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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject Re: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]
Date Sun, 23 Feb 2020 15:01:44 GMT
Hi Abad,

>Is there any plan in cTAKES roadmap to have AE's for these attributes
-- Not at the moment.  The ctakes type system was intended to be completely representative
of all desired clinical information.  While this may run counter to a lot of development strategies,
it served a purpose at the time.  At any rate, most of the attributes in the types do not
have corresponding AEs that can populate them.  It is up to the open source ctakes community
to implement and share such code and techniques.

>Does cTAKES offer any class or Extension points which we can extend and do our processing
outside cTAKES
What do you have in mind?  technically you can:
- create an AE to stick to ctakes conventions (e.g. type system) during processing,
- create an AE that translates ctakes types to some other types, performs custom java processing
and then translates the custom types back to ctakes types,
- create an AE that translates ctakes types to some available 3rd party types, performs 3rd
party java processing and then translates 3rd party types back to ctakes types,
- create an AE that translates, runs some external system process and then receives and translates
process output,
- create an AE that translates, sends information to some server process (e.g. rest) and then
receives and translates process output,
- probably something else that doesn't immediately come to mind.

Practically anything is possible, it just depends upon what is already available and / or
easiest for you.

Sean
________________________________________
From: Abad.Ayyub@cognizant.com <Abad.Ayyub@cognizant.com>
Sent: Thursday, February 20, 2020 11:22 PM
To: dev@ctakes.apache.org
Subject: RE: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]

* External Email - Caution *


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://urldefense.proofpoint.com/v2/url?u=https-3A__apc01.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fcwiki.apache.org-252Fconfluence-252Fdisplay-252FCTAKES-252FPiper-252BFiles-26amp-3Bdata-3D02-257C01-257CAbad.Ayyub-2540cognizant.com-257C676e6493d02c474fcaff08d7b48a4f8b-257Cde08c40719b9427d9fe8edf254300ca7-257C0-257C0-257C637176378465583371-26amp-3Bsdata-3DWFbsaBMYkgoIIQDAdCxHpMHk685Sdr9iB8BPxRvjBVE-253D-26amp-3Breserved-3D0&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Ood08xK67TQfUr7T1v8M6wmJ_XCr-CC3bTiuAbS8S-Y&s=dJ1Md8LHAyt5Bmvo-WrlwBWqGx6jmssUmO1-uBsS9P8&e=

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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