Hi Clayton,
The screenshot is not coming through via the newsgroup emails. can you
attach the log file?
vj
On Mon, Jul 7, 2014 at 5:38 PM, Clayton Turner wrote:
> Any update on this issue? I have this problem even if I don't use the ytex
> version of the aggregate text processor (UMLS-indepe
One other thing -- the User install guide says to download the -bin and the Dev
install guide has you checking out from trunk. And the README in the -src
distribution has instructions that only make sense for the -bin distribution.
Are there instructions somewhere for how to install the -src vers
caveat: this may have changed with the new dictionary lookup algorithm, but
fwiw this is base don the old dictionary lookup
The simple answer to 'why no snomed codes by default with ytex?' this is a
cleaner data model, and a faster dictionary lookup. If you want to map
cuis to snomed codes, simpl
It's the latter:
the -src is basically the same as the dev install w/o the subversion
checkout step...
On Tue, Jul 8, 2014 at 7:15 AM, Miller, Timothy <
timothy.mil...@childrens.harvard.edu> wrote:
> One other thing -- the User install guide says to download the -bin and
> the Dev install guide
I don't see a log file when running the CPE. When running the CVD I have
access to a log file within the gui, but that does not seem to be present
here. Is there a specific place that this log file is saved?
On Tue, Jul 8, 2014 at 3:14 AM, vijay garla wrote:
> Hi Clayton,
>
> The screenshot is
Hi there,
I was wondering if there is any way to retrieve CUIs for the tokens of a free
text in CTakes without changing the codebase? I am able to retrieve CUIs for
only medications in a text.
Thanks,
Nick
What gets annotated depends on which pipeline you use.
The pipeline mentioned in the User Guide should also annotate
diseases/disorders, signs/symptoms, procedures, and anatomical sites. So first
would be to check which pipeline you are using.
Or perhaps you do not have the separately downloadab
My bad, the default log4j config just sends everything to the console. Can
you run the cpe, can you redirect the output to a file like this:
runctakesCPE.bat > cpe.log 2>&1
vj
On Tue, Jul 8, 2014 at 6:01 PM, Clayton Turner wrote:
> I don't see a log file when running the CPE. When running the
Thanks James for answering my question.
I am running "ClinicalPipelineWithUmls" which is using
"AggregatePlaintextUMLSProcessor".
The text that I am sending is
"urine culture mos source/body site clean catch culture results
>100,001col/ml escherichia coli final id e.coli amikacin s ampici
The xmi file is attached.
-Original Message-
From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
Sent: Tuesday, July 08, 2014 2:54 PM
To: 'dev@ctakes.apache.org'
Subject: RE: Retrieving CUIs
What gets annotated depends on which pipeline you use.
The pipeline mentioned in the User Gui
Look for things like
org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention
org.apache.ctakes.typesystem.type.textsem.SignSymptomMention
org.apache.ctakes.typesystem.type.textsem.ProcedureMention
For that sample text, using cTAKES 3.1.1, plus the separately downloaded
dictionary, I ge
Nick,
It is fairly easy to extend an annotator (either a java class or groovy
script) to extract just the items for your specific use case.
Check out the HelloWorldAnnotator and Pipeline from ctakes-examples
project. I can write an example that just outputs the CUI if you like, but
I have a hunch
Hi Chen,
I only need CUI. I tried to extend DictoanryLoopkupAnnotator. Is this a writer
approach?
Thanks,
Nick
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Tuesday, July 08, 2014 3:42 PM
To: dev@ctakes.apache.org
Subject: Re: Retrieving CUIs
Nick,
It is fairly
The attachment didn't come through so if the other email I sent didn't help,
please post the xmi somewhere that I can download it from. Thanks.
-Original Message-
From: Nick Nikandish [mailto:snika...@emerginghealthit.com]
Sent: Tuesday, July 08, 2014 2:14 PM
To: dev@ctakes.apache.org
Su
Sorry I meant right approach.
-Original Message-
From: Nick Nikandish [mailto:snika...@emerginghealthit.com]
Sent: Tuesday, July 08, 2014 3:44 PM
To: dev@ctakes.apache.org
Subject: RE: Retrieving CUIs
Hi Chen,
I only need CUI. I tried to extend DictoanryLoopkupAnnotator. Is this a writ
Sure:
http:///org/apache/ctakes/typesystem/type/refsem.ecore";
xmlns:type4="http:///org/apache/ctakes/padtermspotter/type.ecore";
xmlns:cas="http:///uima/cas.ecore";
xmlns:types3="http:///org/montefiore/cri/nlp/culturetests/uima/types.ecore";
xmlns:type6="http:///org/apache/ctakes/smokingstat
The logic should follow what James described. I would write a new
Annotator (or Consumer ) rather than extend DictionaryLookupAnnotator
i.e. run through the complete pipeline, but at the end, iterate through the
IdentifiedAnnotations and get the CUI's from the ontologyConceptArr().
On Tue, Ju
Sure, I will do that.
Thanks.
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Tuesday, July 08, 2014 3:49 PM
To: dev@ctakes.apache.org
Subject: Re: Retrieving CUIs
The logic should follow what James described. I would write a new Annotator
(or Consumer ) rather tha
In your CAS, I see
So it seems like whatever you are doing to try to read out the CUI is not
accessing something correctly.
-- James
-Original Message-
From: Nick Nikandish [mailto:snika...@emerginghealthit.com]
Sent: Tuesday, July 08, 2014 2:46 PM
To: dev@ctakes.apache.org
Subject:
One of the cui that I need to get is for Bactria like " Enterococcus faecium"
but I am not seeing it. I am writing a new annotator to get those cui and save
them in a map. Do you have any applicationContext that I can save those values
and retrieve them in my annotators which are at the end of
Nick,
On why 'Enterococcus faecium' isn't returned:
I think a limitation is that cTAKES will force a mapping of the TUI's semantic
types into a semantic group. If it doesn't exist in the mapping, the
dictionary lookup won't save it.
It would probably be a nice feature to create a "Other" semanti
Thanks Pei,
I will change LookupDesc_Db.xml and test it right now.
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Tuesday, July 08, 2014 4:45 PM
To: dev@ctakes.apache.org
Subject: RE: Retrieving CUIs
Nick,
On why 'Enterococcus faecium' isn't returned:
I
Yes indeed it gets the correct CUI. In the anatomicalSite it return the CUI but
how can I associate the CUI with the text now?
-Original Message-
From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
Sent: Tuesday, July 08, 2014 4:45 PM
To: dev@ctakes.apache.org
Subject: RE: Retrieving
Cancelling the rc-1.
Will send out another vote thread for RC2 shortly.
--Pei
On Tue, Jul 8, 2014 at 10:53 AM, Pei Chen wrote:
> It's the latter:
> the -src is basically the same as the dev install w/o the subversion
> checkout step...
>
>
> On Tue, Jul 8, 2014 at 7:15 AM, Miller, Timothy <
>
Hi all,
The main difference between rc1 and rc2 is that we removed the lvg-res
and assertion-res.jar from the distro. They still need to be
unpacked.
This is a call for a vote on releasing the following candidate (rc2)
as Apache cTAKES 3.2.0.
The major changes include:
- New optional YTEX compon
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