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
otomy 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 some excellent progres
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 file. When I have
> Python read the output text fi
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
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
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 & Regards
Abad Ayyub
Vnet: 406170 | Cell : +91-9447
hanks & 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 values to the
existing dictionary in cTAKES [EXTERNA
f changing 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
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
s is 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
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
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 your suggestions!
Peter
On Tue, Aug 25, 2020
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();
g.
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.rrf, do you see a s
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 actually p
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
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
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
the
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
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,
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
-Original Message-
From: Finan, Sean
S
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
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/Adding values
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:
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
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 again
Peter
Sent from my iPad
> On A
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
>
> From: Tomasz Oliwa
> Sent: Wednesday, J
>
> 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
> >
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
: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 deeper details in this area of the suite
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,
>
> Without
; [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 beyond
this point.
On 6/26/20, 2:33 PM, "Finan, Sean" wrote:
Hi Tom,
Tiny Rest is not really a standalone deal
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
(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)
On 7/1/20, 4:06 PM, "Finan, Sean" wrote:
I had no idea that this was in the install guide:
>$ exports
: 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 objections
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
/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, "Fina
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: Finan, Sean
Sent: Monday, June 29, 2020 11:02 AM
To:
(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.Thread.run(Thread.java:748)
On 7/1/20, 4:06 PM, "Finan, Sean" wrote:
nd java devops to
get to the bottom of this. I really appreciate you taking the time to respond
Sean, and apologize for the java version issue - rookie mistake!
Tom
On 7/1/20, 2:02 PM, "Finan, Sean" wrote:
Hi Tom,
My settings.xml is completely commented. It looks like
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 through
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
ma
kes.
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 availability. He is on the cta
**
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 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
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
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
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
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 Abad,
None of your em
hat 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, Sean
Sent: Thursday, June 11, 2020 9:14 PM
To: dev@ctakes.apache.org; u...@ctakes.apache.org
Subject: Re:
afe :)
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]
[External]
Hi Abad,
The expe
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
, 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 ctakes-core.
> ListAnno
]
* 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: Friday
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
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
?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
ons 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-clinical-pipeli
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
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
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
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/dictionary/looku
-1jMluqo=5v4infTOKs_DKS1MU9guMdb9vBk3jRrvQixooV2M8ZY=
:
where is it finding this other umlsURL???
Tim
On Tue, 2020-12-08 at 17:06 +0000, Finan, Sean wrote:
> * External Email - Caution *
>
>
> Hi Tim, Peter,
>
> Just in case Peter can't get back to you right away,
>
> > I'm actually setting this via
t, but it sounded from your email
> > like
> > there was a patch attachment too that I didn't see. Did that not
> > come
> > through?
> > Tim
> >
> > On Fri, 2020-11-27 at 18:19 +, Finan, Sean wrote:
> > > * External Email - Caution *
>
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
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
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 notice tha
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 +0000, Finan, Sean wrote:
> > * External Email - Caution *
> >
> >
> > Hi Tim and all,
> >
> > Peter kindly ch
eFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=FQFm_YbfeRux_ry1zWBtjd3hgCIPEZvQqmrh1W9UAVE=5acAKSY9--DM3OWA_Kl4H7Uwt7AGhttmPYKUzdnYLEY=
?
Tim
On Tue, 2020-11-24 at 20:14 +0100, Peter Abramowitsch wrote:
> * External Email - Caution *
>
>
> Right, then.
> I'll get that done.
>
> Peter
>
> On Tue, Nov 2
ate their
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
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 important.
C
[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 seemed to work.
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
ming 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 think that i
out 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:
> >
> > Webapp email is
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
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 devlist regularly uses
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]
Hi Eug
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 SNOMED
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
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
genia.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 tried that and it is
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
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
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
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 *
. 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 Abramowitsch
???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
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
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
are 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 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
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 BsvRegexSectionizer
[EXTERNAL] [SUSPICIOUS]
True, true
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
ctionsBsv=/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 containing BsvReg
okups 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 Tom,
>
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
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