>From a users perspective, I would also really appreciate a ready-to-download
>release of 4.0.1. In any case, thanks for the continuous work on cTAKES.
Regards,
Tomasz
From: Greg Silverman
Sent: Wednesday, February 3, 2021 2:32 PM
To: dev@ctakes.apache.o
Sean,
Since you mention a new release, is there any expected time for a new stable
cTAKES release? An up-to-date stable release for the user installation would be
appreciated I think.
Regards,
Tomasz
From: Finan, Sean
Sent: Friday, July 24, 2020 10:45
,WDT,WP,WPS,WRB"
If things still go missing you can just not exclude any pos from lookup - which
is what I do in yet another project.
Sean
________
From: Tomasz Oliwa
Sent: Tuesday, March 13, 2018 6:14 PM
To: dev@ctakes.apache.org
Subject: Re: Sentenc
uld be able to see the part of speech tag for that word.
Tim
________
From: Tomasz Oliwa
Sent: Tuesday, March 13, 2018 5:34 PM
To: dev@ctakes.apache.org
Subject: Re: Sentence splitter [EXTERNAL]
Hi,
I tested SentenceDetectorAnnotatorBIO in cTA
Hi,
I tested SentenceDetectorAnnotatorBIO in cTAKES 4.0.0, simply by replacing
SentenceDetectorAnnotator.xml with SentenceDetectorAnnotatorBIO.xml in
AggregatePlaintextFastUMLSProcessor.xml.
While it seemed to work, I noticed that in one example, an IdentifiedAnnotation
was not found, that was
ponse time if successful.
Best,
Yiming
On Wed, Dec 7, 2016 at 3:15 PM, Tomasz Oliwa wrote:
> Provided you are under Linux, you could just write a bash script that
> takes your input file as argument, creates a temporary directory with
> "mktemp -d", "cp" the file i
Provided you are under Linux, you could just write a bash script that takes
your input file as argument, creates a temporary directory with "mktemp -d",
"cp" the file into it, and then runs a Java class that calls
org.apache.uima.examples.cpe.SimpleRunCPE on this temporary directory.
The init a
Bandeep,
I am using the JVM from Oracle Java 8 with cTAKES. My cTAKES build from SVN is
3.2.3, but not the latest, possibly a more recent commit broke something?
There is a resolved issue for JDK 8 in the JIRA
https://issues.apache.org/jira/browse/CTAKES-399 , you might want to take a
look at
executor.shutdown();
}
}
You may hit a maximum efficiency because i/o will cause disk thrashing, but 10
threads might be an ok start.
Sean
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 14, 2016 2:08 PM
To: dev@ctakes.apache.org
Sub
Hi,
I have working code to deserialize XCAS files and read-only process them
further, it is based on CASConsumerTestDriver.java, an example is :
// inputs to the CAS file and the AE from cTAKES, templates here
String xCasLocation = ;
String taeDescriptionLocation =
;
Hi,
I am sometimes seeing the "Couldn't find parse for" message in the terminal
from cTAKES, I assume it is from the MaxentParserWrapper.
However, in the CVD I can still see the TreebankNode entries with a tree and
nodes with a grammatical nodeType in these cases. How is this possible? What
a
xtend that class as it is
immutable.
Sean
-Original Message-----
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, June 01, 2016 3:20 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES false positives, case-insensitivity
Another idea would be to create the dictionary without lower
,
Tomasz
From: Tomasz Oliwa [ol...@uchicago.edu]
Sent: Wednesday, June 01, 2016 11:07 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES false positives, case-insensitivity
Thank you all for the suggestions.
Sean, by "make the AE case-sensitive" d
helps.
Sean
-----Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, June 01, 2016 11:28 AM
To: dev@ctakes.apache.org
Subject: cTAKES false positives, case-insensitivity
Hi,
I have encountered false positives annotated with cTAKES that seem to come from
case-in
Hi,
I have encountered false positives annotated with cTAKES that seem to come from
case-insensitivity of the annotation lookup, such as:
Pt uses hearing aids. -> "aids" is found as DiseaseDisorderMention
cui=C0001175, Acquired Immunodeficiency Syndrome
Pt values are all stable. -> "all" is fo
,
Just in case nobody has a better answer: I think that you might need to may a
new array at size n-1 , then copy all ontology concepts that you do want, then
set the annotation's ontology concept array to be the new one.
Sean
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicag
How can I delete an OntologyConcept from a JCas using an Annotator?
