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[bioontology-support] tokenization function in Annotator?

Yannick Pouliot PhD ypouliot at
Mon Oct 31 09:09:59 PDT 2011

From: Leyla Jael Garcia Castro [mailto:lj_garcia at]
Sent: Monday, October 31, 2011 3:07 AM
To: Yannick Pouliot PhD; support at
Subject: Re: [bioontology-support] tokenization function in Annotator?

Hi Yannick,

There is a parameter wholeWordOnly I guess that could do the trick but you 
could also have more annotations that you are looking for. Maybe give it a 
try and see whether it gives you what you need.

Thx, I did notice that parameter but I believe it will likely introduce more 
noise because it is not a selective truncation as is done with tokenization.

Q: I’m pretty sure that you’ve got a tokenization function in your parser (I 
forget its name). If true, any chance of implementing it?

Thx again,




From: Yannick Pouliot PhD <ypouliot at>
To: support at
Sent: Sunday, October 30, 2011 10:58 PM
Subject: [bioontology-support] tokenization function in Annotator?

Howdy.  The Annotator doesn’t recognize the term “heparinized” but does 
recognize “heparin”. Q: Is there a function I can invoke to ask for 
tokenization (i.e., removal of parts of terms associated with plurals, 
adjectives, etc) when invoking the Annotator via REST?



Yannick Pouliot, PhD MBA
Bioinformatics Specialist

Butte Laboratory
Division of Systems Medicine

Room X-147, MSOB
Stanford University School of Medicine
 <mailto:ypouliot at> ypouliot at


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