P4 and hyperlinks in text

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P4 and hyperlinks in text

Melanie Courtot-2
Hi,

I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."

Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)

Cheers,
Melanie

[1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
---
Mélanie Courtot
MSFHR/PCIRN Ph.D. Candidate,
Terry Fox Laboratory - BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada








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Re: P4 and hyperlinks in text

Helen Parkinson
Agree with Melanie that this would be a very handy feature, esp. for
external refs.

thanks

Helen

On 19/06/2012 21:43, Melanie Courtot wrote:

> Hi,
>
> I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
> I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."
>
> Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)
>
> Cheers,
> Melanie
>
> [1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
> ---
> Mélanie Courtot
> MSFHR/PCIRN Ph.D. Candidate,
> Terry Fox Laboratory - BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

--
Helen Parkinson, PhD
Team Leader
Functional Genomics Group
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi
www.ebi.ac.uk/fgpt/

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Re: P4 and hyperlinks in text

Matthew Horridge-2
Administrator
In reply to this post by Melanie Courtot-2
Hi Melanie, Helen,

It depends upon exactly what you want, but in the latest release of P4 if you enter an http://.... in an annotation it should be recognised as a link.  At the moment, entity names aren't linked, but this should be easy to add (since the support for embedded links is already there).   Would this cover most of what you're after, or do you need something more elaborate?

Cheers,

Matthew


On 19 Jun 2012, at 13:43, Melanie Courtot wrote:

Hi,

I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."

Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)

Cheers,
Melanie

[1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
---
Mélanie Courtot
MSFHR/PCIRN Ph.D. Candidate,
Terry Fox Laboratory - BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada








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Re: P4 and hyperlinks in text

Melanie Courtot-2
Hi Matthew,

I just downloaded and checked that using hyperlinks worked fine with P4.2 beta (I am still running the latest "stable" release, 4.1.239) That is really going to be extremely helpful, thanks!

Linking entity names would be helpful for browsing, and potentially in my case to ensure I didn't mess up the names of sometimes long properties (i.e., the ones I reference in definitions/comments are indeed the ones defined)

Cheers,
Melanie


On 2012-06-20, at 2:18 PM, Matthew Horridge wrote:

> Hi Melanie, Helen,
>
> It depends upon exactly what you want, but in the latest release of P4 if you enter an http://.... in an annotation it should be recognised as a link.  At the moment, entity names aren't linked, but this should be easy to add (since the support for embedded links is already there).   Would this cover most of what you're after, or do you need something more elaborate?
>
> Cheers,
>
> Matthew
>
> <PastedGraphic-2.png>
> On 19 Jun 2012, at 13:43, Melanie Courtot wrote:
>
>> Hi,
>>
>> I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
>> I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."
>>
>> Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)
>>
>> Cheers,
>> Melanie
>>
>> [1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
>> ---
>> Mélanie Courtot
>> MSFHR/PCIRN Ph.D. Candidate,
>> Terry Fox Laboratory - BCCRC
>> 675 West 10th Avenue
>> Vancouver, BC
>> V5Z 1L3, Canada
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

---
Mélanie Courtot
MSFHR/PCIRN Ph.D. Candidate,
Terry Fox Laboratory - BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada








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Re: P4 and hyperlinks in text

Matthew Horridge-2
Administrator
Hi Melanie,

I just downloaded and checked that using hyperlinks worked fine with P4.2 beta (I am still running the latest "stable" release, 4.1.239) That is really going to be extremely helpful, thanks!

Great!  If this doesn't quite meet your needs please let us know.

Linking entity names would be helpful for browsing, and potentially in my case to ensure I didn't mess up the names of sometimes long properties (i.e., the ones I reference in definitions/comments are indeed the ones defined)

Ah right - we'll definitely add this functionality.  One tip for now, do you know that the annotation editor features autocompletion for entity names?  You press CTRL+SPACE in the annotation editor.  See screenshot below.

Cheers,

Matthew




Cheers,
Melanie


On 2012-06-20, at 2:18 PM, Matthew Horridge wrote:

Hi Melanie, Helen,

It depends upon exactly what you want, but in the latest release of P4 if you enter an http://.... in an annotation it should be recognised as a link.  At the moment, entity names aren't linked, but this should be easy to add (since the support for embedded links is already there).   Would this cover most of what you're after, or do you need something more elaborate?

Cheers,

Matthew

<PastedGraphic-2.png>
On 19 Jun 2012, at 13:43, Melanie Courtot wrote:

Hi,

I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."

Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)

Cheers,
Melanie

[1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
---
Mélanie Courtot
MSFHR/PCIRN Ph.D. Candidate,
Terry Fox Laboratory - BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada








_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback

_______________________________________________
p4-feedback mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/p4-feedback

---
Mélanie Courtot
MSFHR/PCIRN Ph.D. Candidate,
Terry Fox Laboratory - BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada








_______________________________________________
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[hidden email]
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Re: P4 and hyperlinks in text

Helen Parkinson
In reply to this post by Matthew Horridge-2
Hi Matt,

thanks for the update.

