gacou54 / Chado

the GMOD database schema

Chado

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.

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Introduction

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.

Installation

Please read the included chado/INSTALL.Chado.md document for instructions on how to install the Chado schema.

Running the Docker Image

docker build -t chado .
docker run -it -d chado

Chado Support

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:

[e-mail]

You can browse the schema CVS repository here:

http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/schema/

Authors

Chris Mungall, David Emmert and the GMOD team

Full list of committers:

• a8wright a8wright@224a875b-6a50-0410-9993-82261b5d0d45
• Allen Day [e-mail]
• Ben Faga [e-mail]
• Bobular [e-mail]
• Brian O. [e-mail]
• Brian O'Connor [e-mail]
• Chris Vandevelde [e-mail]
• Chun-Huai Cheng [e-mail]
• cmungall [e-mail]
• Colin Wiel [e-mail]
• Cyril Pommier [e-mail]
• Dave Clements [e-mail]
• David Emmert [e-mail]
• Don Gilbert [e-mail]
• elee [e-mail]
• Eric Just [e-mail]
• Eric Rasche [e-mail]
• Frank Smutniak [e-mail]
• Hilmar Lapp [e-mail]
• Jason Stajich [e-mail]
• Jay Sundaram [e-mail]
• Jim Hu [e-mail]
• Josh Goodman [e-mail]
• Kathleen Falls [e-mail]
• Ken Youens-Clark [e-mail]
• Lacey-Anne Sanderson [e-mail]
• lallsonu lallsonu@224a875b-6a50-0410-9993-82261b5d0d45
• Lincoln Stein [e-mail]
• Malcolm Cook [e-mail]
• Marc RJ Carlson [e-mail]
• Mark Gibson [e-mail]
• Meg Staton [e-mail]
• Monty Schulman [e-mail]
• Nathan Liles [e-mail]
• nm249 [e-mail]
• nmenda [e-mail]
• Nomi Harris [e-mail]
• Peili Zhnag [e-mail]
• Peter Ruzanov [e-mail]
• Pinglei Zhou [e-mail]
• Ram Podicheti [e-mail]
• Richard D. Hayes [e-mail]
• Rob Buels [e-mail]
• Scott Cain [e-mail]
• Seth Redmond [e-mail]
• Sheldon McKay [e-mail]
• Shengqiang Shu [e-mail]
• Stan Letovsky [e-mail]
• Stephen Ficklin [e-mail]
• Tony deCatanzaro [e-mail]
• Yuri Bendana [e-mail]
• zheng zha [e-mail]