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Posted to user@ctakes.apache.org by "Savova, Guergana" <Gu...@childrens.harvard.edu> on 2020/02/17 13:38:43 UTC
RE: Missing body side and laterality attribute in
AnatomicalSiteMention [EXTERNAL]
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/
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
This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored. This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored.
Re: Missing body side and laterality attribute in
AnatomicalSiteMention [EXTERNAL] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <Gu...@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
This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored. This e-mail and any files transmitted with it are for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient(s), please reply to the sender and destroy all copies of the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email, and/or any action taken in reliance on the contents of this e-mail is strictly prohibited and may be unlawful. Where permitted by applicable law, this e-mail and other e-mail communications sent to and from Cognizant e-mail addresses may be monitored.