here else we need to try the changes. Kindly advise
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/Add
followed by us is correct in the case of
addition of ICD and CPT. Is there any other configuration changes required from
our end for getting the "code" attribute populated as expected for ICD and CPT.
Thanks & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447379028
-Or
Hi all,
I am pleased to announce that ctakes has enough presentations to warrant its
own track.
The track will run all 3 days of ApacheCon; it starts Tuesday Sept. 29th and
end Thursday Oct. 1st, running each day between 12:15 pm EDT and 3:pm EDT.
The track schedule can be viewed here:
htt
This is some fantastic information! Thank you for being so thorough and thank
you so much for reaching out to Patrick McLaughlin!
The next time I am in SF I will buy you a beer, coffee, toffee, whatever.
Sean
From: Peter Abramowitsch
Sent: Thursday, Sep
Hi all,
For those of you who did not see the ApacheCon ctakes presentations today, a
few new elements of ctakes were discussed and I promised to provide "locations"
for some of them.
1. Dockhand, the installation gui:
ctakes-dockhand module in trunk.
maven package it.
The jar
SentenceDetectorAnnotatorBIO commented out in favor of the regular
SentenceDetector. Switch the comments to get the SentenceDetectorAnnotatorBIO.
Sean
From: Finan, Sean
Sent: Tuesday, September 29, 2020 3:53 PM
To: dev@ctakes.apache.org
Subject: Revealing my
Hi Peter,
There are untold miles of code that I have never traveled ...
I don't understand the -1. Maybe the original code used some other code (
.start() )that wasn't zero-based?
It seems like nec.begin should not be offset and that down the line consumers
should offset to n-1 or .max(n-1,
Do you already
implement something like that?
4. What about Jira? Do permissions and links come from Apache? I've been
on it briefly in read-only mode.
There's no hurry to respond. I'm on my way back to Italy shortly and will
set up shop there again next week som
Hi Greg,
The simple answer is that we have no answer. yet.
This change in authentication will require some work from ctakes developers and
we haven't yet mapped out the effort.
We will endeavor to have both an implementation and documentation available
before the current authentication is no
Hi Tim and all,
Peter kindly checked this into trunk last week.
I tested that version and it seemed to work.
Another question might be "how do we get this into the/a release?
I haven't looked into whether or not Apache svn servers have a locking
mechanism on release branches, but if not I thi
tors
[EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
* External Email - Caution *
On Tue, 2020-11-24 at 16:29 +, Finan, Sean wrote:
> * External Email - Caution *
>
>
> Hi Tim and all,
>
> Peter kindly checked this into trunk last week.
> I tested that version and it s
t: Re: Changes to UTS Authentication for Authorized Content Distributors
[EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Sean,
I can take up a few things if you can guide me on the same.
On Tue, Nov 24, 2020 at 9:59 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
>
can attach it here if attachments are allowed.
On Tue, Nov 24, 2020 at 7:23 PM Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Gandhi,
That would be great!
I think that an additional test would be useful and putting Peter's
documentation on the wiki is importa
ld that be useful?
Peter
On Tue, Nov 24, 2020 at 6:46 PM Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> On Tue, 2020-11-24 at 16:29 +, Finan, Sean wrote:
> > * External Email - Caution *
> >
> >
> > Hi Tim and all,
> >
> > Peter
gt; I'll get that done.
>
> Peter
>
> On Tue, Nov 24, 2020 at 7:53 PM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > I think so. Whether we can 'release' it or not, branching code
> > from the
> > 4.0 release is probably a fi
eir
dependency version.
Let us keep this rolling,
Sean
From: Finan, Sean
Sent: Tuesday, November 24, 2020 4:02 PM
To: dev@ctakes.apache.org
Subject: Re: Changes to UTS Authentication for Authorized Content Distributors
[EXTERNAL] [SUSPICIOUS] [SUSPICI
trunk becoming 4.1.0-SNAPSHOT? I.e. a new
feature release... when it comes.
Peter
Sent from my iPad
> On Nov 24, 2020, at 22:10, Finan, Sean
> wrote:
>
> Webapp email is killing me ... that email was sent prematurely.
>
>> ctakes-4.0.0-rc3to ctakes-4.0.1
>
> I th
w about 4.0.0 going to 4.0.1
> and trunk becoming 4.1.0-SNAPSHOT? I.e. a new feature release...
> when it comes.
