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 ArabidopsisBeeBase BeetleBaseBovine genome database (BGD) BioHealthBaseBovine QTL ViewerCattle EST Gene Family DatabaseCGDCGLChromDBChromosome 7 Annotation ProjectCSHLmpdDatabase of Genomic VariantsDictyBaseDroSpeGeEchinobaseEcoCycFlyBaseFungal Comparative GenomicsFungal Telomere BrowserGallus Genome BrowserGeneDBGrainGenesGrameneHapMapHuman 2q33Human Genome Segmental Duplication DatabaseIVDBMAGIMarine Biological Lab Organism DatabasesMouse Genome InformaticsNon-Human Segmental Duplication DatabaseOMAPOryGenesDBOryza Chromosome 8Pathway ToolsParameciumDBPeanutMapPlantsDBPlasmoDBPomBasePseudoCAPPossumBasePUMAdbRat Genome DatabaseSaccharomyces Genome DatabaseSGD LiteSmedDBSol Genomics NetworkSoybaseSoybean Gbrowse DatabaseT1DBaseThe Arabidopsis Information ResourceTGDThe Genome InstituteThe Institute for Genomic ResearchTIGR Rice Genome BrowserToxoDBTriAnnot BAC ViewerVectorBasewFleaBaseWormBaseXanthusBaseXenbase
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
See also Biological database Genome project Genomics Genome
References
External links GMOD website