Hi Siamak,
Good question. Yet another shortfall in the documentation ...
There are several ways to set parameters in the PipelineBuilder.
The javadocs for the 4.0.0 release version are here:
http://ctakes.apache.org/apidocs/4.0.0/
You can use the set(..) method to set "global" values, or plac
able, but since they aren't in the any target table,
would the effect be the same as leaving them unchecked (the synonyms of the
unchecked ontologies would be matched when running cTAKES if they were of
the same CUI as the selected ontology)?
Thanks,
Jeff
On Mon, Jun 24, 2019 at 10:58 AM Fina
in the external resource..."
How can do the same for Resource Dependencies in
DictionalyLookuoAnnotatorCSV.xml?
With Best Wishes,
Siamak
On Tue, 25 Jun 2019 at 16:38, Finan, Sean
wrote:
> Hi Siamak,
>
> Good question. Yet another shortfall in the documentation ...
>
> There ar
s". Is there any way to be
able to annotate this typo word as well?
With Best Wishes,
Siamak
On Tue, 25 Jun 2019 at 18:38, Finan, Sean
wrote:
> Ah.
>
> You are trying to use an old annotator. It was never updated to be a
> uimafit component and I think that it may not wo
r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=CST_DJHBnyHs2yZy6bNYrEbg8KH5KIjIbtafSbM9NQQ&s=Yka0I-sYj7AQsBAXKF-s02fd6tpXYdHdT1chqkiJ004&e=
> ) to improve
> recall.
> Unfortunately we had to take if out because the overfitting affected
> precision and increased ambiguity too mu
Hi All,
ctakes-scrubber is not in any ctakes release and it is not in the main
repository. It never went beyond experimental and resides within the ctakes
sandbox. https://svn.apache.org/repos/asf/ctakes/sandbox/
>From what I recall, scrubber does not have "real" name replacement, but
>inste
Hi Maral,
What version of java are you using? Java 8 is the recommended version.
Sean
From: Maral Amir
Sent: Thursday, July 18, 2019 1:39 AM
To: dev@ctakes.apache.org
Subject: Re: Build Error in cTAKES YTEX [EXTERNAL]
Hi Gandhi,
Thank you for your repl
d4gTao&m=nPn3YIWpjzdhxoqmNewNKZVwA8qHAIDHrWMmAsM7N1Y&s=dF8UECpLMGH-1JXOIdBh9G1H-wIsYvELedRo0r8M8S0&e=
[*ERROR*]
[*ERROR*] After correcting the problems, you can resume the build with the
command
[*ERROR*] *mvn -rf :ctakes-ytex*
Thanks,
Maral
On Thu, Jul 18, 2019 at 5:23 AM
Hi Maral,
This might be what you are talking about with respect to the Default Clinical
Pipeline
https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
That lists a command line method for running a set of files and getting xml
output.
The default clinical pipeline config
Hi Tim, Remy,
The fake notes have non- UTF-8 formatting in the smoker/ directory. You can
run the default pipeline on those files and look at various outputs (Pretty
Text, Pretty Property, Pretty Html) and you will see that ctakes maintains
offsets despite the encoding.
The FileTreeReader use
annotated outputs in a
readable format without the help of CVD.
Thanks,
Maral
On Thu, Jul 18, 2019 at 12:52 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Maral,
>
> This might be what you are talking about with respect to the Default
> Clinical Pipeline
>
>
Tao&m=6W89gjAzseX6p7ykbILxuXxSLnkoxvHvx4fb-bXZyd4&s=VdZxU2g1EpC_NsszRn967-ej75GV--bMCJWICUd769s&e=
>
I also have some old Java code that deal with a few of these issues, and
would be happy to share with anyone interested, though it’s far from production
quality and does not ad
PiperFileRunner "$@"
Also,
2. Where is the *"bin"* folder where the bash file resides. Right now I use
this one :
/Users/local/projects/ctakes/trunk/ctakes-distribution/src/main/bin
Thanks,
Maral
On Fri, Jul 19, 2019 at 6:13 AM Finan, Sean <
sean.fi...@childrens.harvard.edu>
I used build profile
"runPiperGui"and it worked beautifully on my custom piper file. I
appreciate it if you kindly direct me to next steps on more run methods. As
I mentioned earlier, my final goal is to develop a OCR+NLP web service.
