Chado - Getting Started

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Status
  • Mature release
  • Active development
  • Active support
Resources

Chado is a relational database 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.

Documentation

Modules

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:


Installation

First you will need database software, or Relational Database Management System (RDBMS). The recommended RDBMS 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. (See Databases and GMOD for more discussion.) Once you've installed your RDBMS you can install Chado.


Download a Stable Release of Chado

See Downloads


Chado From SVN

You can get the most up-to-date, not even released yet, version of Chado from Subversion. To get a copy of the latest Chado source, enter this at the command line:

svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk

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

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

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.

Mailing Lists

Mailing List Link Description Archive(s)
Chado gmod-schema All issues regarding Chado, Chado::AutoDBI, and Bio::Chado::Schema Gmane, Nabble (2010/05+), Sourceforge
gmod-schema-cmts Chado code updates. Sourceforge

Pronunciation

Chado is usually pronounced like this.