Model organism databases

Model organism databases (MODs) are biological databases dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses.[1][2] They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species.[1] Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology[3][4] to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs.[5] Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.[1]

Types of data and services

Model organism databases generate, source and collate species-specific information integratively by combining expert knowledge with literature curation and bioinformatics.

Services provided to biological research communities include:

Some examples are"

Common name Scientific name Wikipedia page Database link-out
Baker's yeast Saccharomyces cerevisiae Saccharomyces Genome Database SGD[6]
Fission yeast Schizosaccharomyces pombe PomBase PomBase[7][8]
Frog Xenopus laevis Xenbase Xenbase[9][10]
Fruitfly Drosophila melanogaster FlyBase FlyBase[11]
Mouse Mus musculus Mouse Genome Informatics MGI[12]
Nematode Caenorhabditis elegans WormBase WormBase[13]
Rat Rattus norvegicus Rat Genome Database RGD[14]
Social amoeba Dictyostelium discoideum DictyBase dictyBase[15]
Thale cress Arabidopsis thaliana The Arabidopsis Information Resource TAIR[16]
Zebrafish Danio rerio Zebrafish Information Network ZFIN[17]
- Candida albicans - CGD[18]
- Escherichia coli EcoCyc EcoCyc[19]

References

  1. 1 2 3 Oliver SG, Lock A, Harris MA, Nurse P, Wood V (2016). "Model organism databases: essential resources that need the support of both funders and users.". BMC Biol. 14 (1): 49. PMC 4918006 Freely accessible. PMID 27334346. doi:10.1186/s12915-016-0276-z.
  2. ↑ Bond M, Holthaus SM, Tammen I, Tear G, Russell C (2013). "Use of model organisms for the study of neuronal ceroid lipofuscinosis.". Biochim Biophys Acta. 1832 (11): 1842–65. PMID 23338040. doi:10.1016/j.bbadis.2013.01.009.
  3. ↑ Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. (2000). "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.". Nat Genet. 25 (1): 25–9. PMC 3037419 Freely accessible. PMID 10802651. doi:10.1038/75556.
  4. ↑ Gene Ontology Consortium (2015). "Gene Ontology Consortium: going forward.". Nucleic Acids Res. 43 (Database issue): D1049–56. PMC 4383973 Freely accessible. PMID 25428369. doi:10.1093/nar/gku1179.
  5. ↑ O'Connor BD, Day A, Cain S, Arnaiz O, Sperling L, Stein LD (2008). "GMODWeb: a web framework for the Generic Model Organism Database.". Genome Biol. 9 (6): R102. PMC 2481422 Freely accessible. PMID 18570664. doi:10.1186/gb-2008-9-6-r102.
  6. ↑ Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, et al. (2012). "Saccharomyces Genome Database: the genomics resource of budding yeast.". Nucleic Acids Res. 40 (Database issue): D700–5. PMC 3245034 Freely accessible. PMID 22110037. doi:10.1093/nar/gkr1029.
  7. ↑ Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, et al. (2012). "PomBase: a comprehensive online resource for fission yeast.". Nucleic Acids Res. 40 (Database issue): D695–9. PMC 3245111 Freely accessible. PMID 22039153. doi:10.1093/nar/gkr853.
  8. ↑ McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, et al. (2015). "PomBase 2015: updates to the fission yeast database.". Nucleic Acids Res. 43 (Database issue): D656–61. PMC 4383888 Freely accessible. PMID 25361970. doi:10.1093/nar/gku1040.
  9. ↑ Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, et al. (2015). "Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.". Nucleic Acids Res. 43 (Database issue): D756–63. PMC 4384024 Freely accessible. PMID 25313157. doi:10.1093/nar/gku956.
  10. ↑ James-Zorn C, Ponferrada VG, Burns KA, Fortriede JD, Lotay VS, Liu Y, et al. (2015). "Xenbase: Core features, data acquisition, and data processing.". Genesis. 53 (8): 486–97. PMC 4545734 Freely accessible. PMID 26150211. doi:10.1002/dvg.22873.
  11. ↑ Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, et al. (2016). "FlyBase: establishing a Gene Group resource for Drosophila melanogaster.". Nucleic Acids Res. 44 (D1): D786–92. PMC 4702782 Freely accessible. PMID 26467478. doi:10.1093/nar/gkv1046.
  12. ↑ Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database Group (2015). "The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease.". Nucleic Acids Res. 43 (Database issue): D726–36. PMC 4384027 Freely accessible. PMID 25348401. doi:10.1093/nar/gku967.
  13. ↑ Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, et al. (2014). "WormBase 2014: new views of curated biology.". Nucleic Acids Res. 42 (Database issue): D789–93. PMC 3965043 Freely accessible. PMID 24194605. doi:10.1093/nar/gkt1063.
  14. ↑ Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, et al. (2015). "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.". Nucleic Acids Res. 43 (Database issue): D743–50. PMC 4383884 Freely accessible. PMID 25355511. doi:10.1093/nar/gku1026.
  15. ↑ Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, et al. (2004). "dictyBase: a new Dictyostelium discoideum genome database.". Nucleic Acids Res. 32 (Database issue): D332–3. PMC 308872 Freely accessible. PMID 14681427. doi:10.1093/nar/gkh138.
  16. ↑ Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, et al. (2012). "The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools.". Nucleic Acids Res. 40 (Database issue): D1202–10. PMC 3245047 Freely accessible. PMID 22140109. doi:10.1093/nar/gkr1090.
  17. ↑ Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, et al. (2013). "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics.". Nucleic Acids Res. 41 (Database issue): D854–60. PMC 3531097 Freely accessible. PMID 23074187. doi:10.1093/nar/gks938.
  18. ↑ Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, et al. (2012). "The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata.". Nucleic Acids Res. 40 (Database issue): D667–74. PMC 3245171 Freely accessible. PMID 22064862. doi:10.1093/nar/gkr945.
  19. ↑ Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, et al. (2013). "EcoCyc: fusing model organism databases with systems biology.". Nucleic Acids Res. 41 (Database issue): D605–12. PMC 3531154 Freely accessible. PMID 23143106. doi:10.1093/nar/gks1027.
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