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 subcla
oting 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 hav
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
> 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 edit
> your
> > xml con
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 help
, 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,
>
>
5JM7mdWjj7wU4Ejfh57A3_jYV0mleqxWmI&s=Nzk8VL74dHhJePx-r_-TOiIb5iwhEVdfbqUuCN7RTaE&e=
On Tue, Feb 14, 2017 at 12:12 PM, David Kincaid
wrote:
> Trello board seems like a good enough idea. I'm willing to help out
> with some testing too.
>
> - Dave
>
> On Tue, Feb 14,
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
1. Sign in
2. Type your medical words in the "term"
The dictionary gui doesn't walk the ontology. There are umls tables that list
relations, wherein things like "isa" (is a) relations may satisfy a hypernym
requirement. If you have the umls rrf files look at mrrel.rrf. The structure
is basically concept1|..| concept2|..|relationtype|.. See s
it for coreference.
Tim
________
From: Finan, Sean
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
relati
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 y
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
ExecutorSe
AM
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 us
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 inc
Hi Andrey,
I gave up on the CDA Sectionizer and created the RegexSectionizer in core. It
is incredibly simple - it just takes in a list of regexes that fit section
headers - and footers if they exist. If you can create a regex that fits most
situations, like a blank line and some short all-c
Virge! Thanks James!
Sean
-Original Message-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Wednesday, March 01, 2017 1:22 PM
To: dev@ctakes.apache.org
Subject: wiki wishlist
In an earlier post I mentioned I was interested in moving away from Confluence
for the cTAKES wiki,
Hi Kean,
You are correct - I moved the collections from the dictionary module to core.
It makes more sense to have them there so that other modules can use them. One
thing that you can try: copy the 3.2.3 core.util.collection package into 3.2.2
core.util.collection.
You can do this easily wi
Hi Martijn,
Since you say that you've created your own dictionary I will assume that you
used the gui in sandbox to do so. If that isn't the case then let me know.
The any dictionary created using the default settings on the gui does have
snomedct and rxnorm codes in addition to the cuis. How
the path for
that class is?
- Martijn
On 07/03/2017, 14:24, "Finan, Sean" wrote:
Hi Martijn,
Since you say that you've created your own dictionary I will assume that
you used the gui in sandbox to do so. If that isn't the case then let me know.
cui: "C1281583"
tui: "T023"
preferredText: "Entire hand"
As you can see, the code is . The concept is present in the UMLS subset
and there is also a SNOMED CT code listed there:
Entire hand [A3421866/SNOMEDCT_US/PT] CUI:C1281583 SCUI:302539009
Am I doing som
ingle item out of that array.
The .xml file lists the snomedct_us table, but the database is empty. I’m sure
that I selected SNOMEDCT_US in the dictionarygui tool. Do you have any idea why
the database could be empty?
Thanks.
- Martijn
On 10/03/2017, 10:33, "Finan, Sean" wr
secondary tables
for the sources I selected, including SNOMEDCT_US.
On Tue, Mar 14, 2017 at 12:18 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Martijn,
> That is very strange. I don't know why the database would have an
> empty table. It is acting like snomed
I selected, including SNOMEDCT_US.
On Tue, Mar 14, 2017 at 12:18 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Martijn,
> That is very strange. I don't know why the database would have an empty
> table. It is acting like snomed codes
rently, my database browser created a new database file instead of opening
the dictionary file (sorry for that!). When I open the correct file, it shows
the SNOMEDCT_US table.
Unfortunately, that doesn’t explain why cTAKES won’t return SNOMED concepts…
On 14/03/2017, 09:44, "Finan, Sean"
DefaultTermConsumer
On 14/03/2017, 09:58, "Finan, Sean" wrote:
You are pointing to your "DictionaryDescriptor" parameter to your custom
.xml configuration file?
