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[bioontology-support] Access rate to Bioportal APIs

Marco Brandizi brandizi at
Mon Jul 6 10:56:32 PDT 2015

Dear Sirs,

I am sending again the message below, since I am not sure you have 
received it the first time.

Thank you in advance for your help,

On 05/06/2015 21:24, Marco Brandizi wrote:
> 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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