ed, Dec 27, 2017 at 8:30 PM, Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
wrote:
Hi Chahal Arora,
That is odd - I have never seen that message. Are you trying to run with
multiple threads? Like most of ctakes, that class was designed to be run in a
single thread. There are thre
Hi Kishore,
From what you can tell, is there anything in your section headers that may not
fit the regex? Are they all on a line by themselves? That is one requirement
for section headers in that pipeline. For instance, this will not work:
SOCIAL HISTORY: Patient is reticent and withdrawn .
and
ICD10).
I'll aim to setup CouchDB for v2 of the ctakes-rest-service. Next step is
to point cTAKES (within the context of the rest service) at MySQL :).
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Dec 18, 2017 at 1:27 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> w
ow can we get JCas object for each document to pass it for
JCasUtil.indexCovered(); Thank you, Kishore.
On Fri, Dec 29, 2017 at 9:45 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Kishore,
>
> From what you can tell, is there anything in your section head
Hi Kishore,
The fastest and easiest way would be to create a new annotator and use regular
expressions detect such cases, then set uncertainty appropriately.
Sean
-Original Message-
From: kishore [mailto:kasaraneni.kish...@gmail.com]
Sent: Tuesday, January 02, 2018 8:12 AM
To: dev@ctak
nnotation = doctimerel != null &&
doctimerel.contains( “Overlap” );
That should give you a start. I am not sure how much each will help, but they
are suggestions of things that you can try.
Sean
From: Ratan Sharma [mailto:ratanc...@gmail.com]
Sent: Tuesday, January 02, 2018 11:20
Are you running the BsvRegexSectionizer?
-Original Message-
From: Ratan Sharma [mailto:ratanc...@gmail.com]
Sent: Wednesday, January 17, 2018 12:17 PM
To: dev@ctakes.apache.org
Subject: Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]
Thanks Timothy for the details. I guess I was
018 12:53 PM
To: dev@ctakes.apache.org
Subject: Re: SubjectClearTkAnalysisEngine not working [EXTERNAL]
No, I guess I am not running it anywhere explicitly. Is that the reason
segment.getPreferredText() is always null for me.
On Wed, Jan 17, 2018 at 11:14 PM, Finan, Sean <
sean.fi...@childrens.harvard
Hi Don,
To run the standard ctakes clinical pipeline you don't need the ytex module, so
indeed do not panic. If you are not getting a proper build because of ytex
then my advice (without analyzing that output) would be to just comment out the
dependency in the main ctakes pom. If you ever do
Hi Erick,
There is a fourth option that should work
cui | tui | text | preferredText
I would create an importer that creates a -fake- cui. The cui need not (in
this case should not) start with 'C'. So, I would import per-owl uri using
something like OWL1.
tui can be empty, in which c
https://www.nlm.nih.gov/databases/umls.html
-Original Message-
From: Ratan Sharma [mailto:ratanc...@gmail.com]
Sent: Tuesday, January 23, 2018 1:14 PM
To: dev@ctakes.apache.org
Subject: Licence : Use of UMLS dictionaries [EXTERNAL]
I just learnt that use UMLS dictionary is not free. Can
> On Jan 22, 2018, at 2:47 PM, Finan, Sean
> wrote:
>
> Hi Erick,
>
> There is a fourth option that should work
>
> cui | tui | text | preferredText
>
> I would create an importer that creates a -fake- cui. The cui need not (in
> this case should not) start
t can help me?
Kind regards,
Erick
> On Jan 23, 2018, at 5:21 PM, Finan, Sean
> wrote:
>
> Hi Erick,
>
> Each synonym gets a single line in the bsv file. So:
>
> OWL00770 | TOOO | Right parietal lobe
> OWL00770 | TOOO | parietal lobe, right
> OWL00770 | TOOO
Hi Manuel,
Your image got scrubbed by a server, but the problem may have been fixed in a
recent xmi writer. The latest xmi writer is in ctakes core and is named
FileTreeXmiWriter. One possible cause for a problem in the writer is if the
document has some unexpected character or character comb
ed. I'm just kinda baffled with the hierarchy defined for this project.
