Hi Abhishek,
You have some interesting timing ...
I can give you the xml specifications that you require if you send me the
format of your dictionary.
Since you are new to the current dictionary module setup, I might also have a
simpler solution for you ...
A couple of days ago I checked a new
> 1) Should we populate IdentifiedAnnotation.severity() and bodylocationof()
> Directly in RelationExtractorAnnotator instead of the template filler?
One minor issue might be the fact that multiple relations of the same type
can (and most likely will be) created for a single Identified Anno
> until we have a definite, well-defined need (from a user).
"Rash on arm and leg"
> I don't follow what you mean by your item B) below
[Rash].getLocationRelation() > [Rash : Arm]
[Rash].getLocation() > [Arm]
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
S
what it
was in cTAKES 3.1 and find out if this is a bug in TemplateFillerAnnotator or
something else.
-- James
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, March 21, 2014 12:30 PM
To: dev@ctakes.apache.org
Subject: RE: getSeverity etc. for relation ex
leg" and I get just one location_of
relation.
And again no location_of relations for "rash on arm and leg"
Sean, what was the exact phrase you used with the incubator version? (or was
that a while ago and lost)
-----Original Message-
From: Finan, Sean [mailto:sean.fi...@
Hi Manu,
Speaking for the developers of that module, we are excited that you and others
in the community are starting to show so much interest in temporal information
extraction - enough to attempt builds and trial runs.
The Temporal module is still in an "academic" experimental phase and there
+1 I think that a factory is a great idea.
I (personally) dislike the descriptor schema, but I think that deprecation is
the way to go until a replacement comes along.
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Tuesday, April 15, 201
Try to open https://uts-ws.nlm.nih.gov
If that works then try
https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser and see if you get a
message like
"This XML file does not appear to have any style information associated with
it. The document tree is shown below."
If that works and you
Those variants are not used by the dictionary lookup. I did look at them to
see if it was worthwhile for the new dictionary, but they are all over the
place so I passed.
From: Miller, Timothy [timothy.mil...@childrens.harvard.edu]
Sent: Thursday, April
+1 false
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Friday, April 18, 2014 2:54 PM
To: dev@ctakes.apache.org
Subject: Re: lvg entries
Thanks for tracking that down Andy.
I am making a pass at UimaFit-izing the configuration parameters fo
rser)
>
> -----Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Thursday, April 17, 2014 12:52 PM
> To: dev@ctakes.apache.org
> Subject: RE: lvg entries
>
> Those variants are not used by the dictionary lookup. I did look at
> th
Hi Vijay,
I did a checkout this morning and I'm getting compile errors from Maven.
If I just run mvn compile then I get an error while building ytex claiming that
the package has not been created. Is there a reversed dependency?
If I run mvn compile package then ytex seems to run through, but
estigate.
>
> -vj
>
>
> On Mon, Apr 28, 2014 at 11:00 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
>> Hi Vijay,
>>
>> I did a checkout this morning and I'm getting compile errors from Maven.
>>
>> If I just run mvn compile
+1
> so I was planning to update
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Friday, May 02, 2014 12:27 PM
To: dev@ctakes.apache.org
Subject: Explict version numbers instead of ranges in pom.xml
Hi,
Are there any opposition to using explicitly depend
>. The newer NER should have in its name the Behavior...
I agree, but the *2 module is a complete replacement for the current lookup.
It does not (really) have any different behavior, just a different
implementation and performance. We plan to swap out the old with the new in
the next release
wsgroup.
On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> >. The newer NER should have in its name the Behavior...
>
> I agree, but the *2 module is a complete replacement for the current
> lookup. It does not (really) have any
pful to
>>>> have thorough documentation on the dictionary lookup, how to
>>>> configure it, and how to create new dictionaries. I would venture
>>>> to say that this is the most important component in cTAKES, and
>>>> probably the one that has generated the most q
Hi Pei,
Nice examples. The pipeline builder could be simpler (divvied), but they
shouldn't leave anybody confused.
+1 for the uimafit annotations!
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Friday, June 27, 2014 11:11 AM
To: Hochheiser, Harry Stew
Hi Nick,
There are ~26,000 T007 Bacterium (falls under Living Being) entries in UMLS
2013aa. They aren't in the cTakes dictionary, but you can build a separate
bacteria dictionary using the dictionary creator tool in cTakes sandbox. It
can create dictionaries formatted for use with both availa
as wondering how to utilize Ctakes to use that library. It will be
> great if
> there were some documents on building a separate dictionary using the
> dictionary creator.
