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 servicesedit
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
^ abcOliver SG, Lock A, Harris MA, Nurse P, Wood V (June 2016). "Model organism databases: essential resources that need the support of both funders and users". BMC Biology. 14 (1): 49. doi:10.1186/s12915-016-0276-z. PMC4918006. PMID 27334346.
^Bond M, Holthaus SM, Tammen I, Tear G, Russell C (November 2013). "Use of model organisms for the study of neuronal ceroid lipofuscinosis". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 1832 (11): 1842–65. doi:10.1016/j.bbadis.2013.01.009. PMID 23338040.
^Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. (May 2000). "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics. 25 (1): 25–9. doi:10.1038/75556. PMC3037419. PMID 10802651.
^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 Biology. 9 (6): R102. doi:10.1186/gb-2008-9-6-r102. PMC2481422. PMID 18570664.
^Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, et al. (January 2012). "Saccharomyces Genome Database: the genomics resource of budding yeast". Nucleic Acids Research. 40 (Database issue): D700-5. doi:10.1093/nar/gkr1029. PMC3245034. PMID 22110037.
^Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J, Wood V (January 2019). "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. doi:10.1093/nar/gky961. PMC6324063. PMID 30321395.
^McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, et al. (January 2015). "PomBase 2015: updates to the fission yeast database". Nucleic Acids Research. 43 (Database issue): D656-61. doi:10.1093/nar/gku1040. PMC4383888. PMID 25361970.
^Lock A, Rutherford K, Harris MA, Wood V (2018). "PomBase: The Scientific Resource for Fission Yeast". Eukaryotic Genomic Databases. Methods in Molecular Biology. Vol. 1757. pp. 49–68. doi:10.1007/978-1-4939-7737-6_4. ISBN978-1-4939-7736-9. PMC6440643. PMID 29761456.
^Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, et al. (January 2018). "Xenbase: a genomic, epigenomic and transcriptomic model organism database". Nucleic Acids Research. 46 (D1): D861–D868. doi:10.1093/nar/gkx936. PMC5753396. PMID 29059324.
^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 (May 2018). "Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database". Eukaryotic Genomic Databases. Methods in Molecular Biology. Vol. 1757. pp. 251–305. doi:10.1007/978-1-4939-7737-6_10. ISBN978-1-4939-7736-9. PMC6853059. PMID 29761462. {{cite book}}: |journal= ignored (help)
^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
^Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ (January 2016). "FlyBase: establishing a Gene Group resource for Drosophila melanogaster". Nucleic Acids Research. 44 (D1): D786-92. doi:10.1093/nar/gkv1046. PMC4702782. PMID 26467478.
^Elsik CG, Tayal A, Unni DR, Burns GW, Hagen DE (2018). "Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects". In Kollmar M (ed.). Eukaryotic Genomic Databases. Methods in Molecular Biology. Vol. 1757. New York, NY: Springer New York. pp. 513–556. doi:10.1007/978-1-4939-7737-6_17. ISBN978-1-4939-7736-9. PMID 29761469.
^Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE (January 2015). "The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease". Nucleic Acids Research. 43 (Database issue): D726-36. doi:10.1093/nar/gku967. PMC4384027. PMID 25348401.
^Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, et al. (January 2014). "WormBase 2014: new views of curated biology". Nucleic Acids Research. 42 (Database issue): D789-93. doi:10.1093/nar/gkt1063. PMC3965043. PMID 24194605.
^Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, et al. (January 2015). "The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease". Nucleic Acids Research. 43 (Database issue): D743-50. doi:10.1093/nar/gku1026. PMC4383884. PMID 25355511.
^Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR (January 2004). "dictyBase: a new Dictyostelium discoideum genome database". Nucleic Acids Research. 32 (Database issue): D332-3. doi:10.1093/nar/gkh138. PMC308872. PMID 14681427.
^Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, et al. (January 2012). "The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools". Nucleic Acids Research. 40 (Database issue): D1202-10. doi:10.1093/nar/gkr1090. PMC3245047. PMID 22140109.
^Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (January 2004). "MaizeGDB, the community database for maize genetics and genomics". Nucleic Acids Research. 32 (Database issue): D393-7. doi:10.1093/nar/gkh011. PMC308746. PMID 14681441.
^Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, et al. (January 2016). "MaizeGDB update: new tools, data and interface for the maize model organism database". Nucleic Acids Research. 44 (D1): D1195-201. doi:10.1093/nar/gkv1007. PMC4702771. PMID 26432828.
