Biology:Model organism database

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Short description: Type of biological database

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:

  • Genome sequence annotations
    • Location of genes and regulatory regions in the genome
  • Functional curation of gene products
    • Discern functions fulfilled by the gene product by looking at a variety of data including Gene Ontology (GO) annotations, phenotypes, gene expression, pathway information
  • Protein/RNA sequence annotations
  • Anatomical information
  • Stock centres
  • Orthology

List of model organism databases

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][9][10]
Clawed frog Xenopus Xenbase Xenbase[11][12]
Sea urchins, starfish, etc. Echinodermata Echinobase Echinobase[13]
Fruitfly Drosophila melanogaster FlyBase FlyBase[14]
Bees, wasps, ants Hymenoptera Hymenoptera Genome Database HGD[15]
Mouse Mus musculus Mouse Genome Informatics MGI[16]
Nematode Caenorhabditis elegans WormBase WormBase[17]
Rat Rattus norvegicus Rat Genome Database RGD[18]
Social amoeba Dictyostelium discoideum DictyBase dictyBase[19]
Ciliate Tetrahymena thermophila Tetrahymena Genome Database TGD
Thale cress Arabidopsis thaliana The Arabidopsis Information Resource TAIR[20]
Maize Zea mays ssp. mays - MaizeGDB[21][22]
Soybean Glycine soja SoyBase SoyBase[23]
Zebrafish Danio rerio Zebrafish Information Network ZFIN[24]
- Candida albicans - CGD[25]
- Escherichia coli EcoCyc EcoCyc[26]
Hay bacillus Bacillus subtilis - SubtiWiki[27]

References

  1. ↑ 1.0 1.1 1.2 "Model organism databases: essential resources that need the support of both funders and users". BMC Biology 14 (1): 49. June 2016. doi:10.1186/s12915-016-0276-z. PMID 27334346. 
  2. ↑ "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. doi:10.1016/j.bbadis.2013.01.009. PMID 23338040. 
  3. ↑ "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics 25 (1): 25–9. May 2000. doi:10.1038/75556. PMID 10802651. 
  4. ↑ Gene Ontology Consortium (January 2015). "Gene Ontology Consortium: going forward". Nucleic Acids Research 43 (Database issue): D1049-56. doi:10.1093/nar/gku1179. PMID 25428369. 
  5. ↑ "GMODWeb: a web framework for the Generic Model Organism Database". Genome Biology 9 (6): R102. 2008. doi:10.1186/gb-2008-9-6-r102. PMID 18570664. 
  6. ↑ "Saccharomyces Genome Database: the genomics resource of budding yeast". Nucleic Acids Research 40 (Database issue): D700-5. January 2012. doi:10.1093/nar/gkr1029. PMID 22110037. 
  7. ↑ "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. doi:10.1093/nar/gky961. PMID 30321395. 
  8. ↑ "PomBase: a comprehensive online resource for fission yeast". Nucleic Acids Research 40 (Database issue): D695-9. January 2012. doi:10.1093/nar/gkr853. PMID 22039153. 
  9. ↑ "PomBase 2015: updates to the fission yeast database". Nucleic Acids Research 43 (Database issue): D656-61. January 2015. doi:10.1093/nar/gku1040. PMID 25361970. 
  10. ↑ "PomBase: The Scientific Resource for Fission Yeast". Eukaryotic Genomic Databases. Methods in Molecular Biology. 1757. 2018. pp. 49–68. doi:10.1007/978-1-4939-7737-6_4. ISBN 978-1-4939-7736-9. 
  11. ↑ "Xenbase: a genomic, epigenomic and transcriptomic model organism database". Nucleic Acids Research 46 (D1): D861–D868. January 2018. doi:10.1093/nar/gkx936. PMID 29059324. 
  12. ↑ "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database". Eukaryotic Genomic Databases. Methods in Molecular Biology. 1757. May 2018. 251–305. doi:10.1007/978-1-4939-7737-6_10. ISBN 978-1-4939-7736-9. 
  13. ↑ Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA, Echinobase: a resource to support the echinoderm research community, Genetics, 2024, doi:10.1093/genetics/iyae002
  14. ↑ "FlyBase: establishing a Gene Group resource for Drosophila melanogaster". Nucleic Acids Research 44 (D1): D786-92. January 2016. doi:10.1093/nar/gkv1046. PMID 26467478. 
  15. ↑ "Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects". Eukaryotic Genomic Databases. Methods in Molecular Biology. 1757. New York, NY: Springer New York. 2018. pp. 513–556. doi:10.1007/978-1-4939-7737-6_17. ISBN 978-1-4939-7736-9. 
  16. ↑ "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. doi:10.1093/nar/gku967. PMID 25348401. 
  17. ↑ "WormBase 2014: new views of curated biology". Nucleic Acids Research 42 (Database issue): D789-93. January 2014. doi:10.1093/nar/gkt1063. PMID 24194605. 
  18. ↑ "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease". Nucleic Acids Research 43 (Database issue): D743-50. January 2015. doi:10.1093/nar/gku1026. PMID 25355511. 
  19. ↑ "dictyBase: a new Dictyostelium discoideum genome database". Nucleic Acids Research 32 (Database issue): D332-3. January 2004. doi:10.1093/nar/gkh138. PMID 14681427. 
  20. ↑ "The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools". Nucleic Acids Research 40 (Database issue): D1202-10. January 2012. doi:10.1093/nar/gkr1090. PMID 22140109. 
  21. ↑ "MaizeGDB, the community database for maize genetics and genomics". Nucleic Acids Research 32 (Database issue): D393-7. January 2004. doi:10.1093/nar/gkh011. PMID 14681441. 
  22. ↑ "MaizeGDB update: new tools, data and interface for the maize model organism database". Nucleic Acids Research 44 (D1): D1195-201. January 2016. doi:10.1093/nar/gkv1007. PMID 26432828. 
  23. ↑ "SoyBase, the USDA-ARS soybean genetics and genomics database". Nucleic Acids Research 38 (Database issue): D843-6. January 2010. doi:10.1093/nar/gkp798. PMID 20008513. 
  24. ↑ "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics". Nucleic Acids Research 41 (Database issue): D854-60. January 2013. doi:10.1093/nar/gks938. PMID 23074187. 
  25. ↑ "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. doi:10.1093/nar/gkr945. PMID 22064862. 
  26. ↑ "EcoCyc: fusing model organism databases with systems biology". Nucleic Acids Research 41 (Database issue): D605-12. January 2013. doi:10.1093/nar/gks1027. PMID 23143106. 
  27. ↑ "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. doi:10.1093/nar/gkx908. PMID 29788229. 



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