Protege vs Jena

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Protege vs Jena

asad ali
Hello

I am new to Semantic Web and confuse about the tools like Protege and Jena.
I mean if I want to create ontologies or doing my master thesis, what will be the tool I have to use? Can we take the same work from Protege which is performed by Jena API? 
Some one told me that Jena is more powerful than Protege?

Plz help

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Re: Protege vs Jena

Luis Enrique Ramos García
Good morning Asad, 


It will mostly depends it the scope of your master thesis, in general you can develop your ontology with protege editor, and play with your ontology, writing axioms, rules and queries. API´s are used when you develop your running applications. 

However, you might also know that JENA is mostly used to work with rdf graphs, while protégé is mostly used with owl. Thus, there are certain differences. 


Best Regards


Luis Ramos






2015-07-27 5:24 GMT-04:30 asad ali <[hidden email]>:
Hello

I am new to Semantic Web and confuse about the tools like Protege and Jena.
I mean if I want to create ontologies or doing my master thesis, what will be the tool I have to use? Can we take the same work from Protege which is performed by Jena API? 
Some one told me that Jena is more powerful than Protege?

Plz help

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



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Re: Protege vs Jena

Don Rolph
In our work we typically create an ontology in Protege and then publish to Jena.

On Mon, Jul 27, 2015 at 7:58 AM, Luis Enrique Ramos García <[hidden email]> wrote:
Good morning Asad, 


It will mostly depends it the scope of your master thesis, in general you can develop your ontology with protege editor, and play with your ontology, writing axioms, rules and queries. API´s are used when you develop your running applications. 

However, you might also know that JENA is mostly used to work with rdf graphs, while protégé is mostly used with owl. Thus, there are certain differences. 


Best Regards


Luis Ramos






2015-07-27 5:24 GMT-04:30 asad ali <[hidden email]>:
Hello

I am new to Semantic Web and confuse about the tools like Protege and Jena.
I mean if I want to create ontologies or doing my master thesis, what will be the tool I have to use? Can we take the same work from Protege which is performed by Jena API? 
Some one told me that Jena is more powerful than Protege?

Plz help

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



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--

73,
AB1PH
Don Rolph

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Re: Protege vs Jena

asad ali
In reply to this post by Luis Enrique Ramos García
Thank you for your reply

So it means it will be suitable for me to learn and grasp hands on Protege rather than Jena because OWL have more strength than Rdf. Right?

On Mon, Jul 27, 2015 at 12:58 PM, Luis Enrique Ramos García <[hidden email]> wrote:
Good morning Asad, 


It will mostly depends it the scope of your master thesis, in general you can develop your ontology with protege editor, and play with your ontology, writing axioms, rules and queries. API´s are used when you develop your running applications. 

However, you might also know that JENA is mostly used to work with rdf graphs, while protégé is mostly used with owl. Thus, there are certain differences. 


Best Regards


Luis Ramos






2015-07-27 5:24 GMT-04:30 asad ali <[hidden email]>:
Hello

I am new to Semantic Web and confuse about the tools like Protege and Jena.
I mean if I want to create ontologies or doing my master thesis, what will be the tool I have to use? Can we take the same work from Protege which is performed by Jena API? 
Some one told me that Jena is more powerful than Protege?

Plz help

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



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



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Re: Protege vs Jena

Luis Enrique Ramos García
Dear Asad

OWL has some more constructor than RDF. Every language has its specific features. For example, RDF is more suitable for working with sparql query engine. 

You should study every language carefully.




Luis Ramos

2015-07-27 10:18 GMT-04:30 asad ali <[hidden email]>:
Thank you for your reply

So it means it will be suitable for me to learn and grasp hands on Protege rather than Jena because OWL have more strength than Rdf. Right?

