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Posted to user@ctakes.apache.org by Franck Dernoncourt <fr...@gmail.com> on 2015/10/04 21:00:16 UTC
How to use cTAKES from the command line?
Hi,
I wonder how to use cTAKES from the command line.
E.g. :
- I have a file note.txt that contains some text like "Patient had
elevated blood sugar but tests confirm no diabetes. Patient's father had
adult onset diabetes."
- I want to use the provided analysis engine
"\apache-ctakes-3.2.2-bin\apache-ctakes-3.2.2\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml"
How can I get the analyse engine's output (viz. the annotations) using the
command line (i.e. without using graphical user interfaces such as UIMA CAS
Visual Debugger or the Collection Processing Engine)? I'd prefer to use to
use the provided JAR files rather than having to compile the code.
The question is fairly simple but I couldn't find the information in
cTAKES's README (https://svn.apache.org/repos/asf/ctakes/trunk/README) or
on Confluence (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0
).
Thanks,
Franck
----
Franck Dernoncourt
francky@mit.edu
http://francky.me
Re: How to use cTAKES from the command line?
Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.
Also, of note, Tika now has support for doing this, either from
cURL (Tika-Server) or the command line (Tika-app):
http://wiki.apache.org/tika/cTAKESParser
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattmann@nasa.gov
WWW: http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-----Original Message-----
From: Pei Chen <ch...@apache.org>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Tuesday, October 6, 2015 at 1:21 PM
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: Re: How to use cTAKES from the command line?
>Hi Franck,
>There was a similar questions on this topic:
>In particular, you can run CPE directly from the command line w/o the UI.
>
>Check out:
>http://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3CCAOsyzK
>3jxpktW5esFnhm2doCv_4JiQpuqQgAOer6wv9FsNAm4Q@mail.gmail.com%3E
>
>On Sun, Oct 4, 2015 at 3:00 PM, Franck Dernoncourt
><fr...@gmail.com> wrote:
>> Hi,
>>
>> I wonder how to use cTAKES from the command line.
>>
>> E.g. :
>> - I have a file note.txt that contains some text like "Patient had
>>elevated
>> blood sugar but tests confirm no diabetes. Patient's father had adult
>>onset
>> diabetes."
>> - I want to use the provided analysis engine
>>
>>"\apache-ctakes-3.2.2-bin\apache-ctakes-3.2.2\desc\ctakes-clinical-pipeli
>>ne\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml"
>>
>> How can I get the analyse engine's output (viz. the annotations) using
>>the
>> command line (i.e. without using graphical user interfaces such as UIMA
>>CAS
>> Visual Debugger or the Collection Processing Engine)? I'd prefer to use
>>to
>> use the provided JAR files rather than having to compile the code.
>>
>> The question is fairly simple but I couldn't find the information in
>> cTAKES's README (https://svn.apache.org/repos/asf/ctakes/trunk/README)
>>or on
>> Confluence
>>(https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0).
>>
>> Thanks,
>> Franck
>>
>>
>> ----
>> Franck Dernoncourt
>> francky@mit.edu
>> http://francky.me
>>
>>
>>
Re: How to use cTAKES from the command line?
Posted by Pei Chen <ch...@apache.org>.
Hi Franck,
There was a similar questions on this topic:
In particular, you can run CPE directly from the command line w/o the UI.
Check out:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201505.mbox/%3CCAOsyzK3jxpktW5esFnhm2doCv_4JiQpuqQgAOer6wv9FsNAm4Q@mail.gmail.com%3E
On Sun, Oct 4, 2015 at 3:00 PM, Franck Dernoncourt
<fr...@gmail.com> wrote:
> Hi,
>
> I wonder how to use cTAKES from the command line.
>
> E.g. :
> - I have a file note.txt that contains some text like "Patient had elevated
> blood sugar but tests confirm no diabetes. Patient's father had adult onset
> diabetes."
> - I want to use the provided analysis engine
> "\apache-ctakes-3.2.2-bin\apache-ctakes-3.2.2\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml"
>
> How can I get the analyse engine's output (viz. the annotations) using the
> command line (i.e. without using graphical user interfaces such as UIMA CAS
> Visual Debugger or the Collection Processing Engine)? I'd prefer to use to
> use the provided JAR files rather than having to compile the code.
>
> The question is fairly simple but I couldn't find the information in
> cTAKES's README (https://svn.apache.org/repos/asf/ctakes/trunk/README) or on
> Confluence (https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0).
>
> Thanks,
> Franck
>
>
> ----
> Franck Dernoncourt
> francky@mit.edu
> http://francky.me
>
>
>