84:
24:
341:
348:
169:
The Chado schema aims to cover many of the classes of data frequently used by modern biologists, from genetic data to phylogenetic trees to publications to organisms to microarray data to IDs to RNA/protein expression. Chado makes extensive use of controlled vocabularies to type all entities in the
1144:
Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel;
1053:
Afgan, E.; Baker, D.; van den Beek, M.; Blankenberg, D.; Bouvier, D.; ÄŚech, M.; Chilton, J.; Clements, D.; Coraor, N.; Eberhard, C.; GrĂĽning, B.; Guerler, A.; Hillman-Jackson, J.; Von Kuster, G.; Rasche, E.; Soranzo, N.; Turaga, N.; Taylor, J.; Nekrutenko, A.; Goecks, J. (8 July 2016).
1145:
Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick (1 October 2010).
174:. When a new type is added to the Sequence Ontology, the feature table requires no modification, only an update of the data in the database. The same is largely true of analysis data that can be stored in Chado as well.
423:
1103:
Cantarel, Brandi L.; Korf, Ian; Robb, Sofia M. C.; Parra, Genis; Ross, Eric; Moore, Barry; Holt, Carson; Sánchez
Alvarado, Alejandro; Yandell, Mark (January 2008).
1331:
170:
database; for example: genes, transcripts, exons, transposable elements, etc., are stored in a feature table, with the type provided by
541:
476:
105:
components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States
1341:
1308:
599:
614:
1523:
263:
936:
Stein LD; Mungall C; Shu S; Caudy M; Mangone M; Day A; Nickerson E; Stajich JE; Harris TW; Arva A; Lewis S. (2002).
1533:
362:
The following organism databases are contributing to and/or adopting GMOD components for model organism databases.
41:
1147:"The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program"
1408:"ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data"
310:
Pathway Tools: tools for metabolic pathway information, and analysis of high-throughput functional genomics data
757:"A Chado case study: an ontology-based modular schema for representing genome-associated biological information"
326:
572:
154:
114:
106:
217:
The full list of GMOD software components is found on the GMOD Components page. These components include:
110:
706:
1056:"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update"
145:
in the life sciences and capture the large volumes of data and information being generated by modern
505:
126:
83:
318:
Pathway Tools: supports definition of regulatory interactions and browsing of regulatory networks
234:
GMODTools: extracts data from a Chado database into common genome bulk formats (GFF, Fasta, etc.)
1202:
Weems, Danforth; Miller, Neil; Garcia-Hernandez, Margarita; Huala, Eva; Rhee, Seung Y. (2004).
387:
1204:"Design, Implementation and Maintenance of a Model Organism Database for Arabidopsis thaliana"
158:
754:
609:
102:
8:
721:
567:
293:
1105:"MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes"
1432:
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1116:
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957:
949:
938:"The generic genome browser: a building block for a model organism system database"
768:
125:
The GMOD project was started in the early 2000s as a collaboration between several
53:
31:
1357:
Chisholm RL; Gaudet P; Just EM; Pilcher KE; Fey P; Merchant SN; Kibbe WA. (2006).
1316:
1330:
Noronha, Antonio; Cui, Changhai; Harris, Robert Adron; Crabbe, John C. (2014).
726:
142:
133:
tools for processing data from sequencing projects. MODs, or organism-specific
46:
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689:
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647:
755:
Christopher J. Mungall; David B. Emmert; The FlyBase
Consortium (2007).
196:
companalysis - augments sequence module with computational analysis data
149:. Rather than each group designing their own software, four major MODs--
1120:
632:
438:
953:
1359:"dictyBase, the model organism database for Dictyostelium discoideum"
674:
430:
299:
254:
Apollo: a Java application for viewing and editing genome annotations
101:) project provides biological research communities with a toolkit of
1356:
1219:
23:
731:
640:
546:
260:
JBrowse: a JavaScript application for displaying genome annotations
134:
130:
796:
1261:"BeetleBase: the model organism database for Tribolium castaneum"
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GBrowse: a CGI application for displaying genome annotations
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Textpresso: a text mining system for scientific literature
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918:
882:
868:
58:
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814:
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832:
277:
CMap: a CGI application for displaying comparative maps
1329:
1259:
Wang L; Wang S; Li Y; Paradesi MS; Brown SJ. (2007).
1143:
1102:
1508:
1515:
228:Chado: the Chado schema and tools to install it.
1406:Arnaiz O; Cain S; Cohen J; Sperling L. (2007).
231:XORT: a tool for loading and dumping chado-xml
1455:Colbourne JK; Singan VR; Gilbert DG. (2005).
161:, and at or run off a Chado schema database.
