Hi Alexandre,
>for user myUserName,:
Notice the comma. The "export" command will export two variables and values
without a comma. Adding a comma to the command adds the comma to the value of
the first variable.
sh-4.3$ export v1=one, v2=two
sh-4.3$ echo $v1
one,
sh-4.3$ export v3=three v
6 8:32 AM
To: dev@ctakes.apache.org
Subject: Re: CTAKES DICTIONARY CREATOR GUI !!!
Hi and happy new year.
why in the data base generator we have exclude list for example in the rxnorm
section we have EXCLUSION_RXNORM = "SY"; ? whats this is about ?
Regards.
On Sun, Dec 13, 2015 at
Hi Patrick,
What version of ctakes are you running? The stack trace looks a little strange.
The Tokenizer used by the smoking status module was changed from
TokenizerAnnotator to tokenizerAnnotatorPTB in version 2.3 on 5/11/2012. But
in your trace it looks like the TokenizerAnnotator class is
CP6r0bcpKGd4f7d4gTao&m=I2RDR92crNxCMkNkHohpBpc_wMG1FJ2xFSfWwgVIxW8&s=v3FlCkQgYLzmZHBhHASLna5gkLUIQ0LqwPrjavSIuew&e=
.
Regards,
Patrick
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Thursday, January 07, 2016 3:12 PM
To: dev@ctakes.apache.org
Subject:
Very cool, thanks Tim
-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
Sent: Tuesday, January 26, 2016 2:59 PM
To: dev@ctakes.apache.org
Subject: umls graph api
I've been working on some code for easy querying of the UMLS relation
graph that I think
. :^)
Sean
From: srinivasa.rao kundeti [mailto:srinivas1...@gmail.com]
Sent: Wednesday, January 27, 2016 11:07 PM
To: dev@ctakes.apache.org; Finan, Sean; pei.c...@childrens.harvard.edu;
srinivasa@philips.com; bruce.tiet...@imatsolutions.com
Subject: I am New to CTakes 3.2.2 : Need Help
Hi Sean/Pie
Hi John,
One thing that you can try is using the "Overlap" version of the dictionary
lookup. It should identify both "right lower quadrant pain" and "left
lower quadrant pain" as Sign/Symptoms.
Check
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+-+Fast+Dictionary+Lookup
Hi Jessica,
You have it correct - LVG will add variants that the dictionary lookup will use
in an attempt to discover terms not explicitly in the dictionary database -
such as the plurals that you saw. However, it does not guarantee "better"
results. The lvg module can add variants that are i
Hi Abhilash,
The fastest way to dive into ctakes development might be to look at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.java
It has a few methods that can build slightly different pipelines and a main(..)
that will run some fake text through a pipeline.
After that you can lo
Has anybody else recently encountered problems unpacking v 3.2.1.1 of
net.sourceforge.ctakesresources.ctakes-resources-lvg2008 ?
Thanks,
Sean
Hi Brandon,
The dictionary creator gui in sandbox automatically adds selected coding
schemes to the concept factory. Is it not doing what you need?
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, March 02, 2016 12:43 PM
To: 'dev@ctakes.a
I can't wait to check it out! Cheers
-Original Message-
From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu]
Sent: Monday, March 14, 2016 3:02 PM
To: 'dev@ctakes.apache.org'
Subject: RE: cTAKES scale-out with DUCC and Shangridocs
WOW, this is fantastic, Chris! Thank you
Hi Tomasz,
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..
Hi Joshua,
The fast dictionary module in ctakes can use flat files with _bar-separated
values_ (.bsv). Checkout
*ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/example/bsv*
for some example formats. Start with *custom_cui_tui_bsv.bsv* as an
Hi Harish,
Not yet. It is high on the "todo" list but nobody has had the time to tackle
it.
As an aside, the fast dictionary module in ctakes can use flat files with
bar-separated values (.bsv). Checkout
ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/loo
The agreement that the ctakes core group was able to achieve with the NLM
(distributor of UMLS) was that ctakes would check a user's access rights upon
every use of any database derived from the UMLS. The reason for this was that
the NLM did not want one valid UMLS user to download the database
n May 16, 2016, at 9:12 AM, Finan, Sean
> wrote:
>
> The agreement that the ctakes core group was able to achieve with the NLM
> (distributor of UMLS) was that ctakes would check a user's access rights upon
> every use of any database derived from the UMLS. The reason for
Hi Jan,
It looks like ou are basically trying to run the equivalent of:
ctakes-clinical-pipeline/desc/../analysis_engine/CuisOnlyPlaintextUMLSProcessor.xml
You could try swapping out the Aggregate... for that one and see what happens.