On Mon, Jul 27, 2015 at 12:58 PM, Luis Enrique Ramos García <[hidden email]> wrote:
Good morning Asad, 


It will mostly depends it the scope of your master thesis, in general you can develop your ontology with protege editor, and play with your ontology, writing axioms, rules and queries. API´s are used when you develop your running applications. 

However, you might also know that JENA is mostly used to work with rdf graphs, while protégé is mostly used with owl. Thus, there are certain differences. 


Best Regards


Luis Ramos






2015-07-27 5:24 GMT-04:30 asad ali <[hidden email]>:
Hello

I am new to Semantic Web and confuse about the tools like Protege and Jena.
I mean if I want to create ontologies or doing my master thesis, what will be the tool I have to use? Can we take the same work from Protege which is performed by Jena API? 
Some one told me that Jena is more powerful than Protege?

Plz help

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



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



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



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Re: Protege vs Jena

Peter Moore
In reply to this post by asad ali
Protege community, 

My team would like to import SNOMED-CT into an ontology authoring tool that we developed that uses an RDF triplestore and has built-in reasoning that supports EL+, which is the expressivity that SNOMED-CT uses.  But when we obtained a license and downloaded this ontology in its native UMLS format, we found it hard to convert it into the RDF/OWL format that our system needs.

So we went looking for other people who have conveted SNOMED-CT into RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania Tudorache posted some RDF/OWL versions of SNOMED-CT, but they are only for portions of it and are for versions that are 5 years old.  She is on vacation for all of August, so I'm hoping that someone else on the Protege team that advise how we can obtain an RDF/OWL version of the entirety of the current version of SNOMED-CT, or at least a recent version, or obtain a parser that helps us do the conversion ourselves.

Thank you!
Peter Moore

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Re: Protege vs Jena

Chris Mungall-2
Kent Spackman may be able to advise, I believe there are perl scripts
for the conversion

On 7 Aug 2015, at 7:17, Peter Moore wrote:

> Protege community,
>
> My team would like to import SNOMED-CT into an ontology authoring tool
> that
> we developed that uses an RDF triplestore and has built-in reasoning
> that
> supports EL+, which is the expressivity that SNOMED-CT uses.  But when
> we
> obtained a license and downloaded this ontology in its native UMLS
> format,
> we found it hard to convert it into the RDF/OWL format that our system
> needs.
>
> So we went looking for other people who have conveted SNOMED-CT into
> RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania
> Tudorache
> posted some RDF/OWL versions of SNOMED-CT, but they are only for
> portions
> of it and are for versions that are 5 years old.  She is on vacation
> for
> all of August, so I'm hoping that someone else on the Protege team
> that
> advise how we can obtain an RDF/OWL version of the entirety of the
> current
> version of SNOMED-CT, or at least a recent version, or obtain a parser
> that
> helps us do the conversion ourselves.
>
> Thank you!
> Peter Moore
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
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VT
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Re: Protege vs Jena

VT
Hi Peter,

Instructions on where to obtain the perl script and how to use it to convert SNOMED CT to OWL can be found in section 4.3.5 'Stated Relationships Guide' of the SNOMED CT Technical Implementation Guide. A PDF version of the Guide is at  http://ihtsdo.org/fileadmin/user_upload/doc/download/doc_TechnicalImplementationGuide_Current-en-US_INT_20140813.pdf?ok. The Guide states that the perl script is included in the release files.

Sadly for us but happily for him, Kent Spackman retired at the end of 2014.