>
> Peter
>
> Sent from my iPad
>
> > On Nov 24, 2020, at 22:10, Finan, Sean <
> > sean.fi...@childrens.harvard.edu> wrote:
> >
> > Webap
Hi Eugenia,
I am glad that you are a fan!
The trunk version has a profile to start the piper file submitter gui defined
in the ctakes-examples pom.
However, the 4.0 release does not have a profile to do so.
If you want to use a pfs gui profile in 4.0 then you will need to edit a
downstream
Oh -- ctakes-clinical-pipeline does not have ctakes-gui as a dependency. So if
you want to put the profile in that pom then you will also need to add
ctakes-gui as a dependency in that pom.
From: Finan, Sean
Sent: Wednesday, November 25, 2020 9:30 AM
To
IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com
-Original Message-----
From: Finan, Sean
Sent: 25 November 2020 14:33
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
Oh -- ctakes-clini
Arg.Yeah. We need to deprecate that module ... I frequently forget that
it exists.
There should not be any problems with having the one class ask permission from
the other.
There shouldn't be any need to duplicate the working code.
From: Peter A
?Thanks Peter,
Happy Thanksgiving all
From: Peter Abramowitsch
Sent: Friday, November 27, 2020 11:47 AM
To: dev@ctakes.apache.org
Subject: 4.0.0 UMLS Authentication Patch - for Developers - Not a release
[EXTERNAL]
* External Email - Caution *
Hi Sean
Give
23683 Email: eugenia.monogy...@nttdata.com
-Original Message-
From: Finan, Sean
Sent: 25 November 2020 16:20
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
>if I make any changes I can simply rename the file and run it again
I haven't t
Hi Eugenia,
>1.
- A few years ago Kean Kaufmann wrote a nice annotator that can discover lab
values. https://issues.apache.org/jira/browse/CTAKES-441
It is in ctakes as org.apache.ctakes.core.ae.LabValueFinder
It may not be exactly what you are looking for, but you can see from the
comments
Hi Eugenia,
In short, I think that you may be stuck.
The only immediate solution that I can offer is to look for a nearby lab value
- by number or by unit. If a value exists then you could assume that it is a
lab result.
Sean
From: Monogyiou, Eugenia
.mil...@childrens.harvard.edu> wrote:
>
> > Peter, I saw the readme attachment, but it sounded from your email
> > like
> > there was a patch attachment too that I didn't see. Did that not
> > come
> > throu
UY3RXS1He-CqwN-1jMluqo&s=5v4infTOKs_DKS1MU9guMdb9vBk3jRrvQixooV2M8ZY&e=
:
where is it finding this other umlsURL???
Tim
On Tue, 2020-12-08 at 17:06 +, Finan, Sean wrote:
> * External Email - Caution *
>
>
> Hi Tim, Peter,
>
> Just in case Peter can't get back to you right awa
both of
those projects. The old lookup now uses the fast lookup's new auth
mechanism. Sorry if that sounded contorted
Peter
On Tue, Dec 8, 2020 at 6:39 PM Finan, Sean
wrote:
> In your dictionary configuration xml file? That would be
> resources/org/apache/ctakes/dictio
Peter, thanks for making the test(s) actually do something.
Just as an aside, since it doesn't much matter right now, but supposedly
maven-surefire-plugin
${maven-surefire-plugin.vers
Argh. And now I notice that there is no /*Tester.java ...
From: Finan, Sean
Sent: Tuesday, December 8, 2020 1:56 PM
To: dev@ctakes.apache.org
Subject: Re: 4.0.0 trial UserTester [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Peter, thanks for
Hi Eugenia,
Within the past few years people have made some user-friendly tools. Check out:
https://razorsql.com/features/hsqldb_gui_tools.html
After you launch it (30 day trial is free), create a new connection as the
first panel indicates.
- Type any name for the connection (line #1)
- for
- it
was just a stub..
Peter
On Tue, Dec 8, 2020 at 9:33 PM Peter Abramowitsch
wrote:
> exactement.
>
> On Tue, Dec 8, 2020 at 8:02 PM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
>> Argh. And now I notic
ta UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com
-Original Message-----
From: Finan, Sean
Sent: 08 December 2020 19:23
To: dev@ctakes.apache.org
Subject: Re: Disambiguation --alignment with SNOMED [EXTERNAL]
H
Hi Peter, Kean and others,
> Seems to me that if we don't do anything,
- I plan to give this 100% of my time starting next week. Well, right after I
clean the basement.
> we will have a flurry of support
> emails in 4.0.0 as soon as the NLM completes its roll-over.
