Difference between revisions of "Chado - Getting Started"

Revision as of 22:05, 13 February 2007

Description

Chado is a relational schema that underlies many GMOD installations. It is capable of representing many of the broad 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

• Chado Manual
• FAQ for Chado
• Getting Started with GMOD

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 audits
• Companalysis - for data from computational analysis
• Contact - for people, groups, and organizations
• Controlled Vocabulary (cv) - for controlled vocabularies and ontologies
• Expression - for RNA and protein expresssion
• General - for identifiers
• Genetic - for genetic data and genotypes
• Library - for descriptions of molecular libraries
• Map - for maps without sequence
• 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

Chado From CVS

To install Chado from source you can get Chado from the schema CVS.

1. Install the prerequisites listed in the [INSTALL document]
2. Install BioPerl
3. Install go-perl
   • Alternatively install the larger go-dev package from the Gene Ontology site at Sourceforge
   • Make sure to set the GO_ROOT variable.
4. Install DBIx::DBStag

Now you can get an anonymous checkout of the gmod schema:

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

Enter blank password.

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

Now cd to the schema/chado directory, and perform these steps:

perl Makefile.PL
make
sudo make install UNINST=1
make load_schema
make prepdb
make ontologies

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) is easy:

1. Modify your /etc/yum.conf file in the way described here on the Biopackages.net website.
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

Pronunciation

Chado is usually pronounced like this.