If you could give me a little bit of clarification in this topic and how to
solve it I would be appreciated.
Thanks for your attention! I'm really looking forward to put this to work.
cTAKES seems awesome. It just need
/resources.
3. Why do we have options in CVD for other languages, but it clearly only
works for the English language?
4. Any other hint you can give me, concerning the big picture of what I'm
trying to build here?
Any additional information you need from my side, just tell me.
T
c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=Dglu7v-Nns-ao41Lbn-oe6MAFF2cEWlkJ-8NQmHv7Xk&e=
2018-01-25 20:43 GMT+00:00 Finan, Sean :
> Hi Manuel,
>
> Thank you for the information. I have a couple of response l
4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=Dglu7v-Nns-ao41Lbn-oe6MAFF2cEWlkJ-8NQmHv7Xk&e=
2018-01-25 20:43 GMT+00:00 Finan, Sean :
> Hi Manuel,
>
> Thank you for the information. I have a couple of
Hi Sekhar,
There may be something better, but this might help ...
There is a small pamphlet that was distributed at a hackathon a year or so
back, and Tim Miller wrote a section describing the essentials of ctakes and
ML. You can find the "pamphlet/manual" on the wiki page :
https://cwiki.apa
It should have nothing to do with the tlink extraction. It copied properties
from events to eventmentions and was in the pipeline after the tlink
annotation, not before.
-Original Message-
From: Lin, Chen [mailto:chen@childrens.harvard.edu]
Sent: Monday, February 12, 2018 10:33 AM
: dev@ctakes.apache.org
Subject: Re: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Thanks to Sean. My bad, I should check the code first before any answer attempt.
Best,
Chen
On 2/12/18, 10:40 AM, "Finan, Sean"
wrote:
>It should have nothing to do w
Hi Gandhi, all,
JdbcDictionary and JdbcConceptFactory are probably the way to go. Just to add,
you don't need to load the dictionary into another database (mysql) to use
Jdbc* classes. They will work out-of-box with the default dictionary.
Sean
-Original Message-
From: Gandhi Rajan N
concept extractor .
But I still stayed true to the interface of umlsdictionarylookupannotator and
validated the credentials of umls as data was dumped from umls.
Regards,
Devi
On 14-Feb-2018 21:42, "Finan, Sean"
wrote:
> Hi Gandhi, all,
>
> JdbcDictionary and JdbcConceptFac
a format that's
convenient for users getting started, so it is really important not to abuse
this.
Tim
On Thu, 2018-02-15 at 14:13 +, Finan, Sean wrote:
> Hi Devi,
>
> There is a lot to say on this topic, and I can't possibly cover it
> all. Disclaimer: the following is no
Unfortunately, writing is not my jam. I wrote about 50% of a paper and then
shoved it aside for other tasks. Now I have no idea where I saved it ...
However, there is an outline of sorts in the code repository within the
ctakes-dictionary-lookup-fast module. The doc/ directory contains a few
UMLS dictionary lookup description [EXTERNAL] [SUSPICIOUS]
[SUSPICIOUS]
Didn't you have some slides at some point as well? I don't know if they are
suitable for public consumption but I remember it was helpful for me at least.
Tim
On Fri, 2018-02-23 at 15:34 +0000, Finan, Sean wrote:
Hi Andrew,
You wrote:
> I ran my script earlier, [...]and only the first run was successful.
Are you saying that one run did succeed? If that is the case then the problem
probably is your network.
The umls credential check will print dots in the log as time progresses, such
as the dots fro
Hi Don,
The default clinical pipeline will provide a little more information:
https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
Sean
-Original Message-
From: Don Flinn [mailto:fl...@alum.mit.edu]
Sent: Tuesday, February 27, 2018 4:16 AM
To: dev@ctakes.apache
Tue, Feb 27, 2018 at 8:21 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Don,
>
> The default clinical pipeline will provide a little more information:
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CT
ave a loop that continually
retries until the operation succeeds?
