Hi Oranit,
While 2011AB is the pre-packaged available version, ctakes can work with any
version of the UMLS. This question has come up before, but I don't believe
that there is a JIRA ticket on it - maybe a ctakes version per umls version, or
every AB version, or ??. There is a tool in
Hi Stuart,
That is strange. Both dictionaries validate the username in the same way, so
if it works for one it should work for the other. I am guessing that this
problem is repeatable, but I have to ask if you've tested the different
dictionaries on different machines or different locations,
Hi Britt,
The dictionary should be using ptb tokenization, but I obviously missed a rule
and separated the . from the following 2 in the dictionary.
I will double-check everything.
Sean
p.s. if you don’t mind my asking, are you looking into all connective tissue
disorders or just Shprintzen?
ng to set
environment variables or muck with the java command line.
> On Oct 26, 2015, at 1:18 PM, Finan, Sean <sean.fi...@childrens.harvard.edu>
> wrote:
>
> You should be able to use ctakes.umlsuser and ctakes.umlspw in the command
> line or as environment variables. If yo
You should be able to use ctakes.umlsuser and ctakes.umlspw in the command line
or as environment variables. If your shell requires, you can replace the dot
with underscore: ctakes_umlsuser ctakes_umlspw
Sean
-Original Message-
From: Peter Szolovits [mailto:p...@mit.edu]
Sent:
n" has 15 rows in the default cTAKES UMLS,
while 24 rows in the 2015 one.
How can I control which subset of synonyms is taken by the dictionarytool per
CUI when the Fast Dictionary is created?
The UMLS metathesaurus itself has (much) more synonyms than 24 for C0231749, so
I image somewher
Hi all,
This is not intended behavior, it is a bug. I will check in a fix soon ...
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Thursday, November 12, 2015 6:53 PM
To: britt fitch; dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
=1RTSCop2kmDAXve36EPdNJo6avl2B2SPpQcxCZZdeFw=2TRn9S89nvbp0TDN_LC1xTglF3VWlqnkgV5KdURu4KM=
It would be great you could check in a fix for it.
Regards,
Tomasz
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Monday, November 16, 2015 10:20 AM
To: dev@ctakes.apache.org
Subject: RE
Sorry, I wrote too quickly. I think that the bin/ contents are meant to be
used only after mvn package and an unpack has been performed. Otherwise, try a
mvn compile with profile runCVD
Sean
-Original Message-
From: Christopher Li [mailto:chri...@augmedix.com]
Sent: Friday, October
Have you tried running from the root? i.e. bash bin/runctakesCVD.sh
-Original Message-
From: Christopher Li [mailto:chri...@augmedix.com]
Sent: Friday, October 16, 2015 3:03 PM
To: dev@ctakes.apache.org
Subject: "Error: Could not find or load main class
org.apache.uima.tools.cvd.CVD"
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, September 21, 2015 10:39 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Hi Brandon,
Sorry for the late reply - I've been out for an extended weekend.
The coding scheme change
GiuUuSTlfo=
++
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++
-Original Message-
From: "Finan,
. sometimes physician writes about
the discussion and sometime the actual surgery. Now I have problem to finalise
if the mentioned procedure/treatment is really happened or just discussed. I
can't just rely on verb in the sentence.
Your help would help me a lot!
On Fri, Oct 9, 2015 at 6:23 PM, Finan
ase might be covered by the "generic" status classifier from the
assertion module? It distinguishes generic mentions of an event from actual
mentions (generic covering both discussions and other things like "she knows
chemotherapy causes side effects" where neither entity is a
4gTao=bLdoNVceobXShsqfGFdPDKSiq2WNSUbGDHdvmrfMj10=CXhGiFUuPnSekOe4GnsuxPOgYHbNp-hAnOD8jmB-lgc=
++
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
+++
Hi Sangram,
Just fyi, users of some email apps (e.g. Outlook) may not be able to reply to a
message with a web address in the title.
Now to your question:
>69 y.o. Caucasian gentleman with a history of prostate cancer s/p open RRP in
>9/2005 for a pT2c, GS3+4 prostate cancer excised with a
Hi,
Is ,
ctakes.umlsp
w=redacted with CHANGEME
something that you wrote to hide your password on this email? If so, that is
fine, it is just a little odd. If not, then can you double-check how your
password is set when you run?
