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

Agravat, Sanjay SAGRAVA at
Mon May 7 12:10:14 PDT 2012

Hi Paul,

I will try that.  BTW, can you point me to the documentation for the BioPortal admin tool; and also how to delete submitted ontologies that didn’t parse correctly due to my previous issues?



On 5/7/12 2:44 PM, "Paul R Alexander" <palexander at> wrote:

 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 properly
  2.  Parse the dummy ontology
  4.  Find the version number for the dummy ontology
  5.  Go to the database on the Virtual Appliance and find the table that corresponds to the dummy version in the 'bioportal_protege' database
  6.  Note the table name (should be something like 'tbl_10000') and delete the table
  7.  Import your parsed version of the real ontology and rename the imported table to match the old dummy table name (ex: 'tbl_10000')
  9.  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?


On May 7, 2012, at 9:09 AM, Agravat, Sanjay wrote:


 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?




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