*Andrew Phillips*
GitHub: github.com/skeledrew
LinkedIn: www.linkedin.com/in/aphillipstech
On 27 February 2018 at 07:18, Finan, Sean
wrote:
> Hi Andrew,
>
> You wrote:
> > I ran my script earlier, [...]a
: www.linkedin.com/in/aphillipstech
On 27 February 2018 at 15:41, Finan, Sean
wrote:
> Hi Andrew,
>
> As far as I know there isn't an explicit timeout imposed by ctakes.
> There is probably a java or system timeout, but I don't know of an
> easy way to change it.
>
> If
Hi Sean,
It looks like you are not using the standard regex file:
> SectionsBsv=E:\ctakes\apache-ctakes-4.0.0\DefaultSectionRegex.bsv
Is it possible that there is a poorly-formed regex?
The sectionizer should time out any regex that takes longer than a few seconds
to complete, but it is possible
Hi Manuel,
The default clinical pipeline runs a piper file located in ctakes-core-res [1].
If you are running using a ctakes binary build, which is how it looks, you can
find the file in:
Resources/org/apache/ctakes/core/pipeline/DefaultFastPipeline.piper
You can edit this file and add a
Hi Kean,
It does sound like you are getting some odd results. I will need to look into
the code, but I won't have time to do so for a few days. My initial thoughts
are below.
>If I add an entry with a comma in it:
>then "chronic kidney disease), stage II" gets picked up, no matter what.
Well
Hi Don,
Oh yes - the file extension ".script" is a bit misleading. You don't need to
execute anything.
We really gloss over it here
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
but basically:
Copy the contents of the .zip file so that they are in the ctakes
Hi Amal,
Could you please provide a full example sentence with expected vs. produced
output? ctakes isn't perfect but something like "fever" should be tagged.
Thanks,
Sean
From: ama...@acolade.co.in
Sent: Friday, March 9, 2018 12:59 AM
To: dev@ctakes.ap
Hi Masoud,
There is a very nice SentenceDetectorBIO in ctakes-core. It will split
sentences based upon features other than just a newline character, which
appears to be what you want.
Sean
From: Masoud Rouhizadeh
Sent: Friday, March 9, 2018 4:41 PM
T
otatorBIO so that it
knows that this is a word-final (i.e. abbreviation-final) and not a
sentence-final period?
Thanks again,
Masoud
On 3/9/18, 5:35 PM, "Finan, Sean" wrote:
Hi Masoud,
There is a very nice SentenceDetectorBIO in ctakes-core. It will split
sentences bas
Arbitrary (pojo?) objects in cas sounds great. serialization must be
interesting.
It is about time that they threw in some garbage collection.
Streaming is great. When I first saw it I thought "so what?" Now I love it.
Thanks for sharing !
From: Mille
Hi Sean,
In case nobody else has replied,
Yes, this would definitely break a whole lot of things. I am not saying that
it is a bad idea, just that the current BinaryTextRelation interface is used
as-is in probably a thousand places, and while some refactoring might be
trivial I wouldn't bet th
Hi Gandhi,
I know that I just sent an email to the devlist, but that seemed like an item
that had wide-impact. Because of some critical work (job that pays the bills)
I am still "dark" as far as ctakes goes - no free nights and only partial
weekends. My apologies. I know that there are a lot
instead of 24 - but Kean's
test code kindly prints the labs and values found so you can look at the test
results.
The code just went into trunk.
Enjoy,
Sean
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, March 28, 2018 9:03 AM
This appears to be a bug in intellij, and oddly enough it just started showing
up in my system today.