- I would call that optimis
back is greatly appreciated :)
Kind Regards,
Eugenia
-Original Message-----
From: Finan, Sean
Sent: 09 December 2020 14:23
To: dev@ctakes.apache.org
Subject: Re: Disambiguation --alignment with SNOMED [EXTERNAL]
Hi Eugenia,
I don't know that anybody on the devlis
Subject: RE: Disambiguation --alignment with SNOMED [EXTERNAL]
* External Email - Caution *
I can't thank you enough!
Kind Regards,
Eugenia
-Original Message-
From: Finan, Sean
Sent: 09 December 2020 16:49
To: dev@ctakes.apache.org
Subject: Re: Disambiguation --alignment with S
only?
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com
-Original Message-
From: Finan, Sean
Sent: 09 December 2020 17:14
To: dev@ctakes.apache.org
Subject
Could you send me the debug lines and/or unit tests?
From: Peter Abramowitsch
Sent: Monday, December 28, 2020 4:45 AM
To: dev@ctakes.apache.org
Subject: Sean... & UMLS [EXTERNAL]
* External Email - Caution *
Hi Sean
Corresponding with Kean on another ma
Sorry for the confusion re: threads.
> Hi Sean
> The debug lines in reference to...?
-- In case you had inserted extra lines in the code to log information for
debugging.
> If you're thinking about my LabValueFinder conversation with Kean the other
> day, I've been working with him on another em
Excellent, thanks! It looks like this component is getting some great
attention!
From: Peter Abramowitsch
Sent: Wednesday, December 30, 2020 11:27 AM
To: dev@ctakes.apache.org
Subject: LabValueFinderTester updated [EXTERNAL]
* External Email - Caution *
commented. You may want to
fix that.
Peter
On Wed, Dec 30, 2020 at 5:43 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Excellent, thanks! It looks like this component is getting some great
> attention!
>
> From: Peter Abr
Hi Eugenia,
The authentication code in trunk is not exactly the same as Peter's original
code. I tried to simplify things so that the user does not need to make any
url changes.
If the url specified in the dictionary properties xml is the old umls user/pass
rest url then the new code automa
Hi Eugenia,
In intellij you can easily run any class containing a main(..) method with a
simple right-click as you have done. In a single module project this works
just fine. However, in a multi-module project like ctakes intellij may not
know to use the entire classpath necessary for the cla
???As some have experienced, the U.S.A. National Library of Medicine (NLM) has
changed the authentication method for using the Unified Medical Language System
(UMLS).
https://www.nlm.nih.gov/research/umls/index.html
Though a bit late in its arrival, Apache cTAKES now has a patch release that
having this problem.
As soon as I witness working links I will let you all know.
Thank you,
Sean
From: Finan, Sean
Sent: Wednesday, January 20, 2021 10:24 AM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: Apache cTAKES 4.0.0.1 : UMLS Authentication
Hi all,
The "Downloads" page on ctakes.apache.org should now be working as expected.
I have tested several mirror servers and they all appear to have the 4.0.0.1
packaged downloads available.
Enjoy,
Sean
____
From: Finan, Sean
Sent: Thursday, January
Hi Tim,
This is really exciting!
Just having this code available to use as a template is extremely useful.
Cheers,
Sean
From: Miller, Timothy
Sent: Sunday, January 24, 2021 11:08 AM
To: dev@ctakes.apache.org
Subject: neural negation model in ctakes [EX
Hi Greg, Peter,
I believe that the performance report comes from a CollectionProcessingEngine
(CPE)
https://uima.apache.org/d/uimaj-current/apidocs/org/apache/uima/collection/CollectionProcessingEngine.html
I think that UIMA's CPE GUI runs the pipeline through a CPE - hence the tool's
name,
Hi Thomas,
Short answer:
You can't do that. The collection of Section definitions is shared through all
of the pipelines.
Long answer:
I think that there might be another approach.
My guess is that within your two different note types there is some common
section header expression, but the co
ionizer SectionsBsv=/my/custom/file.bsv
// Change or remove Sections
add my.java.package.SectionAdjuster
Sean
____
From: Finan, Sean
Sent: Saturday, January 30, 2021 10:00 AM
To: dev@ctakes.apache.org
Subject: Re: Passing SectionsBsv to piper contain
s and add the BSV lookups from the different class loaders. It would
be a lot of work and not as tidy as the kind of thing Sean is suggesting.
But you can lie awake at night thinking about it anyway.
