Maite,
You already have a thread going with me offline. If you have a question please
ask it on that thread to refrain from spamming the devlist. Until I have a
chance to create decent documentation you are stuck with me.
Sean
From: Maite Meseure Hugue
Hi Samir,
Like Tim, I'm a little bewildered and not sure that I understand your
questions.
If you want to run a collection of files, check the code in
org.apache.ctakes.core.cpe.CmdLineCpeRunner.
If you want to iterate through the cas to find its contents, I'd look at the
code in org.apach
Hi Alex,
This is some pretty odd behavior. Obviously, it is indicating that the
resource type loaded or specified is not the correct class. Specification is
(for the standard UMLS pipeline) in
ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
lines #226 and #289
+1 for pushing forward
I may have been one of the voices commenting on memory bloat, but I agree with
Pei re: improving the new. The more use, the more attention and more
improvement (hopefully). I can't speak of the accuracy old v. new as I haven't
actually comparatively tested them. And th
We could, but GetAsStream does not do as complete a search as locateFile.
GetAsStream would not be able to find the resource that was being used at the
time (deepphe custom bsv). getAsStream can be improved - maybe a jira?
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.
Your IDE should have settings that allow custom warnings. Also check out
findbugs -- http://en.wikipedia.org/wiki/FindBugs
There might be a configurable maven plugin.
It is a process ...
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Tuesday, May 05,
7;dev@ctakes.apache.org'
Subject: RE: build tool suggestion
Sorry, I wasn't clear, when I said "at build time", I meant the Jenkins
automated build.
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, May 06, 2015 9:52 AM
To: dev@ctak
Hi Pedro,
Check the cTakesHsql.xml and make sure that the line matches:
https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
In an older version of cTAKES with an output message as you have:
>>11 May 2015 15:59:47 INFO AbstractJCasTermAnnotator - Default - Loading
>>dictionary into memory. I
Argh. Our email server may have mucked with the url that I pasted:
H t t p s : / / uts - ws . nlm . nih . gov / restful / isValidUMLSUser
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, May 11, 2015 5:38 PM
To: dev@ctakes.apache.org
cTAKES was working fine last week and I did not make any config change since
then.
Does anyone have an idea how to resolve this?
On Mon, May 11, 2015 at 4:40 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Argh. Our email server may have mucked with the url that
ake any config change
since then.
Does anyone have an idea how to resolve this?
On Mon, May 11, 2015 at 4:40 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Argh. Our email server may have mucked with the url that I pasted:
>
> H t t p s : / / uts - w
noreCase("true");
in isValidUMLSUser() should be replaced with
result = line.trim().equalsIgnoreCase("true");
Michal
-Message d'origine-
De : Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Envoyé : May-11-15 5:41 PM
À : dev@ctakes.apache
>From the NLM UMLS group:
-Original Message-
From: Emrick, Steve (NIH/NLM) [E] [mailto:emri...@mail.nih.gov]
Sent: Tuesday, May 12, 2015 11:25 AM
To: Finan, Sean; List UMLSUSERS-L
Subject: Re: isValidUMLSUser
All
This happened as part of an update to Java 8 on the UTS side.
Hi Pedro,
> B). If the user has already downloaded the UMLS isn't that already indicative
> that they had a valid account?
As I understand it (I wasn't around at the time) this per-user licensing with a
jit check was the deal that was worked out with the NLM. I think that
repackaging and redis
Hi Pedro,
I just spoke with Pei, who knows a bit more about the history. Another part of
the "validate at runtime" implementation is that NLM wants to monitor use of
the UMLS.
Sean
-Original Message-
From: Pedro [mailto:teixeir...@gmail.com]
Sent: Thursday, May 14, 2015 9:43 AM
To: d
Hi Pankaj,
I haven't seen this exact error before. I guess that my first steps toward a
possible remedy would be:
- check for existence of
/org/apache/ctakes/dictionary/lookup/umls2011ab/umls.properties
- make sure that it (resources/) is in your classpath
- see if it looks like any of the umls
Hi all,
I’m glad that there continues to be interest in the fast alternative to the
dictionary lookup and I welcome all testing.
GBM actually is Glioblastoma Multiforme – hence the “M”. The WHO name is the
abbreviated “Glioblastoma”, but they are actually not (as far as I can discern)
differ
Very cool. It allows quick reproducible testing. For example:
This is extremely useful!
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Friday, June 19, 2015 11:33 AM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: Apache cTAKES hosted demos an
Hi Maite,
I hope to have a paper out on this soon, so I am keeping things kind of quiet
about it - though one can always look at the database and code to get an idea
of what it means.
For anything else in the module, you can look at the wiki page:
https://cwiki.apache.org/confluence/display/CTAK
Hi Maashu,
TimeLanes is currently a prototype gui under development and there is probably
no information about it on the web. It is in sandbox because it isn't part of
the ctakes release and is missing much needed functionality. For instance, It
should display basic information about the pati
mos. Pei just put it up there, thank you very much, Pei!