Sean
-Original Message-
From: Jan Zieher [mailto:jzie
Hi Jose,
There are a lot of ways to do this, and there are examples laying about. I
think that you basically have a 3 step process:
1) Run "mvn package" on the source to build the latest binary.
2) Write a main(..) class that has something like:
CollectionReader collectionReader = --
Hi Tomasz,
Ctakes lookup (both original and fast-) is case insensitive by design. There
have been brief discussions on changing this behavior, but things like
capitalized form entries, list headings, and plain old first word
capitalization have prevented it from being implemented.
One big in
Oh - I should mention:
Increasing the minimum required span cause have unwanted false negatives. A
minimum of 5 will get rid of things like "arm" and "foot". You could make your
own AE that changes this by getting rid of only disease/disorder with character
count < 5 . That would probably be
that
simply removes an annotation based on some criteria like case and semantic
type? Or does cTAKES have such a switch already available?
________
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Wednesday, June 01, 2016 10:56 AM
To: dev@ctakes.ap
arameters or change foldernames for the dictionary-gui to get
a similar numbers?
Thanks,
Tomasz
____
From: Finan, Sean [sean.fi...@childrens.harvard.edu]
Sent: Wednesday, June 01, 2016 2:40 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES false positives, case-i
Hi Vicky,
You can view the current requirements here:
http://ctakes.staging.apache.org/downloads.cgi
Sean
-Original Message-
From: Vicky Chawda [mailto:vicky.cha...@praxify.com]
Sent: Monday, June 20, 2016 7:02 AM
To: dev@ctakes.apache.org
Subject: Hardware Requirement
What is the mini
ick, experimenting with java opts
> settings can get you down pretty low, and you can slim down to the
> barest of needs (pipelines and dictionaries) if needed.
> On Jun 20, 2016 11:46, "Finan, Sean"
>
> wrote:
>
> > Hi Vicky,
> > You can view the current r
Hi Peter,
Our group has used two different approaches, depending upon the note type:
1. Use a custom AE that creates creation time based upon a regex. This works
well for notes that have a header or footer with a known format.
2. Use the last normalized temporal expression. For my test notes
the CAS as a creation time property so that it can be retrieved
later by a client that knows only the serialized CAS?
Peter
On 7/13/16, 11:41 AM, "Finan, Sean"
wrote:
>Hi Peter,
>
>Our group has used two different approaches, depending upon the note type:
>1. Use a cust
Wednesday, July 13, 2016 3:04 PM
To: dev@ctakes.apache.org
Subject: Re: Help needed with document creation time/date
Got it. Thanks
On 7/13/16, 12:00 PM, "Finan, Sean"
wrote:
>DATE_PATTERN.matcher
ings but also against the value of attributes such as POS.
Just like Stanford's TokensRegex
- Peter
On 7/13/16, 12:19 PM, "Finan, Sean"
wrote:
>Pattern.compile( ".*Principal Date\\D+(\\d+) (\\d+).*", DOTALL );
Hi Bandeep,
The gui only works with the new dictionary schema. However, there is an older
command-line (cli) dictionary creator that will create a database in the old
format. The cli version has more options than the gui, but that makes it more
attentive to detail - meaning that you need to b
Hi Vicky,
The closest to an API that I know of is in the clinical pipeline module:
org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory
It has static methods that will return descriptors for the two most commonly
used clinical pipelines. You can look at that class to get an idea of the
"s
Hi Tomasz,
As far as I know, the ae is only instantiated to create the type system, which
is then handed off. So, you shouldn't need to worry about thread safety
problems with the ae. I have an idea for deserializing concurrently, but
you'll notice that I did things slightly differently ...
Hadi is a new member of the NLP group here at Boston Children's Hospital. He
has a background in NLP research and will now be applying his knowledge to the
biomedical domain, and he will be using cTAKES (and why wouldn't he?)
Sean
Hi W.P.,
What is your goal for the run? The easiest thing for you to do might be trying
the "CuisOnlyPlaintextUMLSProcessor" pipeline .xml . That will start you with
a fast pipeline that provides cuis from dictionary lookup. It has commented
lines that you can uncomment, adding one module at
tUMLSProcessor" support or will it do Assertion
Annotation ?
