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terms. They also encode relationships between terms. The Gene
Ontology Project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project also provides gene product annotation data from GO consortium members. FlyBase was one of the three founding members of the Gene Ontology Consortium. GO annotation comprises at least three components: a GO term that describes molecular function, biological role, or subcellular location; an "evidence code" that describes the type of analysis used to support the GO term; and an attribution to a specific reference. GO annotation is useful for both small-scale and large-scale analyses. It can provide a first indication of the nature of a gene product and, in conjunction with evidence codes, point directly to papers with pertinent experimental data. The current priorities for annotation are: homologs of human disease genes, genes that are highly conserved across species, genes involved in biochemical/signaling pathways, and topical genes shown to be of significant interest in recent publications. FlyBase has been contributing GO annotations to the project since it started in August 2006. GO annotations appear on the Gene Report page in FlyBase. GO data are searchable in FlyBase using both TermLink and QueryBuilder. The GO is dynamic and can change on a daily basis, for example the addition of new terms. To keep up, FlyBase loads a new version of the GO every one or two releases of FlyBase. The GO annotation set is submitted to the GOC at the same time as a new version of FlyBase is released.
222:
the help of information on
Drosophila melanogaster in FlyBase. Putative sequence identity was determined using BLAST searches. Sequence matches with E-value scores ≤ −10 were considered significant and were categorized according to the Gene Ontology (GO) classification system based on annotation of the 5 ‘best hit’ matches in BLASTX searches. All D. melanogaster matches were cataloged using FlyBase. Nearly all of these ‘best hit’ matches were characterized with respect to the functionally annotated genes in D. melanogaster using FlyBase. Genetic information is crucial to advancing the understanding of aphid biology, and will play a major role in the development of future non-chemical, gene-based control strategies against these insect pests.
217:, a severe pathogen which causes losses to citrus industries worldwide. The winged form of this aphid can fly long distances with the wind, enabling them to spread the citrus tristeza virus in citrus growing regions. To better understand the biology of the brown citrus aphid and the emergence of genes expressed during wing development, researchers undertook a large-scale 5′ end sequencing project of cDNA clones from winged aphids. Similar large-scale expressed sequence tag (EST) sequencing projects from other insects have provided a vehicle for answering biological questions relating to development and physiology. Although there is a growing database in
121:(Berkeley Drosophila Genome Project) and EDGP (European Drosophila Genome Project) informatics groups. These groups recognized that most genome project and community data types overlapped. They decided it would be of value to present the scientific community with an integrated view of the data. In October 1992, the National Center for Human Genome Research of the NIH funded the FlyBase project with the objective of designing, building and releasing a database of genetic and molecular information concerning
271:
Lynn; Santos, Gilberto dos; Emmert, David; Gramates, L Sian; Falls, Kathleen; Jenkins, Victoria; Matthews, Beverley; Sutherland, Carol; Tabone, Christopher; Zhou, Pinglei; Zytkovicz, Mark; Brown, Nick; Antonazzo, Giulia; Attrill, Helen; Garapati, Phani; Holmes, Alex; Larkin, Aoife; Marygold, Steven; Millburn, Gillian; Pilgrim, Clare; Trovisco, Vitor; Urbano, Pepe; Kaufman, Thomas; Calvi, Brian; Czoch, Bryon; Goodman, Josh; Strelets, Victor; Thurmond, Jim; Cripps, Richard; Baker, Phillip (8 January 2019).
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ontologies used to capture functional, phenotypic, and anatomical data. The database offers several different query tools in order to provide efficient access to the data available and facilitate the discovery of significant relationships within the database. Links between FlyBase and external databases, such as BDGP or modENCODE, provide opportunities for further exploration into other
113:'s lab. Material in these pages presented regular 'catalogs' of mutations, and bibliographies of the Drosophila literature. As computer infrastructure developed in the '80s and '90s, these newsletters gave way and merged with internet mailing lists, and these eventually became online resources and data. In 1992, data on the genetics and genomics of
193:
The second main query tool is called QuickSearch. This is located on the FlyBase homepage. This tool is most useful when you want to look up something quickly that you may only know a little about. Searching can be performed within D. melanogaster only or within all species. Data other than genes can be searched using the ‘data class’ menu.
225:
Enhancing
Drosophila Gene Ontology Annotation: What gene products do and where they do it are important questions for biologists. The Gene Ontology project was established 13 years ago in order to summarize this data consistently across different databases by using a common set of defined vocabulary
221:
of ESTs from insects, most are from
Drosophila melanogaster, with relatively few specifically derived from aphids. The researchers were able to provide a large data set of ESTs from the alate (winged) brown citrus aphid and have begun to analyze this valuable resource. They were able to do this with
192:
There are two main query tools in FlyBase. The first main query tool is called Jump to Gene (J2G). This is found in the top right of the blue navigation bar on every page of FlyBase. This tool is useful when you know exactly what you are looking for and want to go to the report page with that data.
