incorporating an outside ontology in cTAKES pipeline

[Joshua Valdez <jd...@case.edu>]

Hello,

So, I am trying to extend the UMLSlookupannotator with my own .owl
ontology, but I am having difficulty finding any resources on how this
might be done.  Has anyone here tried something like this before?  If so,
could you point me in the direction of any resources that may help in my
efforts?  I am having trouble locating any material on this subject.

Thanks.





*Joshua Valdez*
*Computational Linguist : Cognitive Scientist : Data Scientist
                     *

Home:  (440)-231-0479 | Work: (216)-368-7560
jdv12@case.edu <jd...@uw.edu> | jdv2@uw.edu | joshv@armsandanchors.com
<http://www.linkedin.com/in/valdezjoshua/>

RE: incorporating an outside ontology in cTAKES pipeline

["Savova, Guergana" <Gu...@childrens.harvard.edu>]

Hi Joshua,
You can use any ontology to run cTAKES with as long as it is formatted in the cTAKES expected format. I believe Sean Finan gave you some pointers, but here is it again:
The fast dictionary module in ctakes can use flat files with _bar-separated values_ (.bsv).  Checkout *ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example/bsv* for some example formats.  Start with *custom_cui_tui_bsv.bsv* as an example.  *CustomCuiTuiBsv.xml* is an example property .xml for configuration, but right now it is missing the last *bsv/* subdirectory.

--Guergana

-----Original Message-----
From: Joshua Valdez [mailto:jdv12@case.edu] 
Sent: Tuesday, April 26, 2016 8:59 AM
To: dev@ctakes.apache.org
Subject: incorporating an outside ontology in cTAKES pipeline

Hello,

So, I am trying to extend the UMLSlookupannotator with my own .owl ontology, but I am having difficulty finding any resources on how this might be done.  Has anyone here tried something like this before?  If so, could you point me in the direction of any resources that may help in my efforts?  I am having trouble locating any material on this subject.

Thanks.





*Joshua Valdez*
*Computational Linguist : Cognitive Scientist : Data Scientist
                     *

Home:  (440)-231-0479 | Work: (216)-368-7560 jdv12@case.edu <jd...@uw.edu> | jdv2@uw.edu | joshv@armsandanchors.com <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.linkedin.com_in_valdezjoshua_&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=HvD3B8cNf13hFD2m4L2AfypYi9sEf-HU0AWJ--BjSjc&s=jI_MyQz4nC-jKh9iZGoSMv89mzWVxzktAXA2tPmdqUg&e= >