-Original Message-
From: William Dailey
Hi Jakob,
Where those files exist really depends upon how you are trying to run. They
start in src/main/resources/ directories in their respective -res projects.
If you are running from an IDE, make sure that the -res modules have been added
to your project, and that the src/main/resources/
http://wiredinformatics.com
britt.fi...@wiredinformatics.com
On Jul 8, 2015, at 7:16 PM, Finan, Sean
sean.fi...@childrens.harvard.edumailto:sean.fi...@childrens.harvard.edu
wrote:
Hi Britt,
You’ve got it exactly.
I actually started working on this right before a meeting right before I left
work
Message-
From: Finan, Sean sean.fi...@childrens.harvard.edu
To: dev@ctakes.apache.org dev@ctakes.apache.org
Date: Wed, 8 Jul 2015 21:40:25 +
Subject: RE: Authentication failure - crossposted
Hi,
Is ,
ctakes.umlsp
w=redacted with CHANGEME
something that you wrote to hide your password
- Osceola, MO Sent from mobile
On Jul 8, 2015, at 6:02 PM, Finan, Sean sean.fi...@childrens.harvard.edu
wrote:
About the comma:
What I mean is, it thinks that your username is:
docdailey, ctakes.umlspw=password_here
and that your password is the out-of-box placeholder CHANGEME
for splitting
it out into multiple tasks.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.commailto:britt.fi...@wiredinformatics.com
On Jul 8, 2015, at 2:54 PM, Finan, Sean
sean.fi
=docdailey, ctakes.umlspw=password_here set
CURRENT_DIR=%cd%
password_here replaces my password
with CHANGEME is part of the actual error
-Original Message-
From: Finan, Sean sean.fi...@childrens.harvard.edu
To: dev@ctakes.apache.org dev@ctakes.apache.org
Date: Wed, 8 Jul 2015 21:40:25
By the way, in case you are wondering why it does this … the umls database that
we use has roughly half a million cuis. Storing cuis in the various tables as
longs takes up a lot less space than storing them as 8 character strings.
From: britt fitch [mailto:britt.fi...@wiredinformatics.com]
.maven.org_maven2_org.apache.ctakes_ctakes-2Ddictionary-2Dlookup-2Dfast-2Dres_3.2.1_d=BQIFAgc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=Izx33vJrQxf37pZxy4Ha128D0yl2ak1hSbm4Jp9kX5Es=LbTzcUINCxbwdk3A7ssDgs9MMavHuXKEOQN35OuBd0Ee=
Jakob
-Original Message-
From: Finan
?
Thanks,
Tom
On Fri, Jul 10, 2015 at 11:54 AM, Finan, Sean
sean.fi...@childrens.harvard.edumailto:sean.fi...@childrens.harvard.edu
wrote:
Hi Tom,
Are you interested in catching all allergies or just a few specific allergies
for a study? If you are only concerned with a few
Thanks, just finished testing and closed the ticket.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.commailto:britt.fi...@wiredinformatics.com
On Jul 9, 2015, at 3:44 PM, Finan, Sean
sean.fi
logic though.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.commailto:britt.fi...@wiredinformatics.com
On Jul 10, 2015, at 5:31 PM, Finan, Sean
sean.fi...@childrens.harvard.edumailto:sean.fi
again,
Tom
On Fri, Jul 10, 2015 at 2:12 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Dima, Tom,
I was thinking the same as Dima's first solution. Iterate through the
medication events and see any is included in a phrase as mentioned in
Tom's original email. Each phrase
Checked in, please give it a test and close the ticket if it fits your purposes.
From: britt fitch [mailto:britt.fi...@wiredinformatics.com]
Sent: Thursday, July 09, 2015 3:30 PM
To: dev@ctakes.apache.org
Subject: Re: dictionary-look-fast fails to handle alternative CUIs
Linking ticket here for
-atui ./data/tiny/CtakesAnatTuis.txt -tui
./data/tiny/CtakesSnomedTuis.txt -ol \path\to\file\Umls2015.bsv
Any suggestions?
