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[bioontology-support] NCBO BioPortal connection reset error

Bob Stanley rstanley at
Fri Mar 28 15:10:26 PDT 2014

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 week....

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<mailto:jctoledo at>

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