r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=siIm_idCCJKx_vKf-0UxVEi5frE1bqB3T2dVaYQeKSA&s=MAdp_ACJwKPAjtFqhzzIeGFWZU-icnw3UO4HL8ITDo0&e=
Thanks,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 11, 2017 8
Hi Kathy,
I don't know if the warning indicates a problem for you, but just in case ...
In the ctakes-type-system module there is a file named TypeSystem.xml in
main/resources/.../types/
That file defines types used by ctakes, oncluding the property
multipleReferecesAllowed.
Sean
-Origin
Hi Sirisha,
Are you trying to use a metamorphosis tool with a different version of the nlm
files?
Also, metamorphosis is a gui application. Make sure that you have a display:
> No X11 DISPLAY variable was set, but this program performed an operation
> which requires it.
Sean
-Original Mes
hanks 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 Abilash M
-
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 used [EXTERNAL]
Hi Abilash Mathew,
I haven't evaluated a per-character (or per-word) accuracy, but things look
fair (80-90%? per char)
Hi Melvin,
Thanks. There was originally a reason for not crashing the run, but I think
that this behavior can be changed.
Were you able to get the paths working correctly (piper file found)?
Sean
-Original Message-
From: Melvin Ma [mailto:ma.qian...@gmail.com]
Sent: Tuesday, October 24,
Hi Gandhi, Abilash Mathew,
This is a common problem stemming from the nature of the umls and automated
dictionary creation. I am still (ever so slowly) improving the dictionary
creator code. If anybody can devote some time to help that would be great.
Anyway, if you are using ctakes trunk the
Hi Gandhi,
You can always build ctakes in your sandbox with spring 4 and see if it works.
This may require some "maven magic"(overrides) on your part. If it does seem
to work please create a jira item to upgrade the spring version. Then
hopefully before the next release somebody will thoroug
ely,
Kean
On Wed, Oct 25, 2017 at 9:46 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Gandhi, Abilash Mathew,
>
> This is a common problem stemming from the nature of the umls and
> automated dictionary creation. I am still (ever so slowly) improving
> the
23"?) would come in similarly handy.
Appreciatively,
Kean
On Wed, Oct 25, 2017 at 9:46 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Gandhi, Abilash Mathew,
>
> This is a common problem stemming from the nature of the umls and
> automated dictiona
Hi Melvin,
This has been changed.
Thanks,
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, October 24, 2017 6:27 PM
To: dev@ctakes.apache.org
Subject: RE: Running Piper File [EXTERNAL] [SUSPICIOUS]
Hi Melvin,
Thanks. There was
Hi Melvin,
There shouldn't be any change needed, but let me check ... it could be that I
need to specifically include that piper in the .jar ...
-Original Message-
From: Melvin Ma [mailto:ma.qian...@gmail.com]
Sent: Wednesday, October 25, 2017 12:45 PM
To: dev@ctakes.apache.org
Subject
Dima,
I think that there is an -xmi option or something like that, but for individual
files.
-Original Message-
From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
Sent: Wednesday, October 25, 2017 1:50 PM
To: dev@ctakes.apache.org
Subject: Re: CAS Visual Debugger - [EXTERNAL]
+1
Also, I’
Ok, there is a kludge ...
1. Start the CVD
2. Go to File > load Type System
3. Select your type system
4. Exit
5. Go to your home directory
6. Look at the file named annotViewer.pref
There should be a line starting with " dir.open.xcas=" that points to your type
system.
7. Make a copy of t
Hi Melvin,
This was a bug. I just checked in a fixed pom file.
Thanks,
Sean
-Original Message-
From: Melvin Ma [mailto:ma.qian...@gmail.com]
Sent: Wednesday, October 25, 2017 12:45 PM
To: dev@ctakes.apache.org
Subject: Piper File - [EXTERNAL]
Sean - I am actually replying your earlie
Hi Lani,
I am going to try to address your questions, but I'm not sure that this is the
information that you want.
- The ctakes 4.0 dictionary (sno_rx_16ab) is built using terms from the snomed
ct and rxnorm terminologies as they exist in the 2016AB umls release.
- The codes from the two termi
about the progress.