^Grant D, Nelson RT, Cannon SB, Shoemaker RC (January 2010). "SoyBase, the USDA-ARS soybean genetics and genomics database". Nucleic Acids Research. 38 (Database issue): D843-6. doi:10.1093/nar/gkp798. PMC2808871. PMID 20008513.
^Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, et al. (January 2013). "ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics". Nucleic Acids Research. 41 (Database issue): D854-60. doi:10.1093/nar/gks938. PMC3531097. PMID 23074187.
^Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, et al. (January 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 Research. 40 (Database issue): D667-74. doi:10.1093/nar/gkr945. PMC3245171. PMID 22064862.
^Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, et al. (January 2013). "EcoCyc: fusing model organism databases with systems biology". Nucleic Acids Research. 41 (Database issue): D605-12. doi:10.1093/nar/gks1027. PMC3531154. PMID 23143106.
^Zhu B, Stülke J (January 2018). "SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis". Nucleic Acids Research. 46 (D1): D743–D748. doi:10.1093/nar/gkx908. PMC5753275. PMID 29788229.
January 01, 1970
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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 editModel 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 OrthologyList of model organism databases editCommon 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 edit a b c Oliver SG Lock A Harris MA Nurse P Wood V June 2016 Model organism databases essential resources that need the support of both funders and users BMC Biology 14 1 49 doi 10 1186 s12915 016 0276 z PMC 4918006 PMID 27334346 Bond M Holthaus SM Tammen I Tear G Russell C November 2013 Use of model organisms for the study of neuronal ceroid lipofuscinosis Biochimica et Biophysica Acta BBA Molecular Basis of Disease 1832 11 1842 65 doi 10 1016 j bbadis 2013 01 009 PMID 23338040 Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM et al May 2000 Gene ontology tool for the unification of biology The Gene Ontology Consortium Nature Genetics 25 1 25 9 doi 10 1038 75556 PMC 3037419 PMID 10802651 Gene Ontology Consortium January 2015 Gene Ontology Consortium going forward Nucleic Acids Research 43 Database issue D1049 56 doi 10 1093 nar gku1179 PMC 4383973 PMID 25428369 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 Biology 9 6 R102 doi 10 1186 gb 2008 9 6 r102 PMC 2481422 PMID 18570664 Cherry JM Hong EL Amundsen C Balakrishnan R Binkley G Chan ET et al January 2012 Saccharomyces Genome Database the genomics resource of budding yeast Nucleic Acids Research 40 Database issue D700 5 doi 10 1093 nar gkr1029 PMC 3245034 PMID 22110037 Lock A Rutherford K Harris MA Hayles J Oliver SG Bahler J Wood V January 2019 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 doi 10 1093 nar gky961 PMC 6324063 PMID 30321395 Wood V Harris MA McDowall MD Rutherford K Vaughan BW Staines DM et al January 2012 PomBase a comprehensive online resource for fission yeast Nucleic Acids Research 40 Database issue D695 9 doi 10 1093 nar gkr853 PMC 3245111 PMID 22039153 McDowall MD Harris MA Lock A Rutherford K Staines DM Bahler J et al January 2015 PomBase 2015 updates to the fission yeast database Nucleic Acids Research 43 Database issue D656 61 doi 10 1093 nar gku1040 PMC 4383888 PMID 25361970 Lock A Rutherford K Harris MA Wood V 2018 PomBase The Scientific Resource for Fission Yeast Eukaryotic Genomic Databases Methods in Molecular Biology Vol 1757 pp 49 68 doi 10 1007 978 1 4939 7737 6 4 ISBN 978 1 4939 7736 9 PMC 6440643 PMID 29761456 Karimi K Fortriede JD Lotay VS Burns KA Wang DZ Fisher ME et al January 2018 Xenbase a genomic epigenomic and transcriptomic model organism database Nucleic Acids Research 46 D1 D861 D868 doi 10 1093 nar gkx936 PMC 5753396 PMID 29059324 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 May 2018 Navigating Xenbase An Integrated Xenopus Genomics