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From <Abad.Ay...@cognizant.com>
Subject RE: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]
Date Fri, 21 Feb 2020 04:22:12 GMT
Thank you Sean for your prompt response. As these attributes are very critical info in our
system, Is there any plan in cTAKES roadmap to have AE's for these attributes which is integrated
with cTAKES.  Does cTAKES offer any class or Extension points which we can extend and do our
processing outside cTAKES. Kindly advise.


Thanks & Regards

Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028


-----Original Message-----
From: Finan, Sean <Sean.Finan@childrens.harvard.edu>
Sent: Tuesday, February 18, 2020 9:20 PM
To: dev@ctakes.apache.org
Subject: Re: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]

[External]


Hi Abad,

ctakes does not have annotators that find and assign laterality and body side.

You can add the example ae to a piper file by adding these lines anywhere after the dictionary
lookup (which finds anatomic sites).

package org.apache.ctakes.examples.ae
add BodySideFinder

These instructions are still mostly accurate: https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcwiki.apache.org%2Fconfluence%2Fdisplay%2FCTAKES%2FPiper%2BFiles&amp;data=02%7C01%7CAbad.Ayyub%40cognizant.com%7C676e6493d02c474fcaff08d7b48a4f8b%7Cde08c40719b9427d9fe8edf254300ca7%7C0%7C0%7C637176378465583371&amp;sdata=WFbsaBMYkgoIIQDAdCxHpMHk685Sdr9iB8BPxRvjBVE%3D&amp;reserved=0

You can create a body laterality ae by copying the body side ae code and replacing everything
"side" with a "laterality".  Then add that to the piper file with an 'add' command.

Sean

________________________________________
From: Abad.Ayyub@cognizant.com <Abad.Ayyub@cognizant.com>
Sent: Tuesday, February 18, 2020 9:26 AM
To: dev@ctakes.apache.org
Subject: RE: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]

* External Email - Caution *


Thank you Sean for your response. Actually we already had the annotators you mentioned in
the other mail and still we were not getting those attributes but your example AE worked 
:) . So is it like cTAKES by default doesn’t have an AE to have values for these attributes
or we need to add custom AE when and then required. If custom AE is needed how are we going
to define those in piper files.



Thanks & Regards

Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028



-----Original Message-----
From: Finan, Sean <Sean.Finan@childrens.harvard.edu>
Sent: Tuesday, February 18, 2020 12:14 AM
To: dev@ctakes.apache.org
Subject: Re: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]

[External]


Hi Abad,


I added an example ae to the ctakes-examples module in trunk.


org.apache.ctakes.examples.ae.BodySideFinder


It is really simple, but it is a functional example of an annotator that can find body sides.


Sean


________________________________
From: Abad.Ayyub@cognizant.com <Abad.Ayyub@cognizant.com>
Sent: Monday, February 17, 2020 3:46 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]

* External Email - Caution *


Hello Team,

We introduced cTAKES as our NLP engine to parse clinical data recently in our  profile. Though
we are able to parse the clinical data at high level, we are not able to get values for attributes
like bodySide and bodyLaterality. For eg: for the below text

"He had a slight fracture in the proximal right fibula"

It should have ideally populated values for 'bodySide' and 'bodyLaterality' in the 'AnatomicalSiteMention'
as "right" and  "proximal" respectively. These attributes are critical information in our
profile. We tried different possibilities and still it's not working. We are new to cTAKES
so we would like to know what should be the probable fix for it.  Do we need to add any specific
changes in our piper file to have AnalysisEngine needed for the same. I tried to unit test
using the 'RelationExtractorAnnotatorsTest' coming under 'ctakes-relation-extractor' module
but couldn't find an annotator.xml for the same. Pls. advise on how to proceed


Thanks & Regards
[cid:D3145E69-CD94-48C1-877F-5134EEAFB598]

Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028



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and may contain confidential and privileged information. If you are not the intended recipient(s),
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