Knowledge (XXG)

Model organism database

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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".
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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.).
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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".
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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).
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Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, et al. (January 2015).
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McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, et al. (January 2015).
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Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, et al. (January 2012).
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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: 1643: 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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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).
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Howe DG, Bradford YM, Conlin T, Eagle AE, Fashena D, Frazer K, et al. (January 2013).
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Discern functions fulfilled by the gene product by looking at a variety of data including
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Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. (May 2000).
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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).
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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: 1075: 597: 580: 974: 425: 230: 1155: 546: 193: 736: 240: 350: 323: 1843: 1794: 1745: 1696: 1647: 1598: 1549: 1500: 1451: 1402: 1353: 1304: 1255: 1214: 1139: 1103: 1051: 1018:"Xenbase: a genomic, epigenomic and transcriptomic model organism database" 1002: 951: 902: 853: 804: 755: 704: 655: 606: 565: 1776: 1580: 1482: 1384: 1335: 1196: 933: 786: 686: 1825: 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
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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).
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Location of genes and regulatory regions in the genome
918:"PomBase 2015: updates to the fission yeast database" 478: 436: 523: 521: 519: 1320:"WormBase 2014: new views of curated biology" 8: 101: 1833: 1784: 1735: 1686: 1637: 1588: 1539: 1490: 1441: 1392: 1343: 1294: 1204: 1163: 1093: 1041: 992: 941: 892: 843: 794: 745: 735: 694: 671:"Gene Ontology Consortium: going forward" 669:Gene Ontology Consortium (January 2015). 645: 596: 555: 545: 515: 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 1876: 1848: 1847: 1837: 1805: 1799: 1798: 1788: 1756: 1750: 1749: 1739: 1707: 1701: 1700: 1690: 1658: 1652: 1651: 1641: 1609: 1603: 1602: 1592: 1560: 1554: 1553: 1543: 1511: 1505: 1504: 1494: 1462: 1456: 1455: 1445: 1413: 1407: 1406: 1396: 1364: 1358: 1357: 1347: 1315: 1309: 1308: 1298: 1266: 1260: 1259: 1225: 1219: 1218: 1208: 1176: 1170: 1169: 1167: 1134: 1128: 1127: 1121: 1117: 1115: 1107: 1097: 1062: 1056: 1055: 1045: 1013: 1007: 1006: 996: 962: 956: 955: 945: 913: 907: 906: 896: 864: 858: 857: 847: 815: 