Roshan
On Thu, Oct 6, 2016 at 5:43 PM, Finan, Sean < sean.fi...@childrens.harvard.edu>
wrote:
> Hi W.P.,
>
> What is your goal for the run? The easiest thing for you to do might
> be trying the "CuisOnlyPl
cpKGd4f7d4gTao&m=nCyxC3bK1JwXOPno_KJMfXkiA2HNiP3bs_BsTnl9DTM&s=SiEDKygCD5kLW3hQU564Vx1IvuY0RIKDdtHxlSpP67M&e=
comes as an original Apache repository file and ran the CAS Visual Debugger and
ClinicalPipelineWithUmls.java
I feel like I had miscommunication. but I hope it'll be clear n
Hi Bandeep,
So you are successfully identifying the relations but need more human-readable
output?
Try using the PropertyTextWriter. It will output properties and relations in a
more readable manner. You can look at the code there to see the basics of
grabbing and outputting relation informat
Hi Murali,
I appreciate the volunteerism! However, much of the "fervor" as you put it, is
new functionality. We at the Boston Children's Hospital CHIP-NLP group (
http://www.chip.org/research ) are preparing for a cTAKES usability hackathon
at the Amia 2016 Annual Symposium:
https://sites.go
Hi Yiming,
Thank you very much for letting the community know what has and has not worked
for you. I have also had better results with the Assertion annotators than the
ClearTk alternatives, but that could be because of the note types/formats that
I am using.
Regarding the "Clear" in names, i
f but almost identical F1 scores. But
> for that dataset the tradeoff negex provided was preferred by our
> collaborators. (I think negex had better recall of negated terms but worse
> precision).
>
> Tim
>
>
>
>
> From: Finan
Sure - can you do that?
Thanks,
Sean
-Original Message-
From: Joern Kottmann [mailto:kottm...@gmail.com]
Sent: Wednesday, October 19, 2016 7:52 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES Couldn't find parse for:
This can easily be fixed in the OpenNLP Parser. Should we open an iss
Hi Bandeep,
I myself and several colleagues have be building and running ctakes with jdk 8.
Ctakes 3.2.3-snapshot (trunk) actually requires java 8 as the code uses
lambdas, streams and functions, etc.
We have not needed to do anything beyond pointing to jdk/jre 8. Has this not
worked for you
Hi Melvin,
Thank you for reporting the test bug and going through the effort of tracking
down the root. You can post a bug report on
https://issues.apache.org/jira/browse/CTAKES/?selectedTab=com.atlassian.jira.jira-projects-plugin:summary-panel
1. Search emails using something like MarkMail h
1 release.
Jörn
On Thu, Oct 20, 2016 at 1:57 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Sure - can you do that?
>
> Thanks,
> Sean
>
> -Original Message-
> From: Joern Kottmann [mailto:kottm...@gmail.com]
> Sent: Wednesday, October 19, 201
Hi Xi,
There are a number of things that I can recommend, but first I need to ask if
you are using the pre-built version downloaded from the ctakes website or if
you are using code. Your answer to this question will impact how I can best
provide help.
Sean
-Original Message-
From: Xi
Hi Arron,
Ctakes discovers text words and phrases by lookup using a subset of the UMLS
https://uts.nlm.nih.gov/home.htmlctakes then assigns a code to everything
that it finds.
While you can employ various workarounds to remove "epilepsy" in when within
"epilepsy clinic", these are not part
Hi Patrick,
Are you running on a 64 bit machine? Ctakes requires 3 GB to run the standard
clinical pipeline, and for the system to address that much memory it needs 64
bits. You should also make certain that you are running 64 bit Java.
Sean
-Original Message-
From: Patrick Casimir [
Hi Shyam,
Instead of getting all Identified annotations:
JCasUtil.select( jcas, IdentifiedAnnotation.class )
You can get desired subclasses:
JCasUtil.select( jcas, AnatomicalSiteMention.class )
JCasUtil.select( jcas, DiseaseDisorderMention.class )
JCasUtil.select(
Hi Peter, Patrick,
Just in case I am the "Sean" in question, I will say that Peter provided an
excellent answer. ctakes doesn't send patient information over the network.
As Peter indicated, in order to protect information you should run ctakes in a
HIPAA compliant environment - just as you w
Hi Murali,
Before we make an rc, we must go through the list of currently open tars and
requests. SOP. A list needs to be compiled of what should be closed as fixed
or n/a plus another list of outstanding bugs that need to be dealt with and an
estimate of effort. Then we should try to gather
s hold up a release.
