Hi Avanish,
I think that Apache email services do not allow markups, embedded images or
attachments. Your images didn't come through for me. Can you paste the code
as text? If it is online somewhere public (e.g. github) you can add a link to
the repository for people to inspect.
Thanks,
Sea
Hi Sean,
That is great - thank you for sharing your solution!
Sean
-Original Message-
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Tuesday, June 06, 2017 11:19 AM
To: Finan, Sean; dev@ctakes.apache.org
Subject: RE: ctakes 4.0.0 YTEX DBConsumer not populating
318)
at
org.apache.uima.json.JsonCasSerializer.serialize(JsonCasSerializer.java:308)
at Main.result(Main.java:62)
at Main.main(Main.java:96)
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, June 06, 2017 8:37 PM
To: dev@ctakes.apache.org
Su
Hi Erin,
Do you have any classes in ctakes-typesystem (org.apache.ctakes.type.system)?
It could be that jcasgen needs to be run.
Just out of curiosity, how huge is your jar file? You may be able to decrease
the size ...
Sean
-Original Message-
From: Erin Gustafson [mailto:erin.gusta
: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, June 08, 2017 10:24 AM
To: dev@ctakes.apache.org
Subject: RE: Pipeline executable
Hi Erin,
Do you have any classes in ctakes-typesystem (org.apache.ctakes.type.system)?
It could be that jcasgen needs to be run.
Just out of
But there are other pipelines
within the project for doing location relation and temporal relation
extraction. I'm still learning Java and how to use tools like gradle/maven, so
it's definitely possible that I don't need all of those dependencies listed
above. I was just erring
You can see example files in ctakes dictionary-lookup-res. Start with the
simplest 2:
Cui to term text:
http://svn.apache.org/repos/asf/ctakes/tags/ctakes-4.0.0/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example/bsv/custom_cui_bsv.bsv
Cui and tu
ggestions! I'll work on paring the project down to the bare
essentials.
Any thoughts on what could be causing the type error or how to go about
diagnosing the problem?
Best,
Erin
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, June
ery noticeable.
Dima
> On Jun 5, 2017, at 10:42, Finan, Sean
> wrote:
>
> Hi Dima,
>
> It looks like the UriCollectionReader that you are using never sets a
> document id (type DocumentID) in the cas. However, this shouldn't be a
> problem as each document will
Oops, I misquoted.
"Make it work, make it right, make it fast".
http://wiki.c2.com/?MakeItWorkMakeItRightMakeItFast
Sean
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, June 22, 2017 12:04 PM
To: dev@ctakes.apache.org
Cc: Mille
2:32 PM
To: dev@ctakes.apache.org
Cc: Miller, Timothy
Subject: Re: negation/uncertainty: pipeline runs very slowly [EXTERNAL]
On Thu, Jun 22, 2017 at 9:04 AM Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> There is some suboptimal looping in AssertioncCleartkAnalysisEn
Hi Andrey,
Thank you for the input. Thank you also Hadrian.
With regard to a smaller ctakes, I know that a couple of people (including
yours truly) are currently working on trimming some fat. A few areas have been
targeted, with the old/huge umls dictionary being at the top of the list. It
Hi Sekhar,
With regard to what Chris wrote ... He is correct, you should somehow get the
patient notes into a raw text format. ctakes does not directly handle pdf
files, which contain metadata and instructions in addition to the raw text. If
your ocr tool can save directly to text, please try
-Original Message-
From: Finan, Sean
Sent: Monday, June 26, 2017 1:25 PM
To: 'Hari, Sekhar'
Subject: RE: Visit segregation and extraction [EXTERNAL]
Hi Sekhar,
I don't know of any open source straight convertors. Perhaps somebody on the
devlist does? Does anybody
Hi Tanmay,
Good question. The short answer to
>Does this AE contain annotator to annotate Lab data?
Is "no".
> can someone suggest any different annotator that could identify lab values.
Kean Kaufmann was kind enough to contribute an annotator that creates
labmentions. A great description plu
Hi all,
> I would like to have (and work on it) much leaner distribution
One bigfoot is the clearparser_models.jar in ctakes-dependency-parser-res. As
far as I know this is not used by default or in any checked-in non-default
configuration. As it is 1/4 GB, I would like to move it to its own m
plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=yrWhlRsdzUvgRqXN81TQaszcXtCx5Ehe5cymnXHSNwU&s=jodby0LDvZ4fJmeVjXK_2-4zhZpvKCu9HseL25pjgQ0&e=
On 06/27/2017 07:36 PM, Hadrian Zbarcea wrote:
> Speaking of lvg. Does anybody know where the source code for
> lvgdist-2016.0.jar is?
