Difference between revisions of "Chado - Getting Started"
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| + | Chado is a [[Glossary#Database Schema|relational database schema]] that underlies [[GMOD_Users|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== | ==Documentation== | ||
| + | * [[Introduction to Chado]] | ||
| + | * [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i337?ijkey=QYeUct9uLSzefgk&keytype=ref Chado paper in Bioinformatics] | ||
| + | * [[Chado Tutorial]] | ||
* [[Chado Manual]] | * [[Chado Manual]] | ||
* [[Chado FAQ|FAQ for Chado]] | * [[Chado FAQ|FAQ for Chado]] | ||
| − | * [[ | + | * [[Chado_Tables|Chado Tables]] |
| + | * [[Chado_Best_Practices|Chado Best Practices]] | ||
| + | * [[Sample_Chado_SQL|Sample Chado SQL]] | ||
| + | * [[PostgreSQL Performance Tips]] | ||
==Modules== | ==Modules== | ||
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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: | 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: | ||
| − | + | {{ChadoModules}} | |
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==Installation== | ==Installation== | ||
| + | First you will need database software, or Relational Database Management System (RDBMS). The recommended RDBMS for Chado currently is [http://www.postgresql.org/ 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. | ||
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| − | + | ===Download a Stable Release of Chado=== | |
| − | + | See [[Downloads]] | |
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| − | + | <!-- | |
| + | * Go to [http://sourceforge.net/project/showfiles.php?group_id=27707 GMOD at Sourceforge] | ||
| + | * Download the latest '''gmod''' (the Chado source code is contained within this package) | ||
| + | * Follow the instructions in the {{CVS|schema/chado/INSTALL.Chado}} file | ||
| + | --> | ||
| − | + | === 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://svn.code.sf.net/p/gmod/svn/schema/trunk | |
| − | + | Once the package has been downloaded <code>cd</code> to the <code>trunk/chado</code> directory. | |
| − | + | Follow the instructions in the <tt>INSTALL.Chado</tt> file, including the installation of the prerequisites. Or read <tt>{{SF_SVN|schema/trunk/chado/INSTALL.Chado|INSTALL.Chado}}</tt> online. | |
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| − | == | + | ==Loading Data== |
| − | + | After completing these steps, you can load your chado schema with data in a number of ways: | |
| − | + | * [[Load_RefSeq_Into_Chado|Load RefSeq into Chado HOWTO]] | |
| − | + | * [[Load_GFF_Into_Chado|Load GFF into Chado HOWTO]] | |
| − | + | * Using [[XORT]] | |
| − | + | You can also use the application [[Apollo]] to curate data in Chado. | |
| − | == | + | == Mailing Lists == |
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| + | {{MailingListsFor|Chado}} | ||
==Pronunciation== | ==Pronunciation== | ||
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''Chado'' is usually pronounced [[Media:Chado.mp3|like this]]. | ''Chado'' is usually pronounced [[Media:Chado.mp3|like this]]. | ||
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[[Category:Chado]] | [[Category:Chado]] | ||
| + | [[Category:Database Tools]] | ||
| + | [[Category:GMOD Components]] | ||
Latest revision as of 18:08, 13 February 2014
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.
Contents
Documentation
- Introduction to Chado
- Chado paper in Bioinformatics
- Chado Tutorial
- Chado Manual
- FAQ for Chado
- Chado Tables
- Chado Best Practices
- Sample Chado SQL
- PostgreSQL Performance Tips
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 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://svn.code.sf.net/p/gmod/svn/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.
