up descriptors for a lookup using the bsv
>files they point to. If you want your bsv lookup to complement the
>default lookup it's possible to just have two dictionaries running with
>different lookup descriptors. I think it's also possible to have a lookup
>descriptor have multiple
Sorry for the very wordy contribution here Following on Tim's
answer, I've found the historyOf mechanism to be very weak in its ability
to detect more than just a few possible permutations, and one frequent
issue is span where history Of modifies a series of concepts.
-
iptors. I think it's also possible to have a lookup
>descriptor have multiple lookup types (i.e. multiple
>sections inside ) but I can't guarantee that works!
>Tim
>
>
>From: Abramowitsch, Peter
>Sent: Thursday, January 4, 2018 7:51 AM
&
amp;r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=j2h_timB4skc
>lRz6ICf0XlmaUgJekZOOgGo_WF-iuDw&s=qbZInrnxDgeP2prW-pOoOFkVLFweja-ct48H8NWy
>dIM&e=
>
>Tim
>
>
>From: Abramowitsch, Peter
>Sent: Thursday, January 4, 2018 7:28 AM
>To: dev
Further to my previous message, Sean, I was wondering if you could tell me
whether this answer you gave in 2015, is still the right way to do things in
ctakes4.x
permalink: http://markmail.org/message/s3ztinppusvsciss
Subject:RE: How to update cTAKES so that new top level categories co
Can someone point me to any up-to-date how-tos on how to include external
CSV/BSV type resources to add synonyms, and other terms for dictionary lookup
to augment the FAST UMLS resources that comes out of the box. Perhaps I have
missed something, but looking at the CTakesDictionaryCreator UI,
I have built a type of medical summary module, but the ctakes output was
only a part of the data source and where it was, there was a great deal of
post processing on the CAS, so I suppose it doesn't really classify as a
Ctakes module. However, I'd be interested in any attempts that others have
mad
ection if you
>have something better than ctakes.
>
>-Original Message-
>From: Abramowitsch, Peter [mailto:pabramowit...@hearst.com]
>Sent: Friday, March 31, 2017 3:47 AM
>To: dev@ctakes.apache.org
>Subject: Re: Labs annotator?
>
>I know I'm probably too late into this
I know I'm probably too late into this discussion, but I think the extra
effort to pull out the unit of measure and normalize it will make it
possible to parse notes where a parameter's units are described
differently from one to the next. It would be a pain for each user of
Ctakes to have to pars
oofpoint.com/v2/url?u=http-3A__scholar.harvard.edu_gu
>ergana-5Fk-5Fsavova_biocv&d=DwIFAw&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7
>CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=uOutBBTdNsYiDP3HAuF-_UFIGcTT6qqeuYEBj7dQ
>N2I&s=lj2ltefhatVPII-9YxnA0QHcsvaeL22-sVSCFLZ_QQM&e=
>
>--
There is another, more generic NLP engine, StanfordCoreNLP which does
have more advanced CORel annotation capabilities, but it is not
specifically tuned to clinical concepts and relationships. So for
instance, causal relationships might be detected if expressed in standard
english, but certainly n
I've had some experience pipelining ctakes behind a servlet (not the demo
servlet) and, without going deep into the code, My feeling is that there
are no globally static data resources with instance level content. It's
all just configuration and dictionaries. Threading errors would only
occur if
Hi Melvin
I suggest you have a look at the company Mmodal.
They have gone a very long way toward clinically tuned speech recognition
+ NLP + populating and acting on spoken clinical data
I am not directly connected with them but had the opportunity to meet
their team and see the capabilities of th
Hi Erica
In many cases (I would say most cases) there is not enough semantic
information in incoming text to resolve to a leaf level SNOMED code, so
the CUI is a good cut at mapping the concept. Applications can then
surface just the relevant SNOMED codes/descriptions and have the human who
has m
If by security you mean, protection of data, this would depend entirely on the
architecture in which CTakes is situated.
CTakes itself does not send anything beyond its perimeter except the UMLS login
credentials. So if it were running entirely within a HIPAA compliant
environment then yes.