>
Hi Andrew,
Can you xWin (or other) to the server to launch gui applications?
If so, try the dictionary creator gui:
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
Sean
-Original Message-
From: Andrew Phillips [mailto:aphilli...@luc.edu]
Sent: Wednesday, Jun
man may imagine things that are false, but he can only understand things
that are true, for if the things be false, the apprehension of them is not
understanding." - Isaac Newton
On 28 June 2017 at 12:35, Finan, Sean
wrote:
> Hi Andrew,
>
> Can you xWin (or other) to the serve
files have
hundreds of words) and the slowdown was barely noticeable. When running the
same pipeline on the MIMIC files, the slowdown becomes very noticeable.
Dima
> On Jun 5, 2017, at 10:42, Finan, Sean
> wrote:
>
> Hi Dima,
>
> It looks like the UriCollectionReader that y
to process 300 files from the THYME corpus (where the files have
> hundreds of words) and the slowdown was barely noticeable. When running the
> same pipeline on the MIMIC files, the slowdown becomes very noticeable.
>
>
> Dima
>
>
>
>> On Jun 5, 2017, at 10:42
Hi Raga,
The topic of grabbing data from a db has come up several times within the last
six months or so. There are some classes in ctakes-core cr/ that deal with
databases, but they are not documented and do require configuration for
site-specific schema.
Is anybody out there familiar with t
s for your help.
Andrew
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 28 June 2017 at 19:31, Finan, Sean
wrote:
> Hi Andrew,
>
> You will need to download the umls data from the nlm. Go to their
> website
> https://urldefense.pro
Hi Tim,
I don't know anything about the history, but the constants in PersonTitleFSM
are:
mr
ms
mrs
dr
The execute(..) method iterates through all four.
Sean
p.s. We need to be a little more careful with javadocs (jd) ...
The jd for getTitleMachine() appears to be only partially true:
Perhaps for clarity I should have started with:
ContextDependentTokenizerAnnotator is the only class in ctakes that creates
PersonTitleAnnotation using PersonTitleToken.
ContextDependentTokenizerAnnotator uses PersonTitleFSM to create those tokens.
Sean
-Original Message-
From: Mille
Hi Justin, Kean,
Kean: cheers for some great answers!
Justin:
>> cTakes did not identify any words in any of these sentences:
>> "The patient fell."
>> "The patient fell again after using the restroom."
>> "The patient has not fallen since the afternoon."
My immediate thought is that Kean's asse
Hi Justin,
> To accomplish this I'm using a modified version of the FastPipeline.
>And in the sno_rx_2016ab.xml, instead of DefaultTermConsumer, I'm using the
>PrecisionTermConsumer.
This is the correct approach for your stated goal.
> cTakes picks up "peripheral arterial disease" but it also p
Hi Kean,
> Has anybody done this? I've glanced at the cTAKES wiki, but the install
> instructions don't seem to address this level of customization;
Ctakes basically uses lvg as a 3rd party "black box". So you probably won't
find any in-depth lvg discussion or answers in the ctakes documentat
Hi Sam,
I cannot see the image. It may have been removed by a server.
The url for the 4.0 release:
https://svn.apache.org/repos/asf/ctakes/branches/ctakes-4.0.0/
The url for trunk:
https://svn.apache.org/repos/asf/ctakes/trunk/
I don’t know what your version of Eclipse needs to check out a rep
Subject: Re: Cannot Download CTakes on Eclipse [EXTERNAL]
Sean,
Here is the image. Again, my problem is that whenever I try to input the trunk
url into the SCM URL box, it displays this error message:
On Fri, Jul 14, 2017 at 9:30 PM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
Subversion connector from the plug-in
connectors update site.
If connectors already installed then you can change the selected one at:
Window->Preferences->Team->SVN->SVN Connector.
On Sat, Jul 15, 2017 at 5:53 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
&g
Hi A.S.,
If you are interested in showing medical terms discovered in text to
non-nlpers, you could try adding the html writer to your pipeline.
ctakes-core org/apache/ctakes/core/cc/pretty/html/HtmlTextWriter.java
It creates an html file that displays the document text marked with green, r
ml.HtmlTextWriter OutputDirectory
Validates fine (yellow button in the pipeline creator), but the option to
actually run it (green button) not available yet. I'm guessing I'm missing some
pipe bits?