Regards,
Gandhi
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 25, 2017 7:28 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]
Hi Gandhi,
You can always build ctakes in your sandbox wit
Hi Marcello,
I am hoping that somebody will answer your question with a "Yes, I have a fhir
/ owl / bioc / json writer to share".
Unfortunately I am not aware of any that are publicly available for ctakes
output. BioC should be fairly easy to do as an -xml- rearrangement of what
ctakes can pr
e is also reviewing and testing my
rest service changes. He will provide more info to us once we are done with our
testing. So that we can discuss about productizing the same.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday,
Oq31Y4PRf5muS_U0cyd_auCRZh4ktFD3cK4a6tMk9uU&s=hKBU6HEMwwZgk1UCPAitjL1thyV9inbHjed9rT_ObUI&e=
6. Work on preparing the solution for the cTAKES core codebase. I will
prepare it with a very rich README.
I will provide my updates over the coming days.
Thanks,
Matthew Vita
www.matthewvita.com
On
Hi Bhagwat,
If you are interested in the default clinical pipeline, you can look at the
wiki here:
https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
For a visual representation of what Tim described.
The AEs used for the ctakes 4.0 default clinical pipeline are show
Hi Melvin,
To see how the sno_rx_16ab was created, please see:
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
That page will also instruct you on making one that contains things like "teary
eyes", which comes from the MDR vocabulary and not snomed or rxnorm. It is
po
Hi Abilash Mathew,
Attachments and Embedded images tend to be removed by the time I get them. Can
you please describe the gui?
Thanks,
Sean
From: abilash.mat...@cognizant.com [mailto:abilash.mat...@cognizant.com]
Sent: Friday, November 03, 2017 1:48 AM
To: dev@ctakes.apache.org
Subject: CTAKES
ppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=sa3olNLhgBOetJKc_UpjYUOs2jRqKxw4L5KaCmWs79s&s=Xp_UltsNR-MB60C8L25iqsD62D1AjfzBjJ8Ehrr5dks&e=
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
ty helpful to get the better understanding of source code.
> >
> > I have run ctakes-example project that internally executes
> > ClinicalPipelineFactory.getDefaultPipeline() method. This has given
> > results like POS tag, Polarity, etc.
> > Now,
ren't default models, so set specifically
add BackwardsTimeAnnotator
classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
The same goes for the "load X YY=ZZ" statements that look like they are
the ends of comment lines.
Sean
-Original Message---
Hi all,
The Jenkins builds have been failing for about a month now because of internal
Jenkins changes and 'unit' tests in the ctakes-Regression and ctakes-yTEX
modules. This is holding up the build for all of our primary clinical-pipeline
modules.
If anybody can take a look at the problems a
Subject: RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]
Hi Sean,
I can take it up if someone is willing to guide me on this.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 08, 2017 9:45 PM
To: dev
le. please suggest on this.
On 8 November 2017 at 18:39, Finan, Sean
wrote:
> Hi Bhagwat,
>
> The ctakes-temporal module has the components needed to generate tlinks.
> Using trunk, the following can be added to the end of the default
> clinical pipeline piper fil
t?
I have tried to get the HTML output file using below command.
1) add pretty.html.HtmlTextWriter
2) add pretty.html.HtmlTextWriter D:\Bhagwat\output
But it does not generate any output file
Could you please provide some light on this.
On 9 November 2017 at 20:43, Finan, Sean
wrote:
> Hi B
you please guide on this.
On 10 November 2017 at 18:47, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Bhagwat,
To get html output, you just need to add the html writer and set the output
directory.
Your #1 should do that.
add pretty.html.HtmlTextWriter
To set the outpu
ssion tests on Jenkins [EXTERNAL]
Hi Sean,
I can take it up if someone is willing to guide me on this.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 08, 2017 9:45 PM
To: dev@ctakes.apache.org
Subject: Disable yTE
erated. To find the cause, I have checked multiple things with no
success!
However, event-time-relation is captured in xmi with no problem(P.S. Attached).
For your reference my piper file is also attached.
Could you please have a look at the outputs and guide me to find the root cause
or please tel
.org_view_C_view_Apache-2520cTAKES_job_cTAKES-2Dtrunk-2DJava-2D1.8_25_testReport_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=-PwjGWv5MEFT_1Jui9b27fdgkKfFRa29hts-FMalo8I&e=
On Nov 13, 2017 10:41, "F
Hi all,
I checked in Kean's code as LabValueFinder in ctakes-core. Use is fairly
straightforward - you can look at the annotator class or the unit test in
ctakes-regression-test to get a handle on it.