809: 808: 798: 766: 760: 759: 749: 739: 715: 709: 708: 698: 666: 660: 659: 649: 617: 611: 610: 600: 576: 570: 569: 559: 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415:SoyBase 410:SoyBase 221:FlyBase 216:FlyBase 179:Xenbase 174:Xenbase 168:Xenopus 157:PomBase 152:PomBase 1842:  1832:  1793:  1783:  1744:  1734:  1695:  1685:  1646:  1636:  1597:  1587:  1548:  1541:308746 1538:  1499:  1489:  1450:  1443:308872 1440:  1401:  1391:  1352:  1342:  1303:  1293:  1254:  1244:  1213:  1203:  1162:  1102:  1092:  1082:  1050:  1040:  1001:  991:  981:  950:  940:  901:  891:  852:  842:  803:  793:  754:  744:  703:  693:  654:  644:  605:  564:  554:  479:EcoCyc 474:EcoCyc 379:Maize 247:Mouse 37:) are 500:Subti 1840:PMID 1791:PMID 1742:PMID 1693:PMID 1644:PMID 1595:PMID 1546:PMID 1497:PMID 1448:PMID 1399:PMID 1350:PMID 1301:PMID 1252:PMID 1242:ISBN 1211:PMID 1124:help 1100:PMID 1080:ISBN 1048:PMID 999:PMID 979:ISBN 948:PMID 899:PMID 850:PMID 801:PMID 752:PMID 701:PMID 652:PMID 603:PMID 589:1832 562:PMID 502:Wiki 437:ZFIN 373:TAIR 291:Rat 35:MODs 1830:PMC 1822:doi 1781:PMC 1773:doi 1732:PMC 1724:doi 1683:PMC 1675:doi 1634:PMC 1626:doi 1585:PMC 1577:doi 1536:PMC 1528:doi 1487:PMC 1479:doi 1438:PMC 1430:doi 1389:PMC 1381:doi 1340:PMC 1332:doi 1291:PMC 1283:doi 1234:doi 1201:PMC 1193:doi 1160:PMC 1152:doi 1148:227 1090:PMC 1072:doi 1038:PMC 1030:doi 989:PMC 971:doi 938:PMC 930:doi 889:PMC 881:doi 840:PMC 832:doi 791:PMC 783:doi 742:PMC 732:doi 691:PMC 683:doi 642:PMC 634:doi 593:doi 552:PMC 542:doi 457:CGD 351:TGD 307:RGD 263:MGI 241:HGD 135:SGD 1860:: 1838:. 1828:. 1818:46 1816:. 1812:. 1789:. 1779:. 1769:41 1767:. 1763:. 1740:. 1730:. 1720:40 1718:. 1714:. 1691:. 1681:. 1671:41 1669:. 1665:. 1642:. 1632:. 1622:38 1620:. 1616:. 1593:. 1583:. 1573:44 1571:. 1567:. 1544:. 1534:. 1524:32 1522:. 1518:. 1495:. 1485:. 1475:40 1473:. 1469:. 1446:. 1436:. 1426:32 1424:. 1420:. 1397:. 1387:. 1377:43 1375:. 1371:. 1348:. 1338:. 1328:42 1326:. 1322:. 1299:. 1289:. 1279:43 1277:. 1273:. 1250:. 1240:. 1209:. 1199:. 1189:44 1187:. 1183:. 1158:. 1150:. 1146:. 1142:. 1116:: 1114:}} 1110:{{ 1098:. 1088:. 1078:. 1046:. 1036:. 1026:46 1024:. 1020:. 997:. 987:. 977:. 946:. 936:. 926:43 924:. 920:. 897:. 887:. 877:40 875:. 871:. 848:. 838:. 828:47 826:. 822:. 799:. 789:. 779:40 777:. 773:. 750:. 740:. 726:. 722:. 699:. 689:. 679:43 677:. 673:. 650:. 640:. 630:25 628:. 624:. 601:. 587:. 583:. 560:. 550:. 538:14 536:. 532:. 518:^ 495:- 463:- 453:- 443:- 389:- 1846:. 1824:: 1797:. 1775:: 1748:. 1726:: 1699:. 1677:: 1650:. 1628:: 1601:. 1579:: 1552:. 1530:: 1503:. 1481:: 1454:. 1432:: 1405:. 1383:: 1356:. 1334:: 1307:. 1285:: 1258:. 1236:: 1217:. 1195:: 1168:. 1154:: 1126:) 1106:. 1074:: 1054:. 1032:: 1005:. 973:: 954:. 932:: 905:. 883:: 856:. 834:: 807:. 785:: 758:. 734:: 728:9 707:. 685:: 658:. 636:: 609:. 595:: 568:. 544:: 33:( 20:)

Index

Model organism databases
biological databases
model organisms
Gene Ontology
Gene Ontology
Saccharomyces cerevisiae
Saccharomyces Genome Database
SGD
Schizosaccharomyces pombe
PomBase
PomBase
Xenopus
Xenbase
Xenbase
Echinodermata
Echinobase
Echinobase
Drosophila melanogaster
FlyBase
FlyBase
Hymenoptera
Hymenoptera Genome Database
HGD
Mus musculus
Mouse Genome Informatics
MGI
Caenorhabditis elegans
WormBase
WormBase
Rattus norvegicus

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