In fact, does anyone have an example "start to finish" .
also tried running the batch file as administrator but still the same. Do
you have any ideas?
Thanks,
Arron.
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: 17 July 2017 17:32
To: dev@ctakes.apache.org
Subject: RE: Filter CVD output? [EX
ed
annotations / dictionary items would be great. i.e. drug name get picked up,
but the units / dose etc would also be really good.
All the best,
Arron.
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: 17 July 2017 15:01
To: dev@ctakes.apache.org
Subj
Hi Abilash,
I don't know of any module that already does this ... but if anybody does have
even the beginnings of one I am sure a lot of people would be interested!
I think that a possible quick start could be to use a sectionizer to divide up
the note, then focus upon some sections (reason for
Hi Shyam,
Is there any chance that you missed the –Xmx3G in your servlet launch?
Sean
From: Ks Sunder [mailto:shyam...@gmail.com]
Sent: Friday, August 04, 2017 3:57 AM
To: dev@ctakes.apache.org
Cc: Finan, Sean
Subject: Reg : cTakes ubuntu Operating system issue... [EXTERNAL]
Hi ,
I deployed
Hi Chris,
No, you are not missing anything.
The example on the wiki was concocted to display what ctakes should do. There
are a few different negation modules (and you can write your own). Using the
Assertion module you will not get negated lesions. Using the ContextAnnotator
you will.
I d
( ClinicalPipelineFactory.getDefaultPipeline( ) );
builder.add( ContextAnnotator.createAnnotatorDescription( ) );
return builder;
}
}
-Chris
On Tue, Aug 8, 2017 at 2:36 PM, Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> Hi Chris,
>
> No, you are not missing anything.
>
> The example on the
Hi Sekhar,
You can add the RegexSectionizer in ctakes-core to your pipeline, then code
such as:
final Collection sections = JCasUtil.select( jCas, Segment.class
);
for ( Segment section : sections ) {
System.out.println( section.getId() );
System.out.println( sect
ctionName.equals( "Physical Examination" ) )
.foreach( System.out::println );
}
Or something like that.
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, August 21, 2017 2:37 PM
To: dev@ctakes.apache.org
Cc: u...@ctakes.apache.org
Subject:
Hi Abilash,
The DictionaryCreator2 in sandbox is defunct.
To make a custom dictionary, the dictionary gui in 4.0 (or trunk) should be
used. It does not take the ctakes dictionaries found on sourceforge. It
starts directly with an installation of UMLS .rrf files.
https://www.nlm.nih.gov/re
Hi Matthew,
One of the updates that happened with ctakes 4.0 was the long-awaited update to
use the current version of hypersql (hsqldb) used by components such as the
dictionary lookup modules. That update made all of the older dictionary
databases obsolete as their format does not match that
MLS user/pass to the cTAKES Docker solution and letting it take care of the
rest. I suppose I'm going to have to download and configure a custom UMLS
dataset installation. This is correct?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Aug 27, 2017 at 9:05 PM Finan, Sean < sean
Hi Mathew,
When you ran the dictionary creator gui, did you select those 4 vocabularies as
both sources and targets? If you did so then the dictionary should contain
tables named after them and the DefaultJCasTermAnnotator (must create better
named façade ...) will add those codes to each disc
Hi Dima,
It looks like the temporal demo is up and running.
Sean
From: Dligach, Dmitriy
Sent: Friday, September 1, 2017 4:16 PM
To: cTAKES Developer list
Subject: ctakes demo down [EXTERNAL]
I wanted to demo cTAKES to a physician collaborator and discove
CP6r0bcpKGd4f7d4gTao&m=F20tz1cW9Wqud5ll0V25ppsozN2qquaEtQdi0CPNQTI&s=tejNK_ZDKtCiUgwQpZ6JE4uukYcPEBPPH5tfkcNjjz8&e=
-- James
On Fri, Sep 1, 2017 at 5:50 PM, Finan, Sean wrote:
Hi Dima,
>
> It looks like the temporal demo is up and running.
>
> Sean
>
but I'm pretty sure I am on the right
track! Please let me know if I've missed anything.
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Aug 28, 2017 at 8:48 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Matthew,
>
> The dictionary creator uses a 'ful
Hi Andrey,
So you did set up a travis test for ctakes? Cool.
In my opinion that test should be disabled for automated builds. In addition
to requiring credentials that should not be on a public system, it is basically
a partial integration test that assures that a single workflow runs to
com
ting them and 2) I don't
have the time now to look into a fix.