-Original Message-
From: Martijn
ot;custom2"
code:
oid: "null#custom2"
oui:
score: 0.0
disambiguated: false
cui: "C0010200"
tui: "T184"
preferredText: "Coughing"
On 14/03/2017, 10:24, "Finan, Sean" wrote:
How are you creating your pipeline? Do
ull#custom2"
oui:
score: 0.0
disambiguated: false
cui: "C0010200"
tui: "T184"
preferredText: "Coughing"
On 14/03/2017, 10:24, "Finan, Sean" wrote:
How are you creating your pipeline? Do you run the command line script,
run wi
Hi Leander. I think that you would be better off using the dictionary gui. It
is also in sandbox, and though it was originally a wrapper interface for the
cli tool, it has since been the more active project with new features and bug
fixes.
-Original Message-
From: Leander Melms [mailt
Hi Yiming,
You can try using the lines:
Builder.add(
AnalysisEngineFactory.createEngineDescription(
SubjectAttributeAnalysisEngine.class ) );
Builder.add(
AnalysisEngineFactory.createEngineDescription(
GenericAttributeAnalysisEngine.class ) );
Sean
-Original Message--
ean,
>>
>> Thank you for the fast reply! I imported the dictionary gui into eclipse (as
>> standalone), added the lib folder to the build path and tried to compile
>> with Java 8. Eclipse complained about ~ 200 errors.
>>
>> What am I missing here?
>&
ou make changes, please make them to the trunk version. Thanks.
On Thu, Mar 16, 2017 at 5:12 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Leander,
>
> I thought that I was saving people problems by preselecting English as
> the default ... But you are the
want to choose a different name than ctakes-gui for the
module
On Fri, Mar 17, 2017 at 11:48 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi James,
> I actually do have an expanded version that I was going to check in
> this weekend. I will back out your che
Hi Leander,
There is no single correct way to do this, but a couple of similar classes
exist. Well, one sat in my sandbox for two years until about 5 seconds ago as
I only just checked it in. Anyway, take a look at two classes in ctakes-core
org.apache.ctakes.core
They are TextSpanWriter and
AM9m6E1ypWVaT2hcM&s=Isgii7k_fUy_qLsyqEdh15wKLAnFT6_KeE7zN1dE73Q&e=
>) did this as well.
Thank you
Leander
> On 17 Mar 2017, at 18:33, Finan, Sean
> wrote:
>
> Hi Leander,
>
> There is no single correct way to do this, but a couple of similar
> classes exist.
17 3:05 PM
To: dev@ctakes.apache.org
Subject: Re: Evaluate cTAKES perfomance
Thanks! I'll have a look at it and will try to give something back to the
community!
Leander
> On 17 Mar 2017, at 19:42, Finan, Sean
> wrote:
>
> Ah - you meant best way to test. Sorry, I misread your i
Hi Sekhar,
Short answer: yes. Longer answer: You need to create a custom dictionary and
then set ctakes to use it. You also need to make sure that your output is
providing the icd, loinc, etc. codes in addition to the standard umls cuis.
Our ctakes 4.0 is scheduled to be release in April, and
Hi Lani,
It will remain part of the ytex package. There is some effort being made
toward getting new wsd into ctakes, but it will not be introduced for some
time.
If anybody out there has something that they would like to contribute to
ctakes, please do!
Sean
-Original Message-
Fr
Kean Kaufmann [mailto:k...@recordsone.com]
Sent: Tuesday, March 28, 2017 11:34 AM
To: dev@ctakes.apache.org
Subject: Labs annotator?
On Tue, Mar 28, 2017 at 11:23 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
>
> If anybody out there has something that they would like to
SNOMEDCT? I have downloaded the mapping from
NLM for ICD9CM to SNOMEDCT, ICD10CM to SNOMEDCT as well as ICD10PCS to SNOMEDCT.
Thanks,
Sekhar H.
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: 28 March 2017 18:53
To: dev@ctakes.apache.org
Subject: RE
: Re: SenseDisambiguatorAnnotator in ctakes 4.0?
Hi Sean,
thanks for your reply. I'll try to make the annotator running and see if I can
do more.
