Many thanks for answering me,
cTAKES is the core of my research and I am stuck
How can I generate cTAKES without CVD? is there a command or GUI for that?
How to generate other format such as html or marked text?
------------------------------------------------------------------------------------
The way I know is :
There is misunderstanding for sure here.
We feed CVD with text such as "This patient has diabetes and no signs for
kidney failure"
we also provide the Run > Load AE with the pipeline we are going to use.
Once we click on Run AE, cTakes work and analyse the provided text.
Then we save the results as .XMI which can be taken to any tool suck as UIMA to
display results visually
am I right here?
Thanks
On Tuesday, 17 December 2019, 02:54:03 am AEDT, Finan, Sean
<[email protected]> wrote:
Hi Akram,
Gandhi has provided some good links, and I agree that you should read that
information.
In case you haven't found it, there is also a "quick start" manual is on this
page: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
Under "Documentation", there is a download named "A pamphlet/manual on cTAKES
basics".
It was meant to have an accompanying human tutor, but it does contain some
handy information.
> I can get CVD run on the binary version of cTAKES.
-- Excellent!
> but I have problem on the Developer version.
-- Are you using an IDE? There might be a maven profile listed named "runCVD".
You can try to compile ctakes with that profile.
>From a command line: "mvn compile -PrunCVD"
-- Regardless, if you've already built a binary then at least you can run it
there. The CVD is not a ctakes product, but is bundled with uima. So if you
change ctakes code CVD will still remain the same.
-- https://uima.apache.org/d/uimaj-current/tools.html#ugr.tools.cvd
I think that there is a misunderstanding here:
>When I try to Load AE on the CVD (Development Version) I get this error
-- The CVD is meant to display output from ctakes.
-- If you run ctakes to produce an .xmi file(s) then you can load the .xmi file
into the CVD and view what ctakes discovered in the document.
While the CVD is very good for debugging and roaming details, you can also
produce simpler output types such as html and marked text.
Other output types might be easier for new users, and they do not require
running a second tool (CVD).
Sean
________________________________________
From: Akram <[email protected]>
Sent: Sunday, December 15, 2019 6:35 AM
To: [email protected]
Subject: Re: How does cTAKES work? [EXTERNAL]
Warning: Email originated outside Boston Children's. Don't click
links/attachments unless you know sender & content seems safe.
**********************************************************************
Thanks Gandhi
I can get CVD run on the binary version of cTAKES.
but I have problem on the Developer version.
When I try to Load AE on the CVD (Development Version) I get this error
When I try to load : AggregatePlaintextProcessor.xml
I get Error : org.apache.uima.resource.ResourceInitializationException: More
detailed information in the log file
When I try to load : AggregatePlaintextFastUMLSProcessor.xml
I get Error : org.apache.uima.resource.ResourceInitializationException: an
import could not be resolved. No file with name
"org/apache/ctakes/drugner/types/TypeSystem.xml" was found in the class path
or data path
(Descriptor:file:/D:/cTAKES/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml)
More detailed information in the log file
P.S. I changed CTAKES_HOME to D:\cTAKES which is the development folder that
has all code)
How can I fix that?
=================================================Error 1:
<date>2019-12-15T22:23:11</date> <millis>1576408991483</millis>
<sequence>7</sequence> <logger>org.apache.uima</logger> <level>SEVERE</level>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>handleException(527)</method> <thread>24</thread> <message>Exception
occurred</message> <exception>
<message>org.apache.uima.resource.ResourceInitializationException</message>
<frame>
<class>org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl</class>
<method>load</method> <line>82</line> </frame>
=================================================Error 2:
<date>2019-12-15T22:32:54</date> <millis>1576409574952</millis>
<sequence>9</sequence> <logger>org.apache.uima</logger> <level>SEVERE</level>
<class>org.apache.uima.tools.cvd.MainFrame</class>
<method>handleException(527)</method> <thread>24</thread> <message>An import
could not be resolved. No file with name
"org/apache/ctakes/drugner/types/TypeSystem.xml" was found in the class path or
data path. (Descriptor:
file:/J:/__cTAKES/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml)</message>
<exception>
<message>org.apache.uima.resource.ResourceInitializationException: An import
could not be resolved. No file with name
"org/apache/ctakes/drugner/types/TypeSystem.xml" was found in the class path or
data path. (Descriptor:
file:/J:/__cTAKES/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml)</message>
<frame>
<class>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl</class>
<method>initialize</method> <line>165</line> </frame> <frame>
<class>org.apache.uima.impl.AnalysisEngineFactory_impl</class>
<method>produceResource</method> <line>94</line> </frame>
On Sunday, 15 December 2019, 05:46:24 pm AEDT, gandhi rajan
<[email protected]> wrote:
Hi Akram,
I would prefer to have a look at the following link:
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2BUser-2BInstall-2BGuide&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xWsLlr2p_eCQrJQdreWNUdMv0gchC_6EB3QxoTfWeKw&s=qxZURGVbSA4ymygrHulseFwwUMkwDW5dyrRJTsw_1k4&e=
And for loading custom dictionaries you gotta look at the following link:
https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2BDictionaries-2Band-2BModels&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xWsLlr2p_eCQrJQdreWNUdMv0gchC_6EB3QxoTfWeKw&s=eQMp1QR1LlSy17WiuET0TT87CkBF-TMbH5on4i7CJiU&e=
On Sun, Dec 15, 2019 at 9:19 AM Akram <[email protected]> wrote:
> Hi
> I have 2 questions, and would appreciate the help.
> The first question
> ==================
> I have been trying to get how cTAKES work and not so much luck
> I know that we build .piper file through "cTAKES Simple Pipeline
> Fabricator"
> we get a .piper file
> Then the process is not clear
> my understanding and I am not sure if I am right here
> is that we create a .xml file from the .piper file through
> I tried using "cTAKES Pipe File Submitter"
> I loaded HelloWorld.piper but I got this error
> org.apache.uima.resource.ResourceInitializationException: MESSAGE
> LOCALIZATION FAILED: Can't find resource for bundle
> java.util.PropertyResourceBundle, key No Analysis Component found for
> ContextDependentTokenizerAnnotator
> I read Sean's email in the mail archive
> and Replaced
> add ContextDependentTokenizerAnnotator
> with
> add org.apache.ctakes.contexttokenizer.ae
> .ContextDependentTokenizerAnnotator
> but still getting the same error
>
> The 2nd question
> ===============
> After creating the .xml the next step will be
> Loading the result file in the "CAS Visual Debugger (CVD)"
> and build .xmi file
> but what is next?
> How can I view the the NER values? and where is the coloured screen that
> highlight each token in a colour and each NER in a different colour?
> and where I train cTAKES to take ICD10 or SNOMED or any other dataset?
>
>
--
Regards,
Gandhi
"The best way to find urself is to lose urself in the service of others !!!"
