UMLS-Interface


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

=item 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.

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'.
     
=head1 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


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