none of them switch over the rendering view.

 

Looking at the over the owl source however I see…

 

<anatomy_metaclass rdf:ID="RID30544">

        <rdfs:subClassOf rdf:resource="#RID30543"/>

        <Preferred_name rdf:datatype="&xsd;string"

           >wall of right uterine tube proper</Preferred_name>

        <Synonym rdf:datatype="&xsd;string"

            >right uterine tube proper wall</Synonym>

        <FMAID rdf:datatype="&xsd;string">18503</FMAID>

        <rdfs:label rdf:datatype="&xsd;string">RID30544</rdfs:label>

 

It is apparent that the ‘Preferred_name’ should be visible / applicable in this case. Any further suggestions…

 

Regards,

Pete

 

From: protege-user [mailto:[hidden email]] On Behalf Of Tania Tudorache
Sent: 24 March 2014 17:32
To: [hidden email]
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

 

If Preferred_name is an annotation property (probably it is), then go to View menu -> Render by annotation property -> and select Preferred_name.

Tania


On 03/24/2014 10:19 AM, Woodward, Peter J wrote:

When I load the RadLex owl ontology into Protege,  I get the RadLex identifiers rather than the domain terms.

 

The Protege 3.5 download notes for RadLex states:

 

"The Protege version of RadLex available from the web has been pre-processed to make it suitable for display on the Bioportal web site.  This process sets the display value to the RadLex ID (RID), rather than the English preferred name.  In order to set your version to display English in the left-hand box that displays the hierarchy, go to the Forms tab and click  through the hierarchy on the left (Form Browser) to get to radlex_metaclass.  Then on the right (Form Editor), select Preferred_name as the value for Display Slot"

 

Can anyone advise how I can do this in V4.3 as ‘forms tab’ interface component is not present/visible in this version of Protege.

 

thanks,

Peter Woodward

 

 

Peter Woodward. Research Associate.

Simulation and Modelling in Medicine and Surgery (SiMMS group)

Faculty of Medicine (Department of Surgery and Cancer)

Imperial College London.

St. Mary's Hospital. Room 46, 2nd Floor, Paterson Centre

South Wharf Road. London W2 1BL

(t) +44 (0)203 312 6379

http://www.imperial.ac.uk/medicine/people/peter.woodward/




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

 


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: RadLex Owl in Protege 4.3

pwoodwar

There is a NOT missing from the message below.

 

As in “the Preferred_name is NOT offered as an annotation property”

 

Apologies

 

From: protege-user [mailto:[hidden email]] On Behalf Of Woodward, Peter J
Sent: 24 March 2014 17:51
To: 'User support for WebProtege and Protege Desktop'
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

 

Tania,

 

Unfortunately the Preferred_name is offered as an annotation property I’ve tried 4 view options -> (i) render by name (rdf:id) / (ii) by label (rdf:label) and render by annotation property -> (iii) comment  / (iv) label and none of them switch over the rendering view.

 

Looking at the over the owl source however I see…

 

<anatomy_metaclass rdf:ID="RID30544">

        <rdfs:subClassOf rdf:resource="#RID30543"/>

        <Preferred_name rdf:datatype="&xsd;string"

           >wall of right uterine tube proper</Preferred_name>

        <Synonym rdf:datatype="&xsd;string"

            >right uterine tube proper wall</Synonym>

        <FMAID rdf:datatype="&xsd;string">18503</FMAID>

        <rdfs:label rdf:datatype="&xsd;string">RID30544</rdfs:label>

 

It is apparent that the ‘Preferred_name’ should be visible / applicable in this case. Any further suggestions…

 

Regards,

Pete

 

From: protege-user [[hidden email]] On Behalf Of Tania Tudorache
Sent: 24 March 2014 17:32
To: [hidden email]
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

 

If Preferred_name is an annotation property (probably it is), then go to View menu -> Render by annotation property -> and select Preferred_name.

Tania


On 03/24/2014 10:19 AM, Woodward, Peter J wrote:

When I load the RadLex owl ontology into Protege,  I get the RadLex identifiers rather than the domain terms.

 

The Protege 3.5 download notes for RadLex states:

 

"The Protege version of RadLex available from the web has been pre-processed to make it suitable for display on the Bioportal web site.  This process sets the display value to the RadLex ID (RID), rather than the English preferred name.  In order to set your version to display English in the left-hand box that displays the hierarchy, go to the Forms tab and click  through the hierarchy on the left (Form Browser) to get to radlex_metaclass.  Then on the right (Form Editor), select Preferred_name as the value for Display Slot"

 

Can anyone advise how I can do this in V4.3 as ‘forms tab’ interface component is not present/visible in this version of Protege.

 

thanks,

Peter Woodward

 

 

Peter Woodward. Research Associate.

