export OBO format

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export OBO format

Jan Hummel

Hello everyone,

Are there any limitations in exporting an ontology (RDF/XML Syntax) with given Instances into the OBO Format?

I am asking because in my case Protégé (version 5.1.0) keeps saying “saving ontology…. with progressbar” forever.

The log window reads:

-->

Saving XeO

Saving ontology to temp file: C:\Users\JAN~1.HUM\AppData\Local\Temp\temp-ontolog

y1046999037451107267

<--

 

How could I further debug this?

 

In the same direction I notices this message in the log file during loading an OBO formatted ontology :

-->

ERROR OBOFormatParser    Error: Instance frames are not supported yet. Parsing stopped at line: 1454

<--

 

Holds the same true for writing an ontology in OBO format?

 

I appreciate any advice!

Thank you for your time and effort.

 

Best regards,

Jan

 


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Re: export OBO format

Chris Mungall-2

Instances are not supported in obo.

What is happening is that untranslateable axioms go as functional syntax into the header which leads to hanging as described here
https://github.com/protegeproject/protege/issues/501



On 10 Feb 2017, at 6:18, Jan Hummel wrote:

Hello everyone,

Are there any limitations in exporting an ontology (RDF/XML Syntax) with given Instances into the OBO Format?

I am asking because in my case Protégé (version 5.1.0) keeps saying “saving ontology…. with progressbar” forever.

The log window reads:

-->

Saving XeO

Saving ontology to temp file: C:\Users\JAN~1.HUM\AppData\Local\Temp\temp-ontolog

y1046999037451107267

<--

 

How could I further debug this?

 

In the same direction I notices this message in the log file during loading an OBO formatted ontology :

-->

ERROR OBOFormatParser    Error: Instance frames are not supported yet. Parsing stopped at line: 1454

<--

 

Holds the same true for writing an ontology in OBO format?

 

I appreciate any advice!

Thank you for your time and effort.

 

Best regards,

Jan

 

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


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