Steve
On Sun, Sep 3, 2017, 14:16 Finan, Sean
wrote:
> Hi Andrey,
>
> So you did set up a travis test for ctakes? Cool.
>
> In my opinion that test should be disabled for automated builds. In
> addition to
Hi Sourabh,
Are you running the ctakes temporal module?
Sean
-Original Message-
From: Sourabh Mukherjee [mailto:sourabh...@gmail.com]
Sent: Friday, September 08, 2017 4:17 AM
To: Apache cTAKES Dev
Subject: ctakes timelanes [EXTERNAL]
Hi,
I followed the steps mentioned in the link "
https
Hi Gandhi,
The demo pom.xml points to ctakes 4.0, which should be static wrt code. It
hasn't changed in 5 months.
It looks like the temporal models are the same as the 3.2.2 versions and
haven't been updated for 2 years.
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo/s
Hi Alexandru,
I am just curious: what is your goal?
Thanks,
Sean
-Original Message-
From: Alexandru Zbarcea [mailto:zbarce...@gmail.com]
Sent: Thursday, September 07, 2017 6:46 PM
To: Apache cTAKES Dev
Subject: WSDL for isValidUMLSUser service [EXTERNAL]
Does anybody has access to the WS
Thanks Hadrian!
Sean
-Original Message-
From: Hadrian Zbarcea [mailto:hzbar...@gmail.com]
Sent: Sunday, September 10, 2017 8:48 PM
To: dev@ctakes.apache.org; Finan, Sean
Subject: Builds are now clean [was: Travis has one test failed [EXTERNAL]]
Hi all,
I had issues with the tests as
Hi Ghandi,
"plan" is a synonym for C0270724: Infantile Neuroaxonal Dystrophy.
One outcome of using generic dictionaries that can be used across multiple
fields of interest is that a valid term in one field can be misapplied to text
from another.
Unwanted terms can be addressed per item by crea
ng to implement auto learning to eliminate the disease terms
we don't want. Is this fine?
@Sean, regarding custom dictionary creation for MedDRA, do we have to add every
terms manually or do we have a DB script (as in case of Snowmed CT & RxNORM) to
load the terms as in our case we are us
-Sep-2017 6:47 PM, "Finan, Sean"
wrote:
> Hi Sourabh,
> Are you running the ctakes temporal module?
> Sean
> -Original Message-
> From: Sourabh Mukherjee [mailto:sourabh...@gmail.com]
> Sent: Friday, September 08, 2017 4:17 AM
> To: Apache cTAKES Dev
> S
Hi Abilash,
What exactly are you looking for?
Sean
-Original Message-
From: abilash.mat...@cognizant.com [mailto:abilash.mat...@cognizant.com]
Sent: Thursday, September 14, 2017 3:13 AM
To: dev@ctakes.apache.org
Subject: semantic Role mapping [EXTERNAL]
Hi,
Please let me know if ther
-----Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 14, 2017 6:48 PM
To: dev@ctakes.apache.org
Subject: RE: semantic Role mapping [EXTERNAL]
Hi Abilash,
What exactly are you looking for?
Sean
-Original Message-
Fro
java:211)
It would be a great help if somebody helps me here since I am new to both
ctakes and Java.
Thanks in advance for your help.
Regards,
Sourabh
On Wed, Sep 13, 2017 at 9:10 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sourabh,
>
> The timelanes gui di
6GWs9O4icmRi04-a1AvIFuF_NfI1lvDet5WJbY&e=
if you are using piper files or uima xml descriptors you will need to adapt
these.
Tim
________
From: Finan, Sean
Sent: Friday, September 15, 2017 9:03 AM
To: dev@ctakes.apache.org
Subject: RE: ctakes timelanes [EXTER
Hi Gandhi, (Hi Tim, find below the best coref chain I have ever seen),
Unfortunately, it looks like the drug-ner module has not been kept up-to-date.
I just checked the cpe xml files and they contain invalid pointers. Anyway,
you should be able to add the DrugMentionAnnotator by using:
Aggr
is appropriate or there is any other method
available in Ctakes 4 to achieve the same.
Thanks,
Abilash Mathew
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, September 15, 2017 6:12 PM
To: dev@ctakes.apache.org
Subject: RE: semantic Role mapping
Hi Matthew,
Go to the directory that has your dictionary and run "grep -i "type 2 diabetes"
.script"
Do you see the line:
INSERT INTO CUI_TERMS VALUES(11860,2,3,'type 2 diabetes','diabetes')
?