Thanks again,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 3:05 PM
To: dev
Subject: RE: Fast Dictionary Update
Thanks Sean, much appreciated. To clarify the example below would create the
dictionary for use for the rare word approach?
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16
Hi Brandon,
I can send you a jar or commit one pre-built. What goes wrong when you try to
build the tool?
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 1:23 PM
To: 'dev@ctakes.apache.org'
Subject: Fast Dictionary
@ctakes.apache.org
Subject: Re: Fast Dictionary Update
If this can helps, I had to replace 'SNOMEDCT' with 'SNOMEDCT_US' in
CtakesSources.txt.
On Wed, Sep 16, 2015 at 2:33 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> I'm not sure that I understand your question. As I sent it,
can't find it.
I'm not too familiar with Java and building projects/jars so it could be my
ignorance causing the problem.
Thanks,
Brandon
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 1:45 PM
To: dev@ctakes.apache.o
Terms 0
..File Line 880 Terms 0
.File Line 8827152 Terms 0
Writing map of Cuis and Texts to \pathto\Umls2015.bsv
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 4:00
to be running as expected now.
Thank you for all your help and patience, Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 9:35 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Did you add it to data
Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 3:34 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
I'm not sure that I understand your question. As I sent it, the anat, snomed
and rxnorm are not separate runs. The args
Hi Andrew,
I'm not sure if this is what you are looking for, but you can look at the
org.apache.ctakes.typesystem.type.structured.MetaData class, which has a
setPatientID(long) method.
org.apache.ctakes.core.util. SourceMetadataUtil has a getPatientNum(JCas)
method.
I don't know of any good
Can anybody out there think of a reason why we shouldn't upgrade to Java 8?
Please comment on Jira.
https://issues.apache.org/jira/browse/CTAKES-377
Thanks,
Sean
be appreciated.
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 10:40 AM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Correct, Hsql should automatically read the .log file upon first use
/to/ctakes/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/UMLS2015/snorx2015:
17 Sep 2015 12:58:58 INFO JdbcConnectionFactory - Database connected
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent
Hi Yangrui,
Great question. Right now I don't think that anybody has made an engine for
ctakes that will navigate and report using the full umls parent/child (or
other) relation web. I think that such a task might be better left to
post-processing, and perhaps some industrious soul out there
formation on
relationships from cTakes? When running with 2011 UMLS dictionary I'm able to
get relationships for BodyLocationMentions but with the dictionary I created I
am not getting this information. Any advice?
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@c
om: Pei Chen <chen...@apache.org>
> > To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
> > Sent: Wednesday, September 16, 2015 2:00 PM
> > Subject: Re: CTAKES-377 : Upgrade to Java 8
> >
> > +1 upgrading to Java 8; been using it unofficially locall
database), so would be happy to write up the steps as I go through it. That
assumes that I can dig up the instructions in the dev list.
- Dave
On Tue, Dec 8, 2015 at 11:36 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alaa,
>
> The -shortest- answer is that you
Fantastic idea
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Tuesday, December 08, 2015 4:41 PM
To: dev@ctakes.apache.org
Subject: ctakes blog
The recent discussion over dictionary building, and someone pointing out it has
come up several
in c takes to make it work with them.
like how to get icd10 codes ?
I am sorry for being noob, hope soon I will understand the whole thing and be
effective.
Thanks in advance
On Wed, Dec 9, 2015 at 1:12 AM, Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> Hi Dave,
>
t when I do I'd
be happy to write up an easy to follow tutorial for building a custom
dictionary assuming I am able to get it to work.
Has anyone considered making this tool available outside of the source code
itself? Like including it in the main cTAKES release? It seems there is demand
for it
nterested can follow the Jira item. (Even better if
>> contributions were open discussion/open development.) --Pei
>>
>> On Tue, Dec 8, 2015 at 10:36 PM, Geise, Brandon D.
>> <bdge...@geisinger.edu> wrote:
>> > I'd be interested in contributing to making the dictio
fer to learn how to generate my own db because I will need to
> create my own later on, so your help is appreciated.
