/ 
UMLS-Interface-0.05
River stage one • 3 direct dependents • 3 total dependents
/ UMLS-Interface

NAME

UMLS-Interface Installation Guide

TESTING PLATFORMS

UMLS-Interface has been developed and tested on Linux primarily using Perl.

SYNOPSIS

perl Makefile.PL

make

make test

make install

DESCRIPTION

REQUIREMENTS

UMLS-Interface REQUIRES that the following software packages and data:

Programming Languages

Perl (version 5.8.0 or better) Java SE Development Kit (JDK)

CPAN Modules DBI

Database

MySQL (version 5 or better)

Data

Unified Medical Language System (UMLS 2008AA or higher)

INSTALLATION STAGES

The installation is broken into five stages:
Stage 1: Install Programming Languages
If already installed you need at minimum: 
    - Perl version 5.8 or better
    - Java SE Development Kit
Stage 2: Install CPAN Modules
Stage 3: Install MySQL
If already installed you need at minimum: 
    - MySQL version 5 or better
Stage 4: Install the UMLS
  If already installed you need at minimum: 
      - the following files in the META directory:
        -- populate_mysql_db.sh script 
	-- MRREL.RFF
	-- MRCONSO.RFF
	-- MRSAB.RFF
	-- MRDOC.RFF
      - the following files in the NET directory
	    --populate_mysql_db.sh script
	    --SRDEF
Stage 5: Load the UMLS into MySQL
  If already installed you need at minimum: 
      - the following tables 
	-- MRREL
	-- MRCONSO
	-- MRSAB
	-- MRDOC
	-- SRDEF
Stage 6: Install UMLS-Interface and set environment variable

More details on how to obtain and install appear below.

Stage 1: Install Programming Languages, if already installed go to Stage 2

Perl (version 5.8.5 or better)

Perl is freely available at http://www.perl.org. It is very likely that you will already have Perl installed if you are using a Unix/Linux based system.

Java SE Development Kit (JDK)

JDK is freely available at http://java.sun.com/. The latest version today is JDK 6 which can be found here:

http://java.sun.com/javase/6/webnotes/install/index.html

I installed JDK 6 on Red Hat Enterprise Linux WS release 4 using rpms. The instructions that I used can be found here:

http://java.sun.com/javase/6/webnotes/install/jdk/install-linux.html#install-rpm

You can also install it using the binaries. Instructions for that can be found here:

http://java.sun.com/javase/6/webnotes/install/jdk/install-linux.html#self-extracting

Stage 2 - Install CPAN modules, if already installed go to Stage 3

CPAN MODULES

DBI

UMLS-Interface uses DBI to access the mysql database containing the UMLS. DBI is freely available at http://search.cpan.org/~timb/DBI/

perl -MCPAN -e shell > install DBI

CPAN modules, and will not be repeated in detail for each module.****

If you have supervisor access, or have configured MCPAN for local install, you can install via:

perl -MCPAN -e shell > install DBI

If not, you can, "manually" install by downloading the *.tar.gz file, unpacking, and executing the following commands.

perl Makefile.PL PREFIX=/space/kulka020/Bit-Vector LIB=/space/kulka020/MyPerlLib make make test make install

Note that the PREFIX and LIB settings are just examples to help you create a local install, if you do not have supervisor (su) access.

You must include /space/kulka020/MyPerlLib in your PERL5LIB environment variable to access this module when running.

Stage 3 - Install MySQL, if already installed go to Stage 4

Requires MySQL (version 5 or better)

MySQL is a freely available database at http://www.mysql.com/. You may be able to install this with you package manager. Otherwise you will have to download the appropriate files from the MySQL website. Either way, make certain that the following are installed:

1. Server
2. Client
3. Shared libraries
4. Headers and libraries

Sometimes the headers and libraries are not installed so you want to double check on that.

