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[bioontology-support] Access rate to Bioportal APIs

Marco Brandizi brandizi at
Thu Jul 9 00:48:41 PDT 2015

Dear Ray,

thank you very much for your reply. I'm sorry to write you back so late, 
my email filters sent your message onto the wrong folder. A few days ago 
I have even write you again, believing I hadn't got an answer the first 
time. Please ignore that.

Kind Regards,

On 12/06/2015 23:04, Ray Fergerson wrote:
> We rate limit at 15 calls/second. If you make sequential calls to the
> annotator from a single process/thread then you will not run up against
> this limit. For a single process or thread then just run as fast as you
> can and we should be able to handle it.
> Ray
> -----Original Message-----
> From: bioontology-support
> [mailto:bioontology-support-bounces at] On Behalf Of Marco
> Brandizi
> Sent: Friday, June 5, 2015 1:25 PM
> To: support at
> Subject: [bioontology-support] Access rate to Bioportal APIs
> Dear Sirs,
> I'm considering to use the Bioportal APIs to perform periodic ontology
> annotations of large volume of data. More precisely, I need to annotate
> sample properties in our Biosamples database
> (, to associate text labels like 'homo
> sapiens' to terms like NCBITax:9096. I have something like 10 million
> properties, which I'd like to annotate this way about once a month (to
> generate our RDF export,
> Every time I do this,
> I plan to have a few thousand requests x minute to an external service
> like the Bioportal annotator (via API), for a time of about 24hrs every
> month (we are currently using ZOOMA for the same purpose,
>, and I'm basing the hereby figures on
> that). My code is already able to measure the server responsiveness and
> throttle down its request load when needed.
> My question is if it would be acceptable for Bioportal that I did that,
> both in terms of your policies (fair usage?) and in technical terms (will
> your server block me? Will it consider me a DoS attacker?)
> Thank you in advance for your help.
> Kind Regards,


Marco Brandizi, PhD <brandizi at>,

Functional Genomics Group - Sr Software Engineer

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

Office V2-26, Phone: +44 (0)1223 492 613, Fax: +44 (0)1223 492 620

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