Difference between revisions of "FlyBase:About"

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The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.
 
The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.
  
−
Please use the contact FlyBase form to write to us.
+
Please use the [http://{{flybaseorg}}/contact/email contact FlyBase] form to write to us.
  
 
:'''FlyBase-Harvard'''
 
:'''FlyBase-Harvard'''
Line 10: Line 10:
 
:USA
 
:USA
  
−
     William Gelbart (PI)
+
     Norbert Perrimon (PI)
 +
    Susan Russo Gelbart (PD)
 
     Kris Broll
 
     Kris Broll
 
     Lynn Crosby
 
     Lynn Crosby
 
     Gil dos Santos
 
     Gil dos Santos
−
    David Emmert
 
 
     L. Sian Gramates
 
     L. Sian Gramates
−
     Kathleen Falls
+
     Victoria Jenkins
 +
    Ian Longden
 
     Beverley Matthews
 
     Beverley Matthews
−
     Susan Russo
+
     Carol Sutherland
−
     Andy Schroeder
+
     Christopher J. Tabone
−
    Susan St. Pierre
 
 
     Pinglei Zhou
 
     Pinglei Zhou
 
     Mark Zytkovicz
 
     Mark Zytkovicz
  
 
:'''FlyBase-Cambridge'''
 
:'''FlyBase-Cambridge'''
−
:Department of Genetics, University of Cambridge
+
:Department of Physiology, Development and Neuroscience, University of Cambridge
−
:Downing Street, Cambridge CB2 3EH
+
:Downing Street, Cambridge CB2 3DY
 
:UK
 
:UK
  
−
     Nick Brown (PI)
+
     Nick Brown (Co-PI)
−
     Boris Adryan
+
     Giulia Antonazzo
 
     Helen Attrill
 
     Helen Attrill
−
     Marta Costa
+
     Damien Goutte-Gattat
 +
    Aoife Larkin
 
     Steven Marygold
 
     Steven Marygold
−
     Peter McQuilton
+
     Alex McLachlan
 
     Gillian Millburn
 
     Gillian Millburn
−
     Laura Ponting
+
     Arzu Öztürk-Çolak
−
     Ray Stefancsik
+
     Clare Pilgrim
−
     Susan Tweedie
+
     Rossana Zaru
  
 
:'''FlyBase-Indiana'''
 
:'''FlyBase-Indiana'''
Line 46: Line 47:
 
:USA
 
:USA
  
−
     Thomas Kaufman (PI)
+
     Brian Calvi (Co-PI)
−
     Kathy Matthews (PI)
+
     Seth Campbell
 
     Josh Goodman
 
     Josh Goodman
−
    Gary Grumbling
 
 
     Victor Strelets
 
     Victor Strelets
 
     Jim Thurmond
 
     Jim Thurmond
  
−
:'''FlyBase-NewMexico'''
+
:'''FlyBase-New Mexico'''
 
:Department of Biology, Castetter Hall - Room 200
 
:Department of Biology, Castetter Hall - Room 200
 
:University of New Mexico,
 
:University of New Mexico,
Line 59: Line 59:
 
:USA
 
:USA
  
−
    Maggie Werner-Washburne (PI)
+
     Richard Cripps (Co-PI)
−
     Richard Cripps (PI)
+
     TyAnna Lovato
−
     Harriett Platero
 
  
 
==FlyBase Publications==
 
==FlyBase Publications==
  
−
:S.J. Marygold, P.C. Leyland, R.L. Seal, J.L. Goodman, J.R. Thurmond, V.B. Strelets, R.J. Wilson and the FlyBase Consortium (2013).  
+
:'''2024'''
−
:FlyBase: improvements to the bibliography.  
+
 
−
:Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350]
+
:Antonazzo G, Gaudet P, Lovering RC, Attrill H (2024)
 +
:    '''Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.'''
 +
:    RNA Biol. 21(1) 36–48 [https://doi.org/10.1080/15476286.2024.2408523 DOI:10.1080/15476286.2024.2408523]
 +
 