Another question regarding ctakes 4.0, will it use the first word or rare word
algorithm?
best,
Lani
On 28.03.2017 17:23, Finan, Sean wrote:
nnotate
* TUIs indicating labs - I use T059, T060 and T121
* CUIs too general to be useful, e.g. C1443182, "Calculated (procedure)"
* Whitelist of words allowed as lab values
* Maximum number of newlines permitted between lab and value (0 = must be on
same line)
I'd need to check i
those from YTEX?
best,
Lani
On 29.03.2017 15:23, Finan, Sean wrote:
> Hi Lani,
>
> The rare word lookup will be the default. The default redistributable
> dictionary will be umls snomed and rxnorm 2016ab.
>
> Sean
>
> -Original Message-
> From: Lani
be really useful. If you would like make a contribution,
> could you please open a Jira and attach the patch or code? When you
> submit a patch via jira/attachment, it has legal verberage about
> donating the code, etc.
>
> --Pei
>
>
> On Wed, Mar 29, 2017 at 9:30 AM, Finan,
s.
I don't know how many times I've had to write conversion routines to do this in
Java, C#, and Ruby... Painful.
Peter
On 3/30/17, 7:05 PM, "Finan, Sean"
wrote:
>Hi Kean,
>
>>org.apache.ctakes.typesystem.type.textsem.LabMention,
>whose labValue is a Resu
ance. What do you think?
>
> Btw could you let me know when enough of the new system is stable
> enough that I should upgrade to it? I'm still back at 3.2.2
>
> - Peter
>
> On 3/31/17, 10:02 AM, "Finan, Sean"
> wrote:
>
> >Hi Peter,
> >
>
Challenging all ytex gurus and officianados ...
One of the main goals for ctakes 4.0 is to get the dictionary databases
upgraded from hsqldb 1.8 to the current 2.3.4.
We have lvg and the fast dictionary lookup straightened out, but we are having
issues with the ytex dictionary. Can anybody out
t; 31 Mar 2017 11:21:08 INFO ENGINE - dataFileCache commit start
> 31 Mar 2017 11:21:08 INFO ENGINE - dataFileCache commit end
> 31 Mar 2017 11:21:08 INFO ENGINE - Database closed
>
> On Fri, Mar 31, 2017 at 11:16 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
&
Hi all,
The code in both apache ctakes trunk and ctakes-resources sourceforge trunk
should be ready to be tagged for a 4.0 release candidate.
Pei, if I remember correctly you wanted to make the tags personally. If that
is still the case then please do.
I implore everybody on this list: Once t
CP6r0bcpKGd4f7d4gTao&m=NHcZww6F_YY4R700a23kknbTpsMYfmlwiNkske5nUQo&s=KmMrxLcMYszPFaxmyBHdr4BjC-kmloJFVQrC3rr74FM&e=
Ph: 832.726.2322
Think Semantics. Tame Silos.
On Thu, Apr 6, 2017 at 12:53 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi all,
>
> The code in both apache ctake
For what it is worth, I don't think that reversion is the best course of
action. As the apache doc that you linked states specifically "for release",
not "for every package build" ... The correct way to handle this is by adding
a releaseProfile.
http://maven.apache.org/maven-release/maven-r
r 4.0 is released. the build process will be
fresh in people's minds and we can set it up and include it in the cTAKES
release manager documentation so it is completely ready for 4.1.
On Mon, Apr 10, 2017 at 12:32 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> For
t of NOT distributing source by default is not appropriate
for any open source project. Sure, there are many ways to work around it, but
I do not see it as a technical issue.
On Mon, Apr 10, 2017 at 12:32 PM, Finan, Sean
wrote:
> For what it is worth, I don't think that reversion is the best c
code during package time,
why not just create a special profile for binaryOnly which should be an
exception rather than the norm for an ASF project?
On Mon, Apr 10, 2017 at 4:03 PM, Finan, Sean
wrote:
>> As the apache doc ... states specifically "for release", not "for every
&g
Hi Dima,
Great question. This is part of the change for v.4.0
You will need to pick up the new dictionary (sno_rx_16ab.zip) from sourceforge:
https://sourceforge.net/projects/ctakesresources/files/
and unzip it in your resources/ directory.
Sno_rx_16ab is a new database in hsqldb 2.3.4 format c
Hi Tim,
Excellent question/point.
