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[bioontology-support] Fwd: quick question

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


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

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].

Best,
Jennifer

[1] http://protege-project.136.n4.nabble.com/Bioportal-import-tool-td4664184.html
[2] http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes#BioPortal_Release_4.10_.28September_2014.29
[3] https://github.com/protegeproject/webprotege/issues/152



On Dec 17, 2015, at 5:26 PM, Haider Syed <haider.syed at dartmouth.edu<mailto:haider.syed at dartmouth.edu>> 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: http://data.bioontology.org/ ...
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.

Best,
Haider

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

The correct URL is http://data.bioontology.org<http://data.bioontology.org/>.

Best,
Jennifer


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

Hi,

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: http://rest.bioontology.org/bioportal/

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

Instead, I have also tried:
http://rest.bioontology.org/bioportal?apikey=my_key
and
http://rest.bioontology.org/bioportal/?apikey=my_key

and
http://rest.bioontology.org/bioportal?apikey token=my_key

and these don't work as well...

Can you please tell me what the endpoint should be?

Thanks,
Haider
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