We are using 4.1 as 4.2 didn't work with Simon's URIgen plugin, we'll
use this when we move up to 4.2

thanks

Helen

On 20/06/2012 22:18, Matthew Horridge wrote:

> Hi Melanie, Helen,
>
> It depends upon exactly what you want, but in the latest release of P4
> if you enter an http://.... in an annotation it should be recognised
> as a link.  At the moment, entity names aren't linked, but this should
> be easy to add (since the support for embedded links is already
> there).   Would this cover most of what you're after, or do you need
> something more elaborate?
>
> Cheers,
>
> Matthew
>
>
> On 19 Jun 2012, at 13:43, Melanie Courtot wrote:
>
>> Hi,
>>
>> I was wondering if there is support for using hyperlinks in P4? The
>> only reference I found was at [1], dated 2009 and saying it is on the
>> list of desired features.
>> I would like to be able to link from one term in my ontology to an
>> external specification document, or a publication providing more
>> information etc. For example, have a comment field with value "For
>> more information see the paper at http://...."
>>
>> Another probably similar feature request would be the ability to link
>> from the definition of one term in the ontology to another. For
>> example in the definition of the term "spatial region", "A spatial
>> region is a continuant entity that is a continuant_part_of space
>> [...]" I would like to link to the object property
>> "continuant_part_of" (like it is possible from within the
>> "description" view)
>>
>> Cheers,
>> Melanie
>>
>> [1]
>> http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
>> ---
>> Mélanie Courtot
>> MSFHR/PCIRN Ph.D. Candidate,
>> Terry Fox Laboratory - BCCRC
>> 675 West 10th Avenue
>> Vancouver, BC
>> V5Z 1L3, Canada
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email] <mailto:[hidden email]>
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
>
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

--
Helen Parkinson, PhD
Team Leader
Functional Genomics Group
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi
www.ebi.ac.uk/fgpt/

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Re: P4 and hyperlinks in text

Melanie Courtot-2
In reply to this post by Matthew Horridge-2
Hi Matthew,

This is getting better and better! (I didn't know about ctrl+space indeed)
Is there a Protege cheat sheet somewhere? If not, maybe we could create a place somewhere to add them when they come to existence (or somebody learns of them :))?

In the specific case I was thinking about we (well Alan, cc) is converting a spec into OWL so there is no "manual" editing of the annotations, so having them being recognized would be helpful; sometimes the label used in the text in one place is different from the label of the actual property used later on in the same spec.

Thanks again,
Melanie


On 2012-06-20, at 3:18 PM, Matthew Horridge wrote:

> Hi Melanie,
>
>> I just downloaded and checked that using hyperlinks worked fine with P4.2 beta (I am still running the latest "stable" release, 4.1.239) That is really going to be extremely helpful, thanks!
>
> Great!  If this doesn't quite meet your needs please let us know.
>
>> Linking entity names would be helpful for browsing, and potentially in my case to ensure I didn't mess up the names of sometimes long properties (i.e., the ones I reference in definitions/comments are indeed the ones defined)
>
> Ah right - we'll definitely add this functionality.  One tip for now, do you know that the annotation editor features autocompletion for entity names?  You press CTRL+SPACE in the annotation editor.  See screenshot below.
>
> Cheers,
>
> Matthew
>
>
> <PastedGraphic-3.png>
>
>>
>> Cheers,
>> Melanie
>>
>>
>> On 2012-06-20, at 2:18 PM, Matthew Horridge wrote:
>>
>>> Hi Melanie, Helen,
>>>
>>> It depends upon exactly what you want, but in the latest release of P4 if you enter an http://.... in an annotation it should be recognised as a link.  At the moment, entity names aren't linked, but this should be easy to add (since the support for embedded links is already there).   Would this cover most of what you're after, or do you need something more elaborate?
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>> <PastedGraphic-2.png>
>>> On 19 Jun 2012, at 13:43, Melanie Courtot wrote:
>>>
>>>> Hi,
>>>>
>>>> I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
>>>> I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."
>>>>
>>>> Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)
>>>>
>>>> Cheers,
>>>> Melanie
>>>>
>>>> [1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
>>>> ---
>>>> Mélanie Courtot
>>>> MSFHR/PCIRN Ph.D. Candidate,
>>>> Terry Fox Laboratory - BCCRC
>>>> 675 West 10th Avenue
>>>> Vancouver, BC
>>>> V5Z 1L3, Canada
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> ---
>> Mélanie Courtot
>> MSFHR/PCIRN Ph.D. Candidate,
>> Terry Fox Laboratory - BCCRC
>> 675 West 10th Avenue
>> Vancouver, BC
>> V5Z 1L3, Canada
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback

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Re: P4 and hyperlinks in text

Alan Ruttenberg-2
Hi Matthew,

This is very helpful. Perhaps recognize a little html such as in comment posting. The links would look a lot better if they could have a label rather than showing the bare URI.