Cheers,
Suzanne




 

> On Aug 7, 2015, at 11:10 AM, "Chris Mungall" <[hidden email]> wrote:
>
> Kent Spackman may be able to advise, I believe there are perl scripts for the conversion
>
>> On 7 Aug 2015, at 7:17, Peter Moore wrote:
>>
>> Protege community,
>>
>> My team would like to import SNOMED-CT into an ontology authoring tool that
>> we developed that uses an RDF triplestore and has built-in reasoning that
>> supports EL+, which is the expressivity that SNOMED-CT uses.  But when we
>> obtained a license and downloaded this ontology in its native UMLS format,
>> we found it hard to convert it into the RDF/OWL format that our system
>> needs.
>>
>> So we went looking for other people who have conveted SNOMED-CT into
>> RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania Tudorache
>> posted some RDF/OWL versions of SNOMED-CT, but they are only for portions
>> of it and are for versions that are 5 years old.  She is on vacation for
>> all of August, so I'm hoping that someone else on the Protege team that
>> advise how we can obtain an RDF/OWL version of the entirety of the current
>> version of SNOMED-CT, or at least a recent version, or obtain a parser that
>> helps us do the conversion ourselves.
>>
>> Thank you!
>> Peter Moore
>> _______________________________________________
>> protege-user mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-user
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Protege vs Jena

Peter Moore
Thank you Suzanne!  I read that Kent had made this perl script but when a Google search didn't turn it up, I didn't know where to find it.  We'll try here!

Best,
Peter

On Fri, Aug 7, 2015 at 11:44 AM, VT <[hidden email]> wrote:
Hi Peter,

Instructions on where to obtain the perl script and how to use it to convert SNOMED CT to OWL can be found in section 4.3.5 'Stated Relationships Guide' of the SNOMED CT Technical Implementation Guide. A PDF version of the Guide is at  http://ihtsdo.org/fileadmin/user_upload/doc/download/doc_TechnicalImplementationGuide_Current-en-US_INT_20140813.pdf?ok. The Guide states that the perl script is included in the release files.

Sadly for us but happily for him, Kent Spackman retired at the end of 2014.

Cheers,
Suzanne





> On Aug 7, 2015, at 11:10 AM, "Chris Mungall" <[hidden email]> wrote:
>
> Kent Spackman may be able to advise, I believe there are perl scripts for the conversion
>
>> On 7 Aug 2015, at 7:17, Peter Moore wrote:
>>
>> Protege community,
>>
>> My team would like to import SNOMED-CT into an ontology authoring tool that
>> we developed that uses an RDF triplestore and has built-in reasoning that
>> supports EL+, which is the expressivity that SNOMED-CT uses.  But when we
>> obtained a license and downloaded this ontology in its native UMLS format,
>> we found it hard to convert it into the RDF/OWL format that our system
>> needs.
>>
>> So we went looking for other people who have conveted SNOMED-CT into
>> RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania Tudorache
>> posted some RDF/OWL versions of SNOMED-CT, but they are only for portions
>> of it and are for versions that are 5 years old.  She is on vacation for
>> all of August, so I'm hoping that someone else on the Protege team that
>> advise how we can obtain an RDF/OWL version of the entirety of the current
>> version of SNOMED-CT, or at least a recent version, or obtain a parser that
>> helps us do the conversion ourselves.
>>
>> Thank you!
>> Peter Moore
>> _______________________________________________
>> 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


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Re: Protege vs Jena

Campbell, James R
In reply to this post by Peter Moore

UMLS is NOT the best source of information on SNOMED CT.  The best resource In the US is NLM knowledge server where the RF2 release is available along with the US extension. 

In preparation for our work on SNOMED CT core ontology for ICD-11, Harold Solbrig was good enough to run the perl script from Kent on the January 2015 SNOMED CT.  The TTL file is 198 Mbytes and I would be glad to post it to a repository of the community's choosing if it would be of benefit

Jim Campbell


From: protege-user [[hidden email]] on behalf of Peter Moore [[hidden email]]
Sent: Friday, August 07, 2015 9:17 AM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege vs Jena

Protege community, 

My team would like to import SNOMED-CT into an ontology authoring tool that we developed that uses an RDF triplestore and has built-in reasoning that supports EL+, which is the expressivity that SNOMED-CT uses.  But when we obtained a license and downloaded this ontology in its native UMLS format, we found it hard to convert it into the RDF/OWL format that our system needs.