and Gene Expression Database Eukaryotic Genomic Databases Methods in Molecular Biology Vol 1757 pp 251 305 doi 10 1007 978 1 4939 7737 6 10 ISBN 978 1 4939 7736 9 PMC 6853059 PMID 29761462 a href Template Cite book html title Template Cite book cite book a journal ignored help 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 Attrill H Falls K Goodman JL Millburn GH Antonazzo G Rey AJ Marygold SJ January 2016 FlyBase establishing a Gene Group resource for Drosophila melanogaster Nucleic Acids Research 44 D1 D786 92 doi 10 1093 nar gkv1046 PMC 4702782 PMID 26467478 Elsik CG Tayal A Unni DR Burns GW Hagen DE 2018 Hymenoptera Genome Database Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects In Kollmar M ed Eukaryotic Genomic Databases Methods in Molecular Biology Vol 1757 New York NY Springer New York pp 513 556 doi 10 1007 978 1 4939 7737 6 17 ISBN 978 1 4939 7736 9 PMID 29761469 Eppig JT Blake JA Bult CJ Kadin JA Richardson JE January 2015 The Mouse Genome Database MGD facilitating mouse as a model for human biology and disease Nucleic Acids Research 43 Database issue D726 36 doi 10 1093 nar gku967 PMC 4384027 PMID 25348401 Harris TW Baran J Bieri T Cabunoc A Chan J Chen WJ et al January 2014 WormBase 2014 new views of curated biology Nucleic Acids Research 42 Database issue D789 93 doi 10 1093 nar gkt1063 PMC 3965043 PMID 24194605 Shimoyama M De Pons J Hayman GT Laulederkind SJ Liu W Nigam R et al January 2015 The Rat Genome Database 2015 genomic phenotypic and environmental variations and disease Nucleic Acids Research 43 Database issue D743 50 doi 10 1093 nar gku1026 PMC 4383884 PMID 25355511 Kreppel L Fey P Gaudet P Just E Kibbe WA Chisholm RL Kimmel AR January 2004 dictyBase a new Dictyostelium discoideum genome database Nucleic Acids Research 32 Database issue D332 3 doi 10 1093 nar gkh138 PMC 308872 PMID 14681427 Lamesch P Berardini TZ Li D Swarbreck D Wilks C Sasidharan R et al January 2012 The Arabidopsis Information Resource TAIR improved gene annotation and new tools Nucleic Acids Research 40 Database issue D1202 10 doi 10 1093 nar gkr1090 PMC 3245047 PMID 22140109 Lawrence CJ Dong Q Polacco ML Seigfried TE Brendel V January 2004 MaizeGDB the community database for maize genetics and genomics Nucleic Acids Research 32 Database issue D393 7 doi 10 1093 nar gkh011 PMC 308746 PMID 14681441 Andorf CM Cannon EK Portwood JL Gardiner JM Harper LC Schaeffer ML et al January 2016 MaizeGDB update new tools data and interface for the maize model organism database Nucleic Acids Research 44 D1 D1195 201 doi 10 1093 nar gkv1007 PMC 4702771 PMID 26432828 Grant D Nelson RT Cannon SB Shoemaker RC January 2010 SoyBase the USDA ARS soybean genetics and genomics database Nucleic Acids Research 38 Database issue D843 6 doi 10 1093 nar gkp798 PMC 2808871 PMID 20008513 Howe DG Bradford YM Conlin T Eagle AE Fashena D Frazer K et al January 2013 ZFIN the Zebrafish Model Organism Database increased support for mutants and transgenics Nucleic Acids Research 41 Database issue D854 60 doi 10 1093 nar gks938 PMC 3531097 PMID 23074187 Inglis DO Arnaud MB Binkley J Shah P Skrzypek MS Wymore F et al January 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 Research 40 Database issue D667 74 doi 10 1093 nar gkr945 PMC 3245171 PMID 22064862 Keseler IM Mackie A Peralta Gil M Santos Zavaleta A Gama Castro S Bonavides Martinez C et al January 2013 EcoCyc fusing model organism databases with systems biology Nucleic Acids Research 41 Database issue D605 12 doi 10 1093 nar gks1027 PMC 3531154 PMID 23143106 Zhu B Stulke J January 2018 SubtiWiki in 2018 from genes and proteins to functional network annotation of the model organism Bacillus subtilis Nucleic Acids Research 46 D1 D743 D748 doi 10 1093 nar gkx908 PMC 5753275 PMID 29788229 Retrieved from https en wikipedia org w index php title Model organism database amp oldid 1198622735, wikipedia, wiki, book, books, library,