Bu
While it is doable, it will need some non trivial post processing. The
approach I suggest below is just an example, there are many ways to
achieve this, but there is no silver bullet.
To do something like that I suggest incorporating a TokensRegex analysis
engine in your pipeline. I have had a lo
Hi Vicky
There are two Time related annotation types and neither of them are
incredibly useful on their own and there's no documentation that I've
found, so far. What I've deduced is by trial and error with short
phrases, trying to reverse engineer the behavior
TimeMention attempts to link a tim
Thank you!
Knowing now that it's a do-it-yourself thing, I might also try adding
those expressions to a RegexAnnotator that I'm using: It allows the
expressions to be added and combined in an external file.
https://logiciels.lina.univ-nantes.fr/redmine/.../uima-tokens-regex-documen
tation.pdf
I
Got it. Thanks
On 7/13/16, 12:00 PM, "Finan, Sean"
wrote:
>DATE_PATTERN.matcher
imerel,
>doctime) together post-process. We are doing this in one project.
>
>Sean
>
>-Original Message-
>From: Abramowitsch, Peter [mailto:pabramowit...@hearst.com]
>Sent: Wednesday, July 13, 2016 2:33 PM
>To: dev@ctakes.apache.org
>Subject: Help needed with d
Hello All
How can I get Ctakes to deduce the document creation datetime from the text. I
have a pipeline including the following engines
Basic Token Processing
FastUMLS
Zoner
ClearNLPDependencyParserAE
PolarityCleartkAnalysisEngine
UncertaintyCleartkAnalysisEngine
HistoryCleartkAnalysisEngi
Vivek
Chris and I responded to you about 12 hours ago.
On 6/28/16, 10:17 AM, "Vivek Venugopal" wrote:
>Hi,
>
>Regarding my query on cTakes and UMLS :
>I haven't got any response. Any info would be helpful.
>
>
>Thanks,
>Vivek Venugopal.
>
Hi Dima
Personally I hate Maven because of how it obscures classpaths and
dependencies (even though it purports to make that easier). My use case
is a little different than yours, but when I launch a little pipeline from
the command line, it looks as simple as this:
Cd into the top of my applic
On second thought... This might be useful
http://stackoverflow.com/questions/18055189/why-my-uri-is-not-hierarchical
On 6/28/16, 9:24 AM, "Abramowitsch, Peter"
wrote:
>Dima
>
>Although I'm not an expert, I don't think Ctakes relies on any Environment
>varia
Dima
Although I'm not an expert, I don't think Ctakes relies on any Environment
variables a priori, unless you have a Ctakes extensions that has added a
dependency. Depending on your error you may need to look in AE or
TypeSystem definition files or in the uimafit types.txt file where search
path
It doesn't actually access the database, It accesses your UMLS license.
- P
On 6/27/16, 11:04 PM, "Vicky Chawda" wrote:
>cTAKES as a REST API in Apache Tika accesses UMLS Database online, How can
>we set it up in offline mode?
>
>Regards,
>
>*Vicky Chawda.*
>*Software Engineer,*
>*Praxify Tech
I created one in about 15 minutes using SparkJava. Basically you look at
the code in the ClinicalPipeline package that gives you the workflow to
create a pipeline, assign incoming text to a newly created Jcas, and then
run the pipeline, finally calling a Json or XmlSerializer on the populated
CAS
I'm not sure of Ytex adds another requirement, but is there any reason you
can't just download the pre-built UMLS tables and use the internal Ctakes
hsql DB mechanism as documented here? :
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Dictionaries+
and+Models.
I would also choose
Help -- I need suggestions for where else to look for a problem adding a
new annotation engine to a pipeline. I've Run out of ideas.
New Annotator is a UimaTokensRegex which builds an annotation called
MultipleWordTermOccurrence.
Here is where I've gotten to:
* Created Cas description of Engin
Hello Ctakes Dev
This is a general set of question which may reflect a bad install on my part or
something going on in the 3.2 version that is more than just a set of boundary
case bugs. I am a newcomer to CTakes, but have spent a lot of time with
StanfordCoreNLP, writing annotators, and with
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