>
>
> Thanks again,
> Nick
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi
+1
Pulled fresh candidate, built, and ran Clinical using CPE without problem.
Other than that, no testing. SVN gave me a problem initially (checked out as
anonymous) asking for a password then flunking the checkout, but an update
completed it. I blame the heat.
__
+1 for the ytex method of handling a umls login before download of the umls
resources. While this also doesn't truly prevent people from sharing files
(data) without a umls account, it is a little bit of a nicer mechanism.
Aside ... Does anybody out there have experience with izpack? (izpack.
Hi Harpreet,
If you are willing to use cTakes 3.2, try the dictionary-lookup-fast module as
a replacement of the default dictionary-lookup. That module has a new
dictionary resource (hsql, not lucene) and slightly different methods for
lookup and matching. In time trials it has been faster th
Hi Tim,
> It would be preferable to me to put sentence breaks in between the sections,
> so
> the first two sentences would be:
>
> 1) PE: Lymphonodes...
> 2) Lungs: normal...
The punctuation is (always) after the logical break, being "Term: " for a
Term:Definition list. I think that the firs
Hi Harpreet,
I don't know if this has yet been answered (I'm still finding vacation-time
emails), but the Snomed-ct, Rx-norm, etc. codes were removed from the -fast
dictionary for speed. Basically, any single UMLS Cui can have multiple
different snomed-ct codes (for instance), and adding extra
Hi Clayton,
I don't know how the ytex dictionary lookup works, so I'm afraid that I can't
help you with an answer. Maybe Vijay is the best person to do this. If you
aren't tied to ytex you could try the new cTakes dictionary-lookup-fast. I
tested "Patient came in with a malar rash" and it fo
gt; >
> > How exactly do you switch to using the cTakes dictionary-lookup-fast.
> > Do I need to go in and alter xml files or is it as simple as adding a
> > certain item to the list of analysis engines?
> >
> >
> > On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean &
.apache.uima.resource.ResourceInitializationException:
> > Could
> > >> not
> > >> access the resource data at
> > >>
> > >>
> > file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTake
> > sSnomed.xml
> > >>
> > &g
cTakes now has a youtube channel named "Apache cTakes". It is empty, but if
you have ever made a training video, presentation on a component (descriptors,
type system, etc.), or demo of integration with another system (UimaFit,
Uima-AS, etc.) then please feel free to post on that channel. When
the dbconsumer analysis engine from ytex (for storing into the
> database with regard to analysis batch).
>
> Any tips for exporting or some simple issue I'm missing?
>
> Thanks,
> Clayton
>
>
> On Mon, Aug 11, 2014 at 2:09 PM, Harpreet Khanduja
>
; If so, then I think I need to look into making/using one of those.
>
>
> On Wed, Aug 13, 2014 at 1:41 PM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Clayton,
> >
> > I'm glad that you got it working. Though I stated that I would, I
iar with that process.
>
> Tim
>
>
> On 08/13/2014 02:11 PM, Clayton Turner wrote:
> > Oh okay, so is the purpose of a CasConsumer to essentially save your
> > data in a representation that you can do some kind of data mining or
> > classification on it? If so, the
Hi John,
Have you (or another) thought about modifying the Uima Simple Server to run a
cTakes pipeline?
http://uima.apache.org/sandbox.html#simple-server
> -Original Message-
> From: John Green [mailto:john.travis.gr...@gmail.com]
> Sent: Thursday, August 21, 2014 3:06 PM
> To: dev@ctake
le get requests with the xml ae for output built into
> the
> existing sandbox code, so I just wanted to hash that first before starting on
> a
> new thread.
>
>
>
>
> Do you have experience with uima simple server?
>
>
>
>
> JG
> —
>
Hi Kim, Pei,
I don't think that I changed anything to which Kim is referring, just a couple
of other things that happen to be in the same segment. From the attached it
looks like Kim's change is to copy a list and sort the copy, while mine were
moving the sort from an inner to outer loop. At
M
To: dev@ctakes.apache.org; Finan, Sean
Subject: Re: Permutations
Hi Pei and Sean,
Sean, any thoughts about this would be helpful.
We also had issues in cTAKES 2.5.
Here is the patch for 2.5. Before I got the patch to 3.0 Sean made his
changes.