491:Human Genome Segmental Duplication Database
274:GBrowse_syn: a GBrowse based synteny viewer
129:(MODs) who shared a need to create similar
357:
266:: a genome browser with a comparative mode
82:
22:
1482:
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1431:
1382:
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1235:
1178:
1128:
1079:
961:
772:
510:Non-Human Segmental Duplication Database
502:Marine Biological Lab Organism Databases
296:: a query-oriented data management system
1457:"wFleaBase: the Daphnia genome database"
177:The existing core modules of Chado are:
164:
1516:
141:and other information about important
17:Generic Model Organism Database (GMOD)
901:"Apollo — Apollo 2.7.0 documentation"
225:GMOD Core (Chado database and tools)
202:genetic - genetic and phenotypic data
184:cv - for controlled-vocabs/ontologies
600:The Arabidopsis Information Resource
1208:Comparative and Functional Genomics
660:
302:: open source data warehouse system
208:natural diversity - population data
13:
1333:Neurobiology of Alcohol Dependence
615:The Institute for Genomic Research
115:USDA Agricultural Research Service
14:
1545:
1502:
251:Genome Editing and Visualization
242:Tripal: a web front end based on
181:sequence - for sequences/features
815:"Chado - Getting Started - GMOD"
417:Chromosome 7 Annotation Project
401:Cattle EST Gene Family Database
346:
339:
193:pub - publication and references
187:general - currently just dbxrefs
1448:
1399:
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1096:
1046:
1032:
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996:
978:
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700:Manatee: Manual Annotation Tool
95:Generic Model Organism Database
911:
905:genomearchitect.readthedocs.io
893:
875:
861:
843:
825:
807:
789:
748:
1:
1313:www.bioinformatics.ksu.edu/Be
774:10.1093/bioinformatics/btm189
742:
573:Saccharomyces Genome Database
155:Saccharomyces Genome Database
107:National Institutes of Health
455:Fungal Comparative Genomics
424:Database of Genomic Variants
337:
205:expression - gene expression
7:
1418:(Database issue): D439–44.
715:
212:
111:National Science Foundation
10:
1550:
1369:(Database issue): D423–7.
1271:(Database issue): D476–9.
707:Open Biomedical Ontologies
120:
711:Sequence Ontology Project
621:TIGR Rice Genome Browser
593:Soybean Gbrowse Database
190:organism - taxonomic data
65:
52:
40:
30:
21:
1524:Model organism databases
797:"GMOD Components - GMOD"
506:Mouse Genome Informatics
458:Fungal Telomere Browser
290:Database querying tools
127:model organism databases
1534:Bioinformatics software
697:Genomics Unified Schema
358:Participating databases
199:map - non-sequence maps
1474:10.1186/1471-2105-6-45
1060:Nucleic Acids Research
463:Gallus Genome Browser
388:Bovine genome database
143:experimental organisms
1163:10.1101/gr.108175.110
585:Sol Genomics Network
271:Comparative Genomics
165:Chado database schema
159:Mouse Genome Database
1004:"GBrowse syn - GMOD"
627:TriAnnot BAC Viewer
610:The Genome Institute
315:Regulatory Networks
307:Biological Pathways
282:Literature curation
103:open-source software
722:Biological database
568:Rat Genome Database
523:Oryza Chromosome 8
18:
1461:BMC Bioinformatics
1424:10.1093/nar/gkl777
1375:10.1093/nar/gkj090
1277:10.1093/nar/gkl776
1121:10.1101/gr.6743907
1072:10.1093/nar/gkw343
851:"GMODTools - GMOD"
398:Bovine QTL Viewer
16:
1412:Nucleic Acids Res
1363:Nucleic Acids Res
1343:978-0-12-407155-1
1265:Nucleic Acids Res
1157:(10): 1459–1468.
954:10.1101/gr.403602
767:(13): i337–i346.
658:
657:
355:
354:
172:Sequence Ontology
91:
90:
36:Windows, Mac OS X
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1319:on 13 July 2006.
1315:. Archived from
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986:"JBrowse - GMOD"
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948:(10): 1599–610.
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919:"GBrowse - GMOD"
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661:Related projects
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32:Operating system
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1151:Genome Research
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1109:Genome Research
1101:
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1038:
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997:
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917:
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883:"Apollo - GMOD"
881:
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1503:External links
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1214:(4): 362–369.
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1066:(W1): W3–W10.
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1022:"CMap - GMOD"
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833:"XORT - GMOD"
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1509:GMOD website
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1415:
1411:
1401:
1366:
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1352:
1336:. Elsevier.
1332:
1325:
1317:the original
1312:
1309:"BeetleBase"
1303:
1268:
1264:
1254:
1211:
1207:
1197:
1154:
1150:
1139:
1112:
1108:
1098:
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1040:"Textpresso"
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532:ParameciumDB
374:Arabidopsis
361:
345:
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239:MOD website
216:
176:
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124:
98:
94:
92:
1115:: 188–196.
1042:. gmod.org.
871:. gmod.org.
648:XanthusBase
559:PossumBase
520:OryGenesDB
486:Human 2q33
471:GrainGenes
384:BeetleBase
137:, describe
1518:Categories
942:Genome Res
743:References
637:wFleaBase
633:VectorBase
556:PseudoCAP
536:PeanutMap
439:Echinobase
77:/Main_Page
1228:1531-6912
1171:1088-9051
675:Biopython
577:SGD Lite
435:DroSpeGe
431:DictyBase
323:Analysis
300:InterMine
135:databases
1529:Genomics
1493:15752432
1442:17142227
1393:16381903
1295:17090595
1246:18629167
1189:20647237
1090:27137889
1026:gmod.org
1008:gmod.org
990:gmod.org
972:12368253
923:gmod.org
887:gmod.org
869:"Tripal"
855:gmod.org
837:gmod.org
819:gmod.org
801:gmod.org
783:17646315
732:Genomics
716:See also
641:WormBase
596:T1DBase
588:Soybase
551:PomBase
547:PlasmoDB
542:PlantsDB
420:CSHLmpd
412:ChromDB
213:Software
131:software
113:and the
1433:1669747
1384:1347453
1286:1669707
1237:2447457
1180:2945195
1130:2134774
1081:4987906
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