As an example, the following process method from an Annotator loops over all
IdentifiedAnnotations, and is supposed to simply remove all OntologyConcepts.
However, it does not remove anything from the CAS. I can still see all
Patrick,
I have the smoking-status component of cTAKES running without exceptions. I
also combined it into the AggregatePlaintextFastUMLSProcessor, on
https://issues.apache.org/jira/browse/CTAKES-370 you can find my
AggregatePlaintextFastUMLSProcessor.xml and the necessary steps on how to
inte
ext span J
discardSpans.add( spanKeyJ );
}
}
}
return discardSpans;
}
Good luck,
Sean
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Thursday, November 19, 2015 12:08 PM
To: dev@ctakes.apache.org
Subject: TermConsumers
Hi,
H
If you look at the bottom of your Exception you will see:
...
Caused by: java.io.FileNotFoundException: No File exists at
resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script
at
org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at
Hi,
How can I run a different TermConsumer on already generated CAS files?
I have CAS files created by the AggregatePlaintextFastUMLSProcessor with the
DefaultTermConsumer set in cTakesHsql.xml.
Now I would like to apply the PrecisionTermConsumer on these CAS files without
having to do the wh
anks,
Sean
-Original Message-----
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Monday, November 16, 2015 11:36 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
Sean,
I created a JIRA entry for this bug at:
https://urldefense.proofpoint.com/v2/u
AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES dictionary lookup behavior question
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
Those are just some quick examples. It depends heavily on what the ontology
contains though.
Cheers,
Britt
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com
On Nov 12, 2015, at 6:27 PM, Tomasz Oliwa
mailto:ol
Hi,
cTAKES has a dictionary lookup behavior that I cannot explain, you can verify
the queries via the cTAKES demo that has been posted here at:
http://52.27.22.206:8080/index.jsp but it also happens with the current 3.2.2
version and the fast dictionary UMLS lookup
SENTENCE: Took the baby to
eliveryUtil have some experimental code that is not used by
default, but one could always play around.
I know that -official- documentation outside of doc/howto.txt would be great.
However I would rather spend free time throwing a gui around the tool to make
things more intuitive.
Sean
-Ori
e.org>
Subject: RE: Fast Dictionary Update
Sean,
I added that and still had the same issue.
Thanks,
Brandon
_
From: Finan, Sean
mailto:sean.fi...@childrens.harvard.edu><mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fas
nan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>
And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?
-Original Message-
From: Tomasz Ol
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>
And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 16, 2015 7
I have exactly the same problem with the tool.
A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.
From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fa
Hi,
Check out a recent thread that discussed this:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201504.mbox/%3CCAPqz87rdRx=6uctkwy_ooyzcguzodyyhuj0izt07wj_yuwk...@mail.gmail.com%3E
You could for instance create an object of
org.apache.uima.examples.cpe.SimpleRunCPE, and give it as argumen
The code used for
training is also in the project- it should be in the **/eval/* name
spaces. I believe the gold standard was created in xml (either
knowtator or anafora).
Hope that helps.
--Pei
On Thu, Jul 23, 2015 at 10:33 AM, Tomasz Oliwa wrote:
> What format (features, labels) is best
What format (features, labels) is best suitable for some more training examples?
The SubjectCleartkAnalysisEngine class loads a
/org/apache/ctakes/assertion/models/subject/model.jar, which contains a
liblinear cleartk model.
The model has 3 features, label 12 3.
But what are the features exa
Pei,
The SubjectCleartkAnalysisEngine is currently broken in cTAKES, I tried it with
more examples, it just returns "patient" as subject.
You mentioned that this is the new Subject Classifier.
1. What was the old module that was capturing the subject of a UmlsConcept?
2. How can this old mod
Hi,
I am interested in the design decision of the sentence detector.
Why does it split a sentence of the form "WORD1: WORD2 WORD3." into two
sentences "WORD1:" and "WORD2 WORD3."? Do other components of cTAKES require
such a sentence splitting?
It would seem to me that it should remain one s
https://issues.apache.org/jira/browse/CTAKES-369 is open now.
Thanks for looking into this. If there is something I could additionally test,
let me know.
Hi,
I think there is a regression in the way cTAKES discovers the subject status
("patient", "familiy_member", etc.) of an UmlsConcept. Using cTAKES 3.2.2 and
the AggregatePlaintextFastUMLSProcessor in the CVD:
1. "Patient's brother has a myocardial infarction."
"myocardial infarction" and "in
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