=== modified file
'src/edu/mayo/bmi/loo
Hi Nick,
I think that the bottleneck is probably the lookup module itself. So, I just
sent you a secure email/ftp link. It contains a build of the new
dictionary-lookup-fast module. Should you choose to try it, let me know how
things turn out.
Sean
F
recoreds
Hi Sean,
Many thanks, I will try it tomorrow. Do you have any special instruction to run
that scrip or I have to use it with cTakes?
Thanks,
Nick
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, September 09, 2014 4:24 PM
To: dev
, Nick Nikandish <
snika...@emerginghealthit.com> wrote:
> Great. I will do that. Thanks again.
>
> Nick
>
> -Original Message-
> From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
> Sent: Tuesday, September 09, 2014 4:39 PM
> To: dev@ctakes.apache.org
&g
ndbox area?
Sent from my iPhone
> On Sep 9, 2014, at 5:24 PM, "Finan, Sean"
> wrote:
>
> There is a tool to generate a dictionary in the new format using the UMLS
> MR*** files.
>
> The module can also read directly from a file with bar-separated values:
>
reds
(Trying to avoid passing individual jars via email)
Sent from my iPhone
> On Sep 9, 2014, at 5:26 PM, "Chen, Pei"
> wrote:
>
> Sean-
> Aren't the scripts to generate the DB already available in the sandbox area?
>
> Sent from my iPhone
>
>
---
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, September 09, 2014 4:39 PM
To: dev@ctakes.apache.org
Subject: RE: Ctakes to process 5000K recoreds
Just use it with cTakes. Instead of removing other modules from the pipeline,
replace the dictionary-lookup with dictionar
t file:org/apache/ctakes/dictionary/fast/cTakesHsql.xml.
Where should I add it to the classpath?
Thanks,
Nick
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, September 09, 2014 4:39 PM
To: dev@ctakes.apache.org
Subject: RE: Ctakes to process 5000
Steve Bethard wrote:
> I spent some time writing a script for diff-ing CASes
I urge anyone interested in comparing cTakes CASes / output to use this type of
approach. Comparison of program output is a post-process task, and unless
absolutely necessary code to juggle data and metadata belongs th
ch Corp
http://www.perfectsearchcorp.com/
On 10/07/2014 07:30 AM, Finan, Sean wrote:
> Steve Bethard wrote:
>> I spent some time writing a script for diff-ing CASes
> I urge anyone interested in comparing cTakes CASes / output to use this type
> of approach. Comparison of program
ing with the same configuration outputs different data
under different moons. Having consistent results helps us know if we've made
improvements to our quality or not. c
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 10/07/2014 08:50 AM, Finan, Sean wr
>> outputs different data under different moons. Having consistent
>> results helps us know if we've made improvements to our quality or
>> not. Having output that is in a predictable order makes checking to
>> see if there are differences much cheaper when you a
gt; really interested in cTakes behaving well, so we are usually pretty
> careful in testing our changes before committing anything.
>
> Thanks,
>
> Kim Ebert
> 1.801.669.7342
> Perfect Search Corp
> http://www.perfectsearchcorp.com/
>
> On 10/07/2014 10:46 AM, Finan, Sea
disign decision, but it would be nice if we are consistently
right, or consistently wrong. Many other instances of this result in similar
issues.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 10/07/2014 12:43 PM, Finan, Sean wrote:
> I'm just about sapped on
Hi Bruce,
I would venture to say that this is neither expected nor desired.
Before you fix it (or in addition to a fix), try to run with the new dictionary
lookup. It will have a different behavior, and it will be the default
dictionary lookup in future releases of cTakes – making fixes to the
the necessary dictionary(ies) or how do I build them?
[image: IMAT Solutions] <http://imatsolutions.com> Bruce Tietjen Senior
Software Engineer
[image: Mobile:] 801.634.1547
bruce.tiet...@imatsolutions.com
On Wed, Oct 8, 2014 at 9:46 AM, Finan, Sean < sean.fi...@childrens.harvard.ed
image: IMAT Solutions] <http://imatsolutions.com>
Bruce Tietjen
Senior Software Engineer
[image: Mobile:] 801.634.1547
bruce.tiet...@imatsolutions.com
On Wed, Oct 8, 2014 at 9:46 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Bruce,
>
> I would venture t
lt;mailto:bruce.tiet...@imatsolutions.com>
On Wed, Oct 8, 2014 at 10:02 AM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Bruce,
With Pei's help I just updated the sourceforge repo with the cTakes
dictionaries. Checkout artifact ctakes-resources-snomed-rword-hsqldb-2
01.634.1547
bruce.tiet...@imatsolutions.com<mailto:bruce.tiet...@imatsolutions.com>
On Wed, Oct 8, 2014 at 10:02 AM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Bruce,
With Pei's help I just updated the sourceforge repo with the cTakes
dictionaries. Checko
Hi Chandu,
For your note #2:
> 2)Any new features that can be added to current version of cTakes
> project to make it more useful.
