Generic Model Organism Database
This article provides insufficient context for those unfamiliar with the subject. |
The topic of this article may not meet Wikipedia's general notability guideline. |
The Generic Model Organism Database (GMOD) Project is a loose federation of software applications (components) aimed at providing functionality that is needed by all model organism databases. The applications are linked together by their use of a common database schema known as Chado. This project is funded by the NIH and the USDA Agricultural Research Service.
Software
Chado was designed by FlyBase[1] and BDGP[2] as a modular schema that allows the addition of new modules for new data types.
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 (PRELIMINARY SCHEMA)
- genetic - genetic and phenotypic data (IN DEVELOPMENT)
- expression - gene expression (PRELIMINARY SCHEMA)
Participating members
- WormBase[3]
- FlyBase[4]
- Mouse Genome Informatics[5]
- Gramene[6]
- Rat Genome Database[7]
- TAIR[8]
- EcoCyc[9]
- Saccharomyces Genome Database[10]
Related projects
- Open Biomedical Ontologies
- Ensembl
- Bioperl
- BioJava
- BioXML[11]
- Gene Ontology Software[12]
- DAS[13]
- The Genomics Unified Schema[14]
- Manatee: Manual Annotation Tool Etc, Etc...[15]
- Biocurator.org[16]
- SGD Lite[17]
- Open Biomedical Ontologies