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[bioontology-support] [BioPortal] Feedback from agravina

Alessio Gravina gravina.alessio at
Tue Mar 31 02:41:00 PDT 2020

Thank you so much for your answer. I will follow your advice to use the
virtual appliance.

Thank you for your help.

All the best,

On Mon, Mar 30, 2020 at 5:46 PM John Graybeal <jgraybeal at>

> Hello Alessio,
> I am sorry your work is taking so long. I can give you some suggestions
> you can try right away, but because you are dealing with a very large
> corpus, the virtual appliance definitely will be your best option.
> The key way to accelerate the process is by choosing only the most
> important ontologies to use for annotation.  (This means the Annotator
> won't have to look up annotations in the other 900+ ontologies in the
> system.)  Also, by setting the options Match longest only, Exclude numbers,
> and Exclude synonyms I believe you will minimize annotation time; but I
> have not confirmed this.
> Since system load on the BioPortal side will strongly affect annotation
> rate, you can monitor the response time for your calls and make sure you
> aren't overloading the system to the point of inefficiency. But keeping in
> mind there are millions of API calls per day to BioPortal, I think trying
> to use BioPortal as a high-speed annotation system will not be a satisfying
> user experience for yourself or its other users.
> The OntoPortal Virtual Appliance is described at
> It is
> available in both a form deployable on your own systems (version 2.5), and
> in an AWS AMI (version 2.4). To apply for access, follow the instructions
> in that document. You will have to download into your Virtual Appliance the
> ontologies that you want to use for annotation.
> In a few weeks (by the end of April), we expect to release a version 3.0
> of the OntoPortal Virtual Appliance, which is somewhat easier to set up,
> includes additional annotation capabilities with the AnnotatorPlus, and is
> available in both local and AWS formats.
> Because these systems run only on your own dedicated hardware, they will
> likely be much faster than BioPortal. (And of course, you can increase that
> speed by getting faster or more hardware, so you have much more control
> over the system.)
> I hope this information helps you with your work.
> John
> On Mar 30, 2020, at 2:26 AM, support at wrote:
> Name: agravina
> Email: gravina.alessio at <gravina.alessio at>
> Location:
> *Feedback:*
> reply to: gravina.alessio at
> Hi,
> I am annotating a dataset with your NCBO annotator through REST API.
> Unfortunatelly, with REST API I am able to annotate 8 sentences per second,
> on average. By making some statistics this process will require 4 years.
> So I am asking to you a suggestion to speed up the process. I have read of
> an AWS virtual appliance, do you think it could be beneficial?
> Is the AWS virtual appliance a local version of the web service? or does
> the AWS virtual appliance query the web service though REST API?
> Do you have other suggestion to speed up the process?
> Thank you for your help.
> Kind regards,
> Alessio
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  | ORCID  0000-0001-6875-5360
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