You can always check (or add to) the Jira "future enhancement" page at:
https://issues.apache.org/jira/browse/CTAKES/fixforversion/12323040/?selectedTab=com.atlassian.
By Pei:
> As much as I hate maintaining more desc xml's, but I think it's prudent to
> create a separate one for a patch release temporarily for
> ctakes-dictionary-lookup-fast so users do not get blindsided by the change in
> output.
By Sean:
Excellent idea
-Original Message-
From: M
Hi Andy,
Great stuff! I think that I understand the method, but I have a question about
the statement:
>the content is publicly available per the NCBI policy and license for MedGen
>sources
Does this mean that I, Joe Anybody, could download the content, place some of
the content in a databas
Hi Jun,
Do AE pipelines that do not use the Smoking Status module work?
I think that Smoking Status configuration (via binary install) might be broken
in the last several versions. I thought that I had submitted a Jira long, long
ago, but right now I can't find it so maybe my memory is playing
Hi Brandon,
It sounds like you've got a decent pipeline set up. To increase the speed you
could try swapping out use of ctakes-dictionary-lookup with
ctakes-dictionary-lookup-fast in the AE. Check
ctakes-clinical-pipeline/desc/[ae]/AggregatePlaintextFastUMLSProcessor.xml for
an example. As
Any other suggestions
on performance tuning would be great!
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Friday, December 05, 2014 1:14 PM
To: dev@ctakes.apache.org
Subject: RE: Scaling cTakes
Hi Brandon,
It sounds like you'
Hi Kasie,
cTakes is a community effort, so you've contacted the right people. Assuming
that the "Bug Tracker" link in the navigation bar on the left works, please
submit a report and list all of the orphan links. A kindly volunteer will fix
them as soon as possible.
Thanks,
Sean
-Origin
Hmmm, I can't find it in a search. However, here is a direct link:
https://www.youtube.com/channel/UC8hQoOKz3v4PNEf6cqSkjbQ
Maybe it needs a few videos to register in the search engine ?
Sean
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Monday, December 15, 2014
Wow, I've just spent the last 2 hours doing the exact same thing. That is what
I get for missing a meeting. Mine is extremely similar, though slightly
different language (and without the "improved performance" bar chart - which
may not belong). I also put the "Examples" in a big green button
Anyway, a pretty amazing fresh start, thanks Pei
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Monday, December 15, 2014 4:33 PM
To: dev@ctakes.apache.org
Subject: RE: revamping the Apache cTAKES website
Check out a mockup of a new website proposal:
htt
Hi Yu,
> Also do you know is there any command line I can run to annotate like a
> thousand files automatically rather than copy and paster.
You could try the CPE gui : bin/runctakesCPE.sh
Sean
From: Liang, Yu [mailto:yu.li...@nyumc.org]
Sent: Monday, December 15, 2014 4:51 PM
To: dev@ctakes.a
Hi Praveen,
I think that this question might be better aimed at the nlm umls community.
The standard cTakes installation does not follow this workflow.
Sean
-Original Message-
From: Jay_Ram [mailto:pandupraveen...@gmail.com]
Sent: Tuesday, December 16, 2014 12:10 AM
To: dev@ctakes.apa
er.
>
> JG
>
> On Mon, Dec 15, 2014 at 11:43 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>>
>> Hmmm, I can't find it in a search. However, here is a direct link:
>>
>> https://www.youtube.com/channel/UC8hQoOKz3v4PNEf6cqSkjbQ
video and ctakes youtube : Youtube Apache cTakes Channel
Direct Link
Isnt this to upload for my account? What about to the channel?
On Tue, Dec 16, 2014 at 12:16 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
>
> Hi John,
>
> Look for an "Upload" button i
Well, I guess that it is time for me to speak up …
I must say that I’m happy that people are showing interest in the fast lookup.
