Generic Model Organism Database

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Generic Model Organism Database (GMOD)
Operating system Windows, Mac OS X
Type Bioinformatics
License GPL v3
Website gmod.org/wiki/Main_Page   OOjs UI icon edit-ltr-progressive.svg

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.

Contents

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 [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:

Software

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
    • Tripal: a web front end based on Drupal. [6]
  • 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

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 ViewerCattle EST Gene Family Database
CGDCGLChromDB
Chromosome 7 Annotation ProjectCSHLmpd Database of Genomic Variants
DictyBase [22] DroSpeGe Echinobase EcoCyc
FlyBase Fungal Comparative GenomicsFungal Telomere Browser
Gallus Genome Browser GeneDB GrainGenes
Gramene HapMap Human 2q33
Human Genome Segmental Duplication DatabaseIVDBMAGI
Marine Biological Lab Organism Databases Mouse Genome Informatics Non-Human Segmental Duplication Database
OMAP OryGenesDBOryza Chromosome 8
Pathway Tools ParameciumDB [23] PeanutMap
PlantsDB PlasmoDB PomBase
PseudoCAPPossumBasePUMAdb
Rat Genome Database Saccharomyces Genome Database SGD Lite
SmedDBSol Genomics NetworkSoybase
Soybean Gbrowse DatabaseT1DBase The Arabidopsis Information Resource
TGD The Genome Institute The Institute for Genomic Research
TIGR Rice Genome BrowserToxoDBTriAnnot BAC Viewer
VectorBase wFleaBase [24] WormBase
XanthusBase Xenbase

See also

Related Research Articles

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The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.

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<span class="mw-page-title-main">MicrobesOnline</span>

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References

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