45:. 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. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the
49:(GO) 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. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.
1065:
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".
1137:
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. (2024).
1712:"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"
1228:
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.).
57:
Model organism databases generate, source and collate species-specific information integratively by combining expert knowledge with literature curation and bioinformatics.
820:"PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information"
1245:
1083:
982:
367:
1868:
1863:
431:
129:
1759:
Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, et al. (January 2013).
235:
1810:"SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis"
345:
145:
317:
257:
123:
339:
209:
273:
965:
Lock A, Rutherford K, Harris MA, Wood V (2018). "PomBase: The
Scientific Resource for Fission Yeast".
1563:
Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, et al. (January 2016).
361:
41:, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied
38:
1232:. Methods in Molecular Biology. Vol. 1757. New York, NY: Springer New York. pp. 513–556.
301:
867:
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, et al. (January 2012).
1111:
1367:
Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, et al. (January 2015).
916:
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, et al. (January 2015).
769:
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, et al. (January 2012).
1465:
Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, et al. (January 2012).
530:"Model organism databases: essential resources that need the support of both funders and users"
1839:
1790:
1741:
1692:
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1594:
1545:
1496:
1447:
1398:
1349:
1300:
1271:"The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease"
1251:
1241:
1210:
1179:
Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ (January 2016).
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1731:
1723:
1710:
Inglis DO, Arnaud MB, Binkley J, Shah P, Skrzypek MS, Wymore F, et al. (January 2012).
1682:
1674:
1663:"ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics"
1633:
1625:
1584:
1576:
1535:
1527:
1486:
1478:
1437:
1429:
1388:
1380:
1369:"The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease"
1339:
1331:
1290:
1282:
1233:
1200:
1192:
1159:
1151:
1089:
1071:
1037:
1029:
1016:
Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, et al. (January 2018).
988:
970:
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929:
888:
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839:
831:
790:
782:
741:
731:
690:
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641:
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592:
551:
541:
467:
447:
409:
1661:
Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, et al. (January 2013).
1123:
75:
Discern functions fulfilled by the gene product by looking at a variety of data including
42:
620:
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. (May 2000).
1164:
17:
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1809:
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1711:
1687:
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1613:
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893:
868:
844:
819:
818:
Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J, Wood V (January 2019).
795:
770:
746:
719:
695:
670:
646:
621:
556:
529:
1565:"MaizeGDB update: new tools, data and interface for the maize model organism database"
1540:
1515:
1442:
1417:
1857:
1467:"The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools"
1416:
Kreppel L, Fey P, Gaudet P, Just E, Kibbe WA, Chisholm RL, Kimmel AR (January 2004).
1318:
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, et al. (January 2014).
188:
76:
46:
403:
251:
622:"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium"
1237:
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1103:
1051:
1018:"Xenbase: a genomic, epigenomic and transcriptomic model organism database"
1002:
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1727:
1678:
1629:
1531:
1514:
Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (January 2004).
1433:
1286:
1181:"FlyBase: establishing a Gene Group resource for Drosophila melanogaster"
1033:
884:
835:
279:
581:"Use of model organisms for the study of neuronal ceroid lipofuscinosis"
771:"Saccharomyces Genome Database: the genomics resource of budding yeast"
215:
173:
167:
151:
498:
1269:
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE (January 2015).
1140:"Echinobase: A resource to support the echinoderm research community"
473:
718:
O'Connor BD, Day A, Cain S, Arnaiz O, Sperling L, Stein LD (2008).
198:
1516:"MaizeGDB, the community database for maize genetics and genomics"
1070:. Methods in Molecular Biology. Vol. 1757. pp. 251–305.
720:"GMODWeb: a web framework for the Generic Model Organism Database"
637:
579:
Bond M, Holthaus SM, Tammen I, Tear G, Russell C (November 2013).
383:
262:
79:(GO) annotations, phenotypes, gene expression, pathway information
969:. Methods in Molecular Biology. Vol. 1757. pp. 49–68.
585:
Biochimica et
Biophysica Acta (BBA) - Molecular Basis of Disease
456:
178:
372:
60:
Services provided to biological research communities include:
1761:"EcoCyc: fusing model organism databases with systems biology"
1614:"SoyBase, the USDA-ARS soybean genetics and genomics database"
134:
1612:
Grant D, Nelson RT, Cannon SB, Shoemaker RC (January 2010).