184:
Search
Strategies—Gene reports for genes from all twelve sequenced Drosophila genomes are available in FlyBase. There are four main ways this data can be browsed: Precomputed Files BLAST, Gbrowse, and Gene Report Pages. Gbrowse and precomputed files are for genome-wide analysis, bioinformatics, and
270:
Thurmond, Jim; Goodman, Joshua L; Strelets, Victor B; Attrill, Helen; Gramates, L Sian; Marygold, Steven J; Matthews, Beverley B; Millburn, Gillian; Antonazzo, Giulia; Trovisco, Vitor; Kaufman, Thomas C; Calvi, Brian R; Perrimon, Norbert; Gelbart, Susan Russo; Agapite, Julie; Broll, Kris; Crosby,
108:
has been an experimental organism since the early 1900s, and has since been placed at the forefront of many areas of research. As this field of research spread and became global, researchers working on the same problems needed a way to communicate and monitor progress in the field. This niche was
165:
genetics in the last century. Information on current researchers, and a partial pedigree of relationships between current researchers, was searchable, based on registration of the participating scientist. The site also provides a large database of images illustrating the full genome, and several
58:
expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models, and molecular classification of gene product functions. Query tools allow navigation of FlyBase through DNA or protein sequence, by gene or mutant name, or through terms from the several
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When looking for cytology there are two main tools available. Use
Cytosearch when looking for cytologically-mapped genes or deficiencies, that have not been molecularly mapped to the sequence. Use Gbrowse when looking for molecularly mapped sequences, insertions, or Affymetrix probes.
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Gelbart, WM; Crosby, M; Matthews, B; Rindone, WP; Chillemi, J; Russo
Twombly, S; Emmert, D; Ashburner, M; Drysdale, RA; Whitfield, E; Millburn, GH; de Grey, A; Kaufman, T; Matthews, K; Gilbert, D; Strelets, V; Tolstoshev, C (1997).
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Tweedie, Susan; Ashburner, Michael; Falls, Kathleen; Leyland, Paul; McQuilton, Peter; Marygold, Steven; Millburn, Gillian; Osumi-Sutherland, David; Schroeder, Andrew; Seal, Ruth; Zhang, Haiyan; The FlyBase
Consortium (2009-01-01).
131:, London. In 1998, the FlyBase consortium integrated the information into a single Drosophila genomics server. As of 2022 the FlyBase project was carried out by a consortium of Drosophila researchers and computer scientists at
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181:). The two major tributaries to the database are the large multispecies data sets deposited by the Drosophila 12 Genomes Consortium (Clark et al 2007) and Crosby et al 2007.
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Information in FlyBase originates from a variety of sources ranging from large-scale genome projects to the primary research literature. These data types include mutant
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initially filled by community newsletters such as the
Drosophila Information Service (DIS), which dates back to 1934 when the field was starting to spread from
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Drysdale, Rachel; Flybase
Consortium (2008-07-19). "FlyBase: A Database for the Drosophila Research Community". In Dahmann, Christian (ed.).
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and other resources of biological and molecular information. The FlyBase project is carried out by a consortium of
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Hunter, WB; Dang, PM; Bausher, MG; Chaparro, JX; McKendree, W; Shatters, RG; McKenzie, CL; Sinisterra, XH (2003).
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comparative genomics. BLAST and gene report pages are for a specific gene, protein, or region across the species.
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genome that is updated several times per year. It also included a searchable bibliography of research on
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International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
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and related species were electronically available over the Internet through the funded FlyBase,
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815:"Aphid biology: expressed genes from alate Toxoptera citricida, the brown citrus aphid"
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The following provides two examples of research that is related to or uses FlyBase:
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Drysdale, R (2008). "FlyBase: A Database for the Drosophila Research Community".
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and the primary repository of genetic and molecular data for the insect family
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As of 2022 the FlyBase home page requested a website access fee of
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FlyBase is one of the organizations contributing to the
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448:. Methods Mol. Biol. Vol. 420. pp. 45–59.
1006:, database of protein sequences grouping together
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1241:US National Center for Biotechnology Information
1326:International Society for Computational Biology
33:. For the most extensively studied species and
1393:ISCB Africa ASBCB Conference on Bioinformatics
895:(Database issue). Oxford Journals: D555–D559.
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373:Wilson, RJ; Goodman, JL; Strelets, VB (2008).
334:(Database issue). Oxford Journals: D486–D491.
155:FlyBase contains a complete annotation of the
93:150.00 per person per year, stating that "The
1340:Institute of Genomics and Integrative Biology
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205:The first is a study of expressed genes from
1369:European Conference on Computational Biology
524:"An Introduction to Drosophila Melanogaster"
97:has reduced the funding of FlyBase by 50%".
1404:Research in Computational Molecular Biology
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322:Crosby, Madeline A; et al. (2007).
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67:researchers and computer scientists at
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1320:International Society for Biocuration
1218:European Molecular Biology Laboratory
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526:. BIOLOGY.ARIZONA.EDU. Archived from
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883:Tweedie, Susan; et al. (2009).
