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[bioontology-support] NCBO BioPortal connection reset error

Ray Fergerson ray.fergerson at
Fri Apr 4 17:13:11 PDT 2014


Hope that things are coming together for you on this. Let me know if you
need anything.

I am not sure what you mean by “reference the value
”. If you are talking
about references to our web site we would appreciate anything you might
do. A number of application builders use the BioPortal logo on their
applications or sites.


From: Bob Stanley [mailto:rstanley at]
Sent: Friday, March 28, 2014 3:10 PM
To: Ray Fergerson; Jose Miguel Cruz-Toledo; support at
Cc: Jason Eshleman
Subject: RE: NCBO BioPortal connection reset error

Thanks for the information Ray.

On a somewhat related topic, we have a good design now and are actively
engineering for the new BioPortal API – hopefully to be ready by late next

Also on a related topic, I’m thinking about opportunities to more actively
reference the value we’re seeing through Bioportal and NCBO resources!

All the best,


From: Ray Fergerson [mailto:ray.fergerson at]
Sent: Friday, March 28, 2014 2:52 PM
To: Jose Miguel Cruz-Toledo; support at
Cc: Bob Stanley; Jason Eshleman
Subject: RE: NCBO BioPortal connection reset error

We recently got swamped by annotation calls which bogged down the entire
system so we have installed a 15 call/second throttling on users. If you
exceed this your excess calls will fail with a  429 response. It sounds
more likely though that you were slowed down by the other guys who were
bogging down the system. You might try it again.

The batch commands does not allow you to make multiple resource index
calls. You can pass in more than one class to a RI call but the response
is for documents which are either a union or intersection of those classes
(specified by the mode parameter). This may or may not be what you want.


From: Jose Miguel Cruz-Toledo [mailto:jctoledo at]
Sent: Thursday, March 27, 2014 4:21 PM
To: support at
Cc: Bob Stanley; Jason Eshleman; ray.fergerson at
Subject: NCBO BioPortal connection reset error


I have been making use of the NCBO bioportal REST API using my BioPortal
user’s (jctoledo) API key (dc3e4006-b84c-43b0-8c68-61833811450f ). I wrote
a script that to search for matching class labels using the Search
resource index endpoint against a list of a few thousand terms. During the
past week I have been noticing that the API seems to be blocking my
requests after  about an hour of querying the endpoint. I added to my
script a 5 second sleep call so that we hit the API less frequently but
the problem seems to still appear i.e.: “Connection reset by peer”.

After having read the documentation and from this I have a few questions:

·         Is this an expected behavior from the Bioportal API?

·         Is there a maximum number of calls per second or minute that we
should be doing? I

·         Is there a way of making a batch call to the API with the Search
Resource Index and several terms at once (e.g.

Thank you in advance,

José Cruz-Toledo

Knowledge Engineer

IO Informatics, Inc.
Office:     (613) 323-7506
Email:      jctoledo at


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