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[bioontology-support] NCBO BioPortal connection reset error

Ray Fergerson ray.fergerson at
Fri Mar 28 14:51:43 PDT 2014

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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