Peter
On Sat, Jan 30, 2021 at 4:27 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote
Hi Greg,
just to clarify, 4.0.1 (trunk) is faster than 4.0.0.1 (4.0.0 Patch) ?
Are you asking if/when 4.0.1 (trunk) might become the "latest official release"?
Sean
From: Greg Silverman
Sent: Tuesday, February 2, 2021 10:51 AM
To: dev@ctakes.apache.org
S
n,
Yes to both.
Best!
Greg--
On Tue, Feb 2, 2021 at 10:06 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Greg,
>
> just to clarify, 4.0.1 (trunk) is faster than 4.0.0.1 (4.0.0 Patch) ?
>
> Are you asking if/when 4.0.1 (trunk) might become
You could add an annotator to the end of your pipeline that persistently marks
a document as read, and then a "first" annotator that redirects anything done
to some "null device"
For instance:
// Out this at the end of the pipeline and it will write a list of files that
have been processed to t
Runtime.getRuntime().addShutdownHook( new Thread( () -> {
Files.lines( new File("path/to/my/files/done/list.txt").toPath() )
.map( p -> new File( p ) )
.foreach( f -> f.renameTo( "my/done/dir/"+f.getName() );
} ) );
}
}
_____
a BSV file to use, the B_PipelineRunner uses the
same BSV file regardless of what the B_piper file says.
____
From: Finan, Sean
Sent: Saturday, January 30, 2021 2:32 PM
To: dev@ctakes.apache.org
Subject: Re: Passing SectionsBsv to piper containing BsvRegexSectioniz
Hi Greg,
It looks like the offending class might be
org.apache.ctakes.core.fsm.adapters.DecimalTokenAdapter, which seems to be the
only NumberTokenAdapter without a try/catch around the parse(..).
I made a fix that runs on my tests. Since you say that you cannot build
trunk/4.0.1 locally (cus
Hi Greg,
>From the log that you sent it looks like you didn't set your umls api key for
>that run.
>
10 Feb 2021 18:03:42 ERROR UmlsUserApprover - umlsUser CHANGE_ME not
allowed. It is a placeholder reminder.
10 Feb 2021 18:03:42 ERROR UmlsUserApprover - umlsPass CHANGE_ME not
allowed. It
https://www.youtube.com/watch?v=kZw42pGzyHs
From: Greg Silverman
Sent: Tuesday, February 23, 2021 10:51 AM
To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
Subject: access to presentation on cTAKES at scale [EXTERNAL]
* External Email - Caution *
Hi,
Is
Thanks! No available powerpoint, I presume?
Greg--
On Tue, Feb 23, 2021 at 10:03 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> https://urldefense.com/v3/__https://www.youtube.com/watch?v=kZw42pGzyHs__;!!NZvER7FxgEiBAiR_!8BgV-J
2021 1:36 PM
To: dev@ctakes.apache.org
Cc: Himanshu Shekhar Sahoo
Subject: Re: access to presentation on cTAKES at scale [EXTERNAL]
* External Email - Caution *
👍
On Tue, Feb 23, 2021 at 12:22 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Huh, you are correct. The rest o
Hi Sean (Mullane),
For the original problem:
No Analysis
> > Component found for org.apache.ctakes.core.ae.CuiFilterAnnotator
This means that somewhere in your piper file you have an "add" command for an
analysis engine named "CuiFilterAnnotator".
There is no org.apache.ctakes.core.ae.CuiFilt
branch and recompile.
Thanks,
Sean
-Original Message-----
From: Finan, Sean
Sent: Saturday, February 27, 2021 2:33 PM
To: dev@ctakes.apache.org
Subject: Re: 4.0.0.1 patch [EXTERNAL]
Hi Sean (Mullane),
For the original problem:
No Analysis
> > Component found for org.apache.ctakes.core.ae.Cu
it to be local only, then the
build will sometimes fail because of other dependencies it needs to
update. It's a bit of an octopus.And so, if I were to create a maven
submodule with my permissions, how could I be sure not to contaminate the
global archive when I sure don't want to..?
Peter
Hi Thea and Johanne,
Some of our institutions block attachments and inserted images from unknown
emailers.
Could you post the question with a plain text listing of the error?
Thanks,
Sean
From: Johanne Krogsgaard Jensen
Sent: Thursday, March 18, 2021 7:31
Hi Peter, Eugenia,
I haven't noticed the occurrence, but can believe that this could happen. I am
not sure why or how. I suppose you could run two counts to find out how many
are missing - I don't want to know.
