crosslinking/importing classes from other ontologies

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crosslinking/importing classes from other ontologies

Michael Sinclair

Hello,

 

What is the current best-practices in Protégé (or elsewhere) for linking directly to classes in other ontologies when using object properties?

 

For example, let’s say I want to add to a class the following subclass assertion:

 

hasProperty some ExternalClass,

 

where ExternalClass exists in another ontology.

 

And what is the best way to automatically maintain these links/references is the external ontology should change?  I’ve read there are plugins to do this such as Mireot and Ontofox.  Have people had good success with these plugins in practice?

 

Thanks for any advice!


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Re: crosslinking/importing classes from other ontologies

Chris Mungall-2

Mi Michael

You may want to ask this question on https://groups.google.com/forum/#!forum/obo-discuss

If you create your github repo using the OSK it will set you up with a basic structure for doing this. There is a link to some slides on best practices on the README
https://github.com/INCATools/ontology-starter-kit/

You may also find this useful:
https://github.com/jamesaoverton/obo-tutorial

On 26 Sep 2017, at 21:01, Michael Sinclair wrote:

Hello,

 

What is the current best-practices in Protégé (or elsewhere) for linking directly to classes in other ontologies when using object properties?

 

For example, let’s say I want to add to a class the following subclass assertion:

 

hasProperty some ExternalClass,

 

where ExternalClass exists in another ontology.

 

And what is the best way to automatically maintain these links/references is the external ontology should change?  I’ve read there are plugins to do this such as Mireot and Ontofox.  Have people had good success with these plugins in practice?

 

Thanks for any advice!

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Re: crosslinking/importing classes from other ontologies

Igor Toujilov-2
In reply to this post by Michael Sinclair

Hi Michael,

From my experience I recommend the following. There is no silver bullet when you resolve URIs dynamically because if the third party ontology changes suddenly, and your ontology imports their ontology or even references their entities, then your ontology/application will be in trouble if they did something wrong.

Essentially ontologies are software. So, use software methodologies to manage them:

- establish a regression test suite for your and third party ontologies and applications;

- establish a source code version control, for example, Git, Subversion, etc. for your ontologies and applications;

- import all third parties ontologies into your source code repository and invoke them locally;

- when a third party ontology charges, pull it into your version control work copy manually, and run your regression test suite; if the test passes, happy days: commit the changes to your repository; otherwise revert the changes.

Currently there is no methodology for automatically maintaining links/references to external ontologies when they change.

 

Cheers,

Igor

 
Sent: Wednesday, September 27, 2017 at 5:01 AM
From: "Michael Sinclair" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Cc: "Karen Eilbeck" <[hidden email]>
Subject: [protege-user] crosslinking/importing classes from other ontologies

Hello,

 

What is the current best-practices in Protégé (or elsewhere) for linking directly to classes in other ontologies when using object properties?

 

For example, let’s say I want to add to a class the following subclass assertion:

 

hasProperty some ExternalClass,

 

where ExternalClass exists in another ontology.

 

And what is the best way to automatically maintain these links/references is the external ontology should change?  I’ve read there are plugins to do this such as Mireot and Ontofox.  Have people had good success with these plugins in practice?

 

Thanks for any advice!

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

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Re: crosslinking/importing classes from other ontologies

Michael Sinclair

Thank you Igor, this is very useful advice.

 

From: protege-user [mailto:[hidden email]] On Behalf Of Igor Toujilov
Sent: Wednesday, September 27, 2017 2:45 PM
To: [hidden email]
Subject: Re: [protege-user] crosslinking/importing classes from other ontologies

 

Hi Michael,

From my experience I recommend the following. There is no silver bullet when you resolve URIs dynamically because if the third party ontology changes suddenly, and your ontology imports their ontology or even references their entities, then your ontology/application will be in trouble if they did something wrong.

Essentially ontologies are software. So, use software methodologies to manage them:

- establish a regression test suite for your and third party ontologies and applications;

- establish a source code version control, for example, Git, Subversion, etc. for your ontologies and applications;

- import all third parties ontologies into your source code repository and invoke them locally;

- when a third party ontology charges, pull it into your version control work copy manually, and run your regression test suite; if the test passes, happy days: commit the changes to your repository; otherwise revert the changes.

Currently there is no methodology for automatically maintaining links/references to external ontologies when they change.

 

Cheers,

Igor

 

Sent: Wednesday, September 27, 2017 at 5:01 AM
From: "Michael Sinclair" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Cc: "Karen Eilbeck" <[hidden email]>
Subject: [protege-user] crosslinking/importing classes from other ontologies

Hello,

 

What is the current best-practices in Protégé (or elsewhere) for linking directly to classes in other ontologies when using object properties?

 

For example, let’s say I want to add to a class the following subclass assertion:

 

hasProperty some ExternalClass,

 

where ExternalClass exists in another ontology.

 

And what is the best way to automatically maintain these links/references is the external ontology should change?  I’ve read there are plugins to do this such as Mireot and Ontofox.  Have people had good success with these plugins in practice?

 

Thanks for any advice!

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


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