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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject Re: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL] [SUSPICIOUS]
Date Mon, 17 Feb 2020 15:41:28 GMT
Hi Abad,


If you are using ctakes trunk there are a lot of piper files in the various resources modules
to handle more advanced pipelines.


ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/pipeline/

contains DefaultRelation.piper - which adds detection of modifiers, locations and severities.


If you are not using trunk, just add these lines to the end of your piper:


// Modifiers. Use addLogged to log start and finish of processing.  There aren't default models,
so set specifically
addLogged ModifierExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/modifier_extractor/model.jar

// Degree of severity, etc.
addLogged DegreeOfRelationExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/degree_of/model.jar

// Location.
addLogged LocationOfRelationExtractorAnnotator classifierJarPath=/org/apache/ctakes/relationextractor/models/location_of/model.jar


If you don't care about "starting ..." "done" info statements in your log, you can replace
the 'addLogged' command with 'add'.


Sean







________________________________
From: Savova, Guergana <Guergana.Savova@childrens.harvard.edu>
Sent: Monday, February 17, 2020 8:38 AM
To: user@ctakes.apache.org; dev@ctakes.apache.org
Subject: RE: Missing body side and laterality attribute in AnatomicalSiteMention [EXTERNAL]
[SUSPICIOUS]

* External Email - Caution *


Hi Abad,

Methods for populating these two attributes have not been implemented in cTAKES.  In cTAKES,
there is a method for linking anatomical sites to diseases/disorders, sign/symptoms or procedures:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994852/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC3994852_&d=DwMFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Z5X8hKFLIwIjnXOrGFZcyEpFZdMhdLr5BH7HAXW2fZc&s=EkfOOc3kOW93AA4uAdOCEW40Hy-qfQ5jpL4sqceZEaU&e=>

best,
--
Guergana Savova, PhD, FACMI
Associate Professor
Boston Children's Hospital and Harvard Medical School

[http://web2.tch.harvard.edu/homepagestories/Images/SigBlock.jpg]


From: Abad.Ayyub@cognizant.com [mailto:Abad.Ayyub@cognizant.com]
Sent: Monday, February 17, 2020 3:47 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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