cellfie upload of urls mangled/incomplete

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cellfie upload of urls mangled/incomplete

Nancy Urban
I am uploading data from an excel spreadsheet and having the following issue:
website names are getting chopped off.

In the ontology, the class "Reference" is defined.

In the excel sheet, a class (e.g. "AcademyAward") is in Column A, and a url
reference for it (e.g. www.wikipedia.org/wiki/Academy_Awards) is in column
J.

One JSON rule identifies the website in column J as an individual of Type
Reference (Individual: @J* Types: Reference); another adds the website as an
annotation to the column A class AcademyAwards (Class: @A* Annotations:
reds:seeAlso @J*).

The annotation shows up fine in the ontology as the complete url, but the
individual member of the class gets the main chunk of website info chopped
off and just shows up as "Academy_Awards".

If anyone has any idea why this is happening I'd appreciate some help.
Thank you,
Nancy Urban



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Re: cellfie upload of urls mangled/incomplete

Csongor Nyulas
Administrator
It may be only that you are not seeing the entire IRI because of the
Protege rendering settings (which by default would show you only the
local or prefixed name), but in fact the IRI of the imported entity is
correct.

It is really hard to tell just by reading your email (which contains
some inconsistencies, as well, which may be due to typo).

Would it be possible for you to share JSON file with the mapping rules,
the spreadsheet (or at least a sample of it), and the ontology (or at
least the subset of it containing the relevant entities), so that we can
try to reproduce the problem on our end?

Csongor


On 11/29/18 3:10 PM, Nancy Urban wrote:

> I am uploading data from an excel spreadsheet and having the following issue:
> website names are getting chopped off.
>
> In the ontology, the class "Reference" is defined.
>
> In the excel sheet, a class (e.g. "AcademyAward") is in Column A, and a url
> reference for it (e.g. www.wikipedia.org/wiki/Academy_Awards) is in column
> J.
>
> One JSON rule identifies the website in column J as an individual of Type
> Reference (Individual: @J* Types: Reference); another adds the website as an
> annotation to the column A class AcademyAwards (Class: @A* Annotations:
> reds:seeAlso @J*).
>
> The annotation shows up fine in the ontology as the complete url, but the
> individual member of the class gets the main chunk of website info chopped
> off and just shows up as "Academy_Awards".
>
> If anyone has any idea why this is happening I'd appreciate some help.
> Thank you,
> Nancy Urban
>
>
>
> --
> Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: cellfie upload of urls mangled/incomplete

Nancy Urban
It may be the rendering, because when I export the entities to csv _not_
selecting the "use current rendering instead of IRIs" option, they show up
as the full ontology plus entity iri. It's still odd that in the ontology
view they are incomprehensible, e.g. the imported website
'www.nytimes.com/books/best-sellers/' just shows up as a purple diamond with
no text under the individual view under the class "Reference."

I have created and attached samples for (1) the ontology, (2) the excel file
for upload, (3) the json rules, and (4) the sample ontology with the upload
complete. The upload works, and the reference export shows a reference, but
the individual reference as I noted is not identifiable within the ontology
view.

TestOntologyForURLUpload.owl
<http://protege-project.136.n4.nabble.com/file/t376560/TestOntologyForURLUpload.owl>  
TestExcelforURLupload.xlsx
<http://protege-project.136.n4.nabble.com/file/t376560/TestExcelforURLupload.xlsx>  
TestRulesforURLUpload.json
<http://protege-project.136.n4.nabble.com/file/t376560/TestRulesforURLUpload.json>  
TestOntologyAfterURLUpload.owl
<http://protege-project.136.n4.nabble.com/file/t376560/TestOntologyAfterURLUpload.owl>  

Regards,
Nancy Urban



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Re: cellfie upload of urls mangled/incomplete

Josef Hardi
I think this is a bug. You should be able to write the rule like so:
```
Individual: @J*(IRI)
   Types: Reference
```
to prevent Cellfie adding the default prefix in front of the value found in column J.

I've posted a bug report: https://github.com/protegeproject/mapping-master/issues/24

Best,
Josef

> On Nov 30, 2018, at 1:23 PM, Nancy Urban <[hidden email]> wrote:
>
> It may be the rendering, because when I export the entities to csv _not_
> selecting the "use current rendering instead of IRIs" option, they show up
> as the full ontology plus entity iri. It's still odd that in the ontology
> view they are incomprehensible, e.g. the imported website
> 'www.nytimes.com/books/best-sellers/' just shows up as a purple diamond with
> no text under the individual view under the class "Reference."
>
> I have created and attached samples for (1) the ontology, (2) the excel file
> for upload, (3) the json rules, and (4) the sample ontology with the upload
> complete. The upload works, and the reference export shows a reference, but
> the individual reference as I noted is not identifiable within the ontology
> view.
>
> TestOntologyForURLUpload.owl
> <http://protege-project.136.n4.nabble.com/file/t376560/TestOntologyForURLUpload.owl>  
> TestExcelforURLupload.xlsx
> <http://protege-project.136.n4.nabble.com/file/t376560/TestExcelforURLupload.xlsx>  
> TestRulesforURLUpload.json
> <http://protege-project.136.n4.nabble.com/file/t376560/TestRulesforURLUpload.json>  
> TestOntologyAfterURLUpload.owl
> <http://protege-project.136.n4.nabble.com/file/t376560/TestOntologyAfterURLUpload.owl>  
>
> Regards,
> Nancy Urban
>
>
>
> --
> Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user


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