==head2 Installing on Red Hat Enterprise Linux WS release 4 using rpms

I installed this on Red Hat Enterprise Linux WS release 4 using rpms. So, I downloaded the corresponding rpms:

1. MySQL-server-community-5.0.51a-0.rhel4.i386.rpm
2. MySQL-client-community-5.0.51a-0.rhel4.i386.rpm
3. MySQL-shared-community-5.0.51a-0.rhel4.i386.rpm
4. MySQL-devel-community-5.0.51a-0.rhel4.i386.rpm

I ran into two problems. The first was I had an older version of RedHat that another program was dependent on and it would not let me upgrade. I ended up just removing the program and the older version of MySQL. This was not recommended by the MySQL documentation but after a certain point it just became too frustrating. The second problem that I had was I kept receiving the following error:

Warning: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) in /var/www/html/forum/admin/ db_mysql.php on line 40

Warning: MySQL Connection Failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) in /var/www/html/forum/admin/db_mysql.php on line 40

I don't completely understand this error but after much googling I ended up moving the mysql.sock file to the '/tmp' directory and changed the the socket location in my 'my.cnf' file which was located in the '/etc' directory. I changed the following line: from : socket = /var/lib/mysql/mysql.sock to : socket = /tmp/mysql.sock

In the /var/lib/mysql/ directory I have a mysql.sock= file. I created a symbolic link to that from the /tmp directory

ln -s /var/lib/mysql/mysql.sock= /tmp/mysql.sock

Then everything seemed to work fine.

I then set my root password:

/usr/bin/mysqladmin -u root password 'new-password'

Installing on Fedora using yum

Ted installed mysql on Fedora using yum.

To install mysql using yum, type the following three commands on the command line:

1. yum install mysql
2. yum install mysql-server
3. yum install mysql-devel

After this is complete mysql should be installed. Next you need to start the mysql server by typing the following command:

service mysqld start

Installing on Ubuntu using apt-get

I also installed this on Ubuntu. This was 100 times easier than using the rpms! Type the following commands:

sudo apt-get install mysql-common sudo apt-get install mysql-client sudo apt-get install mysql-server

You are done - much easier!

Reminder

Also for all the installations, remember to set your root password:

/usr/bin/mysqladmin -u root password 'new-password'

Stage 4 - Install UMLS, if already installed go to Stage 5

VERSION

The UMLS-Interface requires version UMLS 2008AA or higher

REMINDER

If you already have the UMLS installed, make certain that you have the populate_mysql_db.sh script in the META directory as well as the MRREL.RFF, MRCONSO.RFF, MRSAB.RFF, and MRDOC.RFF files. If you do not you will need to run the install program (MetamorphoSys) again.

DESCRIPTION OF UMLS

The UMLS is a freely available knowledge representation framework designed to support broad scope biomedical research queries. It includes over 100 controlled medical terminologies and classification systems encoded with different semantic and syntactic structures. The three major sources of UMLS are the Metathesaurus, Semantic Network and SPECIALIST Lexicon. To obtain the UMLS you need to register for a license. For more information please see:

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

The UMLS is installed and the MySQL load scripts are created using MetamorphoSys. MetamorphoSys is the UMLS installation wizard and customization tool included in each UMLS release. It installs one or more of the UMLS Knowledge Sources; when the Metathesaurus is selected, the user can create customized Metathesaurus subsets. MetamorphoSys may be used to exclude vocabularies that are not required or licensed for use in local applications and to select from a variety of data output options and filters. Below are directions for a basic installation - nothing fancy.

There are quite a few steps and substeps here. The steps aren't complicated - there are just alot of different windows that pop up and I tried to break it down into small steps so I wouldn't miss anything. The directions can also be found with in the UMLS documentation:

http://www.nlm.nih.gov/research/umls/load_scripts.html
http://www.nlm.nih.gov/research/umls/meta6.html

Step 1: Download the UMLS

The UMLS is freely available but you need to register for 
a UMLS license prior to downloading. 