Thanks,
Maral
On Fri, Jul 19, 2019 at
> -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g
> org.apache.ctakes.core.pipeline.PiperFileRunner "$@"
>
>
> Also,
>
> 2. Where is the *"bin"* folder where the bash file resides. Right now I use
> this one :
> /Users/local/projects/ctake
Hi all,
I think that there are a lot of things going on here.
Jeff's question is on point - do you actually have the dictionary?
I think that doing all of this with code is unnecessary.
- I don't see anything in the code that cannot be done in a piper file.
- Piper files can set the collection r
Hi Sebastien,
Can you look at the referenced file
org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
It should be in resources/
If it is the default version then it contains the line
Can you look at the referenced directory
resources/org/apache/ctakes/dictionary/lookup/fast/
ll
On Fri, Aug 23, 2019 at 11:26 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sebastien,
>
> Can you look at the referenced file
> org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml ?
>
> It should be in resources/
>
> If it is the d
t 24, 2019 1:09 PM
To: dev@ctakes.apache.org
Subject: Re: Clinical Processor [EXTERNAL]
Oops, I didnt paste the error message!, The message I got was:
ERROR JdbcRareWordDictionary - Could not Connect to Dictionary
sno_rx_16abTerms
On Sat, Aug 24, 2019 at 8:55 AM Finan, Sean <
sean.fi...@chi
Hi all,
I will be attending ApacheCon Europe https://aceu19.apachecon.com. If anybody
is interested in getting together for a cTAKES discussion or some hacking that
week please let me know.
I will also be speaking at 12:00 on 24 October 2019 in room Kesselhaus.
https://aceu19.apachecon.com
anding of the code?
Thanks,
Jeritt
On 2019/07/18 21:22:34, "Finan, Sean" wrote:
> Hi Tim, Remy,
>
> The fake notes have non- UTF-8 formatting in the smoker/ directory. You can
> run the default pipeline on those files and look at various outputs (Pretty
> Text,
Does my thought process make sense with your understanding of the code?
Thanks,
Jeritt
On 2019/07/18 21:22:34, "Finan, Sean" wrote:
> Hi Tim, Remy,
>
> The fake notes have non- UTF-8 formatting in the smoker/ directory. You can
> run the default pipeline on those files an
Hi Greg,
Check your log to see what component is taking all the time.
There is a known problem with the cleartk assertion annotators:
https://issues.apache.org/jira/browse/CTAKES-449
A partial fix was made in the "windowed" sub-package of ctakes-assertion:
org.apache.ctakes.assertion.medfacts.
amp;e=
>>> //load AttributeCleartkSubPipe.piper
>>> load WindowedAttributeCleartkSubPipe
>>>
>>>
>>> All files seem to have been processed fine, but wondering if something
>>> was missed, due to the error. If so, how do I construct the
&
Hi Greg,
Right now that is just a placeholder. There is not an annotator in ctakes to
perform wsd (and toggle that value). I know that at least one ctakes
contributor has worked on it, but so far nothing has been complete enough to
make it into ctakes.
Does anybody out there have a ready-to
Hi Carolina,
ctakes is written for java 8. I don't know if anybody has tested any higher
version. It looks like you are compiling with java version 11.
Are you using Apache maven to build ctakes? ctakes is modular and uses
https://maven.apache.org/.
The most complete instructions of which I
codebase in java 11.
Sent from my iPad
> On Oct 11, 2019, at 11:07, Finan, Sean
> wrote:
>
> Hi Carolina,
>
> ctakes is written for java 8. I don't know if anybody has tested any higher
> version. It looks like you are compiling with java version 11.
>
> Are
Hi Greg,
As far as I know none of the ctakes engines use it.
Sean
From: Greg Silverman
Sent: Tuesday, October 15, 2019 8:48 PM
To: dev@ctakes.apache.org
Subject: score attribute in UmlsConcept annotation [EXTERNAL]
I noticed this was always 0. Is this a
ctakes.core.pipeline.PiperFileRunner.run(PiperFileRunner.java:63)
at org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:30)
Thank you,
Carolina
From: Finan, Sean
Sent: Friday, October 11, 2019 1:07 PM
To: dev@ctakes.apache.org
Subject: Re: PiperFileRunner Error [EXTERNAL]
Hi C
Hi Dima,
At a guess this is a copy - paste artifact.
