This document describes how to build and run the MetaCyc Ontology Loader. The MetaCyc Ontology loader is located in the metacyc-ontology-loader/ subdirectory of the warehouse distribution. For more information regarding the MetaCyc Ontology loader, see the MetaCyc Ontology Manual.

Building the MetaCyc Ontology Loader
Running the MetaCyc Ontology Loader
Testing the MetaCyc Ontology Loader
Documentation

  Building the MetaCyc Ontology Loader

Before building the loader, make sure the environment is configured according to the Environment Setup. Also make sure the schema is loaded into the database as specified in the Schema document.

To build the loader, bring up a shell and navigate to the metacyc-ontology-loader/src/ directory. Then:

MySQL:
osprompt: make clean
osprompt: make db=mysql
Creates the file mysql-metacyc-ontology-loader

Oracle:
osprompt: make clean
osprompt: make db=oracle
If file wh_oracle_util.c is reported missing, re-run the above make command:
osprompt: make db=oracle
Creates the file oracle-metacyc-ontology-loader

Also, a symbolic link named "metacyc-ontology-loader" is created, which points to the newly created executable. This can be used as a synonym for the most recently created DBMS-specific loader if desired.

If the build fails and gives errors about header files which are not found, read the section on configuring the appropriate client in Environment Setup. Posible problems are: improper installation of ProC (Oracle) or library/header files installed in an incorrect place.

  Running the MetaCyc Ontology loader

The MetaCyc Ontology loader can be run from the same machine where the Warehouse database is installed, or it can be run remotely. To run the Oracle loader remotely, use the Net8 configuration assistance to add the remote database. Consult the Oracle documentation for instructions on how to do this. To run the MySQL loader remotely, simply provide the correct host parameter for the location of the MySQL server.

Obtaining the MetaCyc Ontology databases

The MetaCyc Ontology Manual contains information regarding the MetaCyc database. The latest supported data version for the MetaCyc loader is listed in the loader summary table.

See http://biocyc.org/ for information on how to obtain a license and download the data. Also see Pathway/Genome Database (PGDB) for a description of the database file format.

Running the MetaCyc Ontology loader

The metacyc-ontology-loader/src/ directory contains scripts to run the MySQL and Oracle loaders.

MySQL:

    ./run-mysql host database user password datadir version releasedate [-m]
        host - The machine address where the MySQL server/database resides.
        database - Name of the MySQL database to be loaded.
        user - MySQL userid.
        password - MySQL password for userid.
        datadir - Directory which contains the PGDB database files to be loaded.
        version - Version of the MetaCyc database to be loaded. Ex: "10.0"
        releasedate - Release date of the database to be loaded. Ex: "2008-04-01"
        -m - If a dataset named BioCyc exists, merges all loads into it.
             If multiple BioCycs exist, the one with the largest DataSetWID is used.
             If no BioCyc exists, operates normally.

For example:

    ./run-mysql 123.45.67.8 warehouse me mypwd /space/bio/databases/biocyc/metacyc/10.0 "10.0" 2008-04-01

This command loads the MetaCyc ontologies into the MySQL database named warehouse. The data files for MetaCyc are located in the directory /space/bio/databases/biocyc/metacyc/10.0 and the user name and password used to access MySQL are me and mypwd.

Oracle:

    ./run-oracle "user/passwd" datadir version releasedate [-m] 
        user/passwd - User name and password. Ex: "dan/mypwd", "dan/mypwn@mydb"
        datadir - Directory which contains the PGDB database files.
        version - Version of the MetaCyc database to be loaded. Ex: "10.0"
        releasedate - Release date of the database to be loaded. Ex: "2008-04-01"
        -m - If a dataset named BioCyc exists, merges all loads into it.
             If multiple BioCycs exist, the one with the largest DataSetWID is used.
             If no BioCyc exists, operates normally.

For example:

    ./run-oracle "me/mypwd@mydb" /space/bio/databases/biocyc/metacyc/10.0/data "10.0" 2008-04-01

This command loads the MetaCyc ontologies into the Oracle database mydb. The data files for MetaCyc are located in the directory /space/bio/databases/biocyc/metacyc/10.0 and the user name and password used to access Oracle is "me/mypwd".

  Testing the MetaCyc Ontology Loader

Sample output can be found here. In general, the loader may report parse errors.

The database data sets should be queried to ensure the MetaCyc data set is loaded. See the document on Running the Perl Utiltity scripts to check this. Unlike most other loaders, this loader creates three datasets, so all three datasets should be checked to confirm they have populated the Term table. The number of rows in this table for each dataset should match the number of terms loaded as indicated in the loader log.

  Developer Documentation

The following documents are located in the doc directory:

• metacyc-ontology-manual.html
• load-mysql.log