Model organism database explained

Model organism databases (MODs) are biological databases, or knowledgebases, 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 (GO)[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:

List of model organism databases

Common nameScientific nameWikipedia pageDatabase link-out
Baker's yeastSaccharomyces cerevisiaeSaccharomyces Genome DatabaseSGD[6]
Fission yeastSchizosaccharomyces pombePomBasePomBase[7] [8] [9] [10]
Clawed frogXenopusXenbaseXenbase[11] [12]
Sea urchins, starfish, etc.EchinodermataEchinobaseEchinobase[13]
FruitflyDrosophila melanogasterFlyBaseFlyBase[14]
Bees, wasps, antsHymenopteraHymenoptera Genome DatabaseHGD[15]
MouseMus musculusMouse Genome InformaticsMGI[16]
NematodeCaenorhabditis elegansWormBaseWormBase[17]
RatRattus norvegicusRat Genome DatabaseRGD[18]
Social amoebaDictyostelium discoideumDictyBasedictyBase[19]
CiliateTetrahymena thermophilaTetrahymena Genome DatabaseTGD
Thale cressArabidopsis thalianaThe Arabidopsis Information ResourceTAIR[20]
MaizeZea mays ssp. mays-MaizeGDB[21] [22]
SoybeanGlycine sojaSoyBaseSoyBase[23]
ZebrafishDanio rerioZebrafish Information NetworkZFIN[24]
-Candida albicans-CGD[25]
-Escherichia coliEcoCycEcoCyc[26]
Hay bacillusBacillus subtilis-SubtiWiki[27]