Enjoy,
Sean
-Original Message-
From: Kean Kaufmann [mailto:k...@recordsone.com.INVAL
s you mentioned I am sending my piper file, HTML file and clinical note
file to your personal email.
Could you please have a look at it, and provide your thoughts on it.
On 14 November 2017 at 19:16, Finan, Sean
wrote:
> Hi Bhagwat,
>
> To build upon what Tim said, not all of the ctakes
to get the output using the source code in trunk.
On 15 November 2017 at 18:20, Finan, Sean
wrote:
> Hi Bhagwat,
>
> I got your output files, thanks. Tlinks are not present because it comes
> from the ctakes 4.0.0 release, in which the html writer was very
> primitive. It has
BeanInfo for class
> [org.apache.ctakes.ytex.weka.GramMatrixExporterImpl];
> nested exception is java.beans.IntrospectionException: type mismatch
> between read and write methods
>
> Can you do a full build once and try?
>
> Regards,
> Gandhi
>
>
> -Original Message
,
Unfortunately I haven't received it in spam folder too.
On Nov 15, 2017 7:47 PM, "Finan, Sean"
wrote:
> Hi Bhagwat,
>
> I sent the email with the output zipped as it contains a javascript
> file and those are usually blocked as attachments. Check your spam
> folder
y_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=K0KP_M1BTpGUsPOHy6q6q78mS9FKvIj6-B7UEjVOUmc&s=K1pRo0hnemAlUChvke7CvCFXgl7z9uzTgm-oVgSUV6k&e=
On Wed, Nov 15, 2017 at 10:05 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alex,
&g
will come back shortly with a
patch for it.
Checking for a buildID, would make cTAKES dependent on the Apache build service
(Jenkins), making it less portable. I think it would impact adoption for
community.
What do you think?
Alex
On Wed, Nov 15, 2017 at 1:36 PM, Finan,
nk-2DJava-2D1.8_&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Nub-VURn12Fe1c6GYlv6GQNbttfAph_JWwFVGFFHa0Q&s=25NM-JgVwOu3EfTDMgRNPJa6QOsvlt9CK06rB2OsxtA&e=>
On Wed, Nov 15, 2017 at 5:10 PM, Finan, Sean
mailto:sean.fi...@childrens.harvard.ed
yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Nub-VURn12Fe1c6GYlv6GQNbttfAph_JWwFVGFFHa0Q&s=25NM-JgVwOu3EfTDMgRNPJa6QOsvlt9CK06rB2OsxtA&e=>
On Wed, Nov 15, 2017 at 5:10 PM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Alex,
I don't know what you mean about m
--user USER --pass PASS
it is giving following error:
Error: Could not find or load main class
org.apache.ctakes.core.pipeline.PiperFileRunner
On 15 November 2017 at 22:07, Finan, Sean
wrote:
> I just sent it 2 more times ...
>
> -Original Message-
> From: Bhagwat Posane [m
Hi Alex, my responses are below.
>I think is even more convenient than using the apache-release profile. The
>rule of thumb would be that apache-release profile is used only by the person
>assigned by ?the PMC to do the releases
-- Ok, fair enough
>. Yes, the apache-release profile is working f
VKVbB3TtO2SWveKoHZc&s=5yBAv6gio7iSwpVEbMfdJnuGmM_nIx442vpPM_WAVgM&e=
cTAKES+4.0+Developer+Install+Guide
On Thu, Nov 16, 2017 at 10:43 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alex, my responses are below.
>
> >I think is even more convenient than using the apache-release pr
Hi Alex,
Great work,
Cheers,
Sean
-Original Message-
From: Alexandru Zbarcea [mailto:al...@apache.org]
Sent: Thursday, November 16, 2017 7:34 PM
To: Apache cTAKES Dev
Subject: cTAKES Jenkins build is successful. [EXTERNAL]
Hi,
The job:
https://urldefense.proofpoint.com/v2/url?u=https-3
source code.
On 16 November 2017 at 20:23, Finan, Sean
wrote:
> Hi Bhagwat,
>
> I think that you are close, but that workflow won't pan out.