You can register here:      http://umlsks.nlm.nih.gov/ 

The download link is here: http://www.nlm.nih.gov/research/umls/

Download the following files:
  1. <current release>-1-meta.nlm  
  2. <current release>-otherks.nlm    
  3. <current release>-2-meta.nlm  
  4. mmsys.zip	  
  5. <current release>.CHK  
  6. Copyright_Notice.txt  
  7. README.txt

Step 2: Unzip the mmsys.zip file (unzip mmsys.zip)

The following should be created:
  1. linux_mmsys.sh
  2. solaris_mmsys.sh
  3. macintosh_mmsys.sh
  4. windows_mmsys.bat
  5. MMSYS/ (directory)

Step 3: Run MetamorphoSys (the install wizard)

       -- Run the appropriate .sh file for your system 
	       --> I ran ./linux_mmsys.sh

       -- Click 'Install UMLS'

       -- INSTALL UMLS' Window will appear
	  - Type in your destination directory. I used 
	    the same directory as my Source.
	  - At the very least make certain that the Metathesaurus 
	    box is checked. Although, I installed all three of the 
	    Knowledge Sources: 'Metathesaurus', 'Semantic 
	    Network' and 'SPECIALIST Lexicon and Lexical Tools'.
   	  - Click 'OK'

       -- 'Install UMLS' and 'MetamorphoSys Configuration' windows will appear
           - Click 'New Configuration' in the 'MetamorphoSys Configuration' 
		     
       -- 'License Agreement Notice' window will appear
	  - Click 'Accept'

       -- 'Select Default Subset' window will appear
	  - Click 'Level 0 + SNOMEDCT' 		
		- Unless you don't want or do not have a license for 
		  SNOMED-CT. then Click 'Level 0'
	  - Click 'Done'

       -- 'UMLS Metathesaurus Configuration' window will appear
	  - Click on the 'Output Options' tab
	  - Check the 'Write MySQL load script' box 
	        - this is under the heading 'Write Database Load Scripts'
          - Click 'Done' and then 'Begin Subset'
	        - this is the last option on the list of options in the 
	          top left hand corner of the window. 
          - A box will appear asking if you would save the changes 
	        - this is up to you; I clicked 'No'

     Now the UMLS will install and the load scripts will be created 
			
       -- 'Finished' window will appear
          - Click 'Done'

Stage 5 - Load UMLS into MySQL, if already installed go to Stage 6

Step 1: Create the MySQL database

        Log into MySQL and create a database called 'umls' 
	as follows:

	CREATE DATABASE IF NOT EXISTS umls CHARACTER SET utf8 COLLATE utf8_unicode_ci;

Step 2: Modify the 'my.cnf' file.

My 'my.cnf' file is located in the '/etc' directory. I found it by 
typing "whereis my.cnf" on the command line. If you do not have a 
my.cnf file check to see if you have a 'my.ini' file (which one 
you have will depend on your system).

The following options need to be modified to optimize for read 
performance, the MySQL 5 server requires changing buffer sizes 
to make use of the memory available. 

	      key_buffer        = 300M
	      table_cache       = 300
	      sort_buffer_size  = 20M
	      read_buffer_size  = 20M
	      query_cache_limit = 3M
	      query_cache_size  = 100M

Step 3: Populate the MySQL table using the load scripts

Step A: Find the MySQL load script

        Go to your Destination directory that you 
	typed in Step C (this is where I said my 
	source and destination directory were the 
	same)

	go to the: <destination>/2008AA/META directory

	In it you should see the file:

	   populate_mysql_db.sh

	If you don't see this file - you need to start 
	over. Step 3 - F did not get done properly.

Step B: Modify the MySQL load scripts

   In the populate_mysql_db.sh you need to modify the 
   following:

	MYSQL_HOME=<path to MYSQL_HOME>
	user=<username>
	password=<password>
	db_name=<db_name>

   For example, I modified my file as follows:

	MYSQL_HOME=/usr/
	user=bthomson
	password=<well I am not giving you my actual password>
	db_name=umls

Step C: Run the MySQL load scripts

	Run this script by typing on the command line:

	    ./populate_mysql_db.sh

	If you get the following:

	    ./populate_mysql_db.sh: Permission denied.

	You need to change your permissions and try again. To change 
	your permissions type:

	     chmod 755 populate_mysql_db.sh


Now this takes what feels like FOREVER! Now would be a good 
time to go do something else until sometime late tomorrow 
(yes, unfortunately, tomorrow) evening ...

Step D: Modify the my.cnf file (again)

	My 'my.cnf' file is located in the '/etc' directory. I found it by 
	typing "whereis my.cnf" on the command line. If you do not have a 
	my.cnf file check to see if you have a 'my.ini' file (which one 
	you have will depend on your system).