Have you tested the type system with copies removed? It seems like it should
work as the types should be compiled into classes with only a single definition.
Sean
From: Dligach, Dmitriy
Sent: Thursda
Hi Masoud,
I think that the CdaCasInitializer is at least 10 years old. I would not
expect it to conform to any recent standards.
Does anybody else have a reader or transformer that can handle HL7 CDA r2?
Sean
p.s.
If anybody is involved with HL7 International, you may want to get some
movem
Hello Naga Eskala,
To put it simply, sometimes a system configuration may block connection to an
address until it is informed that the address is acceptable.
One route that you may be able to take to remedy the situation is:
1. Open a browser.
2. Visit https://uts-ws.nlm.nih.gov/restful/
_
type Status report
message Request method 'GET' not supported
description The specified HTTP method is not allowed for the requested resource.
Apache Tomcat/7.0.70
-----Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.
Hi Carolina,
If you are using a binary installation of ctakes 4.0.0 and editing an examples
piper in the root resources/ directory then you may have a problem such as you
describe.
There is an unwanted ctakes-examples-res.jar in the lib/ directory that contain
copies of all the example pipers,
Hi Akram,
You mention
> I have followed the instuctions in this page
What page are you reading?
I just followed the instructions from page:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide#cTAKES4.0DeveloperInstallGuide-IntelliJIDEAstepbystepinstallinstruc
Hi Akram,
That was never released with ctakes. It is in ctakes sandbox as a "proof of
concept" project.
https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/
The original author Pei Chen might be able to say more.
It has nothing to do with the released "ctakes-gui" module, which contains
Hi Akram,
Gandhi has provided some good links, and I agree that you should read that
information.
In case you haven't found it, there is also a "quick start" manual is on this
page: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
Under "Documentation", there is a download named "A
Copy of internal email for devlist archival purposes.
From: Finan, Sean
Sent: Tuesday, December 17, 2019 10:08 AM
To: Akram
Subject: Re: How does cTAKES work? [EXTERNAL]
Hi Akram,
To clarify:
There are a lot of ways to run ctakes.
There are a lot of ways
eRunner an appropriate pipeline for
CdaCasInitializer?
Thank you so much for your help in advance.
Masoud
On 11/8/19, 8:30 AM, "Finan, Sean" wrote:
Hi Masoud,
I think that the CdaCasInitializer is at least 10 years old. I would not
expect it to conform to any recent
arser.parse(Unknown Source)
I am not sure what would be causing this.
I don't run CDA, so I can't speak to the operational status of those components
or the pipeline in general.
Does anybody else out there use CDA?
Sean
________
From: Finan, Sean
Sent: W
?Hi Akram,
I am not sure why you are seeing that error message.
That method will search the classpath for "ChunkerSubPipe.piper", which
includes the ctakes-chunker-res*.jar in the lib/ directory of a binary
installation or the ctakes-chunker-res/src/main/resources/ directory tree in a
source
ent: Sunday, December 22, 2019 7:54 PM
To: dev@ctakes.apache.org; Finan, Sean
Subject: Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL]
* External Email - Caution *
I have checked the file ChunkerSubPipe.piper for sure exists in
ctakes-chunker-res\target\classes\org\apache\c
Hi Yatrik,
1. Download the full umls from nlm.
https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
2. Extract everything that you want using MetamorphoSys.
3. Use the ctakes dictionary creator gui to create a ctakes-compatible
database.
https://cwiki.apache.org/
Hi Greg,
The default umls version used by the ctakes 4.0 default clinical pipeline is
extracted from umls 2016ab.
It is fairly easy to create a ctakes dictionary based upon other umls versions.
Sean
From: Greg Silverman
Sent: Monday, January 6, 2020 5:1
Hi Jeff,
There shouldn't be any problems doing that.
And here is a secret
In the class DefaultTermConsumer there is the ability to read in a "blacklist"
of terms that should be excluded. This is in the trunk version of ctakes.
If you are comfortable reading java code you can have a look an
Hi Masoud,
For simple negation you could try to see if the context annotator is fast
enough for your purposes:
add ContextAnnotator
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+NE+Contexts
In case you are creating a custom installation/configuration , this requires
that you
Hi Jeff,
I think that sentence splitting is possibly a cause for this behavior and is
worth checking.
