Return-Path: X-Original-To: apmail-incubator-ctakes-commits-archive@minotaur.apache.org Delivered-To: apmail-incubator-ctakes-commits-archive@minotaur.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 13E65D48F for ; Fri, 28 Dec 2012 16:49:07 +0000 (UTC) Received: (qmail 67016 invoked by uid 500); 28 Dec 2012 16:49:07 -0000 Delivered-To: apmail-incubator-ctakes-commits-archive@incubator.apache.org Received: (qmail 66986 invoked by uid 500); 28 Dec 2012 16:49:07 -0000 Mailing-List: contact ctakes-commits-help@incubator.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: ctakes-dev@incubator.apache.org Delivered-To: mailing list ctakes-commits@incubator.apache.org Received: (qmail 66978 invoked by uid 99); 28 Dec 2012 16:49:07 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 28 Dec 2012 16:49:07 +0000 X-ASF-Spam-Status: No, hits=-2000.0 required=5.0 tests=ALL_TRUSTED X-Spam-Check-By: apache.org Received: from [140.211.11.4] (HELO eris.apache.org) (140.211.11.4) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 28 Dec 2012 16:49:05 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id 0E9D423889E0 for ; Fri, 28 Dec 2012 16:48:46 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r844139 - in /websites/staging/ctakes/trunk/content: ./ ctakes/3.0.0/user-guide-3.0.html Date: Fri, 28 Dec 2012 16:48:45 -0000 To: ctakes-commits@incubator.apache.org From: buildbot@apache.org X-Mailer: svnmailer-1.0.8-patched Message-Id: <20121228164846.0E9D423889E0@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Author: buildbot Date: Fri Dec 28 16:48:45 2012 New Revision: 844139 Log: Staging update by buildbot for ctakes Modified: websites/staging/ctakes/trunk/content/ (props changed) websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html Propchange: websites/staging/ctakes/trunk/content/ ------------------------------------------------------------------------------ --- cms:source-revision (original) +++ cms:source-revision Fri Dec 28 16:48:45 2012 @@ -1 +1 @@ -1426567 +1426576 Modified: websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html ============================================================================== --- websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html (original) +++ websites/staging/ctakes/trunk/content/ctakes/3.0.0/user-guide-3.0.html Fri Dec 28 16:48:45 2012 @@ -90,42 +90,57 @@

Installation

Basic installation:

Download one of the cTAKES archives
It is recommended that you verify the downloaded file using signatures downloaded from our main distribution directory (not from one of the mirrors). -Unpack the archive.
Download one of the cTAKES 3.0.0 archives
It is recommended that you verify the downloaded file using a signature downloaded from our main distribution directory (not from one of the mirrors).
Unpack the archive.

If you plan to use the full LVG resource (recommended)

Download either the full version or the lite version from NIH Lexical Tools
Download either the full version or the lite version from NIH Lexical Tools
Extract the tgz file that you downloaded to a temporary directory. If you are on Windows, you can use a tool like 7-zip (available online).
On some operating systems, like Windows, this may need to be done in two steps: +
This may need to be done in two steps: 1) to uncompress and 2) to unzip.
Replace the directory /resources/lvgresources/lvg/data/HSqlDb with data/HSqlDb from your extracted download. Replacing the entire directory is appropriate.

If you plan to use the UMLS resources:

-
Download and unpack the UMLS resources and add them to the resources directory from +
Download the UMLS resources from http://sourceforge.net/projects/ctakesresources/files/
+
Unpack the UMLS resources and add them to the resources directory
+
Also either set/export env variables like this

export ctakes.umlsuser=[username], ctakes.umlspw=[password]

or add the system properties to the java args

-Dctakes.umlsuser=[username] -Dctakes.umlspw=[password]

Usage

To run a basic pipeline without the UMLS resources:

Run bin/runctakesCVD
Load an AE (analysis engine)

Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor

Enter note or other text
Run analysis engine

NOTE: The included example dictionary is very small. Try a sentence such as: + Patient took aspirin for knee pain

To run with the UMLS resources:

Run bin/runctakesCVD
Load an AE (analysis engine)

Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor -- Enter note or other text -- Run analysis engine

NOTE: The included example dictionary is very small. If you did not download the UMLS resource, -try a sentence such as:

Patient took aspirin for knee pain

Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor

Enter note or other text
Run analysis engine