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[bioontology-support] Support request for the Cardiovascular Research Grid project

Paul R Alexander palexander at
Mon May 7 11:44:01 PDT 2012

Unfortunately, we don't support loading ontologies from a Protege 
database. You can attempt to swap a Protege database back-end table with 
the one used in BioPortal, but it's not a straightforward process. 
However, if you want to give it a shot, you would need to:

 1. Submit a dummy ontology file with all of the information for the
    real ontology. This file should be something small that will parse
 2. Parse the dummy ontology
 3. Find the version number for the dummy ontology
 4. Go to the database on the Virtual Appliance and find the table that
    corresponds to the dummy version in the 'bioportal_protege' database
 5. Note the table name (should be something like 'tbl_10000') and
    delete the table
 6. Import your parsed version of the real ontology and rename the
    imported table to match the old dummy table name (ex: 'tbl_10000')
 7. Using the BioPortal Admin tool: 1) calculate metrics and 2) index
    the ontology

Give that a shot and let me know if you run into problems.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

On 5/7/12 10:35 AM, Trish Whetzel wrote:
> Hi Sanjay,
> I believe there is a mechanism to swap in the Protege database table 
> into the Protege backend for BioPortal.
> Paul, is this what you would recommend and/or can help Sanjay with 
> this item?
> Trish
> On May 7, 2012, at 9:09 AM, Agravat, Sanjay wrote:
>> Hi,
>> I have a local instance of bioportal running  and I'm having a 
>> problem loading my ontology into bioportal.   The ontology is stored 
>> in the protégé database so I tried uploading the .pprj file with the 
>> database located on the same server as bioportal and that didn't 
>> work.  I also tried converting the .pprj to use .pins and .ponts but 
>> that didn't work because the upload form doesn't take the classes or 
>> instances file as input.
>> I am not able to export the ontology to .owl since the ontology is 
>>  very large and protégé doesn't seem to be able to do it.  Do you 
>> have any suggestions?
>> Thanks,
>> Sanjay
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