> I suggest just we mark anything that hasn’t been fixed in Jira into the next
> release and push forward- I’ll volunteer to do that right now.
> In the past, the documentation on the website also shouldn’t hold up a
> release either.
>
> > On Dec 6, 20
MSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SSX4hTAgVD9Hauv28TZlIg6CjaFdtBrFBQJXI3eauzs&s=WE-LsxWpvhEVtVAi1tdjMeBbEFM1vU22JDmuU8MVc0M&e=
>] - change concept type <>On Dec 6, 2016, at 11:20 AM, Jeff Headley
wrote:
>
> I realize I’m not a committer and
uch a sentence splitting?
It would seem to me that it should remain one sentence. For example, the
smoking status detector has its own SentenceAdjuster that merges some of such
sentences back into one, because of this design.
Thanks, Tomasz
From: Finan,
dev aspects of cTAKES as I have so far
been mostly been a user of it.
Can you tell me if the information under the "NegationAnnotator.xml" and
"Updating Negex Patterns" headings on this page is still current?
Thanks,
Sean
-Original Message-----
From: Finan,
This is a great question. mvn compile requires -DskipTests otherwise the build
breaks. This is very poor form and everybody that installs runs into this. It
would be great if we could fix this before the release. Any volunteers?
Sean
-Original Message-
From: Andrey Kurdumov [mailto:
Hi Andrey,
The requirement of skipping tests for a successful build is something that all
ctakes developers have stumbled across, but after initial setup we all forget
about it and it has never been handled. Apologies.
The github mirror is something that would be great to have, but getting it
ueqTsyc_T5Aetds4ipSzuYo&e=
> ).
> I saw issue
>
> CTAKES-185
>
> which could be appropriate for that, and I could create patch for that
> change. During the course of my next project, very likely I would be
> involved in the activities similar to cTakes, so I potential
:chen...@apache.org]
Sent: Tuesday, December 13, 2016 11:15 AM
To: dev@ctakes.apache.org
Subject: Re: Infrastructures questions.
What release are you referring to?
On Tue, Dec 13, 2016 at 11:08 AM, Finan, Sean
wrote:
> By the way, did we ever vote on the release?
> https://urldefense.proofpoint.com/v2
next few days- otherwise, let’s tag this Fri and prepare
>> and push forward?
>>
>>> On Dec 6, 2016, at 11:52 AM, Finan, Sean
>>> wrote:
>>>
>>> Hi Pei,
>>>
>>> Thank you for starting step 1: compiling a list of tars and their
> > > > > >
> > > > > > Also I start looking how cTakes working, and investigate
> > dependencies
> > > > > > between packages, and found following comment: "Temporary
> > workaround: Adding
> > > > > > i
, December 16, 2016 3:40 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org
Subject: Re: Dictionary in cTAKES
Thanks Sean and Nishant for the help. Sean, the document you sent was really
helpful. I was able to successfully create a dictionary using the
dictionary-gui. But I'm still not able to us
Hi Andrey,
I am not going to address the errors that you mention in your email, but I will
just say that you can stop with "mvn package". If you go to the directory
ctakes-distribution/target/ there should be an
apache-ctakes-3.2.3-SNAPSHOT-bin.zip file. This is the ctakes binary package
for
y.
If this is gives you too much trouble, I apologize for that.
I soon will start updating dependencies to have latest versions where possible.
If you think it would be valuable to cTakes itself, I could share my changes
when I finish upgrade process.
Thanks
Andrey.
2016-12-19 2:50 GMT+06:00 Finan,
Hi Erica,
You are correct: ctakes normalizes to CUI. If you fetch Snomed codes then you
will get all snomed codes that match the CUI, which may be > 1/1.
The reason for this is that those snomed codes are synonymous (or not truly
unique) as determined by somebody who contributes to the umls.
tences "WORD1:" and "WORD2 WORD3."? Do other components of
> cTAKES require such a sentence splitting?
>
> It would seem to me that it should remain one sentence. For example,
> the smoking status detector has its own SentenceAdjuster that merges
> some of such
Hi Pratik,
Because combinations of strength, route, form, etc. for medications amount to
an enormous number of unique terms, the possible combinations are not included
in the default ctakes dictionary.
