# Generic Model Organism Database

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.

## History

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.

## Chado database schema

The Chado 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:
* 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
* natural diversity - population data

## Software

The full list of GMOD software components is found on the GMOD Components 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
* Tripal: a web front end based on Drupal.
* Genome Editing and Visualization
* Apollo: a Java application for viewing and editing genome annotations
* GBrowse: a CGI application for displaying genome annotations
* JBrowse: a JavaScript application for displaying genome annotations
* Pathway Tools: a genome browser with a comparative mode
* Comparative Genomics
* GBrowse_syn: a GBrowse based synteny viewer
* CMap: a CGI application for displaying comparative maps
* Literature curation
* Textpresso: a text mining system for scientific literature
* Database querying tools
* BioMart: a query-oriented data management system
* InterMine: open source data warehouse system
* Biological Pathways
* Pathway Tools: tools for metabolic pathway information, and analysis of high-throughput functional genomics data
* Regulatory Networks
* Pathway Tools: supports definition of regulatory interactions and browsing of regulatory networks
* Analysis
* Galaxy
* MAKER

## Participating databases

The following organism databases are contributing to and/or adopting GMOD components for model organism databases.
| NISEED | AntonosporaDB | Arabidopsis |
| BeeBase | BeetleBase | Bovine genome database (BGD) |
| BioHealthBase | Bovine QTL Viewer | Cattle EST Gene Family Database |
| CGD | CGL | ChromDB |
| Chromosome 7 Annotation Project | CSHLmpd | Database of Genomic Variants |
| DictyBase | 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 | 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 | WormBase |
| XanthusBase | Xenbase |

## Related projects

* Bioperl, BioJava, Biopython, BioRuby, etc.
* Ensembl
* Gene Ontology
* DAS
* Genomics Unified Schema
* Manatee: Manual Annotation Tool
* Biocurator.org
* Open Biomedical Ontologies
* Sequence Ontology Project