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[bioontology-support] Using the Annotator with Python

Ray Fergerson ray.fergerson at
Fri Nov 21 15:06:30 PST 2014

I’m not sure exactly what behavior you are seeing. Are you saying that you 
annotate the same piece of text multiple times and that eventually one of 
the calls will fail? This seems unlikely. Are saying that you repeatedly 
call the annotator with a collection of short text strings and that 
eventually one of these will fail (a different one every time)?

We don’t know of any problems with the system that would cause anything like 
what you may be reported. That doesn’t necessarily mean that there isn’t a 
problem though…

Also please let us know if you are accessing the system with multiple 
threads. An please include the exact error message that you get back. 


From: bioontology-support 
[mailto:bioontology-support-bounces at] On Behalf Of Jacob 
Sent: Tuesday, November 18, 2014 12:51 PM
To: support at
Subject: [bioontology-support] Using the Annotator with Python


I am an Undergraduate Researcher at Indiana University working on a project 

involves classifying a large number papers by categories. Your annotator 
seems to work very well for this purpose. However, there seems to be a limit 
when I try to run it over and over on any portion of text. That is, no 
matter how large I make the string size from the paper, the annotator will 
eventually throw an internal service error after some number of iterations. 
Could you fill me in on what is happening here and what I can do to avoid 
these errors? Any information you can give would be great.

Here is my advisor's information for confirmation if you need it.


Jacob Weimer

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