592:"FlyBase:About - FlyBase Consortium"
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273:"FlyBase 2.0: the next generation"
16:Database on Drosophilidae genetics
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1575:Insect developmental biology
1497:List of biological databases
1016:Protein Information Resource
622:Methods in Molecular Biology
237:List of Drosophila databases
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990:European Nucleotide Archive
630:10.1007/978-1-59745-583-1_3
454:10.1007/978-1-59745-583-1_3
385:(Database issue): D588–93.
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209:(meaning "having wings")
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242:Model Organism Databases
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61:model organism databases
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998:China National GeneBank
158:Drosophila melanogaster
137:University of Cambridge
124:Drosophila melanogaster
106:Drosophila melanogaster
79:in the United Kingdom.
77:University of Cambridge
40:Drosophila melanogaster
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994:DNA Data Bank of Japan
889:Nucleic Acids Research
691:Nucleic Acids Research
328:Nucleic Acids Research
277:Nucleic Acids Research
1487:Computational biology
1002:Secondary databases:
215:citrus tristeza virus
984:Sequence databases:
682:"FlyBase: enhancing
522:Pete Geiger (2002).
258:Notes and references
1280:Whitehead Institute
1068:Rat Genome Database
863:"The Gene Ontology"
560:10.1093/nar/25.1.63
290:10.1093/nar/gky1003
211:Toxoptera citricida
1517:Sequence alignment
1224:Flatiron Institute
901:10.1093/nar/gkn788
831:10.1093/jis/3.1.23
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391:10.1093/nar/gkm930
341:10.1093/nar/gkl827
177:2007-03-24 at the
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133:Harvard University
111:Thomas Hunt Morgan
73:Indiana University
69:Harvard University
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1512:Sequence database
1026:Protein Data Bank
1020:Other databases:
755:Precomputed Files
639:978-1-58829-817-1
548:Nucleic Acids Res
530:on 2 August 2013.
463:978-1-58829-817-1
379:Nucleic Acids Res
283:(D1): D759–D765.
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31:Drosophilidae
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22:is an online
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1441:Nexus format
1436:NeXML format
1431:FASTQ format
1426:FASTA format
1414:File formats
1176:Institutions
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866:. Retrieved
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797:. Retrieved
793:the original
789:"Cytosearch"
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698:(Database).
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1421:CRAM format
1342:(CSIR-IGIB)
554:(1): 63–6.
498:"Home page"
1564:Categories
1507:Sequencing
1471:GTF format
1466:GFF format
1461:VCF format
1451:SAM format
1214:(EMBL-EBI)
1140:SOAP suite
1060:VectorBase
1022:BioNumbers
1008:Swiss-Prot
799:2011-11-24
684:Drosophila
618:Drosophila
446:Drosophila
163:Drosophila
101:Background
65:Drosophila
48:phenotypes
1334:(ISCB-SC)
1304:(EMBL-AR)
1237:(MPI-CBG)
978:Databases
716:0305-1048
433:modENCODE
56:wild-type
1536:Category
1406:(RECOMB)
1356:Meetings
1310:(EMBnet)
1160:Server:
1135:SAMtools
1130:PANGOLIN
1093:Software
1072:PHI-base
1064:WormBase
1034:InterPro
919:18948289
849:15841239
734:18948289
648:18641940
601:24 April
507:24 April
472:18641940
409:18160408
360:17099233
309:30364959
247:WormBase
231:See also
175:Archived
151:Contents
143:and the
86:(GMOD).
27:database
1548:Commons
1383:(InCoB)
1328:(ISCB)
1316:(INSDC)
1298:(ASBCB)
1202:(DBCLS)
1196:(COSBI)
1110:Clustal
1056:FlyBase
1030:Ensembl
1004:UniProt
986:GenBank
910:2686450
777:Gbrowse
725:2686450
578:9045212
502:FlyBase
400:2238994
351:1669768
300:6323960
252:Xenbase
219:GenBank
52:alleles
20:FlyBase
1389:(CIBB)
1377:(ISMB)
1371:(ECCB)
1348:(JSBi)
1254:(NBIC)
1243:(NCBI)
1231:(JCVI)
1220:(EMBL)
1208:(DDBJ)
1162:ExPASy
1145:TopHat
1125:MUSCLE
1115:EMBOSS
1105:Bowtie
1080:GISAID
1040:, and
1012:TrEMBL
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868:31 May
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840:524662
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825:: 23.
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569:146418
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139:(UK),
1400:(PSB)
1322:(ISB)
1271:(SIB)
1260:(PGC)
1190:(CBD)
1154:Other
1120:HMMER
1100:BLAST
766:BLAST
738:S2CID
207:alate
95:NHGRI
1082:and
1048:BOLD
1038:KEGG
1014:and
996:and
915:PMID
870:2017
845:PMID
730:PMID
712:ISSN
644:PMID
634:ISBN
603:2022
574:PMID
509:2022
468:PMID
458:ISBN
422:BDGP
405:PMID
356:PMID
305:PMID
119:BDGP
91:US$
71:and
905:PMC
897:doi
835:PMC
827:doi
720:PMC
704:doi
700:OUP
626:doi
564:PMC
556:doi
450:doi
395:PMC
387:doi
346:PMC
336:doi
295:PMC
285:doi
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.