>
> If you want to run just like the ctakes release, run maven package,
> then go to the target/ directory in -distribution and unzip
llation of cTakes. [EXTERNAL]
[SUSPICIOUS] [SUSPICIOUS]
Hi Sean,
I am using Eclipse Mars IDE.
Could you please tell me how to to set up an ide to run directly using the
source code.
On 16 November 2017 at 20:23, Finan, Sean
wrote:
> Hi Bhagwat,
>
> I think that you are close, but that
Hi Tim, Alex,
Great ideas. I like your (Tim) idea to
1. start with commented code removal.
Then maybe move on to
2. sanity-test type unit tests - Little two or three-line "does this method
crack" tests.
And another that is simply
3. "populate a test cas with type(s) X" and a factory with "g
Is anybody that was involved with ytex still out there?
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, November 18, 2017 9:53 AM
To: dev@ctakes.apache.org
Subject: Test case failure [EXTERNAL]
Hi All,
I did a fresh check out of c
g more and more with cTAKES and would love to contribute more to the
project.
Just my thoughts.
- Dave
On Sat, Nov 18, 2017 at 11:10 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Tim, Alex,
>
> Great ideas. I like your (Tim) idea to 1. start with commented co
> optional switch,
> >of course - I believe it may be best to rewrite this in Java
> > should this be
> >included with the solution)
> >5. Test the output in my web viewer:
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.c
ightweight branching for focused development, as it helps me
keep a cleaner working directory. But that adds some additional annoying steps.
Tim
From: Finan, Sean
Sent: Saturday, November 18, 2017 1:23 PM
To: dev@ctakes.apache.org
Subject: RE: Contribut
piper
--user yourUmlUsername
--pass yourUmlsPassword
But I am getting this error : Could not find or load main class
org.apache.ctakes.core.pipeline.PiperFileRunner
Could you please provide some inputs on it.
On 17 November 2017 at 22:04, Finan, Sean
wrote:
> Hi Bhagwat,
>
> It is a
CtgGvLG2s_KqVRWx_tZAcaMSh_KKH4aqc6HGTP3dmtA&e=
>
> with those I guess the suggested workflow is to work off of that repo
> and then just submit patches to someone who commits with svn rather
> than committing directly.
>
> I've been using the git-svn connector mysel
total
Are all these resources still relevant? Is there a way to generate them?
I do not wish to open the Pandora box though, Alex
On Mon, Nov 20, 2017 at 9:29 AM, Finan, Sean wrote:
> Thanks Tim!
>
> -Original Message-
> From: Miller, Timothy [mailto:timothy.mil...@childre
mentioned quite a bit. Last
week I was at the HSPC meeting in Indianapolis where, again, very few knew
about cTakes.
If the project is interested I could find more resources for the project and
help with growing adoption.
Cheers,
Hadrian
On 11/20/2017 10:41 AM, Finan, Sean wrote:
> Hi Alex,
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
There
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 fil
/ }
// }
return allCovering;
}
I think this needs to be fixed, not sure though.
I have few more quires I will write it in separate thread.
On 20 November 2017 at 20:09, Finan, Sean
wrote:
> Hi Bhagwat,
>
> I have no idea why that isn't working. Ctakes-examples
tps-3A__en.wikipedia.org_wiki_Domain-2Dspecific-5Flanguage&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Z1PqE3gYYReZ9DTKn8orPn035tOYJSebS_S_Yq39mHY&s=k5C2cLaa5HI6YU7YX0nXqzUWbrV_KHNqDzSWGyN_jqc&e=
On Tue, Nov 21,
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.
https://cwiki.apache.org/confluence/display/
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, Sean [mail
,
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, Sean
scussion if there is some
indecisio (for example, a 1Gb model that offers 2% improvement on relation
extraction, is that worth it?) Sometimes I've checked things in that run in
experimental projects where they may or may not make it into default models.
Tim
On Tue, 2017-11-21 at 14:21
!= null) { LOGGER.info( "Using custom
descriptor file path: " + _customDescriptorFilePath ); _descriptorFilePath =
_customDescriptorFilePath; }
Is this approach fine?
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, November 21, 2017 9:
Dictionary Descriptor file [EXTERNAL]
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
ce with previous output.
