Hi CTAKES Team,
We have started exploring CTAKES API for the Medical record summarization use
case. Is there a module which would help us to do the medical record
summarization post the entity extraction in CTAKES?
Thanks,
Abilash Mathew
This e-mail and any files transmitted with it are for
Thank you Sean for the inputs. We will let you know the progress.
Thanks,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, July 27, 2017 7:04 PM
To: dev@ctakes.apache.org
Subject: RE: Medical record summarization [EXTERNAL]
Hi
Thanks Perter for the details. We are now exploring the solution at our end. It
would be great , if you can share some insight into the approach that you have
followed.
Thanks,
Abilash Mathew
-Original Message-
From: Abramowitsch, Peter [mailto:pabramowit...@hearst.com]
Sent: Monday, Au
Just a basic question, are we using any deep learning techniques in CTAKES? If
yes, then which module.
Thanks,
Abilash Mathew
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 t
Hi,
I am trying to add ICD 9 and ICD 10 dictionaries to the CTAKES code. I
downloaded the ctakesicd2015.script and ctakesicd2015.properties file from the
link
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Dictionaries+and+Models
Then, from the ctakes-dev mailing list archive
Hi Team
I created a custom dictionary with SNOMED, RXNORM, ICD codes and CPT
vocabularies.
The annotator "DefaultJCasTermAnnotator" performs look up only with CUI_TERMS
table
The annotator "UmlsDictionaryLookupAnnotator" performs look up only with SNOMED
and RXNORM Dictionaries.
But I want
Hi,
Please let me know if there is a method in CTAKES other than
dumpSRLOutput(Annotation annotation to get the semantic Role mapping of input
sentences.
Does DependencyNodeWriter.java has any role in this?
Thanks,
Abilash Mathew
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Hi Sean,
I am looking for the relation between the semantic groups to get printed in the
output text file.
For example in the sentence, "The patient underwent a CT scan in April which
did not reveal lesions in his liver"
I want the "Semantic Role Labeling"( as in the below image) - re
Tim & Sean,
I used DefaultFastPipeline.piper to run CTakes 4.0 code and got the semantic
groups tagged(after lookup with Dictionary) at the output (like
Anatomy,Disorder,Drug,etc).
Now I am trying to find the relation between the tagged words.
>From the link
>https://cwiki.apache.org/conflue
Hi ,
During the recent discussions , I could see that there are many annotators
mentioned in the email communications. Just curious to know, Is there any
documentation available which talks about all the annotators that are part of
CTAKES?
Thanks,
Abilash Mathew
This e-mail and any files trans
Hi All,
I have recently come across below YouTube video and the documentation on IBM
Watson Medical Records Text Analytics Solution (MRTAS). Based on my analysis,
it follows the same approach as CTAKES ( uses same architecture and dictionary
lookups) and also does the same kind of data extr
Hi All,
We are currently using CDASegmentAnnotator for segmenting the medical records.
It is a pattern based annotator, I would like to know is there a better
annotator available to segmenting the documents. It is very difficult to
accommodate all the patterns in CDASegmentAnnotator as we are d
Sean,
When I tried with pattern based approach , during the testing we got into
issues for correctly identifying the segments. I was searching for better
solution and could find couple of articles talks about NLP and statistical
model based approaches. See below couple of links. Let me know if
Hi All,
Can you guys give some of the OCR engines used for Medical record text
extraction from images? I am currently using tesseract and seeing some text
extraction quality issues.
Thanks,
Abilash Mathew
This e-mail and any files transmitted with it are for the sole use of the
intended recip
Thanks Sean fir the quick reply and providing the valuable information.
Regards,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, October 16, 2017 8:17 PM
To: dev@ctakes.apache.org
Subject: RE: OCR engine used [EXTERNAL]
Hi Abila
Sean,
What is the accuracy that you get from OCR? We are at 60-70% accuracy. Most
of the documents are 200 DPI ones. Also, are you using any other software like
Matlab for the OCR pre or post processing.
Thanks,
Abilash Mathew
-Original Message-
From: Mathew, Abilash (Cognizant)
Sen
Yes, that is correct. But, we are looking for a non-cloud options.
Thanks,
Abilash Mathew
-Original Message-
From: Melvin Ma [mailto:ma.qian...@gmail.com]
Sent: Thursday, October 19, 2017 11:03 AM
To: dev@ctakes.apache.org
Subject: Re: OCR engine used [EXTERNAL]
In the context of ctakes,
Thank you Sean for sharing your experience. I will reach out to Tesseract
forum for further queries.