You can go through the possible solutions here (I haven't tried):
https://stackoverflow.com/questions/20496239/maven-plugins-can-not-be-found-in-intellij
There are probably other solutions out t
By the way, if you use the exec goal you can do things like pass more memory or
start with the default clinical pipeline, etc. Sean
clinicalGui
clinicalGui
Hi Ewan,
We use Tim's SentenceDetectorAnnotatorBIO in a project that has run hundreds of
notes that contain newline-spanning sentences and it does work very well. As
Tim wrote, it does sometimes lump lines together if they aren't prose. One
example is lines of text in a list. There are a few
Hi Reed,
Wow, you went through a lot of trouble. There actually is a much simpler
solution. It does need proper documentation as it is only hinted at in [1] and
[2]. You can put a dictionary anywhere you want. Then either in your piper
file (configures pipeline) or the command line, or in t
pache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml"
to the VM options in the run configurations for my intellij project? Can
this be a comma-seperated list of locations?
On Fri, Apr 6, 2018 at 9:32 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Reed,
>
> Wow,
, 2018 at 9:52 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Reed,
>
> lookupXml is a parameter that is sent to ctakes, not the vm. But yes, you
> can place "--lookupXml " or simply "-l " to the command line if
> you are running the defaul
Hi Lohitaksh Yogi,
Wow, I wish that you had asked 2 weeks ago as I was actually working in
Charlotte for the week. I could have met you on-site.
There is a small pamphlet available that might help. Visit
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
and click the second link un
Hi Sander Puts,
The trunk version of the dictionary creator will use languages other than
English. You will know if you have the correct version because there will be a
list of checkboxes with ISO language codes.
Make sure that when you extract your umls .rrf files using the nih tool that
you
Hi Rehan,
You have my apologies if somebody already replied to this. I am trying to
catch up with older emails and I am probably missing quite a few in my rush.
Could you please create a jira item for the functionality and attach the
modified code? Then it can be reviewed and added to ctakes.
lass that is
> MySQL-friendly
> - Gandhi and Sandeep are working with me on some JSON changes
> - Shane and I are working on a refactor of the friendly web ui
>
> Thanks,
>
> Matthew Vita
> www.matthewvita.com
>
> On Tue, Jan 2, 2018 at 7:34 AM, Finan, Sean <
>
Negation annotator, Context annotator
etc.. and its short description if I'm right for the write-up.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Monday, April 30, 2018 8:28 PM
To: dev@ctakes.apache.org; Shane Chesnutt ; D
There shouldn't be any difference, but it looks like you may have found one.
From: Peter Abramowitsch
Sent: Wednesday, May 30, 2018 7:22 PM
To: dev@ctakes.apache.org
Subject: for sean, chenpei or james-masanz [EXTERNAL]
Just a quick question -- Is there a
ty
is still with Java 1.8 and above.
Regards. Peter
On Thu, May 31, 2018, 2:09 PM Finan, Sean
wrote:
> There shouldn't be any difference, but it looks like you may have found
> one.
>
> From: Peter Abramowitsch
> Sent: Wednesday, May
Hi Ritika,
It is a little easier to start the clinical pipeline as outlined here:
https://cwiki.apache.org/confluence/display/CTAKES/Default+Clinical+Pipeline
One thing that may cause problems would be a space or special character in the
username or password. Even if it is valid for the umls br
I am missing?
Ritika
-Original Message-
From: Finan, Sean
Sent: Wednesday, July 18, 2018 11:10 PM
To: dev@ctakes.apache.org
Subject: Re: Re: Cannot authenticate license on REST API TRACKING:000308016
[EXTERNAL]
Hi Ritika,
It is a little easier to start the clinical pipeline as out
this help? I generated the logs
Ritika
-Original Message-
From: Finan, Sean
Sent: Thursday, July 19, 2018 12:28 AM
To: dev@ctakes.apache.org
Subject: Re: Re: Cannot authenticate license on REST API TRACKING:000308016
[EXTERNAL]
Hi Ritika,
In your ctakes directory there might be a file
Nq_i1ipVgUNx8o&s=ESavY32g_DgQihKCacFRT0UuB4IQlrcq8rCvseHVCUY&e=
for user ritikajain:
01:41:17,563 ERROR [UmlsUserApprover] Connection timed out: connect
-Original Message-
From: Finan, Sean
Sent: Thursday, July 19, 2018 1:32 AM
To: dev@ctakes.apache.org
Subject: Re: Re: Cannot authenticate lice
ly 19, 2018 9:18 AM
To: dev@ctakes.apache.org
Subject: Re: Cannot authenticate license on REST API TRACKING:000308016
[EXTERNAL]
I am using a proxy.
