Preserving indentations in text copied into create hierarchy

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Preserving indentations in text copied into create hierarchy

Michael DeBellis-2
I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael

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Re: Preserving indentations in text copied into create hierarchy

samsontu
Michael,

The vocabulary is MESH, right? You can download a RDF/TTL version from Bioportal.


With best regards,
Samson


On Dec 5, 2019, at 11:15 AM, Michael DeBellis <[hidden email]> wrote:

I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael
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Re: Preserving indentations in text copied into create hierarchy

Leila Kiani
Hi Sam,
In reply to your email, I wanted to say that the structure of MeSH in Bioportal is different from the MeSH tree in the browser.  
Here is the link of MeSH: https://meshb-prev.nlm.nih.gov/treeView
Thanks, Leila.


On Thu, Dec 5, 2019 at 2:28 PM Samson Tu <[hidden email]> wrote:
Michael,

The vocabulary is MESH, right? You can download a RDF/TTL version from Bioportal.


With best regards,
Samson


On Dec 5, 2019, at 11:15 AM, Michael DeBellis <[hidden email]> wrote:

I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael
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Re: Preserving indentations in text copied into create hierarchy

samsontu

On Dec 5, 2019, at 11:49 AM, Leila Kiani <[hidden email]> wrote:

Hi Sam,
In reply to your email, I wanted to say that the structure of MeSH in Bioportal is different from the MeSH tree in the browser.  
Here is the link of MeSH: https://meshb-prev.nlm.nih.gov/treeView
Thanks, Leila.

Thanks for pointing out the discrepancy between Bioportal and NLM versions of the MeSH vocabulary. The Bioportal version seems to be corrupted.  I’ve reported the discrepancy to Bioportal staff.

I am not sure why Michael can’t paste the hierarchy into Protege’s Tools/Create class hierarchy… panel. I myself have no difficulty pasting an indented list of lines (which still needs some editing).

With best regards,
Samson




On Thu, Dec 5, 2019 at 2:28 PM Samson Tu <[hidden email]> wrote:
Michael,

The vocabulary is MESH, right? You can download a RDF/TTL version from Bioportal.


With best regards,
Samson


On Dec 5, 2019, at 11:15 AM, Michael DeBellis <[hidden email]> wrote:

I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael
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Re: Preserving indentations in text copied into create hierarchy

Leila Kiani
Thank you very much for your follow up, Sam.
And for the pasting MeSH tree to the tool in Protege, I have tried the same thing, and like what Michael has said, I could paste it, but I couldn't have it like a hierarchy format. I need to edit them manually.
Thanks a lot again.
Best, Leila.

On Fri, Dec 6, 2019 at 12:38 PM Samson Tu <[hidden email]> wrote:

On Dec 5, 2019, at 11:49 AM, Leila Kiani <[hidden email]> wrote:

Hi Sam,
In reply to your email, I wanted to say that the structure of MeSH in Bioportal is different from the MeSH tree in the browser.  
Here is the link of MeSH: https://meshb-prev.nlm.nih.gov/treeView
Thanks, Leila.

Thanks for pointing out the discrepancy between Bioportal and NLM versions of the MeSH vocabulary. The Bioportal version seems to be corrupted.  I’ve reported the discrepancy to Bioportal staff.

I am not sure why Michael can’t paste the hierarchy into Protege’s Tools/Create class hierarchy… panel. I myself have no difficulty pasting an indented list of lines (which still needs some editing).

With best regards,
Samson




On Thu, Dec 5, 2019 at 2:28 PM Samson Tu <[hidden email]> wrote:
Michael,

The vocabulary is MESH, right? You can download a RDF/TTL version from Bioportal.


With best regards,
Samson


On Dec 5, 2019, at 11:15 AM, Michael DeBellis <[hidden email]> wrote:

I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael
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Re: Preserving indentations in text copied into create hierarchy

samsontu
You are right that, on Windows, the indentations are lost. On my Mac, the indentations are present. 

However, I am not sure what Protege can do. Pasting to Note, WordPad, and Note++ still result in a flat list.

With best regards,
Samson


On Dec 6, 2019, at 10:25 AM, Leila Kiani <[hidden email]> wrote:

Thank you very much for your follow up, Sam.
And for the pasting MeSH tree to the tool in Protege, I have tried the same thing, and like what Michael has said, I could paste it, but I couldn't have it like a hierarchy format. I need to edit them manually.
Thanks a lot again.
Best, Leila.

