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[bioontology-support] Posting on behalf of Robert Stevens

Ray Fergerson ray.fergerson at
Fri Apr 11 16:54:33 PDT 2014



The production annotator was never really a standalone system. It exists
as part of the overall BioPortal system. You can either use the public
BioPortal instance through its REST API, or you can install a BioPortal VM
at your site and run annotations against that. You can load into your VM
just the ontologies that you are interested int. If you have restricted
data or ontologies then you need to use your own VM. Otherwise you may be
able to use the public one.


Documentation for the annotator (public or VM) is available at:


If you want the VM then please provide us with information below and I can
point you to the download pages.    




For our record keeping can you please give us the following information: 
- your BioPortal user name - if you need one go to
- a one to two sentence description of your project 
- why you want to use the VM rather than the public instance? For example,
do you want host non-biomedical or proprietary ontologies or annotate
private data? Do you have performance concerns?



From: Nigam Shah [mailto:nigam at] 
Sent: Friday, April 11, 2014 11:05 AM
To: support at
Cc: Ray Fergerson
Subject: Posting on behalf of Robert Stevens


I was interested in using the stand-alone NCBO anotator mentioned at

However, the wiki reporting about the web service doesn't mention it any
more and  and this sort of implies the stand-aklone version no-longer
exists or is out of date (

If you could tell me the state of play it would be great.


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