—
Regards, Ritika
> On 19-Jul-2018, at 9:03 AM, Finan, Sean
> wrote:
>
> Hi Ritika,
>
> The last line of this log is:
>
>
Hi Abhishek,
There is a very short introduction to building pipelines in ctakes 4.0 in a
pamphlet that can be found at
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0 , section
"Documentation", second link. Pamphlet section 5.2, page 5.
There is a runnable example that prints di
Hi all,
Hsqldb is used as the (local) db server and the timeout most likely it is
causing a timeout when read / write is inactive. If anybody has the time it
should be possible to manually disconnect after some ctakes inactivity and then
manually connect when processing (re)starts.
I am reall
while testing web service connecting to MySQL DB. So just
wondering is there any time out setting option available in cTAKES
implementation to retain connectivity?
-Original Message-
From: Finan, Sean
Sent: Tuesday, August 21, 2018 7:33 PM
To: dev@ctakes.apache.org
Subject: RE: ctake web
Hi all,
I have been using 111 - which turned 2 years old last month.
When we first ported ctakes 4.0 to java8 I was using java 8 update 60 - now
over 3 years old.
Peter,
what version were you using?
Thanks,
Sean
From: Peter Abramowitsch
Sent: Monday,
ility. It just
happened that some new code in ctakes-temporal 4.0.1 no longer compiled
under that version. Do you think it will soon be time to move forward off
of eight?
Peter
On Mon, Nov 12, 2018, 4:29 PM Finan, Sean Hi all,
>
> I have been using 111 - which turned 2 years old last mont
Thanks Tim!
From: Miller, Timothy
Sent: Thursday, December 20, 2018 3:24 PM
To: dev@ctakes.apache.org
Subject: ctakes-web-rest changes [EXTERNAL] [SUSPICIOUS]
Hello all,
I've been trying out the ctakes-web-rest module for a project that uses python
where
Hi Tim,
SemanticCleanupTermConsumer does something slightly different than what you are
asking.
Like PrecisionTermConsumer, longer terms of a semantic group subsume fully-
enclosed terms of the same semantic group. Overlapping terms are not subsumed,
just those that are fully covered.
Semant
Hi Sana,
When you say:
>i want to use dictionary_lookup "UmlsLookupAnnotator"
are you talking about the xml descriptor in ctakes-dictionary-lookup-fast? If
so that is great.
>The problem is that identifiedAnnotation given by UmlsLookupAnnotator does
not include Sign/Symptoms, Disease/Disorder o
Hi Kalyani,
At a guess, each parallel instance of ctakes is attempting to write some log
file concurrently and the system does not approve.
Have other people out there witnessed and overcome this problem?
Sean
From: Kalyani Unnikrishnan
Sent: Friday, J
that? becuase i didnt
had to do anything like that for the plaintext. Can you please elaborate
this point too, I am really naive to cTAKES yet so i might be not getting
it right.
PS I am not getting any error or warning related to this in the compiling
logs.
Warm Regards
Sana Riaz
On Thu, Jan
Hi Sana,
This might be related to
https://issues.apache.org/jira/browse/CTAKES-450?filter=-5&jql=project%20%3D%20CTAKES%20AND%20resolution%20%3D%20Unresolved%20AND%20%22Attachment%20count%22%20%3C%3D%20%222%22%20AND%20%22Attachment%20count%22%20%3E%3D%20%221%22%20order%20by%20priority%20DESC%2Cup
dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=1stOSUyvduxWyRf5ExkM407a94mlzdOtd52cdYQb3WQ&s=eSMr6VoSvH5sGvOa4s3OzFHOWPSUigB1hED4x2wu27A&e=
Tim
-Original Message-
From: "Finan, Sean"
mailto:%22Finan,%20sean%22%20%3csean.fi...@childrens.harvard.edu%3e>>
Rep
in. Sorry about that.