Simulation and Modelling in Medicine and Surgery (SiMMS group)

Faculty of Medicine (Department of Surgery and Cancer)

Imperial College London.

St. Mary's Hospital. Room 46, 2nd Floor, Paterson Centre

South Wharf Road. London W2 1BL

(t) +44 (0)203 312 6379

http://www.imperial.ac.uk/medicine/people/peter.woodward/



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

 


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: RadLex Owl in Protege 4.3

Tania Tudorache
Indeed, I looked at Radlex 311, and Preferred_name is a datatype property and not an annotation property, as it was probably intended.

The classes are also punned (they are also individuals), so the only solution is to convert Preferred_name to an annotation property.

It is easy to do, but requires some manual editing of the file.

In the Radlex311 file, search for the definition of Preferred_name (search for: rdf:ID="Preferred_name"), and convert it to an annotation property (replace with text below):

    <owl:AnnotationProperty rdf:ID="Preferred_name">
        <rdf:type rdf:resource="&owl;FunctionalProperty"/>
       <!-- <rdfs:domain>
            <owl:Class>
                <owl:unionOf rdf:parseType="Collection">
                    <owl:Class rdf:about="&owl;Thing"/>
                    <owl:Class rdf:about="#radlex_metaclass"/>
                </owl:unionOf>
            </owl:Class>
        </rdfs:domain>
        -->
        <rdfs:range rdf:resource="&xsd;string"/>
        <rdfs:label rdf:datatype="&xsd;string">Preferred_name</rdfs:label>
    </owl:AnnotationProperty>

We'll let the Radlex developers know, and ideally, they should make this change for future Radlex releases.

Tania


On 03/24/2014 10:54 AM, Woodward, Peter J wrote:

There is a NOT missing from the message below.

 

As in “the Preferred_name is NOT offered as an annotation property”

 

Apologies

 

From: protege-user [[hidden email]] On Behalf Of Woodward, Peter J
Sent: 24 March 2014 17:51
To: 'User support for WebProtege and Protege Desktop'
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

 

Tania,

 

Unfortunately the Preferred_name is offered as an annotation property I’ve tried 4 view options -> (i) render by name (rdf:id) / (ii) by label (rdf:label) and render by annotation property -> (iii) comment  / (iv) label and none of them switch over the rendering view.

 

Looking at the over the owl source however I see…

 

<anatomy_metaclass rdf:ID="RID30544">

        <rdfs:subClassOf rdf:resource="#RID30543"/>

        <Preferred_name rdf:datatype="&xsd;string"

           >wall of right uterine tube proper</Preferred_name>

        <Synonym rdf:datatype="&xsd;string"

            >right uterine tube proper wall</Synonym>

        <FMAID rdf:datatype="&xsd;string">18503</FMAID>

        <rdfs:label rdf:datatype="&xsd;string">RID30544</rdfs:label>

 

It is apparent that the ‘Preferred_name’ should be visible / applicable in this case. Any further suggestions…

 

Regards,

Pete

 

From: protege-user [[hidden email]] On Behalf Of Tania Tudorache
Sent: 24 March 2014 17:32
To: [hidden email]
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

 

If Preferred_name is an annotation property (probably it is), then go to View menu -> Render by annotation property -> and select Preferred_name.

Tania


On 03/24/2014 10:19 AM, Woodward, Peter J wrote:

When I load the RadLex owl ontology into Protege,  I get the RadLex identifiers rather than the domain terms.

 

The Protege 3.5 download notes for RadLex states:

 

"The Protege version of RadLex available from the web has been pre-processed to make it suitable for display on the Bioportal web site.  This process sets the display value to the RadLex ID (RID), rather than the English preferred name.  In order to set your version to display English in the left-hand box that displays the hierarchy, go to the Forms tab and click  through the hierarchy on the left (Form Browser) to get to radlex_metaclass.  Then on the right (Form Editor), select Preferred_name as the value for Display Slot"

 

Can anyone advise how I can do this in V4.3 as ‘forms tab’ interface component is not present/visible in this version of Protege.

 

thanks,

Peter Woodward

 

 

Peter Woodward. Research Associate.

Simulation and Modelling in Medicine and Surgery (SiMMS group)

Faculty of Medicine (Department of Surgery and Cancer)

Imperial College London.

St. Mary's Hospital. Room 46, 2nd Floor, Paterson Centre

South Wharf Road. London W2 1BL

(t) +44 (0)203 312 6379

http://www.imperial.ac.uk/medicine/people/peter.woodward/



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

 



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


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

Re: RadLex Owl in Protege 4.3

pwoodwar
Tania,

Unfortunately this is not feasible as the definition of Preferred_name is missing from the RadLex 311 owl document. Were you able to locate this node in the RadLex file you were editing ?

If so could you post me a link to this version ?