I think that you are welcome to follow any online instructions. We are aware
that the wiki is far from complete, and one thing that I welcome everybody to
do is become active on documentation.
So, if you find instructions for installation, workflow, etc. plea
Yes indeed. The chip-nlp and upmc Deep Phenome team uses ctakes as a maven
dependency.
If the project uses maven just add ctakes poms as dependencies. For instance,
if you want to add everything necessary for the clinical pipeline:
org.apache.ctakes
ctakes-clinical-pip
‘svn up’ this morning,
dictionary lookup started to work without doing the additional steps Sean
describes below.
Dima
> On Apr 11, 2017, at 11:50, Finan, Sean
> wrote:
>
> Hi Dima,
>
> Great question. This is part of the change for v.4.0
>
> You will
Hi Dima,
Where did you get that class? I don't have UmlsLookupPipeline or the package
org.apache.ctakes.pipelines.
If you want to run from command-line I highly recommend that you use the
PiperFileRunner class in core.pipeline.
To run the clinical pipeline use cli parameters:
-p DefaultFastPi
It is probably worth mentioning
I am revealing ctakes 4.0 (or trunk) functionality. Piper files do not exist
in previous versions.
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, April 14, 2017 12:35 PM
To: dev@ctakes.apache.org
Subject
P6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SSpp0I&e=
(This is the UmlsLookupPipeline class).
It runs fine in Eclipse but fails when I run from command line.
I will look into the solution you are suggesting (thanks!).
Dima
> On Apr 14, 2
> I'd rather not get into the definition of "basic", just like I'd rather not
> discuss the definition of obvious with another mathematician.
--> Lol. My wife can't stand it when I say "obviously".
Fwiw, I think that cutting a new rc sooner rather than later is comparatively
little work compare
It happens to us all. Just the other day my sourceforge repository was several
days behind ... ;^)
-Original Message-
From: James Masanz [mailto:masanz.ja...@gmail.com]
Sent: Saturday, April 15, 2017 12:12 AM
To: dev@ctakes.apache.org
Subject: Re: Release Apache cTAKES 4.0.0 (rc2)
Sor
gt;Pei Chen
> Wired Informatics
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__bit.ly_1pHmTcL&d=
> DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI
> 2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=if2F9Ti4D02juzTUQo
> XtsUPoO
Murali,
You are the man! When everything is done do you want to send out a new copy of
Pei's original vote: email?
Thanks,
Sean
+1 for releasing rc3
I am really happy that testing the rc was taken seriously and I'd like to thank
everybody that took part.
Sean
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Monday, April 17, 2017 11:48 PM
To: dev@ctakes.apache.org
Subject: [VOTE] Release Ap
Thank you James - great explanation and information.
Hi David,
There is a new version of the dictionary creator gui distributed with ctakes
4.0. It is 99% the same as the version in sandbox. One important difference
is that it now produces a database in hsqldb 2.3.4 - compatible with ctakes
4
Keep in mind one very important thing:
You need to be very careful about redistribution of a umls database. Many
years ago ctakes had to get special permission to post a copy on sourceforge.
As you all know, use of that distribution requires a umls username and password
check per-ctakes launc
Hi John,
The dockerized ctakes that we use is very specialized. It builds from the
latest trunk, grabs and unpacks a custom dictionary, copies files to and from a
secure s3 area, uses a custom cas consumer, etc. It sets up an s3 tool, preps
input and output directories, etc. So, I have never
- MESSAGE LOCALIZATION FAILED: Can't
find resource for bundle java.util.PropertyResourceBundle, key No Analysis
Component found for ContextDependentTokenizerAnnotator
Any thoughts?
Best,
Dima
> On Apr 14, 2017, at 11:35, Finan, Sean
> wrote:
>
> Hi Dima,
&g
es and
it would be nice to be able to run them from command line.
So, are there any plans to finally fix this old “URI is not hierarchical”
problem? Do we at least know what’s causing it?