You can get some quick debug output by adding a writer to the end of your
pipeline.
add pretty.plaintext.PrettyTextWriterFit SubDirectory=POS
The SubDirectory= parameter is optional.
This wri
Hi Abad,
If you are using ctakes trunk there are a lot of piper files in the various
resources modules to handle more advanced pipelines.
ctakes-relation-extractor-res/src/main/resources/org/apache/ctakes/relationextractor/pipeline/
contains DefaultRelation.piper - which adds detection of mod
Hi Abad,
I added an example ae to the ctakes-examples module in trunk.
org.apache.ctakes.examples.ae.BodySideFinder
It is really simple, but it is a functional example of an annotator that can
find body sides.
Sean
From: abad.ay...@cognizant.com
Sent: Mo
quired. If custom AE is needed how are we going to define those in piper
files.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Tuesday, February 18, 2020 12:14 AM
To: dev@ctakes.apache.org
Subject: Re: Missing bod
rocessing outside cTAKES.
Kindly advise.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Tuesday, February 18, 2020 9:20 PM
To: dev@ctakes.apache.org
Subject: Re: Missing body side and laterality attribute in
AnatomicalSiteM
Hi Akram,
As you have guessed, the specific tags that interest you are created by the
dictionary lookup.
The ones that you don't want come from the annotators in that tokenizer
pipeline.
The dictionary lookup requires the annotations created by the tokenizer
pipeline. It looks up words with
Hi Ryan,
Your piper has a lot of things that you don't need.
Try this:
// set the location of the input file and use a reader that treats each line
like a different document.
set InputFileName=C:/path/to/input/file.txt
reader LinesFromFileCollectionReader
// Use the default section, sentence,
Hi Ryan,
Here is some code for a writer that will do what you want.
To use it, get rid of those first two lines in the piper that I sent (set,
reader).
The default reader will work just fine, and it will allow you to process
multiple surgery lists in on run.
Then just add SentenceFirstCuiWrit
th "add
> SentenceFirstCuiWriter" in the piper file or do I need both?
>
> 3.) If the SentenceFirstCuiWriter is unable to find a valid CUI, will it
> leave a blank, N/A, or NaN value? Having any of these values would
> definitely help when I have Python parse the output text f
th Biopsy()
Ex Laparotomy Total abdominal hysterectomy with Salpingo Oophorectomy
Robot Assisted Prostatectomy Robot Assisted Pelvic Lymphadenectomy
Thank You,
Ryan Young
On Tue, Mar 31, 2020 at 10:44 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Ryan,
>
> You made so
Hi Akram,
To get values for polarity, uncertainty, conditional and generic, add this line
after "load DictionarySubPipe":
load AttributeCleartkSubPipe
Sean
From: Savova, Guergana
Sent: Thursday, April 30, 2020 8:12 AM
To: dev@ctakes.apache.org
Subject:
Peter is absolutely correct.
It is possible to use ctakes and the UMLS dictionary completely offline, but it
isn't recommended for regular use. If you have any way to connect to the
internet please use the standard methods.
Many years ago the initial creators of ctakes negotiated with the NLM
Hi Abad,
None of your embedded images are visible to me, so I don't have whatever
information is contained within those images.
It sounds like you are using the SentenceDetectorBIO. Very cool.
It does have a few idiosyncrasies, one of which you have identified.
There are two helper AEs in
extraction right?.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Thursday, June 11, 2020 8:20 PM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: Re: Sentence detector changes [EXTERNAL]
[External]
Hi Aba
ve issues where sentences are splitted on encountering decimals or '.'
separated dates. If it can what are the changes that we need to do in the piper
file to incorporate the same.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan,
during this
lock down. Stay safe :)
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Friday, June 12, 2020 9:06 PM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: Re: Sentence detector changes [EXTERNAL]
[Ext
Hi Honey,
ctakes efforts on lab values have been light, mostly because they exist in
structured database entries.
There is an annotation engine named "LabValueFinder" that can create a
LabMention annotation and fill in an associated value. It was contributed by
Kean Kaufmann several years ago
cessing to fix mistakes.
Tim
________
From: Finan, Sean
Sent: Friday, June 12, 2020 1:20 PM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: Re: Sentence detector changes [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Abad,
I can't say anything about Timothy Miller's a
Hi Tom,
Tiny Rest is not really a standalone deal, but utilization is pretty simple
once you know what it is for.
