Difference between revisions of "Chado - Getting Started"
From GMOD
(New page: Chado, properly pronounced. [[files/chado.mp3 [[Image:speaker_0.gif]]]] This is a stub document for describing the Chado schema at a high level. Until this is fleshed out a little more...) |
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| − | Chado, properly pronounced. [[ | + | Chado, properly pronounced. [[[[Image:speaker_0.gif]]]] |
This is a stub document for describing the Chado schema at a high level. | This is a stub document for describing the Chado schema at a high level. | ||
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Until this is fleshed out a little more, here are a few useful links: | Until this is fleshed out a little more, here are a few useful links: | ||
| − | * [[ | + | * [[FAQ for chado]] |
* [http://gmod.sourceforge.net/schema/index.shtml The old schema summary page] | * [http://gmod.sourceforge.net/schema/index.shtml The old schema summary page] | ||
* [http://gmod.sourceforge.net/schema/doc/ The autogenerated documentation] | * [http://gmod.sourceforge.net/schema/doc/ The autogenerated documentation] | ||
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As well as these documents that are a good reference for new comers to Chado: | As well as these documents that are a good reference for new comers to Chado: | ||
| − | * [[ | + | * [[Chado_Schema_Documentation.doc]], a MS Word document giving a detailed explaination of many Chado concepts (older), |
| − | * [[ | + | * [[Chado Manual]], a set of html pages automatically generated from tex files, where some of those tex files were automatically generated from sql files (newer). |
| − | * [[ | + | * [[chado-scenarios.xml]], an XML file with Chado usage scenarios. This document has an xslt applied to it, so hopefully your browser will support that as well as mine. |
* [http://www.gmod.org/schema-cvs/chado/doc/ChadoCSHMay03Slides.pdf ChadoCSHMay03Slides.pdf], a presentation given by Stan Letovsky at the May, 2003 GMOD meeting to introduce the basic concepts in Chado. | * [http://www.gmod.org/schema-cvs/chado/doc/ChadoCSHMay03Slides.pdf ChadoCSHMay03Slides.pdf], a presentation given by Stan Letovsky at the May, 2003 GMOD meeting to introduce the basic concepts in Chado. | ||
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You can create a working chado instance in a few ways. First, if you are running the Fedora Core 2 linux distribution, you are in luck! Allen Day has created a set of RPM files for installing Chado and all of the prerequisites. See [http://www.biopackages.net/ biopackages.net] for directions to install Chado with yum. | You can create a working chado instance in a few ways. First, if you are running the Fedora Core 2 linux distribution, you are in luck! Allen Day has created a set of RPM files for installing Chado and all of the prerequisites. See [http://www.biopackages.net/ biopackages.net] for directions to install Chado with yum. | ||
| − | To install Chado from source, my best current advice is to get chado from the schema cvs. See [[ | + | To install Chado from source, my best current advice is to get chado from the schema cvs. See [[this FAQ]] for a description of how to get it and install it. |
Below are the documation for the various modules. | Below are the documation for the various modules. | ||
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| − | * [[ | + | * [[1. Documentation in CVS]] |
| − | * [[ | + | * [[Audit Module]] |
| − | * [[ | + | * [[Companalysis Module]] |
| − | * [[ | + | * [[Contact Module]] |
| − | * [[ | + | * [[Controlled Vocabulary Module]] |
| − | * [[ | + | * [[Expression Module]] |
| − | * [[ | + | * [[General Module]] |
| − | * [[ | + | * [[Genetic Module]] |
| − | * [[ | + | * [[Library Module]] |
| − | * [[ | + | * [[Map Module]] |
| − | * [[ | + | * [[Organism Module]] |
| − | * [[ | + | * [[Phylogeny Module]] |
| − | * [[ | + | * [[Publication Module]] |
| − | * [[ | + | * [[Sequence Module]] |
Revision as of 18:39, 25 January 2007
Chado, properly pronounced. [[File:Speaker 0.gif]]
This is a stub document for describing the Chado schema at a high level.
Until this is fleshed out a little more, here are a few useful links:
As well as these documents that are a good reference for new comers to Chado:
- Chado_Schema_Documentation.doc, a MS Word document giving a detailed explaination of many Chado concepts (older),
- Chado Manual, a set of html pages automatically generated from tex files, where some of those tex files were automatically generated from sql files (newer).
- chado-scenarios.xml, an XML file with Chado usage scenarios. This document has an xslt applied to it, so hopefully your browser will support that as well as mine.
- ChadoCSHMay03Slides.pdf, a presentation given by Stan Letovsky at the May, 2003 GMOD meeting to introduce the basic concepts in Chado.
THIS IS A WORKING DOCUMENT:
The GMOD schema, known as Chado, is the foundation on which GMOD applications interoperate, so consistent use of the database is crucial. It is a modular schema, designed in such a way as to allow the addition of new modules for new data types. It was designed by FlyBase and BDGP. The existing core modules are:
- sequence - for sequences/features
- cv - for controlled-vocabs/ontologies
- general - currently just dbxrefs
- organism - taxonomic data
- pub - publication and references
- companalysis - augments sequence module with computational analysis data
- map - non-sequence maps (PRELIMINARY SCHEMA)
- genetic - genetic and phenotypic data (IN DEVELOPMENT)
- expression - gene expression (PRELIMINARY SCHEMA)
CREATING A WORKING CHADO INSTANCE
You can create a working chado instance in a few ways. First, if you are running the Fedora Core 2 linux distribution, you are in luck! Allen Day has created a set of RPM files for installing Chado and all of the prerequisites. See biopackages.net for directions to install Chado with yum.
To install Chado from source, my best current advice is to get chado from the schema cvs. See this FAQ for a description of how to get it and install it.
Below are the documation for the various modules.
