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[bioontology-support] Fwd: quick question

Jennifer Leigh Vendetti vendetti at
Fri Dec 18 10:15:09 PST 2015

From: Jennifer Vendetti <vendetti at<mailto:vendetti at>>
Subject: Re: [bioontology-support] quick question
Date: December 18, 2015 at 10:14:38 AM PST
To: Haider Syed <haider.syed at<mailto:haider.syed at>>

Hi Haider,

I just noticed that you posted a message to the Protege User support list yesterday regarding the BioPortal Import plug-in [1].  This plug-in was developed by the Protege team using an old version of our REST API.  The old version of the REST API was retired in September of 2014 [2], and according to Tania’s reply, the Protege team has never updated the source code of the plug-in to work with the new version of our REST API.

Unfortunately, I’m not aware of any way to make this Protege plug-in work, short of updating the code to use the new API.  It looks like the Protege team has entered an issue in GitHub to track the status of if/when this plug-in will be updated to use the new API [3].



On Dec 17, 2015, at 5:26 PM, Haider Syed <haider.syed at<mailto:haider.syed at>> wrote:

Hi Jennifer,

Thanks for the response.  I'm not sure if you have any experience with using the BioPortal Import Tool in Protege.

I used the url you provided now; when I hit Test BioPortal Connection, it says:

Testing the BioPortal connection for REST base: ...
Retrieving ontology list from BioPortal...

But it just doesn't populate the list and nothing happens even after you leave it running for a long time...

Any ideas on what the issue might be?

Thanks for the help.


On Thu, Dec 17, 2015 at 7:35 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:
Hi Haider,

The correct URL is<>.


On Dec 17, 2015, at 3:24 PM, Haider Syed <haider.syed at<mailto:haider.syed at>> wrote:


I am trying to use the Bioportal Import Plugin in Protege - the plugin uses Bioportal's REST services. Specifically, it requries the BioPortal REST service base URL, which by default is specified as:

However, when I try this link, I get a page that say Not Found

Instead, I have also tried:

and token=my_key

and these don't work as well...

Can you please tell me what the endpoint should be?

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