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Posted to user@ctakes.apache.org by Ab...@cognizant.com on 2020/02/17 08:46:30 UTC
Missing body side and laterality attribute in AnatomicalSiteMention
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.
RE: Missing body side and laterality attribute in
AnatomicalSiteMention [EXTERNAL]
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
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]
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
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]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <Ab...@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 <Se...@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 <Ab...@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 <Se...@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 <Ab...@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
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 unauthl ized 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.
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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]
Posted by Ab...@cognizant.com.
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 <Se...@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&data=02%7C01%7CAbad.Ayyub%40cognizant.com%7C676e6493d02c474fcaff08d7b48a4f8b%7Cde08c40719b9427d9fe8edf254300ca7%7C0%7C0%7C637176378465583371&sdata=WFbsaBMYkgoIIQDAdCxHpMHk685Sdr9iB8BPxRvjBVE%3D&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 <Ab...@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 <Se...@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 <Ab...@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
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 unauthl ized 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.
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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]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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://cwiki.apache.org/confluence/display/CTAKES/Piper+Files
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 <Ab...@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 <Se...@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 <Ab...@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
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 unauthl�ized 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 solh \�Hو H[�[�Y �X�\Y[�
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RE: Missing body side and laterality attribute in
AnatomicalSiteMention [EXTERNAL]
Posted by Ab...@cognizant.com.
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 <Se...@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 <Ab...@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
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 unauthl�ized 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 solh \�Hو H[�[�Y �X�\Y[�
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Re: Missing body side and laterality attribute in
AnatomicalSiteMention [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <Ab...@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
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.