Generic Model Organism Database
Model Organism Databases (MODs) describe genome and other information about
important experimental organisms in the life sciences. Also called
organism-specific databases, these databases capture the large volumes
of data and information being generated by modern biology.
Behind every MOD is a software system that is designed to help
manage the data within the MOD, and to help users query and access
those data. In the past, every MOD project developed its own software
tools.
More recently, the Generic Model Organism Database (GMOD) Project began as an effort to create reusable software tools for
developing MODs. GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by many or all model organism databases. Some of these software components are linked together by their use of a common database schema known as Chado. This project is funded by the US NIH and the USDA Agricultural Research Service.
Additional recommended knowledge
Software
The full list of GMOD software components is found on the
GMOD home page. These components
include:
- GMOD Core (Chado database and tools)
- Chado : the Chado schema and tools to install it.
- XORT : a tool for loading and dumping chado-xml
- GMODTools : extracts data from a Chado database into common genome bulk formats (GFF, Fasta, etc)
- MOD website
- gmod-web/Turnkey : a generic web front end for browsing database contents.
- Genome Editing and Visualization
- Apollo : a Java application for viewing and editing genome annotations
- GBrowse : a CGI application for displaying genome annotations
- Comparative Genomics
- SynBrowse : a GBrowse based synteny viewer
- CMap : a CGI application for displaying comparative maps
- Literature curation
- PubSearch : a Java servlet web application for annotating genes from literature
- PubFetch : a tool to facilitate literature collection for curators' use
- Textpresso : a text mining system for scientific literature
- Database querying tools
- BioMart : a query-oriented data management system
- Biological Pathways
- Pathway Tools : tools for metabolic pathway information, and analysis of high-throughput functional genomics data
Chado database schema
Chado makes extensive use of controlled vocabularies to type all entities in the database, so there is a feature table where gene, transcripts, exons, transposable elements, etc. are stored and their type is provided by the Sequence Ontology. When a new datatype comes along, the feature table requires no modification, only an update of the data in the database. The same is largely true of analysis data that can be stored in Chado as well.
The existing core modules of Chado 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
- genetic - genetic and phenotypic data
- expression - gene expression
References
- Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. (2002). "The generic genome browser: a building block for a model organism system database.". Genome Res. 12: 1599-610.
- Colbourne JK, Singan VR, Gilbert DG. (2005). "wFleaBase: the Daphnia genome database.". BMC Bioinformatics. 6: 45.
- Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA. (2006). "dictyBase, the model organism database for Dictyostelium discoideum.". Nucleic Acids Res. 34(Database issue): D423-7..
- Wang L, Wang S, Li Y, Paradesi MS, Brown SJ. (2007). "BeetleBase: the model organism database for Tribolium castaneum.". Nucleic Acids Res. 35(Database issue): D476-9.
- Arnaiz O, Cain S, Cohen J, Sperling L. (2007). "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.". Nucleic Acids Res. 35(Database issue): D439-44.
Participating databases
The following organism databases are contributing to and/or adopting GMOD components
for model organism databases.
ANISEED
| AntonosporaDB
| ATIDB
|
BeeBase
| BeetleBase
| BGD
|
BioHealthBase
| Bovine QTL Viewer
| Cattle EST Gene Family Database
|
CGD
| CGL
| ChromDB
|
Chromosome 7 Annotation Project
| CSHLmpd
| Database of Genomic Variants
|
DictyBase
| DroSpeGe
| EcoCyc
|
FlyBase
| Fungal Comparative Genomics
| Fungal Telomere Browser
|
Gallus Genome Browser
| GeneDB
| GrainGenes
|
Gramene
| HapMap
| Human 2q33
|
Human Genome Segmental Duplication Database
| IVDB
| MAGI
|
Marine Biological Lab Organism Databases
| MGI
| Non-Human Segmental Duplication Database
|
OMAP
| OryGenesDB
| Oryza Chromosome 8
|
Pathway Tools
| ParameciumDB
| PeanutMap
|
PlantsDB
| PlasmoDB
| PseudoCAP
|
PossumBase
| PUMAdb
| RGD
|
SGD
| SGD Lite
| SmedDB
|
SOL Genomics Network
| Soybase
| Soybean Gbrowse Database
|
T1DBase
| TAIR
| TGD
|
TGI
| TIGR
| TIGR Rice Genome Browser
|
ToxoDB
| TriAnnot BAC Viewer
| VectorBase
|
wFleaBase
| WormBase
|
XanthusBase
| Xenbase
|
Related projects
See also
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