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From "Akhilesh Patel" <akhilesh.pa...@citiustech.com>
Subject RE: corresponding versions ctakes and stakes-resource
Date Wed, 15 Jul 2015 14:03:48 GMT
Hi Justin,

 

I have not worked on smoking status however  I am able to capture “Side effects” and “Drug
annotation” information from clinical notes. Both the module working form me.

I am using following xml files to extract the information

 

       <delegateAnalysisEngine key="DrugMentionAnnotator">

         <import location="../../ctakes/ctakes-drug-ner/desc/analysis_engine/DrugMentionAnnotator.xml"/>

       </delegateAnalysisEngine>

 

<delegateAnalysisEngine key="SideEffect">

<import location="../../ctakes/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE.xml"/>

</delegateAnalysisEngine>

 

Ctakes version I am using is 3.2.2-SNAPSHOT.

 

Thanks,

Akhilesh

 

From: Justin Zhang [mailto:justinzhang.xl@gmail.com] 
Sent: Wednesday, July 15, 2015 7:22 PM
To: user@ctakes.apache.org
Subject: Re: corresponding versions ctakes and stakes-resource

 

Hello again,

For the same purpose as the first email: I have put a lot of efforts in order to run this
few pipelines with different versions ctakes/resources and different computer systems, and
did not succeed. Most errors are "URIs" or "File (xml) not found". 

I am so eager to move forward. Could anyone help me through the steps for "Smoking Status",
and then "Side effects"/"Drug Annotations"? I would need the information of specific ctakes
binary version and correct match resources, and relevant necessary steps. 

Great appreciation!!!

Justin

 

On Tue, Jul 14, 2015 at 4:04 PM, Justin Zhang <justinzhang.xl@gmail.com> wrote:

Hello Everyone,

 

I am looking to load following AE (analysis engine) from runctakesCVD.sh

 

·  <cTAKES_HOME>/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE.xml
(The annotator to obtain document or patient-level smoking status)

·  <cTAKES_HOME>/desc/ctakes-side-effect/desc/analysis_engine/SideEffectAggregateTAE_UMLS.xml
(The annotator to find side effect mentions and sentences from clinical documents)

·  <cTAKES_HOME>/desc/ctakes-drug-ner/desc/analysis_engine/DrugAggregatePlaintextUMLSProcesor.xml
(The annotator to obtain drug annotations)

 

What corresponding ctakes binary and ctakes resource should I use?

 

In download page, current resource versions are 3.0.1, 3.10, 3.13, 3.2.0, 3.2.1.1

 

current ctakes versions are 3.1.0, 3.1.1, 3.2.0, 3.2.1, 3.2.2

 

thanks, 

 

-- 

Justin




-- 

Justin




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