>
> On Thu, Dec 10, 2015 at 9:13 AM, Alaa al Barari
> <alaa.albar...@gmail.com>
> wrote:
>
>> Thank, but what I endup with is
>> wrong ?
>&
"ICD10PCS", "ICD9CM",
"RXNORM", "SNOMEDCT" );
On Thu, Dec 10, 2015 at 7:02 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alaa,
>
> No worries, it can be pretty confusing.
>
> 1 The tool is a prototype hack. So, it
: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Sunday, December 13, 2015 12:05 AM
To: dev@ctakes.apache.org
Subject: CTAKES DICTIONARY CREATOR GUI !!!
Well, a dictionary creator gui prototype.
I have checked a functioning prototype into ctakes sandbox named dictionary-gui.
Select
rrays.asList( "ICD10PCS", "ICD9CM",
"RXNORM", "SNOMEDCT" );
On Thu, Dec 10, 2015 at 7:02 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alaa,
>
> No worries, it can be pretty confusing.
>
> 1 The tool is a prototype
2 AM
To: dev@ctakes.apache.org
Subject: Re: CTAKES DICTIONARY CREATOR GUI !!!
Hi and happy new year.
why in the data base generator we have exclude list for example in the rxnorm
section we have EXCLUSION_RXNORM = "SY"; ? whats this is about ?
Regards.
On Sun, Dec 13, 2015 at 7:
les, not XMI CAS files. I can use
XCasWriterCasConsumer to write the CAS files, but I cannot find any XCAS
Collection Reader to initially read them in.
Is such a reader available?
Regards,
Tomasz
____
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Se
Hi Pei, thanks for the link to our Jira dashboard. From my 3 second
run-through I would say that there remains a lot of outstanding work slated for
the 3.2.3 release. Below are the Blocker, Critical and Major items. Some may
actually have been or can be quickly resolved, but it looks like we
Hi Jose,
There are a lot of ways to do this, and there are examples laying about. I
think that you basically have a 3 step process:
1) Run "mvn package" on the source to build the latest binary.
2) Write a main(..) class that has something like:
CollectionReader collectionReader =
Hi Tomasz,
Ctakes lookup (both original and fast-) is case insensitive by design. There
have been brief discussions on changing this behavior, but things like
capitalized form entries, list headings, and plain old first word
capitalization have prevented it from being implemented.
One big
Oh - I should mention:
Increasing the minimum required span cause have unwanted false negatives. A
minimum of 5 will get rid of things like "arm" and "foot". You could make your
own AE that changes this by getting rid of only disease/disorder with character
count < 5 . That would probably be
y low, and you can slim down to the
> barest of needs (pipelines and dictionaries) if needed.
> On Jun 20, 2016 11:46, "Finan, Sean"
> <sean.fi...@childrens.harvard.edu>
> wrote:
>
> > Hi Vicky,
> > You can view the current requirements here:
>
. :^)
Sean
From: srinivasa.rao kundeti [mailto:srinivas1...@gmail.com]
Sent: Wednesday, January 27, 2016 11:07 PM
To: dev@ctakes.apache.org; Finan, Sean; pei.c...@childrens.harvard.edu;
srinivasa@philips.com; bruce.tiet...@imatsolutions.com
Subject: I am New to CTakes 3.2.2 : Need Help
Hi Sean/Pie
Has anybody else recently encountered problems unpacking v 3.2.1.1 of
net.sourceforge.ctakesresources.ctakes-resources-lvg2008 ?
Thanks,
Sean
Very cool, thanks Tim
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Tuesday, January 26, 2016 2:59 PM
To: dev@ctakes.apache.org
Subject: umls graph api
I've been working on some code for easy querying of the UMLS relation
graph that I think
Hi Jessica,
You have it correct - LVG will add variants that the dictionary lookup will use
in an attempt to discover terms not explicitly in the dictionary database -
such as the plurals that you saw. However, it does not guarantee "better"
results. The lvg module can add variants that are
Hi Abhilash,
The fastest way to dive into ctakes development might be to look at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.java
It has a few methods that can build slightly different pipelines and a main(..)
that will run some fake text through a pipeline.