 +
 
 +
:Marygold SJ (2024)
 +
:    '''The alpha-ketoacid dehydrogenase complexes of Drosophila melanogaster.'''
 +
:    MicroPubl Biol. 001209 [https://doi.org/10.17912/micropub.biology.001209 DOI:10.17912/micropub.biology.001209] [https://{{flybaseorg}}/reports/FBrf0259508 FBrf0259508]
 +
 
 +
 
 +
:Alliance of Genome Resources Consortium (2024)
 +
:    '''Updates to the Alliance of Genome Resources Central Infrastructure.'''
 +
:    Genetics 227(1) iyae049 [https://doi.org/10.1093/genetics/iyae049 DOI:10.1093/genetics/iyae049] [https://{{flybaseorg}}/reports/FBrf0259417 FBrf0259417]
 +
 
 +
 
 +
:Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold SJ, Novoa EM, Motorin Y, Roignant JY (2024)
 +
:    '''Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster.'''
 +
:    Nucleic Acids Res 52(6) 2848-2864 [https://doi.org/10.1093/nar/gkae139 DOI:10.1093/nar/gkae139] [https://{{flybaseorg}}/reports/FBrf0259352 FBrf0259352]
 +
 
 +
 
 +
:Öztürk-Çolak A, Marygold SJ, Antonazzo G, Attrill H, Goutte-Gattat D, Jenkins VK, Matthews BB, Millburn G, dos Santos G, Tabone CJ, the FlyBase Consortium (2024)
 +
:    '''FlyBase: updates to the Drosophila genes and genomes database.'''
 +
:    Genetics 227(1) iyad211 [https://doi.org/10.1093/genetics/iyad211 DOI:10.1093/genetics/iyad211] [https://{{flybaseorg}}/reports/FBrf0259457 FBrf0259457]
 +
 
 +
 
 +
:Attrill H, Antonazzo G, Goodman JL, Thurmond J, Strelets VB, Brown NH; FlyBase Consortium (2024)
 +
:    '''A new experimental evidence-weighted signaling pathway resource in FlyBase.'''
 +
:    Development 151(3) dev202255 [https://doi.org/10.1242/dev.202255 DOI:10.1242/dev.202255] [https://{{flybaseorg}}/reports/FBrf0258673 FBrf0258673]
 +
 
 +
 
 +
:'''2023'''
 +
 
 +
:Attrill H (2023)
 +
:    '''Comparing the history of signalling pathway research using the research publication record of representative genes.'''
 +
:    MicroPubl Biol. 000998 [https://doi.org/10.17912/micropub.biology.000998 DOI:10.17912/micropub.biology.000998] [https://{{flybaseorg}}/reports/FBrf0258056 FBrf0258056]
 +
 
 +
 
 +
:Gene Ontology Consortium (2023)
 +
:    '''The Gene Ontology knowledgebase in 2023.'''
 +
:    Genetics 224(1) iyad031. [https://doi.org/10.1093/genetics/iyad031 DOI:10.1093/genetics/iyad031]
 +
 
 +
 
 +
:Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Chen W, Li F, Chao T, Mohr SE, Brown NH, Perrimon N. (2023)
 +
:    '''PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.'''
 +
:    Nucleic Acids Res 51(W1) W419--WW426. [https://doi.org/10.1093/nar/gkad331 DOI:10.1093/nar/gkad331] [https://{{flybaseorg}}/reports/FBrf0256969 FBrf0256969]
 +
 
 +
 
 +
:Marygold SJ and the FlyBase Consortium (2023)
 +
:    '''Exploring FlyBase Data Using QuickSearch (Updated protocol)'''
 +
:    Current Protocols 3:e731. [https://doi.org/10.1002/cpz1.731 DOI:10.1002/cpz1.731] [https://{{flybaseorg}}/reports/FBrf0256232 FBrf0256232]
 +
 
