Generic Model Organism Database

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Generic Model Organism Database (GMOD)
Repository
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    Operating systemWindows, Mac OS X
    TypeBioinformatics
    LicenseGPL v3

    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

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    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

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    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:

    • 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

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    The full list of GMOD software components is found on the GMOD Components page.[2] These components include:

    • GMOD Core (Chado database and tools)
      • Chado: the Chado schema and tools to install it.[3]
      • XORT: a tool for loading and dumping chado-xml[4]
      • GMODTools: extracts data from a Chado database into common genome bulk formats (GFF, Fasta, etc.)[5]
    • MOD website
    • Genome Editing and Visualization
      • Apollo: a Java application for viewing and editing genome annotations[7][8]
      • GBrowse: a CGI application for displaying genome annotations[9][10]
      • JBrowse: a JavaScript application for displaying genome annotations[11]
      • Pathway Tools: a genome browser with a comparative mode
    • Comparative Genomics
      • GBrowse_syn: a GBrowse based synteny viewer[12]
      • CMap: a CGI application for displaying comparative maps[13]
    • Literature curation
      • Textpresso: a text mining system for scientific literature [14]
    • 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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    Participating databases

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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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    See also

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    References

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