Medical record summarization

2017-07-27 Thread Abilash.Mathew
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

RE: Medical record summarization [EXTERNAL]

2017-08-04 Thread Abilash.Mathew
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

RE: Medical record summarization [EXTERNAL]

2017-08-08 Thread Abilash.Mathew
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

Deep learning

2017-08-17 Thread Abilash.Mathew
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

ICD10 lookup

2017-08-22 Thread Abilash.Mathew
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

CTAKES lookup

2017-08-30 Thread Abilash.Mathew
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

semantic Role mapping

2017-09-14 Thread Abilash.Mathew
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 This e-mail and any files transmitted with it are for the sol

RE: semantic Role mapping [EXTERNAL]

2017-09-14 Thread Abilash.Mathew
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

RE: semantic Role mapping [EXTERNAL] [SUSPICIOUS]

2017-09-17 Thread Abilash.Mathew
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

annotator Wiki

2017-09-21 Thread Abilash.Mathew
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

IBM MRTAS

2017-10-04 Thread Abilash.Mathew
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

segmentation

2017-10-11 Thread Abilash.Mathew
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

RE: segmentation [EXTERNAL]

2017-10-11 Thread Abilash.Mathew
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

OCR engine used

2017-10-16 Thread Abilash.Mathew
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

RE: OCR engine used [EXTERNAL]

2017-10-16 Thread Abilash.Mathew
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

RE: OCR engine used [EXTERNAL]

2017-10-18 Thread Abilash.Mathew
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

RE: OCR engine used [EXTERNAL]

2017-10-18 Thread Abilash.Mathew
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,

RE: OCR engine used [EXTERNAL]

2017-10-20 Thread Abilash.Mathew
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

RE: OCR engine used [EXTERNAL]

2017-10-20 Thread Abilash.Mathew
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

false positive

2017-10-25 Thread Abilash.Mathew
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

RE: false positive [EXTERNAL]

2017-10-25 Thread Abilash.Mathew
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

CTAKES Timelane

2017-11-02 Thread Abilash.Mathew
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

RE: CTAKES Timelane [EXTERNAL]

2017-11-03 Thread Abilash.Mathew
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

Lab report

2017-11-13 Thread Abilash.Mathew
Hi All, Can CTAKES process LAB reports and able to extract key findings from the report? 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 the intended

RE: Lab report [EXTERNAL]

2017-11-14 Thread Abilash.Mathew
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

Lab Value Finder dictionary

2017-12-19 Thread Abilash.Mathew
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

non Medical entity extraction

2017-12-21 Thread Abilash.Mathew
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

Lab Value - Range finder

2018-02-07 Thread Abilash.Mathew
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

RE: Lab Value - Range finder

2018-02-12 Thread Abilash.Mathew
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...

RE: Lab Value - Range finder

2018-02-28 Thread Abilash.Mathew
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

RE: Lab Value - Range finder

2018-03-02 Thread Abilash.Mathew
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

range Token

2018-03-08 Thread Abilash.Mathew
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

Rest API

2018-04-09 Thread Abilash.Mathew
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

RE: Rest API

2018-04-09 Thread Abilash.Mathew
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