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Generic Model Organism Database
Collection of interconnected applications and databases that biologists use as repositories and as tools

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.

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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 Chado1 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.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-xml4
    • 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 annotations78
    • GBrowse: a CGI application for displaying genome annotations910
    • JBrowse: a JavaScript application for displaying genome annotations11
    • Pathway Tools: a genome browser with a comparative mode
  • Comparative Genomics
    • GBrowse_syn: a GBrowse based synteny viewer12
    • CMap: a CGI application for displaying comparative maps13
  • 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

Participating databases

The following organism databases are contributing to and/or adopting GMOD components for model organism databases.

NISEED17AntonosporaDBArabidopsis18
BeeBaseBeetleBase1920Bovine genome database (BGD)
BioHealthBase21Bovine QTL ViewerCattle EST Gene Family Database
CGDCGLChromDB
Chromosome 7 Annotation ProjectCSHLmpdDatabase of Genomic Variants
DictyBase22DroSpeGeEchinobaseEcoCyc
FlyBaseFungal Comparative GenomicsFungal Telomere Browser
Gallus Genome BrowserGeneDBGrainGenes
GrameneHapMapHuman 2q33
Human Genome Segmental Duplication DatabaseIVDBMAGI
Marine Biological Lab Organism DatabasesMouse Genome InformaticsNon-Human Segmental Duplication Database
OMAPOryGenesDBOryza Chromosome 8
Pathway ToolsParameciumDB23PeanutMap
PlantsDBPlasmoDBPomBase
PseudoCAPPossumBasePUMAdb
Rat Genome DatabaseSaccharomyces Genome DatabaseSGD Lite
SmedDBSol Genomics NetworkSoybase
Soybean Gbrowse DatabaseT1DBaseThe Arabidopsis Information Resource
TGDThe Genome InstituteThe Institute for Genomic Research
TIGR Rice Genome BrowserToxoDBTriAnnot BAC Viewer
VectorBasewFleaBase24WormBase
XanthusBaseXenbase

See also

References

  1. 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. https://doi.org/10.1093%2Fbioinformatics%2Fbtm189 ↩

  2. "GMOD Components - GMOD". gmod.org. http://gmod.org/wiki/GMOD_Components ↩

  3. "Chado - Getting Started - GMOD". gmod.org. http://gmod.org/wiki/Chado ↩

  4. "XORT - GMOD". gmod.org. http://gmod.org/wiki/XORT ↩

  5. "GMODTools - GMOD". gmod.org. http://gmod.org/wiki/GMODTools ↩

  6. "Tripal". gmod.org. http://gmod.org/wiki/Tripal ↩

  7. "Apollo - GMOD". gmod.org. http://gmod.org/wiki/Apollo ↩

  8. "Apollo — Apollo 2.7.0 documentation". genomearchitect.readthedocs.io. https://genomearchitect.readthedocs.io/en/latest/ ↩

  9. "GBrowse - GMOD". gmod.org. http://gmod.org/wiki/GBrowse ↩

  10. 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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187535 ↩

  11. "JBrowse - GMOD". gmod.org. http://gmod.org/wiki/JBrowse ↩

  12. "GBrowse syn - GMOD". gmod.org. http://gmod.org/wiki/GBrowse_syn ↩

  13. "CMap - GMOD". gmod.org. http://gmod.org/wiki/CMap ↩

  14. "Textpresso". gmod.org. http://gmod.org/wiki/Textpresso ↩

  15. Afgan, E.; Baker, D.; van den Beek, M.; Blankenberg, D.; Bouvier, D.; Čech, M.; Chilton, J.; Clements, D.; Coraor, N.; Eberhard, C.; Grüning, B.; Guerler, A.; Hillman-Jackson, J.; Von Kuster, G.; Rasche, E.; Soranzo, N.; Turaga, N.; Taylor, J.; Nekrutenko, A.; Goecks, J. (8 July 2016). "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update". Nucleic Acids Research. 44 (W1): W3 – W10. doi:10.1093/nar/gkw343. PMC 4987906. PMID 27137889. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987906 ↩

  16. Cantarel, Brandi L.; Korf, Ian; Robb, Sofia M. C.; Parra, Genis; Ross, Eric; Moore, Barry; Holt, Carson; Sánchez Alvarado, Alejandro; Yandell, Mark (January 2008). "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes". Genome Research. 18: 188–196. doi:10.1101/gr.6743907. PMC 2134774. http://gmod.org/wiki/MAKER ↩

  17. Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010). "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research. 20 (10): 1459–1468. doi:10.1101/gr.108175.110. ISSN 1088-9051. PMC 2945195. PMID 20647237. https://genome.cshlp.org/content/20/10/1459.short ↩

  18. Weems, Danforth; Miller, Neil; Garcia-Hernandez, Margarita; Huala, Eva; Rhee, Seung Y. (2004). "Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana". Comparative and Functional Genomics. 5 (4): 362–369. doi:10.1002/cfg.408. ISSN 1531-6912. PMC 2447457. PMID 18629167. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447457 ↩

  19. Wang L; Wang S; Li Y; Paradesi MS; Brown SJ. (2007). "BeetleBase: the model organism database for Tribolium castaneum". Nucleic Acids Res. 35 (Database issue): D476–9. doi:10.1093/nar/gkl776. PMC 1669707. PMID 17090595. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669707 ↩

  20. "BeetleBase". www.bioinformatics.ksu.edu/Be. Archived from the original on 13 July 2006. https://web.archive.org/web/20060713200536/http://www.bioinformatics.ksu.edu/BeetleBase/ ↩

  21. Noronha, Antonio; Cui, Changhai; Harris, Robert Adron; Crabbe, John C. (2014). Neurobiology of Alcohol Dependence. Elsevier. ISBN 978-0-12-407155-1. 978-0-12-407155-1 ↩

  22. Chisholm RL; Gaudet P; Just EM; Pilcher KE; Fey P; Merchant SN; Kibbe WA. (2006). "dictyBase, the model organism database for Dictyostelium discoideum". Nucleic Acids Res. 34 (Database issue): D423–7. doi:10.1093/nar/gkj090. PMC 1347453. PMID 16381903. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347453 ↩

  23. Arnaiz O; Cain S; Cohen J; Sperling L. (2007). "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data". Nucleic Acids Res. 35 (Database issue): D439–44. doi:10.1093/nar/gkl777. PMC 1669747. PMID 17142227. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669747 ↩

  24. Colbourne JK; Singan VR; Gilbert DG. (2005). "wFleaBase: the Daphnia genome database". BMC Bioinformatics. 6: 45. doi:10.1186/1471-2105-6-45. PMC 555599. PMID 15752432. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC555599 ↩