existing ontology with invalid URI

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existing ontology with invalid URI

Vatsala

Hi,

 

I have downloaded an ontology from an online source, and I was thinking of extending it to suit my application’s requirements. However, the URI supplied with the ontology seems invalid, hence the latest version of Protégé (5) cannot import the ontology from the import utility on the URI provided.

 

So, that leaves me with one option which is to actually save the file as a local file and instead of importing it, actually open it in Protégé and extend it.

 

I have tried contacting the authors of the ontology, but did not hear from them.

 

Can you please suggest what would be the best way to go in such a case? Should I add the authors’ name in the annotation properties or use a metadata ontology as a way to cite them?

 

Best Regards,

Vatsala

 


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Re: existing ontology with invalid URI

Csongor Nyulas
Administrator
It is really up to the ontology authors to say if they are OK with you building on their work, and how they would be liked to be recognized. I would try to reach them on different channels, including alternative email addresses that you can find for them on the internet, as people may have moved to different companies/institutions over the years. Also I would suggest to have a bit of patience. Many people are in vacation over the summer, so it may take a week or two to get an answer. If you still did not hear from them, maybe send another email, with a subject that would attract more attention. If you won't get any reaction to any of these attempts, you can just mention in the ontology metadata that this ontology is based on the initial work of X., Y. and Z., or something. I think, this should be fine, especially if they make it publicly available for download, and don't have any specific licensing notes or terms of use. This is all I can say, without having any concrete knowledge about the ontology that we are talking about.

Csongor



On 06/20/2017 05:52 AM, Nundloll, Vatsala wrote:

Hi,

 

I have downloaded an ontology from an online source, and I was thinking of extending it to suit my application’s requirements. However, the URI supplied with the ontology seems invalid, hence the latest version of Protégé (5) cannot import the ontology from the import utility on the URI provided.

 

So, that leaves me with one option which is to actually save the file as a local file and instead of importing it, actually open it in Protégé and extend it.

 

I have tried contacting the authors of the ontology, but did not hear from them.

 

Can you please suggest what would be the best way to go in such a case? Should I add the authors’ name in the annotation properties or use a metadata ontology as a way to cite them?

 

Best Regards,

Vatsala

 



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Re: existing ontology with invalid URI

samsontu
I think it’s also important, when the ontology IRL doesn’t resolves to a downloadable ontology, you document the site from which you downloaded the ontology.

In terms of the metadata fields to use, it would be good to use some standard such as Dublin Core [1].

With best regards,
Samson

On Jun 20, 2017, at 2:46 PM, Csongor Nyulas <[hidden email]> wrote:

It is really up to the ontology authors to say if they are OK with you building on their work, and how they would be liked to be recognized. I would try to reach them on different channels, including alternative email addresses that you can find for them on the internet, as people may have moved to different companies/institutions over the years. Also I would suggest to have a bit of patience. Many people are in vacation over the summer, so it may take a week or two to get an answer. If you still did not hear from them, maybe send another email, with a subject that would attract more attention. If you won't get any reaction to any of these attempts, you can just mention in the ontology metadata that this ontology is based on the initial work of X., Y. and Z., or something. I think, this should be fine, especially if they make it publicly available for download, and don't have any specific licensing notes or terms of use. This is all I can say, without having any concrete knowledge about the ontology that we are talking about.

Csongor



On 06/20/2017 05:52 AM, Nundloll, Vatsala wrote:
Hi,
 
I have downloaded an ontology from an online source, and I was thinking of extending it to suit my application’s requirements. However, the URI supplied with the ontology seems invalid, hence the latest version of Protégé (5) cannot import the ontology from the import utility on the URI provided.
 
So, that leaves me with one option which is to actually save the file as a local file and instead of importing it, actually open it in Protégé and extend it.
 
I have tried contacting the authors of the ontology, but did not hear from them.
 
Can you please suggest what would be the best way to go in such a case? Should I add the authors’ name in the annotation properties or use a metadata ontology as a way to cite them?
 
Best Regards,
Vatsala
 


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




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Re: existing ontology with invalid URI

Biswanath Dutta


Yes, as Csongor also mentioned, I think it would be okay if you acknowledge and name the original authors in the ontology metadata (you may use rdfs:comment for this purpose). 

With regards,
Biswanath Dutta 



On Wed, Jun 21, 2017 at 3:28 AM, Samson Tu <[hidden email]> wrote:
I think it’s also important, when the ontology IRL doesn’t resolves to a downloadable ontology, you document the site from which you downloaded the ontology.

In terms of the metadata fields to use, it would be good to use some standard such as Dublin Core [1].

With best regards,
Samson

On Jun 20, 2017, at 2:46 PM, Csongor Nyulas <[hidden email]> wrote:

It is really up to the ontology authors to say if they are OK with you building on their work, and how they would be liked to be recognized. I would try to reach them on different channels, including alternative email addresses that you can find for them on the internet, as people may have moved to different companies/institutions over the years. Also I would suggest to have a bit of patience. Many people are in vacation over the summer, so it may take a week or two to get an answer. If you still did not hear from them, maybe send another email, with a subject that would attract more attention. If you won't get any reaction to any of these attempts, you can just mention in the ontology metadata that this ontology is based on the initial work of X., Y. and Z., or something. I think, this should be fine, especially if they make it publicly available for download, and don't have any specific licensing notes or terms of use. This is all I can say, without having any concrete knowledge about the ontology that we are talking about.

Csongor



On 06/20/2017 05:52 AM, Nundloll, Vatsala wrote:
Hi,
 
I have downloaded an ontology from an online source, and I was thinking of extending it to suit my application’s requirements. However, the URI supplied with the ontology seems invalid, hence the latest version of Protégé (5) cannot import the ontology from the import utility on the URI provided.
 
So, that leaves me with one option which is to actually save the file as a local file and instead of importing it, actually open it in Protégé and extend it.
 
I have tried contacting the authors of the ontology, but did not hear from them.
 
Can you please suggest what would be the best way to go in such a case? Should I add the authors’ name in the annotation properties or use a metadata ontology as a way to cite them?
 
Best Regards,
Vatsala
 


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https://mailman.stanford.edu/mailman/listinfo/protege-user

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

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




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