What you can try is:
Create the jar for ctakes-dockhand using "mvn package". You can put that jar
file anywhere, even a system that doesn't have ctakes.
Run that jar in a graphic
**
One thing that I must point out, in case you are using a vm ... make certain
that the vm has enough memory to run ctakes.
From: Thomas W Loehfelm
Sent: Friday, June 26, 2020 5:04 PM
To: dev@ctakes.apache.org
Subject: ctakes-tiny-rest - any guidance on
Hi all,
General admission to ApacheCon 2020 is free:
https://hopin.to/events/apachecon-home
I think that price of admission and travel costs have held back ctakes users
from attending past conferences, and lack of a sizable audience has diminished
the comparative value of ctakes presentatio
6r0bcpKGd4f7d4gTao&m=pUTbexmiZnykTq7rQgTwZdj0cSAzpWfjzJzMSmD_07c&s=pcCpMxdVbxWvYPBx912AgjRUbL5FuLW8RCXHafDNpuM&e=
) -> [Help 1]
1. And this is where I am stuck. I understand that ctakes-tiny-rest:jar must
not exist in 4.0.0 or 4.0.1 repositories, but am not sure how to get beyon
al Message-----
From: Finan, Sean
Sent: Wednesday, July 01, 2020 5:25 AM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running? [EXTERNAL]
Hi Tom,
first, let me offer my commiseration regarding the ytex failure. I think that
at some point I will write the community for
Repository
https://repo.maven.apache.org/maven2
default
false
Yours should be the same.
Sean
________
From: Finan, Sean
Sent: Wednesday, July 1, 2020 3:58 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running? [EXTERNAL] [SUS
t just dockhand,
I tried that too from a fresh svn checkout of ctakes, cd {ctakes-dockhand} >
mvn package and run the jar, but same issue.
Ah well - I just don't have enough understanding of maven and java devops to
get to the bottom of this. I really appreciate you taking the time t
149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)
On 7/1/20, 4:06 PM, "Finan, Sean" wrote:
I had
riate?
P.S. Are you related to Tim Finan by any chance?
________
From: Finan, Sean
Sent: Monday, June 29, 2020 11:02:26 AM
To: dev@ctakes.apache.org
Subject: ApacheCon 2020 [Bulk]
Hi all,
General admission to ApacheCon 2020 is free:
https://urldefense.proofpoin
e to have a rough head
count for attendance estimation. If you think that you will watch any
presentation of ctakes then please send me ( seanfi...@apache.org ) an email
with the subject "Attend" and "+1" in the body.
Cheers,
Sean
From: Fi
Sean
From: Finan, Sean
Sent: Monday, July 6, 2020 9:08 AM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: ApacheCon 2020
Hi all,
The ctakes representation at ApacheCon 2020 is looking good!
ApacheCon 2020 runs September 29 through October 1.
Submission runs th
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thre
ore/sentdetect/model.jar
Is that the same fix you submitted?
On 7/6/20, 10:49 AM, "Finan, Sean" wrote:
Hi Tom,
Were you using the "Prose Sentences" option? If so, I think that I may
have found the problem (my fault, not the engine's). I checked in a fix but it
.bsv
//LookupXml is the param to specify a custom dictionary xml
//I use this to change the term consumer from Default to Precision or
SemanticCleanup
add org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
LookupXml=path/to/sno_rx_16ab.xml
Tom
On 7/6/20, 12:10 PM, "Finan, Sea
Hi Sreejith,
Without seeing an example of text I can't say whether my next words will help
you or not.
If you are using trunk then you should have access to two 'new' annotation
engines in ctakes-core.
ListAnnotator- Annotates formatted List Sections by detecting them
using Regular Exp
r.
On Fri, Jul 24, 2020, 3:51 AM Finan, Sean
wrote:
> Hi Sreejith,
>
> Without seeing an example of text I can't say whether my next words will
> help you or not.
>
> If you are using trunk then you should have access to two 'new' annotation
> engines in c
ERNAL]
* External Email - Caution *
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: F
Obviously Jeff is correct in all of his answers. Thank you Jeff!
One comment: DictionaryDescriptor is a deprecated parameter name that is picked
up by the piper creator when it inspects the code. However, I am not sure why
the deprecated parameter name isn't working ...
The wiki needs additio
t; Peter
>
> On Fri, Jul 31, 2020 at 4:28 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Obviously Jeff is correct in all of his answers. Thank you Jeff!