On Friday, January 11, 2019, Finan, Sean
wrote:
> Hi Sana,
>
> This might be related to
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.org_jira_browse_CTAKES-2D450-3Ffilter-3D&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
faced issues related to connectivity timeout using mysql db. But
never faced concurrency issue in our testing. Is it hsql db specific by any
chance?
On Friday, January 11, 2019, Finan, Sean
wrote:
> Hi Kalyani,
>
> At a guess, each parallel instance of ctakes is attempting to write some
&
zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=gPZ5JJ-v0kMpDC-vOJTwHP3Ygmn5Ayabo1Rt2xwetpM&s=Ec0ElrVtO9JsYMvjj46U0V07C6KOBvt3Hstk82MR-Og&e=
>
>
>
>
>
> patch
> process-sources
>
> apply
>
>
>
>
Hi Jeff,
The short answer: No, LVG is not in the pipeline created by the
DefaultFastPipeline.piper
Longer answer:
In older versions of dictionary lookup the Lexical Variant Generator module
(LVG) was recommended to capture lexical variants of terms. However, the
dictionary resource already co
Hi Zakir,
In order for me to help you, I need to know more about:
Your primary dictionary:
LookupXml=org/apache/ctakes/dictionary/lookup/fast/tinyDictSpec.xml
Your custom dictionary lookup #1:
add
org.apache.ctakes.raxactakes.dictionary.lookup2.ae.RaxaJCasTermAnnotator
LookupXml=org/apache/ctakes
Consumer
org.apache.ctakes.dictionary.lookup2.consumer.DefaultTermConsumer
*RaxaDefaultJcasTermAnnotator* is similar to the
org.apache.ctakes.dictionary.lookup2.ae.*DefaultJCasTermAnnotator* , I have
only changed the value of _minimumLookupSpan (to
above
scenario using a *single dictionary instance*. please let me know.
On Fri, Feb 22, 2019 at 6:52 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Zakir,
>
> Thank you for the information. Just out of curiosity, why did you decide
> to go with 3 xml files instead of
the things I have
learned along the way setting up ctakes.
On Tue, Feb 19, 2019 at 12:14 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Jeff,
>
> The short answer: No, LVG is not in the pipeline created by the
> DefaultFastPipeline.piper
>
> Longer ans
I think that this might be for Tim
From: Kathy Ferro
Sent: Monday, March 4, 2019 10:57 PM
To: dev@ctakes.apache.org
Subject: Re: ctake web service [EXTERNAL]
Sean,
What machine do you hosting the WS and mysql on? I am on window 10
server. mySQL ini file
Hi Zakir,
I doubt that this has much to do with decreasing the minimum character size for
the dictionary lookup.
> Because if I increase the time between the subsequent user creation and Time
> delay between the subsequent call, I am not getting any exception.
>I am creating 10 users(threads)
Hi all,
I guess that a quick test could be run with a multi-threaded pipeline. Tim,
for some reason I recall you checking in one with a dockerfile. Maybe not, and
it might not be the default in the service. Anyway, you could set the procs to
something like 50 and throw 50 users at it. It de
cop calls which every WS is available and keep
> track of WS statuses. With all this processing going, it might kill the
> power for blocks.
>
> On Fri, Mar 8, 2019 at 10:34 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi all,
> >
> > I gue
i once I feel I have a solid
grasp on it.
Peter- have you made your pipeline pool code available anywhere?