After that you can
Hi Tomasz,
Just in case nobody has a better answer: I think that you might need to may a
new array at size n-1 , then copy all ontology concepts that you do want, then
set the annotation's ontology concept array to be the new one.
Sean
-Original Message-
From: Tomasz Oliwa
Hi Brandon,
The dictionary creator gui in sandbox automatically adds selected coding
schemes to the concept factory. Is it not doing what you need?
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, March 02, 2016 12:43 PM
To:
Wednesday, July 13, 2016 3:04 PM
To: dev@ctakes.apache.org
Subject: Re: Help needed with document creation time/date
Got it. Thanks
On 7/13/16, 12:00 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
>DATE_PATTERN.matcher
as a creation time property so that it can be retrieved
later by a client that knows only the serialized CAS?
Peter
On 7/13/16, 11:41 AM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
>Hi Peter,
>
>Our group has used two different approaches, depending upo
such as POS.
Just like Stanford's TokensRegex
- Peter
On 7/13/16, 12:19 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
>Pattern.compile( ".*Principal Date\\D+(\\d+) (\\d+).*", DOTALL );
Hi Erin,
Where did you get that copy of the umls? I have 2016AA and it has the standard
.rrf filenames.
As long as your .aa/.ab files have the standard mrconso.rrf format, you should
be able to rename them to mrconso.rrf.
Sean
https://www.ncbi.nlm.nih.gov/books/NBK9685/
-Original
@ctakes.apache.org
Subject: RE: jcas work with a list of schemas
Thanks. I was hoping for away to fetch only whats needed for performance
enhancement.
On Feb 6, 2017 8:09 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
> Yes. You do not need to use the code directly if
To: dev@ctakes.apache.org
Subject: RE: jcas work with a list of schemas
Thanks sean but internally this fetch data for all schemas then filter the
needed schema right ?
On Feb 6, 2017 7:57 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
> Hi Al
ed 3. This would be much faster.
On Feb 6, 2017 8:21 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
Hi Alaa,
Are you a java developer or do you have a different background? If you are
not a developer, could you please enumerate exactly what you nee
Hi Alaa,
Have a look at the OntologyConceptUtil class in ctakes-core. You can use the
getCodes(..) method to obtain the codes for a scheme.
For all codes of all annotations:
Collection allCodes = OntologyConceptUtil.getCodes( jcas, schemeName );
For all codes of all annotations in a window
Hi all,
I just have a couple of notes to expand upon what Guergana wrote.
Anafora requires a schema for annotation and it requires text files to be in a
certain structure. I just checked in text files for annotation and the schema
that we plan to use in ctakes-examples-res
to see if that particular class is present?
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org; Finan, Sean; kant2...@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml
this bug a few weeks ago.
Thanks,
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org; Finan, Sean; kant2...@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well
if you
don't personally use the CPE, how to you batch process documents?
I would like to just run the AggregatePlaintextFastUMLSProcessor.xml on all
files in a given directory - perhaps with *some* control over the output
filenames.
Thanks,
Arron.
On Fri, 20 Jan, 2017 at 4:38 PM, Finan, Sean
e your poms?
> >
> > I also noticed you are not using the opennlp-uima integration, is
> > that not working for cTAKES? We could try to find a solution which
> > works for you without duplicating our effort.
> >
> > Jörn
> >
> >
> > On Wed, 201
Hi Pei,
I am a little taken back by your statement:
> I do not see an need for BCH to override existing volunteers.
>From what James wrote, I don't get the feeling that he is trying to override
>other RM volunteers or in any way take control of the release. His email
>stated specifically
Hi Jorn,
Great idea! Have you done any testing with the latest release? I think that
ctakes has 3 dependencies on opennlp libraries. We should try to get our
integration with that update (and others) solidified for the upcoming release.
The boston children's hospital nlp team just gained a
Hi Andrey,
You have recently been a great contributor to ctakes , and I really appreciate
that. You have answered devlist questions and your LVG update is a seriously
big deal. Because of this, you are probably very interested in the upcoming
release. You may have read emails that were on
Hi Charlotte,
I honestly don't know if ctakes will break from a guava update. I suspect that
it won't for two main reasons. First, the only code that I've seen in ctakes
using guava just uses calls to their collections framework, as far as I can
remember, just to create collections. That
To: dev@ctakes.apache.org
Subject: Re: jcasPool problem
Thanks Sean, I will try that, whats the difference between cas and jcas ?