You can:
1. Add a custom dictionary with your fully-defined terms of interest, or
2. Create
Hi Vighnesh,
1. Does ctakes depend upon exact word match?
By default, yet. The fast clinical pipeline uses
"DefaultJCasTermAnnotator" or some such horribly named class. There is also an
"OverlapJCasTermAnnotator". Equally horrible name, slightly different
functionality. Given: "Blo
give valuable solution, and one example.
regards,
shyam k.
On Thu, Dec 22, 2016 at 9:16 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Shyam,
>
> I think that the key to your first question
> > how can execute the single function to run all this jobs in sh
csv file.
please give me a solution and example..
regards,
shyam k.
On Thu, Jan 12, 2017 at 8:48 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Shyam,
>
> Have a look at the LinesFromFileCollectionReader class in ctakes-core.
> It doesn't use csv files,
case.
TextSpan ts = new DefaultTextSpan( BaseToken, 0 );
Thanks & Regards
Vighnesh
On Thu, Jan 12, 2017 at 10:12 PM, Sparsh K wrote:
> Thanks for clarification sean.
>
> On Thu, Jan 12, 2017 at 8:43 PM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
>
13, 2017 at 8:19 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Shyam,
>
> I'm not sure what the [4] is doing in your nextLine String processing.
>
> That aside, are you seeing the pipeline being initiated multiple times?
> This could be the problem.
&g
Hi Joyce,
If you are building from source then you should not need to manually download
the resources. Maven should be doing it for you. Well, that is the behavior
of 3.2.3 ... I honestly cannot remember what 3.2.2 did ...
Otherwise, I think that if the latest was the 3.2.1.1 then that is pro
nal Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 10:57 AM
To: dev@ctakes.apache.org
Subject: [EXTERNAL] RE: New to CTAKES
Hi Joyce,
If you are building from source then you should not need to manually download
the resources. Maven shou
k into the next release may take some effort.
I did notice several packages in the sandbox version of the code. Is there any
plans to bring any of those new packages into the trunk?
Thanks,
Joyce
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tues
27;ve
just graduated the code into the existing ctakes-core and ctakes-
coreference modules once it's ready.
Tim
On Tue, 2017-01-17 at 18:22 +0000, Finan, Sean wrote:
> Hi Joyce,
>
> Thank you for the information on your background and what is being
> done for/by
Hi Joyce,
Ctakes is actually umls version-agnostic, it just requires that the umls be in
a format that it can understand. As you noticed, the umls bundles repackaged
for ctakes are 2011AB.
You can package any version and flavor of the umls for ctakes 3.2.3. The
Dictionary Gui in ctakes sandb
ubject: RE: cTAKES/UMLs Versions
Thanks Sean,
Do you know if YTEX which works with a SQL Database is also version-agnostic?
Thanks,
Joyce
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Tuesday, January 17, 2017 3:11 PM
To: dev@ctakes.apache.org
Hi Andrey,
I won't have time to test this until next week or maybe even after that. If
there are no showstoppers then you have done the community a great favor!
Others and I have wanted to update LVG and hsqldb for so, so long. I hope that
somebody out there can have a look at this as I woul
ideally get:
Castor Oil 793 MG --> codes:[309035]
Instead, I still get:
Castor --> codes:[2129]
Oil --> codes:[1021284]
793 MG --> codes:[]
Please help me understand how this is actually picking out the covered text,
and if there's a way I can modify the pattern so that it giv
An answer to the question "I have a code, how do I get the term text?":
In order to get the preferred text and available synonyms of a term, using its
snomedct (or other) code you can use the umls metathesaurus:
https://uts.nlm.nih.gov/metathesaurus.html
You’ll need to login, then on the left sel
Hi Arron Lacey,
That particular cas consumer java class is a uimafit-paradigm implementation,
and from my memory the CPE gui does not play well with Uimafit. I could be
wrong - I never use the cpe anymore.
You might be able to get things working by changing line #23 in the .xml file
from
o
but I am curious if you
don't personally use the CPE, how to you batch process documents?
I would like to just run the AggregatePlaintextFastUMLSProcessor.xml on all
files in a given directory - perhaps with *some* control over the output
filenames.
Thanks,
Arron.
On Fri, 20 Jan, 201
see if that particular class is present?
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org; Finan, Sean; kant2...@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml
bug a few weeks ago.
Thanks,
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Saturday, January 21, 2017 1:42 PM
To: dev@ctakes.apache.org; Finan, Sean; kant2...@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Have put username and password (umls) in custom.xml as well
those done by others the new “fast” lookup has as good or
better accuracy depending upon the test corpus. Plus it is runs in 1/500th the
time. I recommend that you stick to it.
