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obo

alexandergarciacastrobalu
I am using protege 5.2.0. I am opening an OBO file and I am trying to save it
as an obo file (file /save as/ obo file type/name of the file). protege gets
on an endless loop giving me a "saving ontologies NAME" window. so, I can
open the OBO file but I cant save it as an OBO file?

Also, I found something called robot at the obo website. if protege does the
conversion from obo to rdf and owl and viceversa then why is robot needed?
does protege really deal with obo files or better to stick to the obo editor
instead?

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Re: obo

Jim Balhoff-3
> On Sep 13, 2018, at 10:14 AM, alexander garcia <[hidden email]> wrote:
>
> Also, I found something called robot at the obo website. if protege does the
> conversion from obo to rdf and owl and viceversa then why is robot needed?
> does protege really deal with obo files or better to stick to the obo editor
> instead?

ROBOT is a command-line tool for performing operations on ontologies, while Protégé is an interactive graphical user interface. You would use ROBOT as part of an automated quality control pipeline or release process for an ontology project (for example). ROBOT and Protégé both use the OWL API for handling OWL files, and so both use the same code to read and write OBO files.

Best regards,
Jim

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Re: obo

Wynne, Robert (NIH/NCI) [C]
If used directly with rdf/xml input (the protégé export), the owlapi should be capable of saving in the OBO format.

Questions on use of the owlapi should be directed to [hidden email]

Rob

-----Original Message-----
From: Jim Balhoff <[hidden email]>
Sent: Thursday, September 13, 2018 11:11 AM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-user] obo

> On Sep 13, 2018, at 10:14 AM, alexander garcia <[hidden email]> wrote:
>
> Also, I found something called robot at the obo website. if protege
> does the conversion from obo to rdf and owl and viceversa then why is robot needed?
> does protege really deal with obo files or better to stick to the obo
> editor instead?

ROBOT is a command-line tool for performing operations on ontologies, while Protégé is an interactive graphical user interface. You would use ROBOT as part of an automated quality control pipeline or release process for an ontology project (for example). ROBOT and Protégé both use the OWL API for handling OWL files, and so both use the same code to read and write OBO files.

Best regards,
Jim

_______________________________________________
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