If not, then it wasn't added when your dictionary was created. The dictionary
will only contain term
Hi Gandhi,
> So in this case will be able to see drug attributes in the output XML?
As long as you have the DrugMentionAnnotator in your pipeline you should be
able to find drug attributes in the xml output file.
> we also saw some code changes needs to be done to use drug-ner module. Is it
> s
gator noted that this patient was suffering
worsening fatigue and got tired getting out of his chair"
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 18, 2017 10:02 PM
To: dev@ctakes.apache.org
Subject: RE: Ena
@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
Thanks for the response Sean. Your help is really appreciated.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 20, 2017 6:20 PM
To: dev
/ 02 or 27Aug2002 as in the below example. Please let us know how to
> enhance the system to identify such date patterns.
> E.g " On 20Aug02, the investigator noted that this patient was suffering
> worsening fatigue and got tired getting out of his chair"
>
> Regards,
>
have a requirement to identify the patient names and sex
>
>> available in narrative texts. Please let us know how to achieve the
>
>> same as its not identifying the proper nouns and the relationship with
>>the patient?
>
>> Eg. "This male patient named Tom Ha
,
pharmacology, etc.
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 20, 2017 8:50 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
[SUSPICIOUS]
Hi Gandhi,
I don't have
Hi Abilash,
Superb question. Unfortunately, I think that components are created and
modified faster than they are documented. Being open source, there are authors
of documentation who are not authors of the code - which is fantastic! Being
the lazy developer that I am I wish that there was
any simple annotator that you would suggest us to
look into to get better understanding on annotators for us to proceed further.
Thanks in advance.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 21, 2017 7:59 AM
Hi Alexz,
If I understand your question and comment ...
Those models are not 3rd party jars. They are part of ctakes, distributed with
and for it. They are machine learning models that have been developed using
expertly-written gold annotations on clinical documents. They are updated with
ve
Thank you both!
Sean
-Original Message-
From: Alexandru Zbarcea [mailto:al...@apache.org]
Sent: Monday, September 25, 2017 10:05 AM
To: dev@ctakes.apache.org
Subject: Re: bitwise operator vs logical operator [EXTERNAL]
Thank you Tim,
Alex
On Sep 25, 2017 09:43, "Miller, Timothy" <
tim
Feature
org.apache.ctakes.typesystem.type.textsem.Predicate:relations is marked
multipleReferencesAllowed=false, but it has multiple references. These will be
serialized in duplicate. Message count indicates messages skipped to avoid
potential flooding. Set FINE logging level for stacktrace.
22
Argh. Apparently that was my fault - I have a sandbox scaleout project, but
the change to the main pom is supposed to be in a separate changelist. Somehow
I managed to check it in. That is what I get for having a dozen unfinished
side projects ...
I have reverted the main pom back to its pre
TAKES-2D457&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bcFo8E6kkJXWkeVjt7Mv_BWS0fLZSfxDBgR2hKwSyiw&s=iMftCmA3LSWDaKBTUC81d-9M9OIj4VNdyDh2T_26rUs&e=
On Wed, Sep 27, 2017 at 4:52 PM, Finan, Sean <
sean.fi
an, we have also made some code changes in
MeasurementFSM.java to identify certain measurements like '20 mg/m2' which was
not identified out of the box. Should we send the code changes to you so that
you can consider the same to be productized ? Please advise."
Regards,
Gandhi
er.
Thank you,
Alex Zbarcea
On Thu, Sep 28, 2017 at 9:36 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alex,
>
> Your 475 shouldn't break anything in my current setup.
>
> I like your 475 update ... I think that it is just a matter of time
> befo
Hi Matthew,
It is possible to both
1. Edit the primary hsql dictionary, and
2. Add secondary dictionaries to your ctakes pipeline.
You can find information on the web related to editing an hsql database. There
is some random info on the web regarding the creation and use of bsv files for
dicti
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 28, 2017 8:21 PM
To: dev@ctakes.apache.org
Cc: Miller, Timothy
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
[SUSPICIOUS]
Hi Gandhi,
I don't recall you
Hi Jeff,
I have no problem running on your example "DIDANOSINE, 250MG (PO Capsule
Delayed Release)" or any other text.