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Tuesday, January 24, 2017 5:50 AM
To: Finan, Sean
Cc: dev
rom “levels”.
I hope that helps,
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Tuesday, January 24, 2017 10:17 AM
To: Finan, Sean
Cc: dev@ctakes.apache.org; kant2...@googlemail.com; pratik agarwal
Subject: Re: Ctakes Dictionary Gui
Hi Sean
I am testing the stuff on the fast and Aggreg
t.
- Some fixes to ytex related tests, that's was required for me to pass mvn
install command.
Assumptions:
- User should update ctakesnormx and other databases from HSQLdb 1.8 to HSQLDB
2.3.4
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Wednesday, January 25, 2017 2:
Hi Jorn,
Great idea! Have you done any testing with the latest release? I think that
ctakes has 3 dependencies on opennlp libraries. We should try to get our
integration with that update (and others) solidified for the upcoming release.
The boston children's hospital nlp team just gained a
is mentioning GENIA, do you still use that?
> >
> > The POS Tagger these days can also be trained directly on the Penn
> > Tree Bank, but you could also use OntoNotes.
> >
> > Should I sent you a patch to update your poms?
> >
> > I also noticed you are not
Hi Pei,
I am a little taken back by your statement:
> I do not see an need for BCH to override existing volunteers.
>From what James wrote, I don't get the feeling that he is trying to override
>other RM volunteers or in any way take control of the release. His email
>stated specifically that
Hi Andrey,
You have recently been a great contributor to ctakes , and I really appreciate
that. You have answered devlist questions and your LVG update is a seriously
big deal. Because of this, you are probably very interested in the upcoming
release. You may have read emails that were on th
Hi all,
I just have a couple of notes to expand upon what Guergana wrote.
Anafora requires a schema for annotation and it requires text files to be in a
certain structure. I just checked in text files for annotation and the schema
that we plan to use in ctakes-examples-res
src/main/resources/
Hi Alaa,
Have a look at the OntologyConceptUtil class in ctakes-core. You can use the
getCodes(..) method to obtain the codes for a scheme.
For all codes of all annotations:
Collection allCodes = OntologyConceptUtil.getCodes( jcas, schemeName );
For all codes of all annotations in a window (pa
PM
To: dev@ctakes.apache.org
Subject: RE: jcas work with a list of schemas
Thanks sean but internally this fetch data for all schemas then filter the
needed schema right ?
On Feb 6, 2017 7:57 PM, "Finan, Sean"
wrote:
> Hi Alaa,
>
> Have a look at the OntologyConceptUtil cl
@ctakes.apache.org
Subject: RE: jcas work with a list of schemas
Thanks. I was hoping for away to fetch only whats needed for performance
enhancement.
On Feb 6, 2017 8:09 PM, "Finan, Sean"
wrote:
> Yes. You do not need to use the code directly if it doesn't fit your
> needs. You
faster.
On Feb 6, 2017 8:21 PM, "Finan, Sean"
wrote:
Hi Alaa,
Are you a java developer or do you have a different background? If you are
not a developer, could you please enumerate exactly what you need?
Thanks
-Original Message-
From: Alaa al
Hi Erin,
Where did you get that copy of the umls? I have 2016AA and it has the standard
.rrf filenames.
As long as your .aa/.ab files have the standard mrconso.rrf format, you should
be able to rename them to mrconso.rrf.
Sean
https://www.ncbi.nlm.nih.gov/books/NBK9685/
-Original Messag
lts selected in the tool? Any thoughts?
Thanks,
Erin
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, February 08, 2017 3:34 PM
To: dev@ctakes.apache.org
Subject: RE: UMLS version in dictionary-gui
Hi Erin,
Where did you get that copy of th
t
certain custom dictionaries from the GUI (T047 only) run fine but others with
more TUIs don't?
Is there any way to still use the custom dictionary in 3.2.2 by modifying the
configuration file to make it compatible?
-Erin
-Original Message-----
From: Finan, Sean [mailto:sean.fi...@childr
Yes, thanks. I will try to look into this a little later.
Sean
From: shahid ashraf [mailto:sha...@trialx.com]
Sent: Friday, February 10, 2017 3:45 PM
To: Finan, Sean
Subject: Re: CAS Pool
Are you looking for these lines
11 Feb 2017 02:13:59 INFO POSTagger - POS tagger model file:
org
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