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| Operating system | Windows, Mac OS X |
|---|---|
| Type | Bioinformatics |
| License | GPL v3 |
| Website | gmod |
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.
The GMOD project was started in the early 2000s as a collaboration between several model organism databases (MODs) who shared a need to create similar software tools for processing data from sequencing projects. MODs, or organism-specific databases, describe genome and other information about important experimental organisms in the life sciences and capture the large volumes of data and information being generated by modern biology. Rather than each group designing their own software, four major MODs--FlyBase, Saccharomyces Genome Database, Mouse Genome Database, and at or run off a Chado schema database.
The Chado [1] schema aims to cover many of the classes of data frequently used by modern biologists, from genetic data to phylogenetic trees to publications to organisms to microarray data to IDs to RNA/protein expression. Chado makes extensive use of controlled vocabularies to type all entities in the database; for example: genes, transcripts, exons, transposable elements, etc., are stored in a feature table, with the type provided by Sequence Ontology. When a new type is added to the Sequence Ontology, 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:
The full list of GMOD software components is found on the GMOD Components page. [2] These components include:
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The following organism databases are contributing to and/or adopting GMOD components for model organism databases.
| NISEED [17] | AntonosporaDB[ citation needed ] | Arabidopsis [18] | |
| BeeBase | BeetleBase [19] [20] | Bovine genome database (BGD) | |
| BioHealthBase [21] | Bovine QTL Viewer | Cattle EST Gene Family Database | |
| CGD | CGL | ChromDB | |
| Chromosome 7 Annotation Project | CSHLmpd | Database of Genomic Variants | |
| DictyBase [22] | DroSpeGe | Echinobase | 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 | Mouse Genome Informatics | Non-Human Segmental Duplication Database | |
| OMAP | OryGenesDB | Oryza Chromosome 8 | |
| Pathway Tools | ParameciumDB [23] | PeanutMap | |
| PlantsDB | PlasmoDB | PomBase | |
| PseudoCAP | PossumBase | PUMAdb | |
| Rat Genome Database | Saccharomyces Genome Database | SGD Lite | |
| SmedDB | Sol Genomics Network | Soybase | |
| Soybean Gbrowse Database | T1DBase | The Arabidopsis Information Resource | |
| TGD | The Genome Institute | The Institute for Genomic Research | |
| TIGR Rice Genome Browser | ToxoDB | TriAnnot BAC Viewer | |
| VectorBase | wFleaBase [24] | WormBase | |
| XanthusBase | Xenbase | ||
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