Salvador's notes: UMLS on Windows

List of steps required to install UMLS in a Windows machine:

Go to UMLS web site:

http://www.nlm.nih.gov/research/umls/

Click on Downloads

http://www.nlm.nih.gov/research/umls/licensedcontent/downloads.html

Click on the UMLS link:

http://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html

Create a folder in your local machine e.g., C:\UMLS

Download all files (see image below), e.g., 2014AB.CHK, 2014... You will need to register an account

After download the files your directory should look like this:

Run mmsys

run.bat or run64.bat according to your environment

Run script and click on Install UMLS

Define the Destination folder, select the same folder "C:\UMLS"

Click on new configuration

Click accept

Select subset

Select MySQL

Save configuration

Click Done and select begin, you will see the progress on the following window:

Install MySQL Server

Download and intall mysql server from here:

http://dev.mysql.com/downloads/mysql/

Select mysql installer

leave the password empty. This will simplify the UMLS installation on the following steps..

Open mysql command line

Create a mysql database. This database will be used to hold the UMLS content :

mysql -u root -p

Create user umls_user and password umls

mysql -u root -p

CREATE DATABASE umls;

CREATE USER umls_user;

SET PASSWORD FOR umls_user = PASSWORD ('umls');

GRANT SELECT ON umls.* TO umls_user;

Change settings on MySQL server on my.ini file. Check this post which explains how to find this file in your system http://blog.sqlauthority.com/2014/01/07/mysql-locate-the-configuration-file-my-ini-or-my-cnf-on-windows-platform/

In my machine the file is located on "C:\ProgramData\MySQL\MySQL Server 5.6\my.ini"

Add the following settings

key_buffer = 600M

table_cache = 300

sort_buffer_size = 500M

read_buffer_size = 200M

query_cache_limit = 3M

query_cache_size = 100M

myisam_sort_buffer_size = 200M

bulk_insert_buffer_size = 100M

join_buffer_size = 100M

If you have defined a root password in the last step, you can remove it using the following command:

open mysql command line

SET PASSWORD FOR root@localhost=PASSWORD('');

Set environment variable MYSQL_HOME

and add it to the path

Go to C:\UMLS\2014AB\META and edit the script populate_mysql_db.bat

You will end with something like the following: (I have removed password and the full path of mysql, since it is available thanks to the environment variable)

::
:: For useful information on loading your Metathesaurus subset
:: into a MySQL database, please consult the on-line
:: documentation at:
::
:: http://www.nlm.nih.gov/research/umls/load_scripts.html
::

::
:: Database connection parameters
:: Please edit these variables to reflect your environment
::
::set MYSQL_HOME="C:\Program Files\MySQL\MySQL Server 5.6"
set user=root
set password=
set db_name=umls

del mysql.log
echo. > mysql.log
echo ---------------------------------------- >> mysql.log 2>&1
echo Starting ... >> mysql.log 2>&1
date /T >> mysql.log 2>&1
time /T >> mysql.log 2>&1
echo ---------------------------------------- >> mysql.log 2>&1
echo MYSQL_HOME = %MYSQL_HOME% >> mysql.log 2>&1
echo user =       %user% >> mysql.log 2>&1
echo db_name =    %db_name% >> mysql.log 2>&1
set error=0
set mrcxt_flag=0

:: Create empty mrcxt if it doesn't exist, expected by mysql_tables.sql script
if not exist MRCXT.RRF set mrcxt_flag=1
if not exist MRCXT.RRF TYPE NUL > MRCXT.RRF

echo     Create and load tables >> mysql.log 2>&1
mysql -vvv -u %user% --local-infile=1 %db_name% < mysql_tables.sql >> mysql.log 2>&1
IF %ERRORLEVEL% NEQ 0 (set error=1
goto trailer)

echo     Create indexes >> mysql.log 2>&1
mysql -vvv -u %user% --local-infile=1 %db_name% < mysql_indexes.sql >> mysql.log 2>&1
IF %ERRORLEVEL% NEQ 0 (set error=1

IF %mrcxt_flag% EQU 1 (
del MRCXT.RRF
echo DROP TABLE IF EXISTS MRCXT; >> drop_mrcxt.sql
mysql -vvv -u %user% --local-infile=1 %db_name% < drop_mrcxt.sql >> mysql.log 2>&1
IF %ERRORLEVEL% NEQ 0 (set error=1
del drop_mrcxt.sql
)

:trailer
echo ---------------------------------------- >> mysql.log 2>&1
IF %error% NEQ 0 (
echo There were one or more errors. Please reference the mysql.log file for details. >> mysql.log 2>&1
set retval=-1
) else (

echo Completed without errors. >> mysql.log 2>&1
set retval=0
)
echo Finished ... >> mysql.log 2>&1
date /T >> mysql.log 2>&1
time /T >> mysql.log 2>&1
echo ---------------------------------------- >> mysql.log 2>&1
exit %retval%

Run the script, this will take some time. After the script has finished you can verify if there were some errors during the process on mysql.log file