--Guergana
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, June 22, 2015 11:36 AM
To: dev@ctakes.apache.org
Subject: RE: TimeLanes
Hi Maashu,
TimeLanes is currently a prototype gui un
(RN)."
In the regular pipeline, the concept array of "gbm" contains the CUI of
"Glioblastoma" only, while in the fast pipeline, the concept array of "GBM"
contains the CUIs of both "Glioblastoma" and "glioblastoma Multiforme".
Best,
Hi Britt,
This did come up briefly wrt NCI custom cuis, but there was no urgency so it
got shoved onto a back burner. I’m glad that you brought it up again as it is
something that I’ve been wanting to enhance.
My thought at the moment is to change CuiCodeUtil (…lookup2.util.) from a
non-insta
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]
Sen
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 [mailto:wdai
=docdailey, ctakes.umlspw= set
CURRENT_DIR=%cd%
replaces my password
"with CHANGEME" is part of the actual error
-Original Message-----
From: "Finan, Sean"
To: "dev@ctakes.apache.org"
Date: Wed, 8 Jul 2015 21:40:25 +
Subject: RE: Authentication
apache.org
Subject: RE: Authentication failure - crossposted
redacted means i edited out my password... set with:
set ctakes.umlsuser=docdailey, ctakes.umlspw= set
CURRENT_DIR=%cd%
replaces my password
"with CHANGEME" is part of the actual error
-Original Message-
Fro
rence 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.com<mailto:britt.fi...@wiredinformatics.com>
On Jul 8, 2015, at 2:54 PM, Finan, Sean
mailto:sean.fi
- Osceola, MO Sent from mobile
> On Jul 8, 2015, at 6:02 PM, Finan, Sean
> wrote:
>
> About the comma:
> What I mean is, it thinks that your username is:
>
> docdailey, ctakes.umlspw=
>
> and that your password is the out-of-box placeholder "CHANGEME"
&
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/ di
http://wiredinformatics.com
britt.fi...@wiredinformatics.com
On Jul 8, 2015, at 7:16 PM, Finan, Sean
mailto: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 right before I went
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 c
;s=LbTzcUINCxbwdk3A7ssDgs9MMavHuXKEOQN35OuBd0E&e=
Jakob
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: den 9 juli 2015 19:54
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor files for
UmlsDictionaryLookupAnnotator
Hi
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 then there is a (possibly)
simple solution. If you are interested in throwing a wider net then I think
that a new module would need to be created; does anybo
ks,
Tom
On Fri, Jul 10, 2015 at 11:54 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu<mailto: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 the
ationMentions here would not be in the
same sentence as the word "ALLERGIES".
Thanks 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
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.com<mailto:britt.fi...@wiredinformatics.com>
On Jul 9, 2015, at 3:44 PM, Finan, Sean
mailto:s
logic though.
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com<mailto:britt.fi...@wiredinformatics.com>
On Jul 10, 2015, at 5:31 PM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
w
Hi Tom,
Just for fun I checked "ctakes-allergy" into sandbox. Great title. While too
simple to be really useful, it might serve as a testing point or example for
future endeavors.
Sean
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Se
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?
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 sandbo
eAggregate();
...
SimplePipeline.runPipeline(reader, aggregateEngine, writer, evaluator);
Best regards,
Jakob
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: den 10 juli 2015 18:29
To: dev@ctakes.apache.org
Subject: RE: Cannot resolve lookup descriptor
Hi Justin,
The UMLS licensing issue has been resolved:
https://issues.apache.org/jira/browse/CTAKES-359
Any version built after May 12th 2015 should have the fix.
Sean
-Original Message-
From: Justin Zhang [mailto:justinzhang...@gmail.com]
Sent: Sunday, July 26, 2015 9:21 AM
To: u...
isCYNYmQCP6r0bcpKGd4f7d4gTao&m=lbEdKoY0da48z2A6Xnehe0DtLHhe9WSu6whMx1DpeS8&s=2Mg1-XF2l5zWbSeV2-H2my6WBXiFuqcHNXpRSy7u-gY&e=
is not valid for user -Dctakes.umlspw=
-Djava.util.logging.config.file=/Logger.properties with CHANGEME
On Mon, Jul 27, 2015 at 8:32 AM, Finan, Sean <
sean.fi...@childre
Hi Justin,
A shot in the dark:
You could create a collection reader that works similarly to
org.apache.ctakes.core.cr.FilesInDirectoryCollectionReader , but instead of
grabbing all of the files in a directory it grabs all the records parsed from a
single .xml and runs a pipeline per record. Ba
data
Thanks Sean for your understanding, and I am in hope now.
Where is the best place to start looking at regarding "create a collection
reader that works similarly to org.apache.ctakes.core.cr.
FilesInDirectoryCollectionReader"?
Justin
On Wed, Aug 5, 2015 at 7:24 PM, Finan, Sean
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 ex
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
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 Upd
ys 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:
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
ETA
-fd ./data/tiny -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,
--Original 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
@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
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
te
Yes, it finds "SNOMEDCT_US".