Dima
> On Apr 14, 2017, at 12:14, Finan, Sean
> wrote:
>
> Ok, thanks. For your original que
existing uimaFIT pipelines and
it would be nice to be able to run them from command line.
So, are there any plans to finally fix this old “URI is not hierarchical”
problem? Do we at least know what’s causing it?
Dima
> On Apr 14, 2017, at 12:14, Finan, Sean
> wrote:
>
>
jKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
(it’s the same as the first one, but the dictionary lookup part is removed).
Dima
> On Apr 26, 2017, at 11:37, Finan, Sean
> wrote:
>
> Hi again Dima,
>
> The piper files are not meant to replace
Hi Tom,
A thousand thanks for the testing and problem report. I will (at some point
today) update the documentation based upon your information. I never noticed
that lvg version error. Poor/incomplete testing on my part - we may need to
create an immediate patch for that one.
Sean
p.s. con
Dear ctakers:
Does anybody know why the CVD profile (and CPE) in the clinical-pipeline
pom.xml has an explicit dependency on lvg-dist? It doesn't make sense to me
and I can run through a typical workflow without it.
Thanks,
Sean
-Original Message-
From: Thomas W Loehfelm [mailto:twloe
ory to using a maven dependency several years ago.
When I updated the artifactId and version of lvg for cTAKES 4.0, I didn't
consider whether the explicit reference could be removed from that profile.
On Thu, Apr 27, 2017 at 2:09 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> w
java_org_apache_ctakes_pipelines_UmlsLookupPipeline.java&d=DwIGaQ&c=
> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiV
kup) runs fine at command line. The error only happens when I
> run pipelines containing dictionary lookup.
>
> Dima
>
>
>
> > On Apr 26, 2017, at 13:36, Finan, Sean
> wrote:
> >
> > Hi Dima,
> >
> > Good news: no uri hierarchical error.
> >
nd you had some suggestions which I’m trying now).
Dima
> On Apr 28, 2017, at 11:54, Finan, Sean
> wrote:
>
> Hi Dima,
> I have a question:
>
> Are you running ctakes-misc directly or do you have a master pom (like
> misc_pom.xml) that includes ctakes-misc(-master) a
ens when I run it from command line.
>>
>> I run it using the following maven command:
>>
>> mvn exec:java -Dexec.mainClass="org.apache.c
>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
>> -Dctakes.umlsuser= -Dctakes.umlspw=&g
Hi Dima,
Most likely things are now out-of-sync since we have 4.0.1-SNAPSHOT.
Since it is just a sandbox project I didn't pay it any attention wrt the 4.0
release. It probably needs to be updated.
Anyway, you probably get the idea - instead of just adding
"ctakes-clinical-pipeline" as a depen
Huh, that is a bit odd. That sandbox module worked when I made it. Obviously
something else needs to be changed/fixed.
Ok, sorry for the misdirect, you can stop running down that road. I chatted
with James a little earlier and he was making great progress with the whole lvg
update. We may
eD-kPkdek6YU2P7IPSF8VaY-FeZNqURVlkk&e=
I swapped in 4.0.0 for ctakes.version, removed my .m2 directory, and it
compiled fine.
On Fri, Apr 14, 2017 at 11:04 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Yes indeed. The chip-nlp and upmc Deep Phenome team uses
t; >>
> >>> Hi Sean,
> >>>
> >>> First of all, a huge thank you for taking time to debug this
> >>> issue. I really appreciate your help.
> >>>
> >>> Second, I think my main message somehow got lost in translation
> (sorry, I
>
vRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=dKDOAG-k6QNwD3cIsI31U4zH
> >> k2lGmqXzRjKXI4ySz_s&e= files/ctakes-resources-4.0-bin.zip/download
> >>
> >>
> >> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy
> >> mailto:ddlig...@luc.edu>>
> >>
Hi David,
Thanks. I made jira #442 and checked a fix into trunk. The Synth look and
feel didn't like the table that I had sent it ...