For the in-line links to other ontology terms, as I mentioned, the desired behavior is offer with confirmation as some words that match ontology terms might not be referring to the same thing, and to be able to adjust display as choice of annotation for label changed. With the little-bit-of-html approach, and local anchors referring to URIs of terms, the display text could be changed with a hook to the renderer to match the current annotation property used for labels.

-Alan


On Thu, Jun 21, 2012 at 1:46 PM, Melanie Courtot <[hidden email]> wrote:
Hi Matthew,

This is getting better and better! (I didn't know about ctrl+space indeed)
Is there a Protege cheat sheet somewhere? If not, maybe we could create a place somewhere to add them when they come to existence (or somebody learns of them :))?

In the specific case I was thinking about we (well Alan, cc) is converting a spec into OWL so there is no "manual" editing of the annotations, so having them being recognized would be helpful; sometimes the label used in the text in one place is different from the label of the actual property used later on in the same spec.

Thanks again,
Melanie


On 2012-06-20, at 3:18 PM, Matthew Horridge wrote:

> Hi Melanie,
>
>> I just downloaded and checked that using hyperlinks worked fine with P4.2 beta (I am still running the latest "stable" release, 4.1.239) That is really going to be extremely helpful, thanks!
>
> Great!  If this doesn't quite meet your needs please let us know.
>
>> Linking entity names would be helpful for browsing, and potentially in my case to ensure I didn't mess up the names of sometimes long properties (i.e., the ones I reference in definitions/comments are indeed the ones defined)
>
> Ah right - we'll definitely add this functionality.  One tip for now, do you know that the annotation editor features autocompletion for entity names?  You press CTRL+SPACE in the annotation editor.  See screenshot below.
>
> Cheers,
>
> Matthew
>
>
> <PastedGraphic-3.png>
>
>>
>> Cheers,
>> Melanie
>>
>>
>> On 2012-06-20, at 2:18 PM, Matthew Horridge wrote:
>>
>>> Hi Melanie, Helen,
>>>
>>> It depends upon exactly what you want, but in the latest release of P4 if you enter an http://.... in an annotation it should be recognised as a link.  At the moment, entity names aren't linked, but this should be easy to add (since the support for embedded links is already there).   Would this cover most of what you're after, or do you need something more elaborate?
>>>
>>> Cheers,
>>>
>>> Matthew
>>>
>>> <PastedGraphic-2.png>
>>> On 19 Jun 2012, at 13:43, Melanie Courtot wrote:
>>>
>>>> Hi,
>>>>
>>>> I was wondering if there is support for using hyperlinks in P4? The only reference I found was at [1], dated 2009 and saying it is on the list of desired features.
>>>> I would like to be able to link from one term in my ontology to an external specification document, or a publication providing more information etc. For example, have a comment field with value "For more information see the paper at http://...."
>>>>
>>>> Another probably similar feature request would be the ability to link from the definition of one term in the ontology to another. For example in the definition of the term "spatial region", "A spatial region is a continuant entity that is a continuant_part_of space [...]" I would like to link to the object property "continuant_part_of" (like it is possible from within the "description" view)
>>>>
>>>> Cheers,
>>>> Melanie
>>>>
>>>> [1] http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Hyperlinks-in-comments-td22237.html
>>>> ---
>>>> Mélanie Courtot
>>>> MSFHR/PCIRN Ph.D. Candidate,
>>>> Terry Fox Laboratory - BCCRC
>>>> 675 West 10th Avenue
>>>> Vancouver, BC
>>>> V5Z 1L3, Canada
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> p4-feedback mailing list
>>>> [hidden email]
>>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>>
>>> _______________________________________________
>>> p4-feedback mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>>
>> ---
>> Mélanie Courtot
>> MSFHR/PCIRN Ph.D. Candidate,
>> Terry Fox Laboratory - BCCRC
>> 675 West 10th Avenue
>> Vancouver, BC
>> V5Z 1L3, Canada
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> p4-feedback mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/p4-feedback
>
> _______________________________________________
> p4-feedback mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/p4-feedback



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Re: P4 and hyperlinks in text

Steve Wartik

My ne plus ultra request is for Matthew and colleagues to recognize that when a literal’s type is rdf:XMLLiteral, Protégé checks to see if the XML is HTML and, if so, displays it using an HTML renderer. But that’s a lot of work. If we don’t want them to implement anything close to a full subset of HTML, would it not make more sense to use a wiki-like language? These tend to be easier to write.

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Alan Ruttenberg
Sent: Thursday, June 21, 2012 2:21 PM
To: Melanie Courtot
Cc: Submit feedback for Protege 4.x
Subject: Re: [p4-feedback] P4 and hyperlinks in text

 

Hi Matthew,

 

This is very helpful. Perhaps recognize a little html such as in comment posting. The links would look a lot better if they could have a label rather than showing the bare URI.

 

For the in-line links to other ontology terms, as I mentioned, the desired behavior is offer with confirmation as some words that match ontology terms might not be referring to the same thing, and to be able to adjust display as choice of annotation for label changed. With the little-bit-of-html approach, and local anchors referring to URIs of terms, the display text could be changed with a hook to the renderer to match the current annotation property used for labels.

 

-Alan

 


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