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF
Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 8:14 PM
To: dev@ctakes.apache.org; dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Sean,
I added that and still had the same issue.
Thanks,
Brandon
_____
From: Finan, Sean
mail
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
the dictionarytool project or should the inserts be put into the .script file
by default on the program execution?
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 9:59 PM
To: dev@ctakes.apache.org
Subject: RE
s would 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
db:file:path/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.ha
kes.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 locally.
> >
> >
> >
> > On Wed, Sep 16, 2015 at 1:3
onary 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...@childrens.harvard.edu]
Sent: Thursday, September 17, 2015 1:18 PM
T
Does your packaging include the ctakes-dictionary-lookup-fast-res ? In our
normal distribution that -res is unpacked into the resources/ directory. If
you are bypassing that then you'll need to make a -res.jar for lib/ - or
follow the rest of your strategy accordingly.
-Original Message
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
Hi Chris,
There are a few ways to do this:
1. Create an additional dictionary with the terms of interest and add it as a
source
2. Create a new dictionary hsqldb that contains everything, old and new
3. Add to the existing hsqldb dictionary
The best approach for you would probably depend upon
GZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=bLdoNVceobXShsqfGFdPDKSiq2WNSUbGDHdvmrfMj10&s=CXhGiFUuPnSekOe4GnsuxPOgYHbNp-hAnOD8jmB-lgc&e=
++
Adjunct Associate Professor, Computer Science Department
University of Southern Californi
+++++++
-Original Message-
From: "Finan, Sean"
Reply-To: "dev@ctakes.apache.org"
Date: Tuesday, October 6, 2015 at 2:04 PM
To: "dev@ctakes.apache.org"
Subject: RE: How to update cTAKES so that new top leve
kj31RvxkVUdnSPQbvWY&s=KFniTLNNLNcMoSDkc497MlyGPi4XiN34ZYZkSqvq8C8&e=
++
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++++++
-Original M
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 neg
tment. 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
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 actual
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" wh
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 1
-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 chan
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: Monday
set
environment variables or muck with the java command line.
> On Oct 26, 2015, at 1:18 PM, Finan, Sean
> wrote:
>
> 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
&g
e pain" 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 somewh
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
d4f7d4gTao&m=1RTSCop2kmDAXve36EPdNJo6avl2B2SPpQcxCZZdeFw&s=2TRn9S89nvbp0TDN_LC1xTglF3VWlqnkgV5KdURu4KM&e=
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
T
trunk' with this fix and run it on the examples from the
Description. It no longer finds the incorrect annotations mentioned in the
Description. I closed the JIRA entry. Thanks for the quick fix.
Regards,
Tomasz
____
From: Finan, Sea
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 Tomasz,
I don't know that anybody has done this. However, you could try running a
pipeline with items in ctakes-core:
XmiCollectionReaderCtakes to read your existing cas xmi files in directory
-- custom refiner AE below -- to remove unwanted umls annotations
XmiWriterCasConsumerCtakes
Hi Arron,
The stack trace is a bit of a bear (our fault), but it has the line:
Caused by: java.sql.SQLException: No Hsql DB exists at Url
Your bash output is a little easier to read (thanks!), and it has:
19 Nov 2015 21:43:59 ERROR FileLocator - Could not find
resources/org/apache/ctakes/dictio
is a registered charity. No. 1138342 | Mae Prifysgol
Abertawe yn elusen gofrestredig. Rhif. 1138342
On 19/11/15 22:08, Finan, Sean wrote:
> Dictionary UmlsHsqlRareWord
AS 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]
Sent: Thursday,
Thanks. It is like that in my sandbox. It is annoying juggling local and
remote versions of trunk pom ...
Checking in ...
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Tuesday, November 24, 2015 3:26 PM
To: dev@ctakes.apache.org
Subject: Re: svn commit: r1716235
Hi Alaa,
The -shortest- answer is that you'll need to run the dictionary creation tool.
There are instructions in older devlist threads. By default the dictionary
creation tool does add icd9 and icd10 tables to the dictionary. The problem is
that in Umls 2011AB those codes weren't very well
S release (as well as a custom
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 -sh
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'll need to run the dictionary
> creation tool. There are instructions in older devlist threa
y not have time to try this out for a while yet, but 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
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 t
ange 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: RE: ctakes with icd10; 2015 versions available on sourceforge!
I'd be interested in contributing to making the dictionary tool more user
friendly with a GUI.
Thanks,
Brandon
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, December 08, 2015
appropriately.
>> Anyone who is interested 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.
>> wrote:
>> > I'd be interested in contributing to making
>
> I prefer 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
>
> wrote:
>
>> Thank, but what I endup with is
>> wrong ?
>> On Dec 10, 20
;, "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 i
icd10; 2015 versions available on sourceforge!
I am really thankful.
I believe the issue is in herestatic public void writeCuiCodes( final
String termFilePath,
final Map>> cuiCodes ) {
final List codeSources = Arrays.asList( "ICD
: 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.
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