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Revision as of 14:48, 5 April 2007
Contents
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 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:
- 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 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
- Go to GMOD at Sourceforge
- Download the latest gmod (the Chado source code is contained within this package)
- Follow the instructions in the schema/chado/INSTALL.Chado 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:
- Modify your
yum.conf
file in the way described here on the Biopackages.net website. This file is usually found in the/etc
directory. - Issue the command
sudo yum update
. - 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.
Contacts
Pronunciation
Chado is usually pronounced like this.