Sean
-Original Message-
From: David Kincaid [mailto:kincaid.d...@gmail.com]
Sent: Sunday, April 30, 2017 6:57 PM
To: dev@ctakes.apache.org
Subject:
SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71AwHMnoopw&s=FYlVTUtO7S8Vj6vFZxnQS2Vgf3rQMYNUQNoCuNjiYRA&e=
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> -Original Message-
> From: Kean Kaufmann [mailto:k...@recordsone.com]
> Sent: Monday
Hi Sean,
Thank you for the heads-up.
Is anybody out there a regular ytex user with confluence edit rights?
Thanks,
Steeltown Sean
-Original Message-
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Monday, May 01, 2017 4:54 PM
To: dev@ctakes.apache.org
Subject: YTE
Hi Andy,
As you can probably see below, our IT adds some lovely obfuscation .. I mean
"protection" to web links in our email, so I am just guessing that the
workflow amounts to "click download". The downloads page is set up to use one
of some dynamically loaded list of available mirrors. It
;>>> trying to handle it as a File, not a stream. :(
> >>>>>
> >>>>> File configFile = new File(dr.getUri());
> >>>>> configFileName = configFile.getPath();
> >>>>>
> >>>>> At first glance, look
Hi Tom,
After you perform a mvn compile there should be a copy of that file in the
resources/ directory under org/apache/ctakes/dictionary/lookup/fast/
Let me know if you don't see it after performing a mvn compile as that would
indicate a bug.
Thanks,
Sean
-Original Message-
From:
install,
even deleting my eclipse installation and starting from scratch.
Tom
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, May 9, 2017 1:19 PM
To: dev@ctakes.apache.org
Subject: RE: Issues changing term consumer
Hi Tom,
After you perf
Hi Erin,
So, just to be clear, you changed line #110 in
TemporalExtractionPipeline_ImplBase, the getFastPipeline() method from:
builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription() );
to:
builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription(
path/to/my/config.xm
Sean
-Original Message-
From: Erin Gustafson [mailto:erin.gustaf...@northwestern.edu]
Sent: Thursday, May 11, 2017 12:59 PM
To: dev@ctakes.apache.org
Subject: RE: Temporal module dictionary
Correct!
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thu
afson [mailto:erin.gustaf...@northwestern.edu]
Sent: Thursday, May 11, 2017 2:04 PM
To: dev@ctakes.apache.org
Subject: Re: Temporal module dictionary
Hi Sean,
The cuis are all within my dictionary.
Erin
From: Finan, Sean
Sent: Thursday, May 11, 2017 12:39 PM
To
Hi Sean,
I am unfamiliar with all things ytex, but a cursory glance at that class makes
me think that it is only meant to write an XMI file.
You can have a look at JdbcWriterTemplate and its parent AbstractJdbcWriter in
ctakes core.cc, which can write to an sql database.
Sean
-Original
From: Mullane, Sean *HS [mailto:sp...@hscmail.mcc.virginia.edu]
Sent: Monday, June 05, 2017 10:06 AM
To: Finan, Sean; dev@ctakes.apache.org
Subject: RE: ctakes 4.0.0 YTEX DBConsumer not populating v_document_cui_sent
Do you know of any example code using JdbcWriterTemplate? I'm loathe to
lto:sha...@trialx.com]
Sent: Monday, May 29, 2017 3:35 AM
To: cTakes developers list; Finan, Sean
Subject: Re: Japanese and portuguese Language support
Also in dictionary builder i have selected mdrjpn and mdrpor dictionaries from
umls. but i did not get any text from these languages in database
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 be assigned a unique id "UnknownDocument"{###} where {###} is a
number incremented per new document with an unknow
Hi Shyam,
Do you see another error message above the SQLException indicating which
username and password were used ?
Sean
From: Ks Sunder [mailto:shyam...@gmail.com]
Sent: Monday, May 22, 2017 5:39 AM
To: dev@ctakes.apache.org; chen...@apache.org; Finan, Sean
Subject: Invalid User for UMLS
Hi Avanish,
For future reference, please provide a snippet of the error when one is thrown
or logged. It can really help others and possibly get you a faster and
possibly more accurate answer. thanks.
The first problem is that SmokerNamedEntityAnnotation is an annotation type and
not an anal
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