869:"PomBase: a comprehensive online resource for fission yeast"
1418:"dictyBase: a new Dictyostelium discoideum genome database"
528:
Oliver SG, Lock A, Harris MA, Nurse P, Wood V (June 2016).
392:
156:
284:
414:
328:
306:
220:
67:
Location of genes and regulatory regions in the genome
918:"PomBase 2015: updates to the fission yeast database"
478:
436:
523:
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519:
1320:"WormBase 2014: new views of curated biology"
8:
101:
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671:"Gene Ontology Consortium: going forward"
669:Gene Ontology Consortium (January 2015).
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1119:
1109:
72:Functional curation of gene products
7:
368:The Arabidopsis Information Resource
25:
1808:Zhu B, Stülke J (January 2018).
98:List of model organism databases
84:Protein/RNA sequence annotations
1:
432:Zebrafish Information Network
130:Saccharomyces Genome Database
1477:(Database issue): D1202-10.
1238:10.1007/978-1-4939-7737-6_17
1230:Eukaryotic Genomic Databases
1076:10.1007/978-1-4939-7737-6_10
1068:Eukaryotic Genomic Databases
967:Eukaryotic Genomic Databases
681:(Database issue): D1049-56.
598:10.1016/j.bbadis.2013.01.009
185:Sea urchins, starfish, etc.
64:Genome sequence annotations
1771:(Database issue): D605-12.
1722:(Database issue): D667-74.
1673:(Database issue): D854-60.
1379:(Database issue): D743-50.
1330:(Database issue): D789-93.
1281:(Database issue): D726-36.
975:10.1007/978-1-4939-7737-6_4
928:(Database issue): D656-61.
346:Tetrahymena Genome Database
236:Hymenoptera Genome Database
27:Type of biological database
1885:
1624:(Database issue): D843-6.
1526:(Database issue): D393-7.
1428:(Database issue): D332-3.
879:(Database issue): D695-9.
781:(Database issue): D700-5.
53:Types of data and services
547:10.1186/s12915-016-0276-z
146:Schizosaccharomyces pombe
1869:Model organism databases
1156:10.1093/genetics/iyae002
737:10.1186/gb-2008-9-6-r102
318:Dictyostelium discoideum
258:Mouse Genome Informatics
124:Saccharomyces cerevisiae
31:Model organism databases
18:Model organism databases
340:Tetrahymena thermophila
210:Drosophila melanogaster
1814:Nucleic Acids Research
1765:Nucleic Acids Research
1716:Nucleic Acids Research
1667:Nucleic Acids Research
1618:Nucleic Acids Research
1569:Nucleic Acids Research
1520:Nucleic Acids Research
1471:Nucleic Acids Research
1422:Nucleic Acids Research
1373:Nucleic Acids Research
1324:Nucleic Acids Research
1275:Nucleic Acids Research
1185:Nucleic Acids Research
1022:Nucleic Acids Research
922:Nucleic Acids Research
873:Nucleic Acids Research
824:Nucleic Acids Research
775:Nucleic Acids Research
675:Nucleic Acids Research
274:Caenorhabditis elegans
87:Anatomical information
111:Knowledge (XXG) page
1864:Biological databases
362:Arabidopsis thaliana
39:biological databases
1777:10.1093/nar/gks1027
1581:10.1093/nar/gkv1007
1483:10.1093/nar/gkr1090
1385:10.1093/nar/gku1026
1336:10.1093/nar/gkt1063
1197:10.1093/nar/gkv1046
934:10.1093/nar/gku1040
787:10.1093/nar/gkr1029
687:10.1093/nar/gku1179
302:Rat Genome Database
1826:10.1093/nar/gkx908
1728:10.1093/nar/gkr945
1679:10.1093/nar/gks938
1630:10.1093/nar/gkp798
1532:10.1093/nar/gkh011
1434:10.1093/nar/gkh138
1287:10.1093/nar/gku967
1034:10.1093/nar/gkx936
885:10.1093/nar/gkr853
836:10.1093/nar/gky961
384:Zea mays ssp. mays
227:Bees, wasps, ants
114:Database link-out
1820:(D1): D743–D748.
1575:(D1): D1195-201.
1247:978-1-4939-7736-9
1085:978-1-4939-7736-9
1028:(D1): D861–D868.
984:978-1-4939-7736-9
830:(D1): D821–D827.
507:
506:
490:Bacillus subtilis
296:Rattus norvegicus
16:(Redirected from
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1191:(D1): D786-92.
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591:(11): 1842–65.
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