svn commit: r1426576 - /incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext

[ja...@apache.org]

Author: james-masanz
Date: Fri Dec 28 16:48:42 2012
New Revision: 1426576

URL: http://svn.apache.org/viewvc?rev=1426576&view=rev
Log:
CMS commit to ctakes by james-masanz

Modified:
    incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext

Modified: incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext?rev=1426576&r1=1426575&r2=1426576&view=diff
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext (original)
+++ incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext Fri Dec 28 16:48:42 2012
@@ -25,42 +25,55 @@ Java 1.6 or later is required to run cTA
 
 Basic installation:
 
-1. 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.
+1. 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)
 
-1. Download either the full version or the lite version from NIH Lexical Tools
+1. Download either the full version or the lite version from [NIH Lexical Tools](http://lexsrv2.nlm.nih.gov/LexSysGroup/Projects/lvg/2008/web/download.html)
 - 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 <cTAKES_HOME>/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:
 
-1. Download and unpack the UMLS resources and add them to the resources directory from 
+1. 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]
+ -Dctakes.umlsuser=[username]  -Dctakes.umlspw=[password]
+
 ##Usage
 
+###To run a basic pipeline without the UMLS resources:
+
 1. Run bin/runctakesCVD 
 - Load an AE (analysis engine)
 
-  Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor
+ 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: 
+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:
 
-   Patient took aspirin for knee pain
+1. Run bin/runctakesCVD 
+- Load an AE (analysis engine)
+
+ Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor
 
+- Enter note or other text
+- Run analysis engine