Difference between revisions of "Chado - Getting Started"

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==Description==
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{{ComponentBox
 
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|{{ChadoResourcesBoxItem}}
Chado is a relational 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 is advised to spend some time becoming familiar with its fundamentals.
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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]]
 
* [[Introduction to Chado]]
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* [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i337?ijkey=QYeUct9uLSzefgk&keytype=ref Chado paper in Bioinformatics]
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* [[Chado Tutorial]]
 
* [[Chado Manual]]
 
* [[Chado Manual]]
 
* [[Chado FAQ|FAQ for Chado]]
 
* [[Chado FAQ|FAQ for Chado]]
 
* [[Chado_Tables|Chado Tables]]
 
* [[Chado_Tables|Chado Tables]]
 
* [[Chado_Best_Practices|Chado Best Practices]]
 
* [[Chado_Best_Practices|Chado Best Practices]]
 
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* [[Sample_Chado_SQL|Sample Chado SQL]]
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* [[PostgreSQL Performance Tips]]
  
 
==Modules==
 
==Modules==
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==Installation==
 
==Installation==
  
First you will need database software, or Relational Database Management System (RDBMS). The recommended RDBMBS 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. Once you've installed your RDBMS you can install Chado.
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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.
  
  
===Chado From CVS===
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===Download a Stable Release of Chado===
  
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:
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See [[Downloads]]
 
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cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
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Enter blank password. Then do:
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cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co schema
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Once the package has been downloaded <code>cd</code> to the <code>schema/chado/</code> directory.
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Follow the instructions in the INSTALL.Chado file, including the installation of the prerequisites. Or read {{CVS|schema/chado/INSTALL.Chado}} online.
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===Download a Stable Release of Chado===
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<!--
 
* Go to [http://sourceforge.net/project/showfiles.php?group_id=27707 GMOD at Sourceforge]
 
* 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)
 
* Download the latest '''gmod''' (the Chado source code is contained within this package)
 
* Follow the instructions in the  {{CVS|schema/chado/INSTALL.Chado}} file
 
* Follow the instructions in the  {{CVS|schema/chado/INSTALL.Chado}} file
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-->
  
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=== Chado From SVN ===
  
===Installation using an RPM===
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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:
  
If you are running the Fedora Core 2 linux distribution or any Unix that uses <code>yum</code> and RPM files then installing many GMOD applications (e.g. Chado, GBrowse, and Textpresso and the prerequisites) should be easy:
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svn co https://svn.code.sf.net/p/gmod/svn/schema/trunk
  
# Modify your <code>yum.conf</code> file in the way described [http://www.biopackages.net/#Configuration here] on the Biopackages.net website. This file is usually found in the <code>/etc</code> directory.
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Once the package has been downloaded <code>cd</code> to the <code>trunk/chado</code> directory.
# Issue the command <code>sudo yum update</code>.
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# Issue the command <code>sudo yum install gmod</code>.
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See [http://www.biopackages.net/ biopackages.net] for more detail.
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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.
  
 
==Loading Data==
 
==Loading Data==
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After completing these steps, you can load your chado schema with data in a number of ways:
 
After completing these steps, you can load your chado schema with data in a number of ways:
  
* Using {{CVS|schema/chado/load/bin/bulk_load_gff3.PLS}}
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* [[Load_RefSeq_Into_Chado|Load RefSeq into Chado HOWTO]]
* Using the closely related script <code>load_gff3.PLS</code> - see the [[HOWTO:LoadGenbankIntoChado|Load Genbank into Chado HOWTO]]
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* [[Load_GFF_Into_Chado|Load GFF into Chado HOWTO]]
 
* Using [[XORT]]
 
* Using [[XORT]]
  
 
You can also use the application [[Apollo]] to curate data in Chado.
 
You can also use the application [[Apollo]] to curate data in Chado.
  
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== Mailing Lists ==
  
==Contacts==
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{{MailingListsFor|Chado}}
 
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* [https://lists.sourceforge.net/lists/subscribe/gmod-schema GMOD Schema Mailing List]
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* [[GMOD_Help_Desk|GMOD Help Desk]]
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==Pronunciation==
 
==Pronunciation==
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''Chado'' is usually pronounced [[Media:Chado.mp3|like this]].
 
''Chado'' is usually pronounced [[Media:Chado.mp3|like this]].
  
 
[[Category:To Do]]
 
 
[[Category:Chado]]
 
[[Category:Chado]]
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[[Category:Database Tools]]
 
[[Category:GMOD Components]]
 
[[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.

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:


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.