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词条 Model organism databases
释义

  1. Types of data and services

  2. List of model Organism databases

  3. References

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[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 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]
Fruitfly Drosophila melanogaster FlyBase FlyBase[13]
Mouse Mus musculus Mouse Genome Informatics MGI[14]
Nematode Caenorhabditis elegans WormBase WormBase[15]
Rat Rattus norvegicus Rat Genome Database RGD[16]
Social amoeba Dictyostelium discoideum DictyBase dictyBase[17]
Thale cress Arabidopsis thaliana The Arabidopsis Information Resource [https://www.arabidopsis.org/ TAIR][18]
Zebrafish Danio rerio Zebrafish Information Network ZFIN[19]
- Candida albicans - CGD[20]
- Escherichia coli EcoCyc EcoCyc[21]

References

1. ^{{cite journal | vauthors = Oliver SG, Lock A, Harris MA, Nurse P, Wood V | title = Model organism databases: essential resources that need the support of both funders and users | journal = BMC Biology | volume = 14 | issue = 1 | pages = 49 | date = June 2016 | pmid = 27334346 | pmc = 4918006 | doi = 10.1186/s12915-016-0276-z }}
2. ^{{cite journal | vauthors = Bond M, Holthaus SM, Tammen I, Tear G, Russell C | title = Use of model organisms for the study of neuronal ceroid lipofuscinosis | journal = Biochimica et Biophysica Acta | volume = 1832 | issue = 11 | pages = 1842–65 | date = November 2013 | pmid = 23338040 | pmc = | doi = 10.1016/j.bbadis.2013.01.009 }}
3. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = Gene ontology: tool for the unification of biology. The Gene Ontology Consortium | journal = Nature Genetics | volume = 25 | issue = 1 | pages = 25–9 | date = May 2000 | pmid = 10802651 | pmc = 3037419 | doi = 10.1038/75556 }}
4. ^{{cite journal | author = Gene Ontology Consortium | title = Gene Ontology Consortium: going forward | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D1049–56 | date = January 2015 | pmid = 25428369 | pmc = 4383973 | doi = 10.1093/nar/gku1179 }}
5. ^{{cite journal | vauthors = O'Connor BD, Day A, Cain S, Arnaiz O, Sperling L, Stein LD | title = GMODWeb: a web framework for the Generic Model Organism Database | journal = Genome Biology | volume = 9 | issue = 6 | pages = R102 | year = 2008 | pmid = 18570664 | pmc = 2481422 | doi = 10.1186/gb-2008-9-6-r102 }}
6. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = Saccharomyces Genome Database: the genomics resource of budding yeast | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D700–5 | date = January 2012 | pmid = 22110037 | pmc = 3245034 | doi = 10.1093/nar/gkr1029 }}
7. ^{{cite journal |last1=Lock |first1=A |last2=Rutherford |first2=K |last3=Harris |first3=MA |last4=Hayles |first4=J |last5=Oliver |first5=SG |last6=Bähler |first6=J |last7=Wood |first7=V |title=PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. |journal=Nucleic Acids Research |date=13 October 2018 |doi=10.1093/nar/gky961 |pmid=30321395}}
8. ^{{cite journal | vauthors = Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG | display-authors = 6 | title = PomBase: a comprehensive online resource for fission yeast | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D695–9 | date = January 2012 | pmid = 22039153 | pmc = 3245111 | doi = 10.1093/nar/gkr853 }}
9. ^{{cite journal | vauthors = McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V | display-authors = 6 | title = PomBase 2015: updates to the fission yeast database | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D656–61 | date = January 2015 | pmid = 25361970 | pmc = 4383888 | doi = 10.1093/nar/gku1040 }}
10. ^{{Cite book |last1=Lock |first1=A |last2=Rutherford |first2=K |last3=Harris |first3=MA |last4=Wood |first4=V |title=PomBase: The Scientific Resource for Fission Yeast |journal=Methods in Molecular Biology |date=2018 |volume=1757 |pages=49–68 |doi=10.1007/978-1-4939-7737-6_4 |pmid=29761456|series=Methods in Molecular Biology |isbn=978-1-4939-7736-9 }}
11. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = Xenbase: a genomic, epigenomic and transcriptomic model organism database | journal = Nucleic Acids Research | volume = 46 | issue = D1 | pages = D861–D868 | date = January 2018 | pmid = 29059324 | pmc = 5753396 | doi = 10.1093/nar/gkx936 }}
12. ^{{Cite book | vauthors = 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 | title = Xenbase: Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database | journal = Eukaryotic Genomic Databases: Methods and Protocols | volume = 1757 | pages = 251–305 | date = May 2018 | pmid = 29761462 | doi = 10.1007/978-1-4939-7737-6_10 | series = Methods in Molecular Biology | isbn = 978-1-4939-7736-9 }}
13. ^{{cite journal | vauthors = Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ | display-authors = 6 | title = FlyBase: establishing a Gene Group resource for Drosophila melanogaster | journal = Nucleic Acids Research | volume = 44 | issue = D1 | pages = D786–92 | date = January 2016 | pmid = 26467478 | pmc = 4702782 | doi = 10.1093/nar/gkv1046 }}
14. ^{{cite journal | vauthors = Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE | title = The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D726–36 | date = January 2015 | pmid = 25348401 | pmc = 4384027 | doi = 10.1093/nar/gku967 }}
15. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = WormBase 2014: new views of curated biology | journal = Nucleic Acids Research | volume = 42 | issue = Database issue | pages = D789–93 | date = January 2014 | pmid = 24194605 | pmc = 3965043 | doi = 10.1093/nar/gkt1063 }}
16. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease | journal = Nucleic Acids Research | volume = 43 | issue = Database issue | pages = D743–50 | date = January 2015 | pmid = 25355511 | pmc = 4383884 | doi = 10.1093/nar/gku1026 }}
17. ^{{cite journal | vauthors = Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR | display-authors = 6 | title = dictyBase: a new Dictyostelium discoideum genome database | journal = Nucleic Acids Research | volume = 32 | issue = Database issue | pages = D332–3 | date = January 2004 | pmid = 14681427 | pmc = 308872 | doi = 10.1093/nar/gkh138 }}
18. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D1202–10 | date = January 2012 | pmid = 22140109 | pmc = 3245047 | doi = 10.1093/nar/gkr1090 }}
19. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D854–60 | date = January 2013 | pmid = 23074187 | pmc = 3531097 | doi = 10.1093/nar/gks938 }}
20. ^{{cite journal | vauthors = Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G | display-authors = 6 | title = 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 | journal = Nucleic Acids Research | volume = 40 | issue = Database issue | pages = D667–74 | date = January 2012 | pmid = 22064862 | pmc = 3245171 | doi = 10.1093/nar/gkr945 }}
21. ^{{cite journal | vauthors = 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 | display-authors = 6 | title = EcoCyc: fusing model organism databases with systems biology | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D605–12 | date = January 2013 | pmid = 23143106 | pmc = 3531154 | doi = 10.1093/nar/gks1027 }}

2 : Biological databases|Model organism databases

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