Thanks for your help,

Pete W

From: Tania Tudorache <[hidden email]>
Organization: Biomedical Informatics Research
Reply-To: User support for WebProtege and Protege Desktop <[hidden email]>
Date: Monday, 24 March 2014 18:12
To: "[hidden email]" <[hidden email]>
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

<owl:AnnotationProperty rdf:ID="Preferred_name">
        <rdf:type rdf:resource="&owl;FunctionalProperty"/>
       <!-- <rdfs:domain>
            <owl:Class>
                <owl:unionOf rdf:parseType="Collection">
                    <owl:Class rdf:about="&owl;Thing"/>
                    <owl:Class rdf:about="#radlex_metaclass"/>
                </owl:unionOf>
            </owl:Class>
        </rdfs:domain>
        -->
        <rdfs:range rdf:resource="&xsd;string"/>
        <rdfs:label rdf:datatype="&xsd;string">Preferred_name</rdfs:label>
    </owl:AnnotationProperty>

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|

[POSSIBLE VIRUS:###] Re: RadLex Owl in Protege 4.3

Tania Tudorache
On 03/24/2014 03:02 PM, Woodward, Peter J wrote:
Tania,

Unfortunately this is not feasible as the definition of Preferred_name is missing from the RadLex 311 owl document. Were you able to locate this node in the RadLex file you were editing ?

Yes, the definition is in there. I got Radlex 311 from BioPortal:
http://data.bioontology.org/ontologies/RADLEX/submissions/30/download?apikey=4ea81d74-8960-4525-810b-fa1baab576ff

I attached the fixed file.

Tania

If so could you post me a link to this version ?

Thanks for your help,

Pete W

From: Tania Tudorache <[hidden email]>
Organization: Biomedical Informatics Research
Reply-To: User support for WebProtege and Protege Desktop <[hidden email]>
Date: Monday, 24 March 2014 18:12
To: "[hidden email]" <[hidden email]>
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

<owl:AnnotationProperty rdf:ID="Preferred_name">
        <rdf:type rdf:resource="&owl;FunctionalProperty"/>
       <!-- <rdfs:domain>
            <owl:Class>
                <owl:unionOf rdf:parseType="Collection">
                    <owl:Class rdf:about="&owl;Thing"/>
                    <owl:Class rdf:about="#radlex_metaclass"/>
                </owl:unionOf>
            </owl:Class>
        </rdfs:domain>
        -->
        <rdfs:range rdf:resource="&xsd;string"/>
        <rdfs:label rdf:datatype="&xsd;string">Preferred_name</rdfs:label>
    </owl:AnnotationProperty>


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


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

Radlex311-fixed.owl.zip (3M) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: [POSSIBLE VIRUS:###] Re: RadLex Owl in Protege 4.3

pwoodwar
Thanks for this Tania, I must have acquired another version of the file from somewhere elseā€¦
This works fine now.

Cheers,
Pete W


From: Tania Tudorache <[hidden email]>
Organization: Biomedical Informatics Research
Reply-To: User support for WebProtege and Protege Desktop <[hidden email]>
Date: Monday, 24 March 2014 22:04
To: "[hidden email]" <[hidden email]>
Subject: [protege-user] [POSSIBLE VIRUS:###] Re: RadLex Owl in Protege 4.3

On 03/24/2014 03:02 PM, Woodward, Peter J wrote:
Tania,

Unfortunately this is not feasible as the definition of Preferred_name is missing from the RadLex 311 owl document. Were you able to locate this node in the RadLex file you were editing ?

Yes, the definition is in there. I got Radlex 311 from BioPortal:
http://data.bioontology.org/ontologies/RADLEX/submissions/30/download?apikey=4ea81d74-8960-4525-810b-fa1baab576ff

I attached the fixed file.

Tania

If so could you post me a link to this version ?

Thanks for your help,

Pete W

From: Tania Tudorache <[hidden email]>
Organization: Biomedical Informatics Research
Reply-To: User support for WebProtege and Protege Desktop <[hidden email]>
Date: Monday, 24 March 2014 18:12
To: "[hidden email]" <[hidden email]>
Subject: Re: [protege-user] RadLex Owl in Protege 4.3

<owl:AnnotationProperty rdf:ID="Preferred_name">
        <rdf:type rdf:resource="&owl;FunctionalProperty"/>
       <!-- <rdfs:domain>
            <owl:Class>
                <owl:unionOf rdf:parseType="Collection">
                    <owl:Class rdf:about="&owl;Thing"/>
                    <owl:Class rdf:about="#radlex_metaclass"/>
                </owl:unionOf>
            </owl:Class>
        </rdfs:domain>
        -->
        <rdfs:range rdf:resource="&xsd;string"/>
        <rdfs:label rdf:datatype="&xsd;string">Preferred_name</rdfs:label>
    </owl:AnnotationProperty>


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


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