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
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Complex phenotypic data
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Ontologies structured as graphs; querying over graph ontologies non-recursively by pre-computing the closure
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Sequence ontology
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Comparative data
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Genetic interactions
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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 chado/INSTALL.Chado.md document for instructions on how to install the Chado schema.
docker build -t chado .
docker run -it -d chadoPlease 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:
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
Full list of committers:
- a8wright a8wright@224a875b-6a50-0410-9993-82261b5d0d45
- Allen Day [email protected]
- Ben Faga [email protected]
- Bobular [email protected]
- Brian O. [email protected]
- Brian O'Connor [email protected]
- Chris Vandevelde [email protected]
- Chun-Huai Cheng [email protected]
- cmungall [email protected]
- Colin Wiel [email protected]
- Cyril Pommier [email protected]
- Dave Clements [email protected]
- David Emmert [email protected]
- Don Gilbert [email protected]
- elee [email protected]
- Eric Just [email protected]
- Eric Rasche [email protected]
- Frank Smutniak [email protected]
- Hilmar Lapp [email protected]
- Jason Stajich [email protected]
- Jay Sundaram [email protected]
- Jim Hu [email protected]
- Josh Goodman [email protected]
- Kathleen Falls [email protected]
- Ken Youens-Clark [email protected]
- Lacey-Anne Sanderson [email protected]
- lallsonu lallsonu@224a875b-6a50-0410-9993-82261b5d0d45
- Lincoln Stein [email protected]
- Malcolm Cook [email protected]
- Marc RJ Carlson [email protected]
- Mark Gibson [email protected]
- Meg Staton [email protected]
- Monty Schulman [email protected]
- Nathan Liles [email protected]
- nm249 [email protected]
- nmenda [email protected]
- Nomi Harris [email protected]
- Peili Zhnag [email protected]
- Peter Ruzanov [email protected]
- Pinglei Zhou [email protected]
- Ram Podicheti [email protected]
- Richard D. Hayes [email protected]
- Rob Buels [email protected]
- Scott Cain [email protected]
- Seth Redmond [email protected]
- Sheldon McKay [email protected]
- Shengqiang Shu [email protected]
- Stan Letovsky [email protected]
- Stephen Ficklin [email protected]
- Tony deCatanzaro [email protected]
- Yuri Bendana [email protected]
- zheng zha [email protected]