svn commit: r1426583 - /incubator/ctakes/site/trunk/content/ctakes/3.0.0/user-guide-3.0.mdtext

[ja...@apache.org]

Author: james-masanz
Date: Fri Dec 28 17:01:40 2012
New Revision: 1426583

URL: http://svn.apache.org/viewvc?rev=1426583&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=1426583&r1=1426582&r2=1426583&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 17:01:40 2012
@@ -33,24 +33,24 @@ If you plan to use the full LVG resource
 
 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). 
-- This may need to be done in two steps:
- 1) to uncompress and 2) to unzip.
+    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 the UMLS resources from 
-http://sourceforge.net/projects/ctakesresources/files/
+[http://sourceforge.net/projects/ctakesresources/files/](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]
+    export ctakes.umlsuser=[username], ctakes.umlspw=[password]
 
- or add the system properties to the java args
+    or add the system properties to the java args
 
- -Dctakes.umlsuser=[username]  -Dctakes.umlspw=[password]
+    -Dctakes.umlsuser=[username]  -Dctakes.umlspw=[password]
 
 ##Usage
 
@@ -59,21 +59,23 @@ http://sourceforge.net/projects/ctakesre
 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. Try a sentence such as: 
-  Patient took aspirin for knee pain
+    Patient took aspirin for knee pain
 
 ### To run with the UMLS resources:
 
 1. Run bin/runctakesCVD 
 - Load an AE (analysis engine)
 
- Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor
+     Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor
 
 - Enter note or other text
 - Run analysis engine
 
+### To process multiple files at once:
+1. Run bin/runctakesCPE