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 The UMLS-Interface package is an interface to the Unified Medical Language System (UMLS) 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 -- MRDEF.RFF -- MRSTY.RFF - the following files in the NET directory --populate_net_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 -- MRDEF -- MRSTY 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 . 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 . The latest version today is JDK 6 which can be found here: I installed JDK 6 on Red Hat Enterprise Linux WS release 4 using rpms. The instructions that I used can be found here: You can also install it using the binaries. Instructions for that can be found here: Stage 2 - Install CPAN modules, if already installed go to Stage 3 CPAN MODULES DBI CPAN modules, and will not be repeated in detail for each module.**** UMLS-Interface uses DBI to access the mysql database containing the UMLS. DBI is freely available at 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=/home/programs LIB=/home/lib 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 /home/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 . 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. 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' If you are not going to be using root as your main entry into mysql - which is probably a good idea - you can create a user account. Here is how I did it: mysql> CREATE USER bthomson IDENTIFIED BY 'psswrd'; Query OK, 0 rows affected (0.00 sec) mysql> GRANT ALL ON *.* TO bthomson; Query OK, 0 rows affected (0.00 sec) Directions are in the mysql documentation: 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, MRDOC.RFF, MRDEF.RFF, MRSTY.RFF and SRDEF.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: 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 a lot 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: 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: The download link is here: Download the following files: 1. -1-meta.nlm 2. -otherks.nlm 3. -2-meta.nlm 4. mmsys.zip 5. .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. This has been put in a different place every version or distribution that I have run this one. I have found it in the '/etc' directory as well as the '/etc/mysql' directory. You can find where yours is by using the find command: sudo find / -name my.cnf 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 for the Metathesaurus 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: /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 for the Metathesaurus In the populate_mysql_db.sh you need to modify the following: MYSQL_HOME= user= password= db_name= For example, I modified my file as follows: MYSQL_HOME=/usr/ user=bthomson password= db_name=umls Step C: Run the MySQL load scripts for the Metathesaurus 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: Find the MySQL load script for the Semantic Network 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: /2008AA/NET In it you should see the file: LoadScripts.zip Unzip this file as follows: unzip LoadScripts.zip The following file then should appear: populate_net_mysql_db.sh If you don't see this file - you need to start over. Step 3 - F did not get done properly. Step E: Modify the MySQL load script for the Semantic Network This is the exact same modifications that were done in the Metathesaurus load script. In the populate_net_mysql_db.sh you need to modify the following: MYSQL_HOME= user= password= db_name= For example, I modified my file as follows: MYSQL_HOME=/usr/ user=bthomson password= db_name=umls Step F: Run the MySQL load script for the Semantic Network Run this script by typing on the command line: ./populate_net_mysql_db.sh If you get the following: ./populate_net_mysql_db.sh: Permission denied. You need to change your permissions and try again. To change your permissions type: chmod 755 populate_net_mysql_db.sh Now this should not take forever. It goes much much quicker! Step G: Modify the my.cnf file (again) This has been put in a different place every version or distribution that I have run this one. I have found it in the '/etc' directory as well as the '/etc/mysql' directory. You can find where yours is by using the find command: sudo find / -name my.cnf This time you are modifying it so the that the UMLS-Interface package (and the utils/ files) can automatically log into the umls database. [client] user = 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 8.04: socket = /var/lib/mysql/mysql.sock and currently on Ubuntu 9.04: socket = /var/run/mysqld/mysqld.sock So the sock file is different and its location is different depending on what version of linux you are running. You can find it using: sudo find / -name mysqld.sock or sudo find / -name mysql.sock This is a huge pain. If you need help just send me an email. The database is whatever you called the database that the UMLS is installed in. Mine 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 or perl Makefile.PL LIB=/home/lib PREFIX=/home will install UMLS-Interface into /home. The first method above will install the modules in /home/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/lib. In either case the executable scripts will be installed in /home/bin and the man pages will be installed in home/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/lib/perl5/site_perl/5.8.3'; if you used the first method or use lib '/home/lib'; if you used the second method. By doing this, the installed modules are found by your program. To run the umls-similarity.pl program, you would need to do perl -I/home/lib/perl5/site_perl/5.8.3 umls-similarity.pl or perl -I/home/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: Now please set the UMLSINTERFACE_CONFIGFILE_DIR environment variable. This will be the location where you don't mind the UMLS-Interface module writing out system files. The system files that created are: 1. __config which is an example configuration file of the the current run 2. __child __parent this files store the upper level taxonomy which is created when connecting multiple sources 3. __table this file contains the path to the root for each concept in the UMLS view. this information is stored in a mysql database of the same name. This really helps speed up the initialization. CONTACT US If you have any trouble installing and using UMLS-Interface, please contact us via the users mailing list : umls-similarity@yahoogroups.com You can join this group by going to: You may also contact us directly if you prefer : Bridget T. McInnes: bthomson at cs.umn.edu Ted Pedersen : tpederse at d.umn.edu