On Thu, Feb 16, 2017 at 6:14 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alaa,
>
> I have no idea what is causing your error using c
Hi Tim,
Definitely not a dumb idea. I think that this possibility and others have been
posted: no lvg, single-thread, uima-as, multiple jvms, wrapping the current lvg
annotator in a singleton and then making a new lvg annotator that makes
synchronized calls to that singleton ...
I think that
imes it should return icd9 and
> other times icd10 based on the request. modifying the xml wont do the trick.
>
> On Tue, Feb 14, 2017 at 4:33 PM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Go into resources/org/apache/ctakes/dictionary/lookup/fast/ and
, February 14, 2017 12:12 PM
To: dev@ctakes.apache.org
Subject: Re: UIMA 3.0.0
Trello board seems like a good enough idea. I'm willing to help out with some
testing too.
- Dave
On Tue, Feb 14, 2017 at 11:01 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Dave,
>
>
=Nzk8VL74dHhJePx-r_-TOiIb5iwhEVdfbqUuCN7RTaE=
On Tue, Feb 14, 2017 at 12:12 PM, David Kincaid <kincaid.d...@gmail.com>
wrote:
> Trello board seems like a good enough idea. I'm willing to help out
> with some testing too.
>
> - Dave
>
> On Tue, Feb 14, 2017 at 11:01 AM,
Yes, thanks. I will try to look into this a little later.
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Friday, February 10, 2017 3:45 PM
To: Finan, Sean
Subject: Re: CAS Pool
Are you looking for these lines
11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
org
Hi Dave,
I haven't tried it. I don't even know what major changes there may be ... Does
anybody out there know? It would be great to test this before the upcoming
ctakes release to see if ctakes is fully compatible ...
Man oh man, we have a lot of testing to do before the release ... any
for, if I dont need them at the moment I
dont want them found. suppose I have icd10 and icd9, I want it to not find icd9
when I am looking for 10 and nice versa.
On Tue, Feb 14, 2017 at 4:13 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Alaa,
>
> I have a q
Hi Alaa,
I have a question for you. Do you want ctakes to never find codes from certain
schemes during processing? Or do you want it to find them, but only return
them when you request them explicitly after processing?
> can I override process(final JCas jcas)
That depends. If you are
in the tool? Any thoughts?
Thanks,
Erin
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, February 08, 2017 3:34 PM
To: dev@ctakes.apache.org
Subject: RE: UMLS version in dictionary-gui
Hi Erin,
Where did you get that copy of the umls? I have
custom dictionaries from the GUI (T047 only) run fine but others with
more TUIs don't?
Is there any way to still use the custom dictionary in 3.2.2 by modifying the
configuration file to make it compatible?
-Erin
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu
Hi Alaa,
There is not a need for LVG. It is supposed to generate lexical variants.
https://www.nlm.nih.gov/research/umls/new_users/online_learning/LEX_004.html
Many already exist in the dictionary. In some tests that I did in the past,
using lvg increased recall about 1%. If it is preventing
Hi Alaa,
I have no idea what is causing your error using caspool. Ctakes and uima both
suffer from a lack of descriptive error output.
Here is something that was used a while ago for testing. The trick is that the
cas pool is just used for storage of reusable cas objects. The Java
From: Finan, Sean <sean.fi...@childrens.harvard.edu>
Sent: Wednesday, February 15, 2017 2:23 PM
To: dev@ctakes.apache.org
Subject: RE: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS]
The dictionary gui doesn't walk the ontology. There are umls tables that list
rel
Hi Shyam,
If I understand you correctly, to get synonyms from the umls, go here:
https://utslogin.nlm.nih.gov/cas/login?service=https%3A%2F%2Futs.nlm.nih.gov%3A443%2F%2Fj_spring_cas_security_check%3Bjsessionid%3D73C54CF8B4F00AD1538881044F2F52FE
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