Could you please help me to resolve this error.
On 21 November 2017 at 18:43, Finan, Sean
wrote:
> Hi Bhagwat,
>
> You can visit the ctakes-assertion-res module for some clues.
>
> Navigate to ctakes-assertion-ressrc/main/resources/
> org/apache/cta
ering( jCas, covered, covering ) );
On Wed, Nov 22, 2017 at 8:40 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Bhagwat,
>
> I have no idea what is going on with your system.
>
> > The method putAll(Map > List>) in the type
> > Map> is no
Hi Chahal Arora,
>1) Is there any piper file available for LabValueFinder that I can use to make
>it work?
The LabValueFinder isn't part of any default workflow. However, it can be
added to any piper with the line:
add LabValueFinder
My recommendation is that you create your own piper file.
eption, it resolved for me
by removing "file:" from command, I suppose this needs to be fixed.
On 22 November 2017 at 23:21, Finan, Sean
wrote:
> Wow, that is really strange.
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org_d
> _uimaf
essfully, it means to get into infinite loop the highlighted
sentence should have at least one sentence with it.
Could you please provide your thoughts on it.
Sorry for lengthy explanation, but I thought it is necessary.
On 24 November 2017 at 01:22, Finan, Sean
wrote:
> Hi Bhagwat,
>
&
The code where it throws exception is -
final Future>> future = _executor.submit( callable ); which
is at line 121 in class RegexSpanFinder of package -
org.apache.ctakes.core.util.regex
Regards
Chahal Arora
Software Engineer
Raxa
On Thu, Nov 23, 2017 at 1:10 AM, Finan, Sean <
sean.fi
mber 2017 at 01:22, Finan, Sean
wrote:
> Hi Bhagwat,
>
> Thanks for the heads up on the "file:" issue. I will check to see if
> the usage has changed and fix the piper.
>
> Sean
>
> -Original Message-
> From: Bhagwat Posane [mailto:bhagwat.pos...@gm
src/main/resources/
> org/apache/ctakes/assertion/pipeline/
> There are two .piper files there. Each one covers a different way to
> get the information that you mentioned.
By following this clues, I am nowhere.
Could you please provide information on which pipeline I should have t
Hi Kathy,
The negation annotator used in the default clinical pipeline is based upon
machine learning and trained on real data. It is possible that such "denies"
lists were underrepresented in the training data. One thing that you can try
is adding another negation annotator. The ContextAnno
;c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=4K9fxMmBiI0QZB0UhriFp_YvXDL8rmXtGRiKVgxMCPE&s=hsCB9xPXLC8fpiwrGXuEW9snw_WZbY0e-E-mhPOO9N8&e=
Thanks again,
Kathy
On Tue, Nov 28, 2017 at 9:31 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Kathy,
te new
cTakescode, not sure though.
On 27 November 2017 at 19:02, Finan, Sean
wrote:
> Hi Bhagwat.
>
> You wrote:
> > Now coming back to our original question for which this thread has
> > been
> initiated.
> > I was trying to get the context out of clinical n
false positive is an example the algorithm calls negated
that is not actually being negated).
Tim
On Tue, 2017-11-28 at 17:22 +, Finan, Sean wrote:
> Hi Kathy,
>
> I am glad that you checked the wiki! I should have pointed to it ...
>
> In the example I sent the "relevan
Excellent answers Tim!
> Is there a way to link all this term to x-ray without have to modify
> fast dictionary for every x-ray entries?
Unfortunately no. The dictionary can only match (give or take) the data that
it contains. I have long had an idea on how to improve this by trickery, but
I
ds,
Gandhi
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 22, 2017 1:21 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNAL]
Hi Gandhi,
You don't need to add that code. There is alre
Hi Shyam k,
Are you sure that you changed your umls credentials? How did you change them?
It doesn't look like your change went through since your error is still:
> is not valid for user CHANGE_ME with CHANGE_ME
Sean
-Original Message-
From: Ks Sunder [mailto:shyam...@gmail.com]
Sent
Hi Alex,
Thank you for the heads-up.
I did notice your checkin and you have nothing but my respect for taking the
initiative. I haven't tested the update on another project for any ill
happenstance, but a colleague and ctakes pmc (Chen Lin, master of doctimerel
among other things) did run (po
Hi Chalal Arora,
You can change values in a piper file in two ways.
