Difference between revisions of "Chado - Getting Started"
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# Install the prerequisites listed in the [INSTALL document] | # Install the prerequisites listed in the [INSTALL document] | ||
# Install [http://www.bioperl.org/ BioPerl] | # Install [http://www.bioperl.org/ BioPerl] | ||
| − | # Install | + | # Install [http://search.cpan.org/search?query=go-perl go-perl] |
#* Alternatively install the larger go-dev package from the [http://sourceforge.net/projects/geneontology/ Gene Ontology site at Sourceforge] | #* Alternatively install the larger go-dev package from the [http://sourceforge.net/projects/geneontology/ Gene Ontology site at Sourceforge] | ||
#* Make sure to set the <code>GO_ROOT</code> variable. | #* Make sure to set the <code>GO_ROOT</code> variable. | ||
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make prepdb | make prepdb | ||
make ontologies | make ontologies | ||
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===Installation using an RPM=== | ===Installation using an RPM=== | ||
Revision as of 20:46, 13 February 2007
Contents
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
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.
- Install the prerequisites listed in the [INSTALL document]
- Install BioPerl
- Install go-perl
- Alternatively install the larger go-dev package from the Gene Ontology site at Sourceforge
- Make sure to set the
GO_ROOTvariable.
- 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 see biopackages.net for directions.
Contacts
Pronunciation
Chado is usually pronounced like this.