So we went looking for other people who have conveted SNOMED-CT into RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania Tudorache posted some RDF/OWL versions of SNOMED-CT, but they are only for portions of it and are for versions that are 5 years old.  She is on vacation for all of August, so I'm hoping that someone else on the Protege team that advise how we can obtain an RDF/OWL version of the entirety of the current version of SNOMED-CT, or at least a recent version, or obtain a parser that helps us do the conversion ourselves.

Thank you!
Peter Moore

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
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Re: Protege vs Jena

Chris Mungall-2
It would be wonderful if you could do this. However, I fear that the
license will prevent you from doing this.

On 8 Aug 2015, at 14:30, Campbell, James R wrote:

> UMLS is NOT the best source of information on SNOMED CT.  The best
> resource In the US is NLM knowledge server where the RF2 release is
> available along with the US extension.
>
> In preparation for our work on SNOMED CT core ontology for ICD-11,
> Harold Solbrig was good enough to run the perl script from Kent on the
> January 2015 SNOMED CT.  The TTL file is 198 Mbytes and I would be
> glad to post it to a repository of the community's choosing if it
> would be of benefit
>
> Jim Campbell
>
> ________________________________
> From: protege-user [[hidden email]] on behalf
> of Peter Moore [[hidden email]]
> Sent: Friday, August 07, 2015 9:17 AM
> To: User support for WebProtege and Protege Desktop
> Subject: Re: [protege-user] Protege vs Jena
>
> Protege community,
>
> My team would like to import SNOMED-CT into an ontology authoring tool
> that we developed that uses an RDF triplestore and has built-in
> reasoning that supports EL+, which is the expressivity that SNOMED-CT
> uses.  But when we obtained a license and downloaded this ontology in
> its native UMLS format, we found it hard to convert it into the
> RDF/OWL format that our system needs.
>
> So we went looking for other people who have conveted SNOMED-CT into
> RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania
> Tudorache posted some RDF/OWL versions of SNOMED-CT, but they are only
> for portions of it and are for versions that are 5 years old.  She is
> on vacation for all of August, so I'm hoping that someone else on the
> Protege team that advise how we can obtain an RDF/OWL version of the
> entirety of the current version of SNOMED-CT, or at least a recent
> version, or obtain a parser that helps us do the conversion ourselves.
>
> Thank you!
> Peter Moore
>
> The information in this e-mail may be privileged and confidential,
> intended only for the use of the addressee(s) above. Any unauthorized
> use or disclosure of this information is prohibited. If you have
> received this e-mail by mistake, please delete it and immediately
> contact the sender.
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Protege vs Jena

Campbell, James R
SNOMED CT is free for use in the US (and UK, Australia...) based upon license with the NLM.  I am copying Jim Case who can tell us if we have any license issues sharing within the user group.
Jim

Jim (Case),
can we share a TTL file with SNOMED CT within the Protégé user group?
Jim (Campbell)

________________________________________
From: protege-user [[hidden email]] on behalf of Chris Mungall [[hidden email]]
Sent: Saturday, August 08, 2015 4:48 PM
To: User support for WebProtege and Protege Desktop
Subject: Re: [protege-user] Protege vs Jena

It would be wonderful if you could do this. However, I fear that the
license will prevent you from doing this.

