Difference between revisions of "Chado - Getting Started"

Revision as of 18:30, 9 March 2007

Description

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 complexity is that the new user is advised to spend some time becoming familiar with its fundamentals.

Documentation

• Introduction to Chado
• Chado Manual
• FAQ for Chado
• Chado Tables
• Chado Best Practices

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:

• Audit - for database audit trails
• Companalysis - for data from computational analysis
• Contact - for people, groups, and organizations
• Controlled Vocabulary (cv) - for controlled vocabularies and ontologies
• Expression - for summaries of RNA and protein expresssion
• General - for identifiers
• Genetic - for genetic data and genotypes
• Library - for descriptions of molecular libraries
• Mage - for microarray data
• Map - for maps without sequence
• Natural Diversity (ND) - for multiple experiments, such as phenotyping and genotyping
• Organism - for taxonomic data
• Phenotype - for phenotypic data
• Phylogeny - for organisms and phylogenetic trees
• Publication (pub) - for publications and references
• Sequence - for sequences and sequence features
• Stock - for specimens and biological collections
• WWW -

Installation

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 this is not the best choice. Since most experienced bioinformatics people work on some version of Unix you'll 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 file, including the installation of the prerequisites. Or read schema/chado/INSTALL.

Download a Stable Release of Chado

• Go to GMOD at Sourceforge
• Download the latest gmod (the Chado source code is contained within this package)
• Follow the instructions in the chado/INSTALL file

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.

Contacts

• GMOD Schema Mailing List
• GMOD Help Desk

Pronunciation

Chado is usually pronounced like this.