	This time you are modifying it so the that the UMLS-Interface 
	package and the umlsCycles.pl program can automatically 
	log into the umls database.

	    [client]
	    user            = <username>
	    password	    = <password>
	    port	    = 3306
	    socket          = /tmp/mysql.sock
	    database        = umls
	    
	    The port number is should already be in the my.cnf file 
	    under the [mysql] heading. I just copied and pasted that. 
	    
	    The socket is what ever socket you used in Stage 3. 

	    Remember we discussed how big of pain this was since 
	    it seemed like the socket location depended on what 
	    operating system you were using. My RedHat is:
		      socket = /tmp/mysql.sock
	    where as on my Ubunutu:	    
	              socket = /var/lib/mysql/mysql.sock

            A pain I know. If you need help just send me an email.

	    The database is whatever you called the database that 
	    the UMLS is installed in. My is 'umls'.

Stage 6 - Install UMLS-Interface and set environment variable

The usual way to install the package is to run the following commands:

 perl Makefile.PL
 make
 make test
 make install


You will often need root access/superuser privileges to run
make install. The module can also be installed locally. To do a local
install, you need to specify a PREFIX option when you run 'perl
Makefile.PL'. For example,

 perl Makefile.PL PREFIX=/home/sid

or

 perl Makefile.PL LIB=/home/sid/lib PREFIX=/home/sid

will install UMLS-Interface into /home/sid. The first method above 
will install the modules in /home/sid/lib/perl5/site_perl/5.8.3 
(assuming you are using version 5.8.3 of Perl; otherwise, the 
directory will be slightly different). The second method will 
install the modules in /home/sid/lib. In either case the executable 
scripts will be installed in /home/sid/bin and the man pages will 
be installed in home/sid/share.

Warning: do not put a dash or hyphen in front of PREFIX, LIB or WNHOME.

In your perl programs that you may write using the modules, you may need
to add a line like so

 use lib '/home/sid/lib/perl5/site_perl/5.8.3';

if you used the first method or

 use lib '/home/sid/lib';

if you used the second method. By doing this, the installed modules are
found by your program. To run the similarity.pl program, you would need
to do

 perl -I/home/sid/lib/perl5/site_perl/5.8.3 similarity.pl

or

 perl -I/home/sid/lib

Of course, you could also add the 'use lib' line to the top of the
program yourself, but you might not want to do that. You will need to
replace 5.8.3 with whatever version of Perl you are using. The
preceding instructions should be sufficient for standard and slightly
non-standard installations. However, if you need to modify other
makefile options you should look at the ExtUtils::MakeMaker
documentation. Modifying other makefile options is not recommended
unless you really, absolutely, and completely know what you're doing!

NOTE: If one (or more) of the tests run by 'make test' fails, you will
see a summary of the tests that failed, followed by a message of the
form "make: *** [test_dynamic] Error Y" where Y is a number between 1
and 255 (inclusive). If the number is less than 255, then it indicates
how many test failed (if more than 254 tests failed, then 254 will still
be shown). If one or more tests died, then 255 will be shown. For more
details, see:

http://search.cpan.org/dist/Test-Simple/lib/Test/Builder.pm#EXIT_CODES

The UMLSINTERFACE environment variable needs to be set to the location 
that the UMLS-Interface package is installed in order to gain access 
to the files in the default_options directory.

For example:

  # in cshell
  setenv UMLSINTERFACE /home/btmcinnes/UMLS-Interface

  # in bash
  export UMLSINTERFACE=/home/btmcinnes/UMLS-Interface

This can be added to your .cshrc or .bashrc file

CONTACT US

If you have any trouble installing and using UMLS-Interface, please contact us via the users mailing list :

umls-query-users@lists.sourceforge.net

You may also contact us directly if you prefer :

Bridget T. McInnes: bthomson@cs.umn.edu Ted Pedersen : tpederse@d.umn.edu

2 POD Errors

The following errors were encountered while parsing the POD:

Around line 50:

'=item' outside of any '=over'

Around line 93:

You forgot a '=back' before '=head1'