On Fri, Dec 6, 2019 at 12:38 PM Samson Tu <[hidden email]> wrote:

On Dec 5, 2019, at 11:49 AM, Leila Kiani <[hidden email]> wrote:

Hi Sam,
In reply to your email, I wanted to say that the structure of MeSH in Bioportal is different from the MeSH tree in the browser.  
Here is the link of MeSH: https://meshb-prev.nlm.nih.gov/treeView
Thanks, Leila.

Thanks for pointing out the discrepancy between Bioportal and NLM versions of the MeSH vocabulary. The Bioportal version seems to be corrupted.  I’ve reported the discrepancy to Bioportal staff.

I am not sure why Michael can’t paste the hierarchy into Protege’s Tools/Create class hierarchy… panel. I myself have no difficulty pasting an indented list of lines (which still needs some editing).

With best regards,
Samson


<PastedGraphic-3.png>

On Thu, Dec 5, 2019 at 2:28 PM Samson Tu <[hidden email]> wrote:
Michael,

The vocabulary is MESH, right? You can download a RDF/TTL version from Bioportal.


With best regards,
Samson


On Dec 5, 2019, at 11:15 AM, Michael DeBellis <[hidden email]> wrote:

I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael
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Re: Preserving indentations in text copied into create hierarchy

Michael DeBellis-2
Samson, Yes, the reason it didn't work for me is because I've been doing development on my Windows machine. But it's good to know it will work on a Mac. I still have a mac desktop that can run Protege if I come across this in the future I'll go back to my Mac. 

Cheers,
Michael

On Fri, Dec 6, 2019 at 11:00 AM Samson Tu <[hidden email]> wrote:
You are right that, on Windows, the indentations are lost. On my Mac, the indentations are present. 

However, I am not sure what Protege can do. Pasting to Note, WordPad, and Note++ still result in a flat list.

With best regards,
Samson


On Dec 6, 2019, at 10:25 AM, Leila Kiani <[hidden email]> wrote:

Thank you very much for your follow up, Sam.
And for the pasting MeSH tree to the tool in Protege, I have tried the same thing, and like what Michael has said, I could paste it, but I couldn't have it like a hierarchy format. I need to edit them manually.
Thanks a lot again.
Best, Leila.

On Fri, Dec 6, 2019 at 12:38 PM Samson Tu <[hidden email]> wrote:

On Dec 5, 2019, at 11:49 AM, Leila Kiani <[hidden email]> wrote:

Hi Sam,
In reply to your email, I wanted to say that the structure of MeSH in Bioportal is different from the MeSH tree in the browser.  
Here is the link of MeSH: https://meshb-prev.nlm.nih.gov/treeView
Thanks, Leila.

Thanks for pointing out the discrepancy between Bioportal and NLM versions of the MeSH vocabulary. The Bioportal version seems to be corrupted.  I’ve reported the discrepancy to Bioportal staff.

I am not sure why Michael can’t paste the hierarchy into Protege’s Tools/Create class hierarchy… panel. I myself have no difficulty pasting an indented list of lines (which still needs some editing).

With best regards,
Samson


<PastedGraphic-3.png>

On Thu, Dec 5, 2019 at 2:28 PM Samson Tu <[hidden email]> wrote:
Michael,

The vocabulary is MESH, right? You can download a RDF/TTL version from Bioportal.


With best regards,
Samson


On Dec 5, 2019, at 11:15 AM, Michael DeBellis <[hidden email]> wrote:

I'm trying to create an OWL version of a medical vocabulary that doesn't exist in OWL yet. You can see the model here:  https://meshb-prev.nlm.nih.gov/treeView  One thing that occurred to me is that I could copy that text and then paste it into the window you get in the Tools>Create class hierarchy option. I tried that and it works but unfortunately it just pastes each class at the same level with no indentation. I've also tried pasting it into Word and then copying from Word into Protege but unfortunately still no luck. I can preserve the hierarchy when I paste it into Word but when I go from Word to Protege I still lose it. 

It's not that big of a deal, I can manually just tab the classes over into the right level of indentation but before I did that I just wanted to see if by chance anyone else has come across this and perhaps found a clever way to preserve the formatting with tabs rather than whatever HTML and Word are using since that would be easier and less prone to error. 

Cheers,
Michael
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