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, October 19, 2017 6:52 PM
To: dev@ctakes.apache.org
Subject: RE: OCR engine
Sure Sean, will update you on the progress.
Regards,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, October 20, 2017 6:41 PM
To: dev@ctakes.apache.org
Subject: RE: OCR engine used [EXTERNAL]
Hi Abilash Mathew,
If you do find a
Hi all,
We are seeing some false positives identified by CTAKES after we tested couple
of medical records samples. Can anyone help us on how to ignore these words
from tagging incorrectly?
Word
Finding
test
Procedure
Page
Procedure
treatment
Procedure
medicine
Drug
medication
Drug
a
Thanks Sean for the help. The information provided below are really helpful for
addressing our challenges.
Regards,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 25, 2017 7:17 PM
To: dev@ctakes.apache.org
Subject: R
Hi,
Can you help me to find below UI feature in CTAKES? The code we downloaded
didn't have this UI.
[http://ctakes.apache.org/images/TimeLanesBig.jpg]
Thanks,
Abilash Mathew
This e-mail and any files transmitted with it are for the sole use of the
intended recipient(s) and may contain confiden
Sean,
I am referring to the timelanes GUI available in the below page.
http://ctakes.apache.org/examples.html
Thanks,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, November 3, 2017 6:20 PM
To: dev@ctakes.apache.org
Subject: R
Hi All,
Can CTAKES process LAB reports and able to extract key findings from the report?
Thanks,
Abilash Mathew
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If you are not the intended
Thanks Sean Kean for the help.
Regards,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 15, 2017 5:40 AM
To: dev@ctakes.apache.org
Subject: RE: Lab report [EXTERNAL]
Hi all,
I checked in Kean's code as LabValueFinde
Hi ,
Based on the experience , can anyone tell me whether the current UMLS
dictionary would help us to find all the major Lab values?
Thanks,
Abilash Mathew
This e-mail and any files transmitted with it are for the sole use of the
intended recipient(s) and may contain confidential and privileg
Hi All,
Is there an option currently available with CTAKES for extracting patient name,
age etc. from Medical records and lab reports?
Thanks,
Abilash Mathew
This e-mail and any files transmitted with it are for the sole use of the
intended recipient(s) and may contain confidential and privileg
Hi All,
I am trying to extend the current Lab Value finder annotator to include the
Range annotation also.
"Blood Urea Nitrogen (BUN) 10 mg/dL 8-23"
Using current module , I am able to pull lab value as " BUN 10 mg" from above
text and trying to tag "8-23" as reference range.
final M
Thanks Kean for the suggestions. I could see setReferenceRangeNarrative method
in LabMention class. Is that the one are you referring? Also, what is your
suggestion to create new class similar to LabValueFinder?
Regards,
Abilash Mathew
-Original Message-
From: Kean Kaufmann [mailto:k...
Kean,
I was able to get the annotation tagged as Range and measurement annotations as
shown below. As a next step, I would like to get the individual token like 42
,52 and 21 etc. I know I can try a pattern or index based search to extract the
information, but I am trying to see if any options c
Thanks Kean. I was able to get the desired output using selectCovered method.
From: Kean Kaufmann [mailto:k...@recordsone.com]
Sent: Friday, March 2, 2018 12:30 AM
To: Mathew, Abilash (Cognizant)
Cc: dev@ctakes.apache.org
Subject: Re: Lab Value - Range finder
Abilash,
The org.apache.uima.fit.ut
Hi,
I am trying to get range annotation from the below lab text. But CTAKES is not
picking the decimal ranges from the text. But, if it is whole number then range
annotator is working.
"creatine level test 0.9 mg/dL 0.7-1.3 \n" ;
It uses RangeFSM class to annotate the range annotator. Any h
Hi,
I have a requirement to expose rest API to a different application. Is the
CTAKES Rest API feature currently available or still in progress?
Thanks,
Abilash Mathew
This e-mail and any files transmitted with it are for the sole use of the
intended recipient(s) and may contain confidential
Thanks Gandhi for the quick response.
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, April 10, 2018 11:05 AM
To: dev@ctakes.apache.org
Subject: RE: Rest API
Hi Abilash,
It is not yet available in CATKES codebase but the module is m
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