Chado General Information

Background

Chado is a relational database schema for managing biological data that was created by FlyBase in 2006. It is currently developed and maintained by the GMOD organization.

Database Dumps

PostgreSQL database dumps of the FlyBase Chado database are available for every release of FlyBase from our FTP site.

Steps to load

This procedure assumes that you have enough disk space to hold the downloaded dump files and the PostgreSQL database files. You should expect to use ~200 GB of disk space for this procedure.

  1. Download all database dump files from the FTP site.
  2. Create your PostgreSQL database using createdb
  3. Load the dump file into your local database instance.
  4. Vacuum your database.

Example:

wget ftp://ftp.flybase.org/releases/current/psql/*.gz.*
createdb -E UTF-8 my_flybase
cat FB2018_03.sql.gz.00 FB2018_03.sql.gz.01 FB2018_03.sql.gz.02 FB2018_03.sql.gz.03 FB2018_03.sql.gz.04 FB2018_03.sql.gz.05 | gunzip | psql my_flybase 
vacuumdb -f -z -v my_flybase

Public Database

If you only need occasional access to the FlyBase Chado database and performance is not a primary concern you can access our public Chado instance via any SQL client that supports PostgreSQL.

hostname: chado.flybase.org

user: flybase

password: <none>

database: flybase

port: 5432

Example using the command line PostgreSQL client psql:

psql -h chado.flybase.org flybase flybase
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