Name: Chado
Owner: Generic Model Organism Database Project
Description: the GMOD database schema
Created: 2011-05-12 23:16:51.0
Updated: 2018-01-15 01:33:49.0
Pushed: 2018-01-11 17:36:56.0
Homepage: http://gmod.org/wiki/Chado
Size: 530056
Language: PLpgSQL
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Chado is a modular schema for handling all kinds of biological data. It is intended to be used as both a primary datastore schema as well as a warehouse-style schema.
Chado was originally conceived as the next generation Flybase database, combining the sequence annotation database gadfly with the Harvard and Cambridge databases. We have avoided organism or project specificity in the schema, and we hope it will be of use to other projects.
The modules currently in chado are:
Module | Description ————————– | —————————— Audit | database audits Companalysis | data from computational analysis Contact | people and groups Controlled Vocabulary (cv) | controlled vocabularies and ontologies Expression | summarized RNA and protein expresssion General | identifiers Genetic | genetic data and genotypes Library | descriptions of molecular libraries Mage | microarray data Map | maps without sequence Organism | species Phenotype | phenotypic data Phylogeny | phylogenetic trees Publication (pub) | publications and references Sequence | sequences and sequence features Stock | specimens and biological collections WWW | generic classes for web interfaces
For documentation on the various modules, see http://www.gmod.org.
Other modules are possible; the existing modules cover a very large variety of use cases.
Chado has a fairly abstract schema, and ontologies and controlled vocabularies (CVs) are utilised where their use is favourable to relational modeling. In particular, the sequence ontology (SO) is vital to the sequence module.
Some (but not all) of the use cases we have discussed are:
Central dogma genome annotations
Genes that break the central dogma (of which there are many Annotated in fly, including polycistronic transcripts, transplicing, selenocysteine readthroughs, rna editing, ….)
Sequence variation data, including SNPs, transposable element insertions, indels, … how this relates to phenotypes, how these effect the central dogma….
Non-wildtype data, including representing a wildtype transcriptome and proteome on a non wildtype genome; implicit and explicit central dogma examples for mutant strains
Complex phenotypic data
Ontologies structured as graphs; querying over graph ontologies non-recursively by pre-computing the closure
Sequence ontology
Comparative data
Genetic interactions
Transgene constructs, complex genetic experiments and their results
The core schema is DBMS independent. The SQL table create files can be found in the chado/modules directory. The main Chado developers are currently using PostgreSQL.
Please read the included INSTALL.Chado document for instructions on how to install the Chado schema.
Please see our website for more information on Chado and the GMOD project:
http://www.gmod.org/
You can send questions to the Chado mailing list:
gmod-schema@lists.sourceforge.net
You can browse the schema CVS repository here:
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/schema/
Chris Mungall, David Emmert and the GMOD team
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