Notes and References

  1. Oliver SG, Lock A, Harris MA, Nurse P, Wood V . Model organism databases: essential resources that need the support of both funders and users . BMC Biology . 14 . 1 . 49 . June 2016 . 27334346 . 4918006 . 10.1186/s12915-016-0276-z . free .
  2. Bond M, Holthaus SM, Tammen I, Tear G, Russell C . Use of model organisms for the study of neuronal ceroid lipofuscinosis . Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease . 1832 . 11 . 1842–65 . November 2013 . 23338040 . 10.1016/j.bbadis.2013.01.009 . free .
  3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G . 6 . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium . Nature Genetics . 25 . 1 . 25–9 . May 2000 . 10802651 . 3037419 . 10.1038/75556 .
  4. Gene Ontology Consortium . Gene Ontology Consortium: going forward . Nucleic Acids Research . 43 . Database issue . D1049-56 . January 2015 . 25428369 . 4383973 . 10.1093/nar/gku1179 .
  5. O'Connor BD, Day A, Cain S, Arnaiz O, Sperling L, Stein LD . GMODWeb: a web framework for the Generic Model Organism Database . Genome Biology . 9 . 6 . R102 . 2008 . 18570664 . 2481422 . 10.1186/gb-2008-9-6-r102 . free .
  6. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED . 6 . Saccharomyces Genome Database: the genomics resource of budding yeast . Nucleic Acids Research . 40 . Database issue . D700-5 . January 2012 . 22110037 . 3245034 . 10.1093/nar/gkr1029 .
  7. Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J, Wood V . PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information . Nucleic Acids Research . 47 . D1 . D821–D827 . January 2019 . 30321395 . 6324063 . 10.1093/nar/gky961 .
  8. Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG . 6 . PomBase: a comprehensive online resource for fission yeast . Nucleic Acids Research . 40 . Database issue . D695-9 . January 2012 . 22039153 . 3245111 . 10.1093/nar/gkr853 .
  9. McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V . 6 . PomBase 2015: updates to the fission yeast database . Nucleic Acids Research . 43 . Database issue . D656-61 . January 2015 . 25361970 . 4383888 . 10.1093/nar/gku1040 .
  10. Book: Lock A, Rutherford K, Harris MA, Wood V . Eukaryotic Genomic Databases . PomBase: The Scientific Resource for Fission Yeast . 2018 . 1757 . 49–68 . 10.1007/978-1-4939-7737-6_4 . 29761456. Methods in Molecular Biology . 6440643 . 978-1-4939-7736-9 .
  11. Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD . 6 . Xenbase: a genomic, epigenomic and transcriptomic model organism database . Nucleic Acids Research . 46 . D1 . D861–D868 . January 2018 . 29059324 . 5753396 . 10.1093/nar/gkx936 .
  12. Book: James-Zorn C, Ponferrada VG, Fisher ME, Burns KA, Fortriede JD, Segerdell E, Karimi K, Lotay VS, Wang DZ, Chu S, Pells TJ, Wang Y, Vize PD, Zorn AM . Eukaryotic Genomic Databases . Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database . Eukaryotic Genomic Databases: Methods and Protocols . 1757 . 251–305 . May 2018 . 29761462 . 10.1007/978-1-4939-7737-6_10 . Methods in Molecular Biology . 6853059 . 978-1-4939-7736-9 .
  13. Echinobase: A resource to support the echinoderm research community . 10.1093/genetics/iyae002 . 2024 . Telmer . Cheryl A. . Karimi . Kamran . Chess . Macie M. . Agalakov . Sergei . Arshinoff . Bradley I. . Lotay . Vaneet . Wang . Dong Zhuo . Chu . Stanley . Pells . Troy J. . Vize . Peter D. . Hinman . Veronica F. . Ettensohn . Charles A. . Genetics . 227 . 11075573 .
  14. Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ . FlyBase: establishing a Gene Group resource for Drosophila melanogaster . Nucleic Acids Research . 44 . D1 . D786-92 . January 2016 . 26467478 . 4702782 . 10.1093/nar/gkv1046 .
  15. Book: Elsik CG, Tayal A, Unni DR, Burns GW, Hagen DE . Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects. 2018 . Eukaryotic Genomic Databases. Methods in Molecular Biology. 1757. 513–556. Kollmar M . New York, NY . Springer New York . 10.1007/978-1-4939-7737-6_17 . 29761469. 978-1-4939-7736-9 .
  16. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE . The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease . Nucleic Acids Research . 43 . Database issue . D726-36 . January 2015 . 25348401 . 4384027 . 10.1093/nar/gku967 .
  17. Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW . 6 . WormBase 2014: new views of curated biology . Nucleic Acids Research . 42 . Database issue . D789-93 . January 2014 . 24194605 . 3965043 . 10.1093/nar/gkt1063 .
  18. Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H . 6 . The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease . Nucleic Acids Research . 43 . Database issue . D743-50 . January 2015 . 25355511 . 4383884 . 10.1093/nar/gku1026 .
  19. Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR . dictyBase: a new Dictyostelium discoideum genome database . Nucleic Acids Research . 32 . Database issue . D332-3 . January 2004 . 14681427 . 308872 . 10.1093/nar/gkh138 .
  20. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E . 6 . The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools . Nucleic Acids Research . 40 . Database issue . D1202-10 . January 2012 . 22140109 . 3245047 . 10.1093/nar/gkr1090 .
  21. Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V . MaizeGDB, the community database for maize genetics and genomics . Nucleic Acids Research . 32 . Database issue . D393-7 . January 2004 . 14681441 . 308746 . 10.1093/nar/gkh011 .
  22. Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ . 6 . MaizeGDB update: new tools, data and interface for the maize model organism database . Nucleic Acids Research . 44 . D1 . D1195-201 . January 2016 . 26432828 . 4702771 . 10.1093/nar/gkv1007 .
  23. Grant D, Nelson RT, Cannon SB, Shoemaker RC . SoyBase, the USDA-ARS soybean genetics and genomics database . Nucleic Acids Research . 38 . Database issue . D843-6 . January 2010 . 20008513 . 2808871 . 10.1093/nar/gkp798 .
  24. Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, Knight J, Mani P, Martin R, Moxon SA, Paddock H, Pich C, Ramachandran S, Ruef BJ, Ruzicka L, Schaper K, Shao X, Singer A, Sprunger B, Van Slyke CE, Westerfield M . 6 . ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics . Nucleic Acids Research . 41 . Database issue . D854-60 . January 2013 . 23074187 . 3531097 . 10.1093/nar/gks938 .
  25. Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G . 6 . 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 Research . 40 . Database issue . D667-74 . January 2012 . 22064862 . 3245171 . 10.1093/nar/gkr945 .
  26. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD . 6 . EcoCyc: fusing model organism databases with systems biology . Nucleic Acids Research . 41 . Database issue . D605-12 . January 2013 . 23143106 . 3531154 . 10.1093/nar/gks1027 .
  27. Zhu B, Stülke J . SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis . Nucleic Acids Research . 46 . D1 . D743–D748 . January 2018 . 29788229 . 5753275 . 10.1093/nar/gkx908 .

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