Hi Sandeep,
I just took a peek at the JavaOcr code, and it looks like they perform image
filtering in the PixelImage class. This would probably cause a problem with
dot matrix images as every corner of every dot would be removed as noise, so
dots that participate in curves on characters such
AM
To: dev@ctakes.apache.org
Cc: Finan, Sean
Subject: RE: cTAKES user interface
Hi all,
Sean Finan (I think is on this group) already wrote a command line CPE runner
like Pei described. I've been using it and would be happy to provide some user
guides if he provides the class,etc.
Todd Lingren
hour.
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, October 30, 2013 11:20 AM
To: Lingren, Todd; dev@ctakes.apache.org
Subject: RE: cTAKES user interface
Sean Finan (I think is on this group) already wrote a command line CPE runner
like
.
Jg
—
Sent from Mailbox for iPhone
On Thu, Oct 31, 2013 at 2:04 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
I don't know if what I write below truly applies to the discussion, but here
it is.
much of a problem list definition may already be contained to varying degrees
in existing
dictionary used by cTAKES?
Ted
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 04, 2013 9:37 AM
To: dev@ctakes.apache.org
Subject: RE: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
I don't know
would possibly be a
route to a solution.
Now that is a challenge!
Cheers for the inspiration and enthusiasm,
Sean
From: John Green [john.travis.gr...@gmail.com]
Sent: Monday, November 04, 2013 10:45 AM
To: Finan, Sean
Subject: RE: Sundry; Problem Lists
Oh goodness
Good stuff - Thanks Richard
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Friday, December 06, 2013 3:30 PM
To: 'dev@ctakes.apache.org'
Subject: RE: cTAKES Groovy...
Thanks Richard! That did the trick
I'll create a JIRA and update the script including
(_), and
leave the dot (.) in the code to be deprecated for now?
--Pei
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Saturday, January 04, 2014 10:10 PM
To: dev@ctakes.apache.org
Subject: RE: UMLS Env variables suggestion
This went in to 3.1 https
On my end it looks like my email was reformatted and some of my -newline-
removed in those last examples ...
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, January 22, 2014 3:42 PM
To: dev@ctakes.apache.org
Subject: RE: sentence
Hi Vijay,
I have yet to run across clinical text from a real EMR where newlines
represent the end of a sentence
Since James pointed out this possibility a couple weeks ago, I have kept my
eyes open. The problem is pretty ubiquitous in a corpus that I'm working with
right now. I just
this if they like.
-vj
On Thu, Feb 6, 2014 at 1:01 PM, Finan, Sean sean.fi...@childrens.harvard.edu
wrote:
Hi Vijay,
I have yet to run across clinical text from a real EMR where
newlines
represent the end of a sentence
Since James pointed out this possibility a couple weeks ago, I have
kept
Hi Andy,
We have been using Uima-as here, but with no third-party wrappings. We have
set it up to run in standalone and lsf cluster environments, but everything is
out-of-box with a few custom bash scripts to set environment settings, etc.
Sean
-Original Message-
From: andy mcmurry
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
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 extractor
until we have a definite, well-defined need (from a user
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...@childrens.harvard.edu]
Sent: Friday, March
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
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
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
.
-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 then I get an error while building ytex
claiming that the package has not been
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 different behavior, just a
different implementation
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 questions on the newsgroup.
On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean
sean.fi
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
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
+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?
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
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 first three
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
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
again:
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
sean.fi...@childrens.harvard.edu
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
/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
haven't yet checked the fidelity of trunk. Urgent data request one
day, must have writing the next
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, 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 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:
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
To: dev@ctakes.apache.org
Subject: RE: Ctakes to process 5000K 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
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
/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 output is a post-process task, and unless
absolutely necessary code
that is in a predictable order makes checking to
see if there are differences much cheaper when you are dealing with larger
data sets.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 10/07/2014 08:50 AM, Finan, Sean wrote:
Hi Kim,
One might want compare
.
Thanks,
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 10/07/2014 10:46 AM, Finan, Sean wrote:
Hi Kim,
It concerns me a bit by making the code return consistent results
would
be so concerning.
Could you please clarify what you mean
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 this topic. What comes below is my final writing.
Kim wrote:
Yes, I mean actual type values not matching.
Ok, this is a very serious problem and should
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 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.edu
wrote:
Hi
: 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 to say that this is neither expected
...@imatsolutions.com
On Wed, Oct 8, 2014 at 10:02 AM, Finan, Sean
sean.fi...@childrens.harvard.edumailto: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-2011ab
Sean
, but that would probably be better than missing the
annotation all together.
[IMAT Solutions]http://imatsolutions.com
Bruce Tietjen
Senior Software Engineer
[Mobile:]801.634.1547
bruce.tiet...@imatsolutions.commailto:bruce.tiet...@imatsolutions.com
On Wed, Oct 8, 2014 at 10:02 AM, Finan, Sean
sean.fi
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:
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 database
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
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.
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've got
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:
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:
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
Maybe it needs a few videos to register in the search engine ?
Sean
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 in the upper-left corner next
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
Software Engineer
[Office:]801.669.7342
kim.eb...@imatsolutions.commailto: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
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
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
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”. In other
words, when your script reports that a cui and/or span is missing,
manually look at the data and see
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:
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
-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 question, but here is
an attempt to help. If I'm oversimplifying
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
-Original Message-
From: Finan, Sean [mailto:sean.fi
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
= 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.
Finan, Sean Sean.Finan@... writes:
Hi Tol (and Maite),
I'm not entirely
Try something like the following for output:
private int extractFeatures( final IdentifiedAnnotation annotation ) {
// Extract the IdentifiedAnnotation itself
final CollectionString umlsInfos = getUmlsInfos( annotation,
_printSnomed );
if ( umlsInfos == null ) {
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
...@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...@childrens.harvard.edu wrote:
Oh yeah - use the -fast dictionary to get
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)
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 out
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.fi...@childrens.harvard.edu]
Sent: Friday, December 19, 2014 11:55 AM
To: dev@ctakes.apache.org; kim.eb
@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.fi
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
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
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
-3A__www.nlm.nih.gov_research_umls_sourcereleasedocs_current_CHV_d=BQIBaQc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTaom=1Bkpeno1tqLjX78o0wYm5DmJHCHlK7hrxpeEgPnGtRMs=-rEmTgTCe0mkSXT34XK56zkiuy_VxIfFvngGJzUwem8e=
On Sun, Feb 22, 2015 at 10:37 AM, Finan, Sean
sean.fi
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
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 probably
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
+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
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,
Hi Pedro,
Check the cTakesHsql.xml and make sure that the line matches:
property key=umlsUrl
value=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
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
property key=umlsUrl value= INSERT URL HERE, NO SPACES /
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent
@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@ctakes.apache.org
Subject: RE
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
().equalsIgnoreCase(Resulttrue/Result);
in isValidUMLSUser() should be replaced with
result = line.trim().equalsIgnoreCase(?xml version='1.0'
encoding='UTF-8'?Resulttrue/Result);
Michal
-Message d'origine-
De : Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Envoyé : May-11-15
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
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
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:
. 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 under
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
contains the CUIs of both Glioblastoma and glioblastoma Multiforme.
Best,
Oranit.
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, June 22, 2015 5:13 PM
To: dev@ctakes.apache.org
Subject: RE: The fast dictionary pipeline vs
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 sean.fi
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.
();
...
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 files
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:
=/Logger.properties with CHANGEME
On Mon, Jul 27, 2015 at 8:32 AM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Justin,
The UMLS licensing issue has been resolved:
https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org
_jira_browse_CTAKES-2D359d=BQIFaQc
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