I am also happy (sort of) that some concerns are being raised – and that there
is now community participation in my little toy. I have some concerns about
what pe
One quick mention:
The cTakes dictionaries are built with UMLS 2011AB. If the Human annotations
were not done using the same UMLS version then there WILL be differences in CUI
and Semantic group. I don't have time to go into it with details, examples,
etc. just be aware that every 6 months cu
com>
Kim Ebert
Software Engineer
[Office:]801.669.7342
kim.eb...@imatsolutions.com<mailto:greg.hub...@imatsolutions.com>
On 12/19/2014 11:31 AM, Finan, Sean wrote:
One quick mention:
The cTakes dictionaries are built with UMLS 2011AB. If the Human annotations
were not done using the same
eer
[Office:]801.669.7342
kim.eb...@imatsolutions.com<mailto:greg.hub...@imatsolutions.com>
On 12/19/2014 11:31 AM, Finan, Sean wrote:
One quick mention:
The cTakes dictionaries are built with UMLS 2011AB. If the Human annotations
were not done using the same UMLS version then there WILL
Hi Bruce,
I'm not sure how there would be fewer matches with the overlap processor.
There should be all of the matches from the non-overlap processor plus those
from the overlap. Decreasing from 215 to 211 is strange. Have you done any
manual spot checks on this? It is really bizarre that y
Hi Bruce,
> Correction -- So far, I did steps 1 and 2 of Sean's email.
No problem. Aside from recreating the database, those two steps have the
greatest impact. But before you change anything else, please do some manual
spot checks. I have never seen a case where the lookup would be so horrib
uce Tietjen
Senior Software Engineer
[Image removed by sender. Mobile:]801.634.1547
bruce.tiet...@imatsolutions.com<mailto:bruce.tiet...@imatsolutions.com>
On Fri, Dec 19, 2014 at 1:27 PM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Bruce,
I'm not sure how there
Bruce Tietjen
> Senior Software Engineer
> [image: Mobile:] 801.634.1547
> bruce.tiet...@imatsolutions.com
>
> On Fri, Dec 19, 2014 at 1:39 PM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>>
>> Sorry, I meant “Do some spot checks on the validity”.
Hi Maite Meseure,
Check the cTakes User guide on UMLS setup:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide#cTAKES3.2UserInstallGuide-(Recommended)AddUMLSaccessrights
which (in part) points you towards obtaining a license to use the NIH UMLS
dictionary:
https:
Go through the error that you got, and look for a message like:
Failed to initilize. Invalid UMLS License
and
Error: Invalid UMLS License. A UMLS License is required to use the UMLS
dictionary lookup.
Error: You may request one at: https://uts.nlm.nih.gov/license.html
Please verify your UML
I don't know. I'm comparing what I think is the 2009 negex trigger set
https://code.google.com/p/negex/source/browse/trunk/GeneralNegEx.Java.v.1.2.05092009/negex_triggers.txt
with the cTakes trigger set in
org.apache.ctakes.core.fsm.machine.NegationFSM.java and it looks like the
cTakes set is
c\main\resources\org\apache\ctakes\ytex\negex\negex_triggers.txt)
Adding triggers requires modifying a text file - much simpler than changing
code and compiling.
-vj
On Mon, Jan 5, 2015 at 8:30 PM, Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> I don't know. I'm comparing
the shared clef 2013
task?
https://sites.google.com/site/shareclefehealth/
I'm looking for something that doesn't have to be the best speed-wise, but that
is the recommended for optimizing F1 measure.
Regards,
James
-Original Message-
From: Finan, Sean [mailto:sean.f
best F1 measure for something like the shared clef 2013
task?
https://sites.google.com/site/shareclefehealth/
I'm looking for something that doesn't have to be the best speed-wise, but that
is the recommended for optimizing F1 measure.
Regards,
James
-Original Message-
From: Fina
Hi Michelle,
Did your error have only "Could not find . as absolute" or did it also have
"or in ... or in ..."? If you see " ... or in ... " then this is a new issue.
If you don't, then you should update your source. If you need to run the
release binary then let me know and I can work o
Hi Tol (and Maite),
I'm not entirely certain that I understand the question, but here is an attempt
to help. If I'm oversimplifying then I apologize.
I think that ExampleAggregatePipeline is intended to represent a very simple
single-note pipeline and that custom code could be produced by usin
job than the CPE-GUI -at least in Eclipse, I haven't managed to
run it via the command line yet.
