File	Date	Author	Commit
jars	2012-07-13	mchoudhari	[21bb8a] initial commit of java code
thesis_experiments	2012-08-02	mchoudhari	[e93f20] added readme files along with experiments' inpu...
umls_java	2012-08-02	mchoudhari	[e93f20] added readme files along with experiments' inpu...
README	2012-08-01	mchoudhari	[20379f] modified readme and added basic config files fo...
build.xml	2012-07-13	mchoudhari	[21bb8a] initial commit of java code
run_it.sh	2012-07-13	mchoudhari	[21bb8a] initial commit of java code

Read Me

This project encapsulates the java implementation of HSO measure of semantic relatedness.
Project uses UMLSKS JAVA API to access UMLS database. To use this project, you will require valid 
credentials to access UTS server database. 
The code under umls_java/src/gov package is generated by UMLSKS  Web Services Description Language (WSDL) and is provided by NLM. 
(For more information visit : https://uts.nlm.nih.gov//doc/devGuide/index.html

To run the project on your machine: 

./run_it.sh <CONFIG_FILE_PATH> <PATTERN_FILE_PATH> <LOGIN_FILE_PATH> <INPUT_FILE_PATH>

Here 

<CONFIG_FILE_PATH> : path to configuration file where UMLS sources (SAB), relations(REL), directions (DIR) and attributes (RELA) are specified.

sample file :

SAB :: include SNOMEDCT
REL :: include PAR
DIR :: include U
 
<PATTERN_FILE_PATH> : path to a pattern file that contains a regular expression mapping the set of allowable path patterns.

sample file:

\bU+\b|\bU+D+\b|\bU+H+\b|\bU+H+D+\b|\bD+\b|\bD+H+\b|\bH+D+\b|\bH+\b


<LOGIN_FILE_PATH> : path to login file that contains credentials to access UTS and optional MySQL credentials is you want to use
caching

username :: <uts-username> ;required
password :: <uts-pwd>      ;required

sql_username :: <mysql-username> ;optional
sql_password :: <mysql-pwd>      ;optional

If the optional MySQL credentials are not supplied, cache is turned off.

MySql Setup to be able to use cache:
  a) start mysql
  b) setup mysql root password
  c) CREATE USER 'umls_user'@'localhost' IDENTIFIED BY 'umls_user';
  d) CREATE database umls_cache;
  e) GRANT ALL ON umls_cache.* TO 'umls_user'@'localhost';


<INPUT_FILE_PATH> : file with CUI pairs for which you want to fins the semantic relatedness

sample file :

C0035078<>C0035078
C0156543<>C0000786
C0018787<>C0027061
C0038454<>C0021308


More sample files can be found under /config folder.