This document describes how to build and run the NCBI Taxonomy Loader. The NCBI Taxonomy loader is located in the ncbi-taxonomy-loader/ subdirectory of the warehouse distribution. For more information regarding the NCBI Taxonomy loader, see the NCBI Taxonomy Manual.

Building the NCBI Taxonomy Loader
Running the NCBI Taxonomy Loader
Testing the NCBI Taxonomy Loader
Documentation

  Building the NCBI Taxonomy 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 ncbi-taxonomy-loader/src/ directory. Then:

MySQL:
osprompt: make clean
osprompt: make db=mysql
Creates the file mysql-ncbi-taxonomy-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-ncbi-taxonomy-loader

Also, a symbolic link named "ncbi-taxonomy-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 NCBI Taxonomy loader

The NCBI Taxonomy 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 NCBI Taxonomy databases

The NCBI Taxonomy Manual contains information regarding the NCBI Taxonomy data set. See the NCBI Taxonomy Homepage for general information about NCBI.

Running the NCBI Taxonomy loader

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

MySQL:

    ./run-mysql host database user password datadir version releasedate 
        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 NCBI Taxonomy data files to be loaded.
        version - Version of source database (typically the date it was downloaded)
        releasedate - Release date of source database (typically the date it was downloaded)
  

For example:

    ./run-mysql 123.45.67.8 warehouse me mypwd /space/bio/databases/NCBI/released "2008-03-13" "2008-03-13" 

This command loads NCBI Taxonomy data into the MySQL database named warehouse. The data files are located in the directory /space/bio/databases/NCBI/released and the user name and password used to access MySQL are me and mypwd.

Oracle:

    ./run-oracle "user/passwd" datadir version releasedate 

        user/passwd - User name and password. Ex: "dan/mypwd", "dan/mypwn@mydb"
        datadir  - Directory which contains the NCBI Taxonomy data files.
        version - Version of source database (typically the date it was downloaded)
        releasedate - Release date of source database (typically the date it was downloaded)
  

For example:

    ./run-oracle "me/mypwd@mydb" /space/bio/databases/NCBI/released "2008-03-13" "2008-03-13" 

This command loads NCBI Taxonomy data into the Oracle database mydb. The data files are located in the directory /space/bio/databases/NCBI/released and the user name and password used to access Oracle is "me/mypwd".

  Testing the NCBI Taxonomy Loader

The loader may report parse errors; this is expected. The expected output for MySQL can be found sample-loader-output-mysql.txt. The expected output when loading Oracle can be found sample-loader-output-oracle.txt.

The database data sets should be queried to ensure NCBI Taxonomy data is loaded. See the document on Running the Perl Utiltity scripts to check this.

  Developer Documentation

The following documents are located in the doc directory:

• NCBI Taxonomy Manual (HTML)