Quantcast

How to save OBO file

classic Classic list List threaded Threaded
3 messages Options
Eva
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

How to save OBO file

Eva
Hi there :
Recently I have used your proteje software to make a domain ontology.
But I need the ontology is saved OBO file. (Because I need to input the ontology in R program next step.)
Unfortunately, I have tried “Save as¬→ Choose OBO format”, but It’s not working.
Attachments are my set up and error message.
So I want to ask what wrong with my set up?
And are there any way to solve this question?
Thanks


Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: How to save OBO file

samsontu
Hi,

The java.io.FileNotFoundException occurs when Java cannot find the file (e.g., because of path name issue) or because the file is not accessible (e.g., because the program has no write access to a read-only file/folder). 

Given that a lot of Windows operating system restricts access to C:Program Files, I suspect the latter (write-access issue). Try to save the ontology to another location where you know you have write-access.

With best regards,
Samson


On Apr 18, 2017, at 6:27 PM, Eva <[hidden email]> wrote:

Hi there :
Recently I have used your proteje software to make a domain ontology.
But I need the ontology is saved OBO file. (Because I need to input the
ontology in R program next step.)
Unfortunately, I have tried “Save as¬→ Choose OBO format”, but It’s not
working.
Attachments are my set up and error message.
So I want to ask what wrong with my set up?
And are there any way to solve this question?
Thanks

<http://protege-project.136.n4.nabble.com/file/n4668175/save1.png>
<http://protege-project.136.n4.nabble.com/file/n4668175/save2.png>



--
View this message in context: http://protege-project.136.n4.nabble.com/How-to-save-OBO-file-tp4668175.html
Sent from the Protege User mailing list archive at Nabble.com.
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: How to save OBO file

Chris Mungall-2

It may also be the case that you are using a superset of what is expressible in obo, and the owlapi is throwing an error which can sometimes be hidden in Protege. Saving as OWL and sending that can help diagnose.

On 19 Apr 2017, at 9:25, Samson Tu wrote:

Hi,

The java.io.FileNotFoundException occurs when Java cannot find the file (e.g., because of path name issue) or because the file is not accessible (e.g., because the program has no write access to a read-only file/folder). 

Given that a lot of Windows operating system restricts access to C:Program Files, I suspect the latter (write-access issue). Try to save the ontology to another location where you know you have write-access.

With best regards,
Samson


On Apr 18, 2017, at 6:27 PM, Eva <[hidden email]> wrote:

Hi there :
Recently I have used your proteje software to make a domain ontology.
But I need the ontology is saved OBO file. (Because I need to input the
ontology in R program next step.)
Unfortunately, I have tried “Save as¬→ Choose OBO format”, but It’s not
working.
Attachments are my set up and error message.
So I want to ask what wrong with my set up?
And are there any way to solve this question?
Thanks

<http://protege-project.136.n4.nabble.com/file/n4668175/save1.png>
<http://protege-project.136.n4.nabble.com/file/n4668175/save2.png>



--
View this message in context: http://protege-project.136.n4.nabble.com/How-to-save-OBO-file-tp4668175.html
Sent from the Protege User mailing list archive at Nabble.com.
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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


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