On Mon, Feb 2, 2015 at 7:12 PM, Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> Hi Tol (and Maite),
>
> I'm not entirely certain that I understand the questio
Hi Steve,
You are right (confirming your finding) - it looks like the first is a no-show
and the second is somebody's personal upload to github (not git.apache.org)
from 3 years ago. The jira claims that the item was closed (fixed), but if you
go to
https://urldefense.proofpoint.com/v2/url?u=
teJCas();
jCas.setDocumentText("some text");
AnalysisEngine tokenizer = createEngine(MyTokenizer.class);
AnalysisEngine tagger = createEngine(MyTagger.class);
runPipeline(jCas, tokenizer, tagger);
for(Token token : iterate(jCas, Token.class)){
System.out.println(token.getTag());
}
Tol O.
ctory. So in our HPC, it spawns a
> > new job for each subfolder (which may have between 5 and 2500 notes).
> >
> > Todd Lingren
> > Biomedical Informatics
> > Cincinnati Children’s Hospital
> > todd.ling...@cchmc.org
> > 513-803-9032
> >
> >
> > ---
@ctakes.apache.org
Subject: Re: Question about the pipeline
Yes, it does but only in Eclipse, not in command line even though I am in the
good directory. I have to look at the classpath more in details probably.
Thanks for your replies.
On Thu, Feb 5, 2015 at 8:08 AM, Finan, Sean < sean
Hi Taposh,
Try the process outlined below. I have screenshots for each step if you want
them. If this works (you are the first tester) then we can put it in the web
documentation.
Sean
Fresh checkout from SVN
===
1. Start IntelliJ IDEa.
2. In the "Quick Start" menu, selec
Try something like the following for output:
private int extractFeatures( final IdentifiedAnnotation annotation ) {
// Extract the IdentifiedAnnotation itself
final Collection umlsInfos = getUmlsInfos( annotation,
_printSnomed );
if ( umlsInfos == null ) {
return 0
Oh yeah - use the -fast dictionary to get preferred text. The fastest way to
get cuis only is with CuisOnlyPlaintextUMLSProcessor. If you want polarity
make sure you uncomment the section with PolarityCleartkAnalysisEngine.
Sean
-Original Message-
From: Maite Meseure Hugues [mailto:me
PM, Maite Meseure Hugues <
meseure.ma...@gmail.com> wrote:
> Thank you for your replies, It's helpful. I was working on 3.2.0
> version, so it looks like 3.2.1 allows to get the UMLS preferred text.
>
> Maite
>
> On Thu, Feb 12, 2015 at 2:25 PM, Finan, Sean <
> sean.fi..
Our request is for a read-only mirror. However, if it ever becomes i/o, I
don't know if this will have what you want, but http://git.apache.org/
Links to documentation (mostly server setup) http://www.apache.org/dev/git.html
and a wiki (check toward middle and bottom for committer info)
https:/
Hi Raymond,
If you use the dictionary-fast module there exists an entry "feeling bad" with
cui 557911 and cui 231218. There is also "feel bad" and "feeling bad
emotionally"
You will find "horrible present pain" but no other entry with "horrible". You
will not find any terms with "awful" and
url?u=http-3A__www.nlm.nih.gov_research_umls_sourcereleasedocs_current_CHV_&d=BQIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1Bkpeno1tqLjX78o0wYm5DmJHCHlK7hrxpeEgPnGtRM&s=-rEmTgTCe0mkSXT34XK56zkiuy_VxIfFvngGJzUwem8&e=
On Sun, Feb 22, 2015 a
Hi all,
It looks like a few people (myself included) are interested in having
information on people, projects, papers, and applications that use cTAKES on
the web page. I have created a form on google that might help us collect this
and other information. Please visit
https://docs.google.com
Hi Michelle,
When it comes to
> multiple instances of cTakes in parallel
You can certainly start as many pipelines as you want as separate JVM
processes, just make sure that you divide your notes among separate batches,
one batch per process. Also keep in mind that you don't want to clobber yo
Hi Tom,
> I am passing my UMLS login and password on startup as arguments ...
> "-Dctakes.umlsuser=myusername -Dctakes.umlspw=mypassword"
That is fine. If I understand correctly you are already running this way
without problem. The comments in the .xml files should probably be extended to
inc
Hi Maite,
> Does anyone know why is it [UmlsDictionaryLookupAnnotator ]so slow?
The top 5 reasons (1-3 are 90% of the problem):
1. The dictionary database is bloated with unwanted entries
2. The dictionary database indexing is sub-optimal
3. The second drug lookup with orangebook filtering take
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