There are probably a few things that could be done to 'cover' this problem, but
t
?That looks like a fun little ms windows problem.
AppData\Local\Packages\Microsoft.Windows.Search_cw5n1h2txyewy\LocalState\ConstraintIndex\Apps_{cf9957f1-d72a-454c-b482-ff422f953a8c}
Did you place the source in a -normal- windows directory such as
"C:\apache\ctakes\" ?
Are you in an old fas
moving the source code to directly under C:\ctakes folder it worked.
On Thu, Mar 18, 2021 at 6:10 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> ?That looks like a fun little ms windows problem.
>
>
>
>
> AppData\Local\Packages\Microsoft.Windows.Search_
Hi Thea and Johanne,
I have a "easy button" recommendation at the end. Feel free to skip to that if
you don't want to look at utility methods and just want to see some example
code.
> Here we try to access the CollectionMap allConceptsMap, which to our
> understanding include all the concep
https://www.oracle.com/java/technologies/javase/javase-jdk8-downloads.html
From: Mullane, Sean *HS
Sent: Wednesday, April 14, 2021 3:56 PM
To: 'dev@ctakes.apache.org'
Subject: JDK situation [EXTERNAL]
* External Email - Caution *
Since Oracle has change
Hi John,
Just out of curiosity, if you have one method that works then why do you want
to use a different method to do the same thing?
I personally use the PIpelineBuilder as you have in your second example when I
need to work with code - though that is extremely rare as piper files can
handle
ive but correct me if I'm wrong.
On Thu, Apr 22, 2021 at 1:58 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi John,
>
> Just out of curiosity, if you have one method that works then why do you
> want to use a different method to do the same thing?
>
>
Hi Javi,
I too would like to get more developers and activity with source available on
Github. Hopefully you can help us do it.
One problem that we had in the past concerning use of Github is caused by large
machine learning models in ctakes. Github has file size limits for
repositories and
Linkedin: es.linkedin.com/in/javiroman
Big Data Blog: dataintensive.info
On Tue, Apr 27, 2021 at 5:15 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Javi,
>
> I too would like to get more developers and activity with source available
> on Github. Hopefully you
and
storing the blob in a location external to the git repository itself, in
this case hosted by GitHub.
This is just an idea.
--
Javi Roman
Twitter: @javiromanrh
GitHub: github.com/javiroman
Linkedin: es.linkedin.com/in/javiroman
Big Data Blog: dataintensive.info
On Tue, Apr 27, 2021 at
To which ctakes component(s) are you referring?
From: Greg Silverman
Sent: Sunday, May 16, 2021 6:02 PM
To: dev@ctakes.apache.org; Himanshu Shekhar Sahoo
Subject: rule-based lookup for custom lexicon [EXTERNAL]
* External Email - Caution *
I looked all
s).
When I Googled around, I stumbled on UIMA Ruta, but couldn't find anything
wrt to cTAKES specifics.
Thanks!
Greg--
On Tue, May 18, 2021 at 10:04 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> To which ctakes component(s) are you referring?
> __
vid container:
> >
> >
> https://urldefense.com/v3/__https://github.com/Machine-Learning-for-Medical-Language/ctakes-covid-container__;!!NZvER7FxgEiBAiR_!7ZopTIhXKalQFx0xET_yET0agN2ZT8JWoa0UyqGSrXa4w-h_9-tRCEeiS4pr6s2Y-T4elV3bYac$
> > Tim
> >
> > _
vantages.
I was thinking about creating some introductory examples for the
combination and usage of UIMA Ruta and cTAKES. If you have a good use
case, let me know.
Best,
(another) Peter
Am 19.05.2021 um 14:30 schrieb Finan, Sean:
> Hi all,
> Correct.
>
> Tim is correct in the sens
Hi John,
>Can you help me with a few questions?
- I will try. Others may offer alternate or additional information.
> If I wanted to create a modified workflow without the entire source code,
> could I create a jar file of the module I wanted to modify and then replace
> that jar file in the U
Hi John, I sent a reply directly to jrcaskey at medicine.wisc.edu
Let me know if you don't get it.
Sean
Hi all,
I am happy to announce that Peter Klugl, creator of Apache UIMA Ruta, will
participate in an informal discussion on Apache's UIMA Rule-based Text
Annotator (Ruta).