To set a value "globally" use the "set" command:
set DISTANCE=14
set BOUNDARY_ANN_TYPE=14
To set a value just for one annotator enter it on the "add" line:
add DrugMentionAnnotator DISTANCE=14 BOUNDARY_ANN_TYPE=14
If the DrugMe
e have any properties files for that...?
please help me..
On Thu, Nov 30, 2017 at 7:42 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Shyam k,
>
> Are you sure that you changed your umls credentials? How did you change
> them? It doesn't look like your change
Hi Alex,
I like the approach.
Sean
-Original Message-
From: al...@apache.org [mailto:al...@apache.org]
Sent: Monday, December 04, 2017 10:58 PM
To: comm...@ctakes.apache.org
Subject: svn commit: r1817150 -
/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/util/JdbcOperationsHel
> > >
> > > Sean,
> > >
> > > Ghandi and I have met and we both agreed that his solution is
> > > superior to the one I was working on. Therefore, I will be helping
> > > to see this project through to the end so we can get it
Hi Sekhar H.,
You could check out the downloads at openfda.gov
https://open.fda.gov/downloads/
The json files in food/event and drug/event might help.
Sean
-Original Message-
From: Hari, Sekhar [mailto:sekhar.h...@cgi.com]
Sent: Thursday, December 07, 2017 7:38 AM
To: u...@ctakes.apa
O) or Human Phenome
Ontology (HPO)?
Sean
-Original Message-
From: Hari, Sekhar [mailto:sekhar.h...@cgi.com]
Sent: Thursday, December 07, 2017 8:04 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: RE: Drug-Allergy Contraindications [EXTERNAL]
Thank you so mu
Ooh - OMIM has released an api:
http://omim.org/api
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, December 07, 2017 8:11 AM
To: Hari, Sekhar
Cc: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: RE: Drug-Allergy
14:16 +, Miller, Timothy wrote:
> I am really interested in this too, just waiting until I have a few
> free hours to look around. Don't want you to think it's not of
> interest.
> Tim
>
>
> On Tue, 2017-12-05 at 19:18 +, Finan, Sean wrote:
> >
>
a while. Would every call re-load the pipeline?
Tim
On Thu, 2017-12-14 at 20:16 +, Finan, Sean wrote:
> Hi Tim,
>
> Many thanks for testing the new rest service! And double that for the
> setup instructions!
>
> >
> > if this whole thing could be wrapped
e old one?
>
> I'll keep poking around, but hopefully this is helpful feedback for
> you guys. Thanks again for getting this off the ground!
>
> Tim
>
>
>
>
> On Thu, 2017-12-07 at 14:16 +, Miller, Timothy wrote:
> >
> > I am really in
Util.select(jcas,
>> > SignSymptomMention.class)){
>> > int begin = ss.getBegin(); // begin offset
>> > int end = ss.getEnd(): // end offset ...
>> > }
>> >
>> > Using the typesystem directly may help you to speed up that code or
Hi Satya,
Could you please let us know what steps you have already taken to create and
integrate the custom dictionary?
Thanks,
Sean
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
-Original Message-
From: satyananda sahu [mailto:satyananda...@gmail.com]
Se
Fantastic!
I am glad that you found the issue - that wouldn't have been a straightforward
causal to track down.
Unfortunately we cannot package and ship any binaries that aren't fully Apache
license compliant etc. However, we can do two different things:
- We can still grab mysql from maven ce
and d) Is
1 of the 2 databases used in OpenEMR so our cTAKES module users wouldn't get
too confused.
Again, that last item is nice to have, don't read into it too much :).
Thoughts?
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Dec 18, 2017 at 7:23 AM, Finan, Sean <
sean.fi..
Do you want your lookup to be case sensitive? If so then new code would be
required. The lookup is case insensitive because it does expect the
dictionary/database to contain only lowercase entries. If you are ok with the
case insensitivity then I propose that you modify your database.
Sean
; I wanted the lookup to be case insensitive. Also wanted to go away
> > with
> the
> > restriction of putting enteries in lowercase in database like the
> > way it was working with BSV.
> >
> > But if lowercase enteries are expected in database then I guess
> > modify
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