Load Scripts

MetamorphoSys can generate custom load scripts in MySQL or Oracle when creating a subset. The files below are guides to loading a subset of the UMLS Metathesaurus into a MySQL or Oracle database by using the scripts and files created by MetamorphoSys. These load scripts have been machine generated from data provided in the MRFILES and MRCOLS tables that come with the UMLS Metathesaurus, and are for informational purposes only. You will need to modify them for local installation. For example, the database name and paths to the individual files are coded into the load scripts; this must be changed.

If you are having problems with the current release, consult the Release Notes and Problems (Bugs). If you are having problems with a previous release, consult the Previous Release Bugs.

Metathesaurus Load Scripts for MySQL

• Original Release Format
• Rich Release Format

Please note: These scripts require MySQL 5.

Instructions for MySQL Users:

• If you are running MetamorphoSys in a Windows environment, in your output directory (after running MetamorphoSys with the "Write MySQL Load Script" box checked) you should see a batch file script called "populate_mysql_db.bat".  This script can be used to load your subset into a MySQL database.   The directory will also contain an SQL script for creating the tables, and an SQL script for creating the indexes..
• Edit the script and configure the four parameters at the top of the script.  These are:
  • set MYSQL_HOME=<path to MYSQL_HOME>
  • set user=<username>
  • set password=<password>
  • set db_name=<db_name>
• MYSQL_HOME should be set to the installation directory of your local MySQL server.  This is likely to be something like "C:\Program Files\MySQL\MySQL Server 5.0".  Remember to enclose the value in quotes if the directory name contains spaces.  After configuring these four parameters, this section of your script may look something like the following:
  • set MYSQL_HOME="C:\Program Files\MySQL\MySQL Server 5.0"
  • set user=myuser
  • set password=p4ssw0rd
  • set db_name=umls
• You are now ready to run the script.  To do so, navigate to your subset directory using the Windows explorer and double-click on the "populate_mysql_db.bat" file you just finished editing.
• Click here for more detailed instructions as well as other operating systems

Metathesaurus Load Scripts for Oracle

• Original Release Format
• Rich Release Format

Instructions for Oracle Users:

• Create a schema specifically for this data.
• Set tablespace at unlimited, or high enough to ensure the amount of space available is what is needed by the data. Granting UNLIMITED TABLESPACE is acceptable as long as "AUTOEXTEND" is turned on to allow for unlimited table space growth.
• Create synonyms for tables or only access tables using the same login used to create them.
• Do not use the SYS/SYSTEM account to load data into the database since the default table space is SYSTEM, which is reserved for the data dictionary.
• Use MTH or another account to insert data into the database; do not use "AS SYSDBA" to see the tables. Setting the proper grants from the beginning will solve this problem.
• The loader script must be changed to SCHEMA.TABLE format to insert data into the proper tables if the SYS/SYSTEM account is used.
• The database must use the UTF-8 character set.

Semantic Network Load Scripts

Semantic Network Load Scripts are provided for illustration purpose only. Scripts are only available in MySQL. Column names have been changed to conform to DBMS restrictions.

Data Model

• Metathesaurus Entity Diagram for RRF Files

Last reviewed: 23 September 2009
Last updated: 23 September 2009
First published: 13 July 2004
Metadata| Permanence level: Permanence Not Guaranteed

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