Difference between revisions of "Chado - Getting Started"

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* [[Chado_Tables|Chado Tables]]
* [[Chado_Tables|Chado Tables]]
* [[Chado_Best_Practices|Chado Best Practices]]
* [[Chado_Best_Practices|Chado Best Practices]]
* [[Sample_Chado_SQL|Sample Chado SQL]]

Revision as of 20:53, 11 May 2007


Chado is a relational schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.



Chado is a modular schema, designed in such a way as to allow the addition of new modules for new data types. The existing modules are:


First you will need database software, or Relational Database Management System (RDBMS). The recommended RDBMBS for Chado currently is Postgres. Postgres is free software, usually used on a Unix operating system such as Linux or Mac OS X. You can also install Postgres, and Chado, on Windows but most Chado installations are found on some version of Unix - you'll probably get the best support by choosing Unix. Once you've installed your RDBMS you can install Chado.

Chado From CVS

If you get Chado from CVS you get the very latest code but it is not as thoroughly tested as the stable release. To do an anonymous checkout of the Chado schema:

cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login 

Enter blank password. Then do:

cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co schema

Once the package has been downloaded cd to the schema/chado/ directory.

Follow the instructions in the INSTALL.Chado file, including the installation of the prerequisites. Or read schema/chado/INSTALL.Chado online.

Download a Stable Release of Chado

Installation using an RPM

If you are running the Fedora Core 2 linux distribution or any Unix that uses yum and RPM files then installing many GMOD applications (e.g. Chado, GBrowse, and Textpresso and the prerequisites) should be easy:

  1. Modify your yum.conf file in the way described here on the Biopackages.net website. This file is usually found in the /etc directory.
  2. Issue the command sudo yum update.
  3. Issue the command sudo yum install gmod.

See biopackages.net for more detail.

Loading Data

After completing these steps, you can load your chado schema with data in a number of ways:

You can also use the application Apollo to curate data in Chado.



Chado is usually pronounced like this.