Hi Sean,
It is run time error.
I have chosen maven-build for ctakes-core, It gave Build Success message
console.
But when I try to run, It has given Error : Error exists in ctakes-core.
Then I have seen LabValueFinder.java file highlighted with cross sign.
In this file when I hover on
Awesome, work. I agree it will certainly ease our process!
I have created a ticket to discuss the next steps with the REST service now
that this is complete (hoping we can delete some unneeded code!):
https://github.com/GoTeamEpsilon/ctakes-rest-service/issues/23
Thanks,
Matthew Vita
Tim, this is extremely informative. Thank you Sean for updating the .xml's.
I will play a little bit more with them and understand the process.
Until then, I can only speculate (please excuse my lack of understanding)
that the *model.jar is produced out of these .txt(raw data)+.xml
(annotations)
Thanks for the detailed explanation Sean. We will have a look at the
PiperFileReader and try to implement the rest module in similar lines.
Will keep you posted. Thanks again.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent:
Hi Gandhi,
You don't need to add that code. There is already a parameter named
"LookupXml" that can be used.
That being said, I just took a look at the code in github. To be honest, I
would not use the DemoServlet class. It uses a hardcoded pipeline, complete
with parameter values.
Hi Sean and Sirisha,
Thanks a lot for the response.
I tried building and deploying the war from the following repo -
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
On server start, it looks for sno_rx_16ab.xml. Not sure what configuration
exactly you are asking for.
I just checked the files into trunk an hour ago, so you'll need to update.
ctakes-examples-res /src/main/resources/
org/apache/ctakes/examples/annotation/anafora_annotated
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Tuesday, November
Yeah, it's definitely hard to do it the most efficient way because the
sensitive nature of our source data. You can see roughly what the
source data looks like in our ctakes-example-res project
(/home/tmill/Projects/ctakes-git/ctakes-examples-
Cheers!
-Original Message-
From: Sirisha Pulivarthi [mailto:sirisha_pulivar...@horizonblue.com.INVALID]
Sent: Tuesday, November 21, 2017 10:48 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi
We can point to the custom xml file explicitly
Hi Gandhi,
You don't need to have sno_rx_16ab* . I don't know exactly how you are
configured, but if you have another dictionary that you want to use instead of
the default sno_rx then you just need to create it and then point the custom
config .xml. This can be done a couple of ways, but
Hi
We can point to the custom xml file explicitly while invoking the pipeline.
Thanks
Sirisha
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 10:44 AM
To: dev@ctakes.apache.org
Subject: [External] RE: Use of
Hi Sean,
When we try to deploy cTAKES as web application, it always looks for
sno_rx_16ab.xml by default on server start. So do you mean we should also have
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?
Regards,
Gandhi
-Original Message-
From: Finan,
Hi Sandeep,
Adding a custom dictionary should never require code modification.
The dictionary creator gui will create a custom dictionary and its .xml
configuration file and place them in your ctakes resources/ directory. No code
changes necessary.
Very informative and a lot of information to digest. I will start with the
pamphlet, per your advice.
So what what I understand is that with a little bit of machine learning
awarness and annotated data, such a process can be built. More than that,
there is a collaboration over this data until the
Hi,
Is there currently any way to use a custom dictionary descriptor file without
making changes to the code or by rebuilding the ctakes-dictionary-lookup-fast
jar file.
Regards,
Sandeep
This email and any files transmitted with it are confidential and intended
solely for the use of the
Hi Alex,
> I know about the importance of these models.
My apologies if I offended.
> I would like to know if there is a way also to generate them.
There is a little bit of documentation on models expertly written by Tim.
Right now it is in a pamphlet that we distributed at a hackathon a
Hi Sean,
I know about the importance of these models. Tim was also kind enough to
explain to me in a previous email on the mailing list about the importance
of them and about the fact that these models were created by experts.
However, I'm not proposing to remove them, but to document better
Hi Bhagwat,
Does
> allCovering.putAll(
Create a build error or a run error? It shouldn't have a build error.
Sean
-Original Message-
From: Bhagwat Posane [mailto:bhagwat.pos...@gmail.com]
Sent: Tuesday, November 21, 2017 5:26 AM
To: dev@ctakes.apache.org
Subject: Re: source code of
Hi Bhagwat,
You can visit the ctakes-assertion-res module for some clues.
Navigate to ctakes-assertion-ressrc/main/resources/
org/apache/ctakes/assertion/pipeline/
There are two .piper files there. Each one covers a different way to get the
information that Tim mentioned. In those
Hi Bhagwat,
It is far from complete, but the wiki is probably the best place to start.
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
This page probably has the best introduction to components:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Component+Use+Guide
Hi Hadrian,
Very true on all points. Any connections that you can make in healthcare are
very welcome.
Sean
-Original Message-
From: Hadrian Zbarcea [mailto:hadr...@apache.org]
Sent: Monday, November 20, 2017 8:11 PM
To: dev@ctakes.apache.org
Subject: Re: Contribute to ctakes: it is
Hi Alex,
The model.jar files are needed and cannot be removed. You may have noticed
that a lot of those hard-coded paths point to these model.jar files.
Sean
-Original Message-
From: Alexandru Zbarcea [mailto:al...@apache.org]
Sent: Monday, November 20, 2017 7:33 PM
To: Apache
Hello Sean,Tim, et al,
I would like to Interpret context out of clinical note, e.g. interpretation
of the procedure, lab tests for a patient. For this, I suppose TLINK
statements would be of much help.
Ex. for the note- "Cystoscopy is planned on 3 / 26 / 2018."
I get TLINK as
Cystoscopy
Hello,
I have got the glimpse of ctakes functionality, now I am interested to
deep dive in the code.
Could anybody please help me to understand the functionality of each
module as a beginner I need to understand the Technologies,framework,coding
standard etc used to develop ctakes.
Any
Hello Sean,
Thank you very much for the help, finally I am able to generate the Html
output file with tlink statement using piper file.
Although I have taken latest trunk update, in LabValuFinder.java the
putAll() method giving build error. this was the culprit. for me to get it
worked, I have
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