On 8 Aug 2015, at 14:30, Campbell, James R wrote:

> UMLS is NOT the best source of information on SNOMED CT.  The best
> resource In the US is NLM knowledge server where the RF2 release is
> available along with the US extension.
>
> In preparation for our work on SNOMED CT core ontology for ICD-11,
> Harold Solbrig was good enough to run the perl script from Kent on the
> January 2015 SNOMED CT.  The TTL file is 198 Mbytes and I would be
> glad to post it to a repository of the community's choosing if it
> would be of benefit
>
> Jim Campbell
>
> ________________________________
> From: protege-user [[hidden email]] on behalf
> of Peter Moore [[hidden email]]
> Sent: Friday, August 07, 2015 9:17 AM
> To: User support for WebProtege and Protege Desktop
> Subject: Re: [protege-user] Protege vs Jena
>
> Protege community,
>
> My team would like to import SNOMED-CT into an ontology authoring tool
> that we developed that uses an RDF triplestore and has built-in
> reasoning that supports EL+, which is the expressivity that SNOMED-CT
> uses.  But when we obtained a license and downloaded this ontology in
> its native UMLS format, we found it hard to convert it into the
> RDF/OWL format that our system needs.
>
> So we went looking for other people who have conveted SNOMED-CT into
> RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania
> Tudorache posted some RDF/OWL versions of SNOMED-CT, but they are only
> for portions of it and are for versions that are 5 years old.  She is
> on vacation for all of August, so I'm hoping that someone else on the
> Protege team that advise how we can obtain an RDF/OWL version of the
> entirety of the current version of SNOMED-CT, or at least a recent
> version, or obtain a parser that helps us do the conversion ourselves.
>
> Thank you!
> Peter Moore
>
> The information in this e-mail may be privileged and confidential,
> intended only for the use of the addressee(s) above. Any unauthorized
> use or disclosure of this information is prohibited. If you have
> received this e-mail by mistake, please delete it and immediately
> contact the sender.
> _______________________________________________
> 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

The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Re: Protege vs Jena

Campbell, James R
In reply to this post by Chris Mungall-2
Speaking with NLM we can post behind the NLM knowledge source server firewall.  Does anyone not have a,license to pull down a file from their site?  After all, that is where UMLS is kept
Jim

James R. Campbell MD
[hidden email]
Office: 402-559-7505
Secretary: 402-559-7299
Pager: 402-888-1230

> On Aug 8, 2015, at 4:48 PM, "Chris Mungall" <[hidden email]> wrote:
>
> It would be wonderful if you could do this. However, I fear that the license will prevent you from doing this.
>
>> On 8 Aug 2015, at 14:30, Campbell, James R wrote:
>>
>> UMLS is NOT the best source of information on SNOMED CT.  The best resource In the US is NLM knowledge server where the RF2 release is available along with the US extension.
>>
>> In preparation for our work on SNOMED CT core ontology for ICD-11, Harold Solbrig was good enough to run the perl script from Kent on the January 2015 SNOMED CT.  The TTL file is 198 Mbytes and I would be glad to post it to a repository of the community's choosing if it would be of benefit
>>
>> Jim Campbell
>>
>> ________________________________
>> From: protege-user [[hidden email]] on behalf of Peter Moore [[hidden email]]
>> Sent: Friday, August 07, 2015 9:17 AM
>> To: User support for WebProtege and Protege Desktop
>> Subject: Re: [protege-user] Protege vs Jena
>>
>> Protege community,
>>
>> My team would like to import SNOMED-CT into an ontology authoring tool that we developed that uses an RDF triplestore and has built-in reasoning that supports EL+, which is the expressivity that SNOMED-CT uses.  But when we obtained a license and downloaded this ontology in its native UMLS format, we found it hard to convert it into the RDF/OWL format that our system needs.
>>
>> So we went looking for other people who have conveted SNOMED-CT into RDF/OWL.  On the Bioportal page for SNOMED-CT, I see that Tania Tudorache posted some RDF/OWL versions of SNOMED-CT, but they are only for portions of it and are for versions that are 5 years old.  She is on vacation for all of August, so I'm hoping that someone else on the Protege team that advise how we can obtain an RDF/OWL version of the entirety of the current version of SNOMED-CT, or at least a recent version, or obtain a parser that helps us do the conversion ourselves.
>>
>> Thank you!
>> Peter Moore
>>
>> The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.
>> _______________________________________________
>> protege-user mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-user
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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