I don't know how you are running ctakes through
com.clientproject.ctakes.processors.CommandLineProcessor, so I don't know how
closely the standard pipeline approximates yours
UQ&s=Tihsi1dyNHsqsYbwyClGANfqk2Ov2nfQL2YuIV1L0CI&e= for
> measurement FSM changes and attached the modified file changes. Could
> someone have a look and know your thoughts please?
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan,
wise, I'll get it figured
out eventually. I suspect it's possibly because we never did anything with the
SNOMEDCT_US in the prior version.
On Mon, Oct 2, 2017 at 10:47 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Jeff,
>
> I have no problem running on
t: Tuesday, October 03, 2017 8:52 AM
To: dev@ctakes.apache.org
Subject: Re: NPE after upgrade in DefaultJCASTermAnnotator [EXTERNAL]
I updated our pom to use the same hsqldb version as what I saw in the ctakes
lib folder. The data coming in is from a SQL Server database.
On Tue, Oct 3, 2017 at
e, Oct 3, 2017 at 9:07 AM, Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> Ok, let me see if I understand your current setup:
>
> Ctakes 4.0 fast lookup,
> Dictionary configuration file points to an sql server, Sql server uses
> cui_terms (cui, rword, rindex, tcoun
rscript with number-1 too. With the changes in
Input, the co-reference between all the entities should still be preserved
right? Do we have any more info or doc on this co-reference module to
understand its complexity better?
Regards,
Gandhi
-----Original Message-
Fr
amp;e= for
> measurement FSM changes and attached the modified file changes. Could
> someone have a look and know your thoughts please?
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sen
amp;d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=L05lBYR93doAn-IsnZW2HMb7Ev0Y_82_0CpE3FYzpEA&s=GohiPyZbSEWfBjnOtC6x3UNnzv-fOBTnPFaIBUnVjm8&e=
Tim
On Tue, 2017-10-03 at 13:52 +, Finan, Sean wrote:
> >
> > With the changes in Input,
aragraph we sent earlier can be in the example notes provided the protocol
number is masked/modified.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, October 03, 2017 7:27 PM
To: dev@ctakes.apache.org
Subject: RE: E
GANfqk2Ov2nfQL2YuIV1L0CI&e= for
> measurement FSM changes and attached the modified file changes. Could
> someone have a look and know your thoughts please?
>
> Regards,
> Gandhi
>
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@children
t sure if I'll get a chance
to look more this week. if you end up picking up looking at it Sean, at
least you know what I've done.
-- James
On Tue, Oct 3, 2017 at 12:25 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Gandhi,
>
> Ctakes is a purely volun
Hi Alex,
I think that it goes against the umls license to have credentials available to
the public. That might be what you were saying in a previous email:
> Exporting the ctakes_umlsuser, ctakes_umlspw makes the whole build
> succeed. But having some credentials in the Jenkins job (official)
Hi Matthew,
I haven't done anything with Tim's Docker, so I don't know how it is handling
lifetimes. As I understand it uima-as runs the pipelines as services, and the
reader is a client. If one reader completes and later on you want to run more
documents, you should be able to run a new rea
Hi Matthew,
Could you explain:
> is there a better annotator ..?
You could take a look at the BxvRegexSectionizer in ctakes-core. It is a
little more robust than the CDASegmentAnnotator, but they are both
pattern-based. One immediate advantage is that the BsvRegexSectionizer has a
default l
Can you, as the user running ctakes, do a "touch /output/TestSample1.xml.xmi" ?
-Original Message-
From: Sirisha Pulivarthi [mailto:sirisha_pulivar...@horizonblue.com.INVALID]
Sent: Wednesday, October 11, 2017 11:22 AM
To: dev@ctakes.apache.org
Subject: ctakes clinical default pipeline is
issions.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 11, 2017 9:24 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]
Can you, as the user running ctakes,
Hi Abilash Mathew,
I have only used Tesseract. Unfortunately, no ocr is perfect.
I am by no means an expert on Tesseract, but perhaps I can help to get you
started ...
There are tricks that you can use to get it to work better with medical notes
(besides training on fonts). Possibly the mos
Hi Gandhi,
For 1) Just to be sure, you are running your pipeline using xml descriptor
files?
For 2) Consider using FileLocator.getAsStream(..).
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, October 14, 2017 3:52 AM
To: d
Hi Sirisha,
Matthew Vita made an excellent video that contains some instructions on
creating a custom dictionary for ctakes. The default dictionary contains only
umls cuis, snomed ct and rx_norm codes.
https://www.youtube.com/watch?v=4aOnafv-NQs
You want to create a dictionary containing CPT co
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