> >
> > One comment: DictionaryDescriptor is a deprecated parameter name that is
> >
x27;t have dockhand (as an example).
Thanks,
Jeff
On Wed, Jul 29, 2020 at 1:31 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Tomasz,
>
> As far as I know there aren't any upcoming releases planned.
>
> Sean
>
gt; > On Fri, Jul 31, 2020 at 7:44 PM Peter Abramowitsch <
> > > pabramowit...@gmail.com>
> > > wrote:
> > >
> > > > I could do it while the experience is fresh, although I only know the
> > > happy
> > > > path and not the deepe
Hi Peter,
I would guess that you are seeing things like "SOFT" because you new dictionary
has a vocabulary that was not included in sno_rx_16ab.
I don't remember if OMIM (which has the 'SOFT' synonym) was included in
sno_rx_16ab. Probably not, omim is a more -specialized- vocabulary for
geneti
ent applications: a superior way of finding the values of
findings and a way of validating/pruning the polarity status of concepts that
are in an semi-grammatical or improperly punctuated sentence - such as “Denies
headache, abdominal pain, temperature normal”
Maybe one day
Thanks a
achine()). Is there any way to add a new machine to this
set, which will probably pick the patterns like "Patient smoking status:
No".
Thanks and Regards,
Sreejith
On Fri, Jul 24, 2020 at 4:20 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Sreejith,
>
> Witho
Hi Peter,
I don't have an answer but I do have a question:
In your mrconso.rrf, do you see a snomed line item for "SOB" or only "SOB
-Shortness of breath" ?
I think that the simple "SOB" and "sob" entries might be from other
vocabularies.
There is (was?) logic in the dictionary creator to mul
t of
recompiling.
So the question is: do you know why the empty version is the default?
Peter
On Fri, Aug 14, 2020 at 4:53 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Peter,
>
> I don't have an answer but I do have a question:
>
> In your mrconso
rivate for
now.
Many thanks for your help.
Peter
On Fri, Aug 14, 2020 at 9:51 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Peter,
>
> shining a flashlight back into the dark ages ...
>
> You have found the advanced configuration directories!
>
> Those
Hi Andrew,
Thank you for the reminder.
If my memory serves correctly, we do use CMS on a few pages.
I can be A point of contact for you. As far as I know there haven't been any
public discussions regarding the cTAKES pages, and there have been formal plans
declared.
I will see if I can get s
rhetorical. Wracking my brain for an explanation I had
possibly missed.
Peter
On Fri, Aug 14, 2020 at 10:27 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
>
> >Finally an explanation that makes sense.
> -- It frequently takes a while to get one of those out of me ...
I think that Kean is correct. I usually create an annotator that removes terms
that I don't want. It is usually fairly easy.
final Predicate is2char
= a -> a.getCoveredText().length() == 2;
final String geneTui = SemanticTui.getTui( "Gene or Genome" ).name();
Ont
ctor in our project.
>From your response and Kean's I'm inferring that there's no way to set the
window size to N and have an exception list of a few items that are of
length < N. Right? If there were, it would be in the chunker, not the
term lookup.
Thanks again for yo
Hi Abad,
I think that you need to make only one minor change.
ctakes uses "tokens" for identification and not the actual text. Tokenization
turns text such as "F84.1" into "F84 . 1" The first token being F84, followed
by a token encompassing '.' and another with '1'. The manner in which th
s tagging things like "F84" as other parts of speech,
so you would have to check on that and modify the exclusionTags accordingly.
You can check by adding at the end of your piper:
add pretty.plaintext.PrettyTextWriterFit
and checking the output files that it creates.
I realize that t
D table using
the fetched CUI? Kindly advise.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-
From: Finan, Sean
Sent: Monday, September 14, 2020 9:35 PM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating/Adding val
have something
additional for cTAKES to recognize the code alone as a separate token Is there
any other way in which we can try to get the respective ICD/CPT code of the
identified annotation from cTAKES, like querying the CPT/ICD table using the
fetched CUI? Kindly advise.
Thanks &
anging the
sentenceDetectorAnnotator going to be huge?
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Original Message-----
From: Finan, Sean
Sent: Tuesday, September 15, 2020 9:06 PM
To: dev@ctakes.apache.org
Subject: Re: Building a new custom dictionary or Updating
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