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[bioontology-support] [BioPortal] Feedback from Francis Nguyen

John Graybeal jgraybeal at
Wed Mar 4 11:46:40 PST 2020

Sergiu (and everyone running open source projects that are accessing BioPortal!),

Thank you for this question!

Yes please, you should keep your API key private, so that others don't use it and the privileges that come with it. We suggest keeping the key in a private repository, or better, setting the key as a run-time/start-up configuration from files accessible only to your project, so that it is not exposed to the public in this way. (After all, if anyone forks your code, you don't want them to use your key in running the software—then we would be asking you questions if their version of the software was doing something bad.)

Can you share with us (offline if you'd rather, or on the list if you want the advertising :->) what project this is used for? We'd like to start keeping track of all the projects that use BioPortal, so it will be very interesting to hear from you.

John (jgraybeal - at -<>)

On Mar 4, 2020, at 10:49 AM, Sergiu Dumitriu <sdumitriu at<mailto:sdumitriu at>> wrote:

Hello Michael,

Sorry for the late reply, I've been away for a few days.

I have a few questions about the API key. Although it belongs to my
"personal" account, we're actually using it in an open source software
project, and the key is public in the source code. Given that we don't
have any custom ontologies associated with the account, at least at the
moment, and we only use the publicly available ones, should we try to
keep the key private?


On 2/28/20 4:39 PM, Michael Dorf wrote:
Super! Thanks a lot!


On Feb 28, 2020, at 1:18 PM, Francis Nguyen
<fr.nguyen at<mailto:fr.nguyen at> <mailto:fr.nguyen at>> wrote:

Oh, my apologies, I wasn't aware this was a public forum -- I just
used the "Contact Us" link at the bottom of the page. I just updated
my API key on our end (And yes, Sergiu and I work together).

Thank you for your help!
-- Francis Nguyen

On Fri, 28 Feb 2020 at 16:02, Michael Dorf <mdorf at<mailto:mdorf at>
<mailto:mdorf at>> wrote:

   Hi Francis,

   Thank you for contacting support. The /submissions endpoint is
   naturally a bit slower, as it retrieves roughly 1000 records
   without the benefit of pagination. That said, we’ve had some
   intermittent performance issues with our REST services around the
   time of your request. The endpoint is working fine on my end now.

   On a different note, this list is a public forum, and sharing your
   private API key with the entire community is never a good idea.
   I’ve invalidated the API key you shared and replaced it with a new
   one. There appears to be a different user attached to the API key
   you were using. Are the two of you part of the same organization?
   In any case, I’ll follow this up with a private email to the owner
   of the original API key (CCd), containing the new API key for the
   account. If you two are related, please ask him or her to share
   the new API key with you.



   On Feb 28, 2020, at 7:13 AM, support at<mailto:support at>
   <mailto:support at> wrote:

   Name: Francis Nguyen

   Email: fr.nguyen at<mailto:fr.nguyen at>
   <mailto:fr.nguyen at>




   I'm trying to access the BioOntology API at:

   Unfortunately, I'm getting a blank page. This URL was working
   yesterday -- did something about the API change?

   Thank you for your time,
   Francis Nguyen

Sergiu Dumitriu
bioontology-support mailing list
bioontology-support at

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

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