Generic Model Organism Database
The Generic Model Organism Database (GMOD) Project began as an effort to create reusable software tools for developing Model Organism Databases (MODs). 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. GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by many or all MODs. 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 United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.
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
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
- 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
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References
- Christopher J. Mungall, David B. Emmert, The FlyBase Consortium (2007). "A Chado case study: an ontology-based modular schema for representing genome-associated biological information". Bioinformatics 23 (13): i337-i346. doi:10.1093/bioinformatics/btm189. PMID 17646315. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i337.
- 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 (10): 1599–610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=187535.
Participating databases
The following organism databases are contributing to and/or adopting GMOD components for model organism databases.
Related projects
See also