This Apache UIMA(tm) component consists of two major parts: An Analysis Engine,
which interprets and executes the rule-b
, "Finan, Sean" wrote:
Hi all,
I am happy to announce that Peter Klugl, creator of Apache UIMA Ruta, will
participate in an informal discussion on Apache's UIMA Rule-based Text
Annotator (Ruta).
This Apache UIMA(tm) component consists of two major parts: An A
Ok, so much for keeping this private ... I should have been more specific about
my email address.
Michael - this was my fault, not yours.
From: Finan, Sean
Sent: Wednesday, May 26, 2021 7:59 AM
To: dev@ctakes.apache.org
Subject: Re: Discussion on Apache
Sorry all, I should have said "If you are interested, send directly to my email
address." I forgot that Apache automatically routes through the lists.
Please send an email to:
sean.fi...@tch.harvard.edu
thanks,
Sean
____
From: Finan, Sean
Sent:
BTW, I have created a new meeting and the invitation below is defunct. You
still need to email me with your info to get an invitation.
Sean
From: Finan, Sean
Sent: Wednesday, May 26, 2021 8:09 AM
To: dev@ctakes.apache.org
Subject: Re: Discussion on
Hi John,
It shouldn't be excluded from ctakes-core, but if you are looking at the binary
distributable or maven central artifact for ctakes 4.0.0.1 then it will
definitely be absent as it didn't exist in that version. It is only in the
trunk version of ctakes currently under development. You
Hi John,
I am not completely sure that I understand what you are asking, and I think
that this is more of an s3 question than a ctakes question, but here are a
couple of comments:
> the cTAKES part of it relies on CTAKES_HOME being set
- Is this requirement on your side? I never bother to set
sure if EFS will be available,
which is why I'm trying to see if I can do it on S3.
On Mon, Aug 2, 2021 at 11:41 AM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi John,
>
> I am not completely sure that I understand what you are asking, and I
> think that t
Without a little more information I cannot tell you exactly why you are getting
that exact error.
ctakes 4.0.0.1 was built with UIMA v2. Trying to use a newer version of uima
and/or uimafit will (frequently) not work.
Any declared dependency on ctakes, such as you have for core and
clinical-
Hi Benjamin,
My first question is: what pipeline are you trying to run?
My second question is: Do you really need to use LVG?
Sean
From: Benjamin hansen
Sent: Wednesday, August 18, 2021 3:07 AM
To: dev@ctakes.apache.org
Subject: An exception occured whil
Hi Peter,
I use the piper files, and temporal sub piper TemporalSubPipe.piper in
ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/pipeline
contains the following:
// Commands and parameters to create a default temporal processing
sub-pipeline. This is not a full pipeline.
//
Hi Peter,
To your question:
>there isn't yet much code that pulls these relations out in any user-friendly
>way?
the answer is mostly no. The relation-related code in ctakes is mostly for
experimentation and not utilization.
Annotations/Events and Relations are translated in a few places into
e edges.
Alternatively you could use Pair as the map key, but more than one
relation type between two annotations would cause problems. Or an ugly
Map>> in which the pairs are constantly added
to the collection ...
Sean
________
From: Finan, Sean
Sent:
I think that you are both correct.
One or more preferred texts for a concept should be available if the user
created a local copy of the umls that contains one a vocabulary that contains a
preferred text. This is the first step in the process of creating a ctakes
dictionary and takes place bef
> let's hope
for lots of those and good holidays for all.
Peter
On Tue, Dec 7, 2021 at 7:05 PM Finan, Sean
wrote:
> I think that you are both correct.
>
> One or more preferred texts for a concept should be available if the user
> created a local copy of the umls that contains
Hi Peter,
I have noticed this and just added a following engine that recognized text
within event spans. It is a lazy solution, but it fit my needs and available
time.
Sean
From: Peter Abramowitsch
Sent: Monday, January 3, 2022 5:03 PM
To: dev@ctakes.a
I see you made some source
changes in that area and will check tomorrow.
Peter
On Mon, Jan 3, 2022 at 2:26 PM Finan, Sean
wrote:
> Hi Peter,
>
> I have noticed this and just added a following engine that recognized text
> within event spans. It is a lazy
Email - Caution *
Hi Sean
Ok.. I was confused whether I was meant to find it in the sources.
But while you're reading this, is there a brief way to describe the
difference between the older:package
org.apache.ctakes.assertion.medfacts.cleartk;
and
org.apache.ctakes.assertion.medfacts.cleartk.
801 - 900 of 1020 matches
Mail list logo