On Fri, Mar 8, 2019 at 12:49 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi all,
>
> >Is there any known reason that you can't create a pipeline pool,
Hi Sekhar,
Perhaps through relationships in the umls you could arrive at such groupings.
https://www.nlm.nih.gov/research/umls/META3_current_relations.html
https://www.ncbi.nlm.nih.gov/books/NBK9679/figure/ch05.F3/
Sean
From: Hari, Sekhar
Sent: Monday,
Hi Raghav,
I think that your dictionary is not specified. The (deeply embedded plus i18n)
error message is:
"Missing name for Dictionary Name"
from
>Caused by:
>org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION
>MESSAGE LOCALIZATION FAILED: java.util.MissingRe
g mapping [EXTERNAL]
Thanks Sean! Looks a little complex to navigate the relationships. Can you
please cite the most appropriate terms in this relationship that may point to
therapeutic area?
Thanks
Sekhar Hari | AI Program Lead | Health Sciences R&D | Asia Pacific Solutions
Delivery Center
+91
Hi Sekhar, Jessie,
I am intrigued by RxMix this app!
Thanks,
Sean
From: Hari, Sekhar
Sent: Tuesday, March 19, 2019 10:34 AM
To: jessie.tenenb...@duke.edu
Cc: dev@ctakes.apache.org
Subject: RE: Therapeutic are - Drug mapping [EXTERNAL]Jessie
Update: I fou
/ help on setting up Lucene index is appreciated.
Thanks,
Raghav
> On Mar 19, 2019, at 7:45 AM, Finan, Sean
> wrote:
>
> Hi Raghav,
>
> I think that your dictionary is not specified. The (deeply embedded plus
> i18n) error message is:
>
> "Mis
Thank you all for your efforts on ctakes!
https://opensource.com/article/19/3/apache-projects?
Sean
Hi Jeff,
> 1) do you think it might not crash yet produce unreliable results when
using the components in the DefaultClinicalPipeline?
-- I am pretty certain that you would get unreliable results. I seem to recall
attempts with the default pipeline crashing, but with a small corpus one could
g
! [EXTERNAL]
This is a great news and feeling happy to be a part of it. Sean, you
deserve a big applause on this journey. Thanks everyone who contributed to
this success.
On Thursday, March 28, 2019, Finan, Sean
wrote:
> Thank you all for your efforts on ctakes!
>
>
> https://urldefense.pr
Hi Jeff,
The 4. default dictionary no longer filters rxnorm to only contain orange book
terms.
If you want to filter your rxnorm terms using orange book it is possible by
filtering your umls db before using the dictionary creator or by culling rxnorm
terms in the created dictionary.
It might
Hi Greg,
What exactly do you need ?
There are a lot of output components that can produce different formats
containing various types of information.
Do you prefer to parse ml ? Or is columnized text output ok? Does this go to
a post-processing engine or a human user?
Thanks,
Sean
_
vy client.
Thanks!
On Wed, May 15, 2019 at 7:43 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Greg,
>
> What exactly do you need ?
>
> There are a lot of output components that can produce different formats
> containing various types of information.
>
&g
Hi all,
The contents of the sno_rx_16ab are a dump of the umls 2016AB snomed and rxnorm
terms with certain symantic types. Nothing was added, but synonyms are
filtered based upon various rules. For instance, unnecessary suffixes are
removed ("Wart (Finding)" -> "Wart"), really long terms are
get "diabetes
mellitus" where as sno_rx_16ab contains both "diabetes" and "dm".
Especially with the addition of "dm" it feels like I must be missing a step
or a setting somewhere.
Thanks!
Jeff
On Sun, Jun 16, 2019 at 8:55 AM Finan, Sean <
sean.fi..
t; contexts and the inheritance that ensues and would like to re-assign them.
>
> Not holding my breath, but just something to keep in mind.
>
> Remy
>
> On Sun, Jun 16, 2019 at 7:16 AM Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > Hi Jeff,
&
T INTO CUI_TERMS VALUES(11849,1,2,'diabetes mellitus','mellitus')
When I created the dictionary from the full cTAKES install tonight, that
error appeared again.
Jeff
On Mon, Jun 17, 2019 at 8:08 PM Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Hi Jeff,
>
>
601 - 700 of 1020 matches
Mail list logo