 +
 
 +
:Court R, Costa M, Pilgrim C, Millburn G, Holmes A, McLachlan A, Larkin A, Matentzoglu N, Kir H, Parkinson H, Brown NH, O'Kane CJ, Armstrong JD, Jefferis GSXE, Osumi-Sutherland D. (2023)
 +
:    '''Virtual Fly Brain-An interactive atlas of the Drosophila nervous system.'''
 +
:    Front Physiol. 14:1076533. [https://doi.org/10.3389/fphys.2023.1076533 DOI:10.3389/fphys.2023.1076533] [https://{{flybaseorg}}/reports/FBrf0255719 FBrf0255719]
 +
 
 +
 
 +
:'''2022'''
 +
 
 +
:Jenkins VK, Larkin A, Thurmond J; FlyBase Consortium. (2022)
 +
:    '''Using FlyBase: A Database of Drosophila Genes and Genetics.'''
 +
:    Methods Mol Biol. 2540:1-34. [https://doi.org/10.1007/978-1-0716-2541-5_1 DOI:10.1007/978-1-0716-2541-5_1] [https://{{flybaseorg}}/reports/FBrf0254317 FBrf0254317]
 +
 
 +
 
 +
:Trovisco V (2022)
 +
:    '''Featured Resource: FlyBase.'''
 +
:    [https://thenode.biologists.com/featured-resource-flybase/resources/ The Node: Resources]
 +
 
 +
 
 +
:Marygold SJ, Chan PP, Lowe TM (2022)
 +
:    '''Systematic identification of tRNA genes in Drosophila melanogaster.'''
 +
:    MicroPubl Biol. 000560 [https://doi.org/10.17912/micropub.biology.000560 DOI:10.17912/micropub.biology.000560] [https://{{flybaseorg}}/reports/FBrf0253514 FBrf0253514]
 +
 
 +
 
 +
:Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews BB, Millburn G, Strelets VB and the FlyBase Consortium (2022)
 +
:    '''FlyBase: A guided tour of highlighted features.'''
 +
:   Genetics 220(4) iyac035 [https://doi.org/10.1093/genetics/iyac035 DOI:10.1093/genetics/iyac035] [https://{{flybaseorg}}/reports/FBrf0253076 FBrf0253076]
 +
 
 +
 
 +
:Alliance of Genome Resources Consortium (2022)
 +
:   '''Harmonizing model organism data in the Alliance of Genome Resources.'''
 +
:   Genetics 220(4) iyac022 [https://doi.org/10.1093/genetics/iyac022 DOI:10.1093/genetics/iyac022] [https://{{flybaseorg}}/reports/FBrf0253213 FBrf0253213]
 +
 
 +
 
 +
:Liu Y,  Li JSS, Rodiger J, Comjean A, Attrill H, Antonazzo G, Brown NH, Hu Y, Perrimon N (2022)
 +
:    '''FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila.'''
 +
:    Genetics 220(3) iyab235 [https://doi.org/10.1093/genetics/iyab235 DOI:10.1093/genetics/iyab235] [https://{{flybaseorg}}/reports/FBrf0252867 FBrf0252867]
 +
 
 +
 
 +
:'''2021'''
 +
 
 +
:Meyer H, Buhr A, Callaerts P, Schiemann R, Wolfner MF, Marygold SJ (2021)
 +
:    '''Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster.'''
 +
:    MicroPubl Biol. 000410 [https://doi.org/10.17912/micropub.biology.000410 DOI:10.17912/micropub.biology.000410] [https://{{flybaseorg}}/reports/FBrf0249415 FBrf0249415]
 +
 
 +
 
 +
:Hu Y, Tattikota SG, Liu Y, Comjean A, Gao Y, Forman C, Kim G, Rodiger J, Papatheodorou I, Dos Santos G, Mohr SE, Perrimon N (2021)
 +
:    '''DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.'''
 +
:    Comput Struct Biotechnol J 19:2018-2026. [https://doi.org/10.1016/j.csbj.2021.04.021 DOI:10.1016/j.csbj.2021.04.021][https://{{flybaseorg}}/reports/FBrf0249044 FBrf0249044]
 +
 
 +
 
 +
:Ahn SJ and Marygold SJ (2021)
 +
:   '''The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis.'''
 +
:    Front Physiol 12 648481 [https://doi.org/10.3389/fphys.2021.648481 DOI:10.3389/fphys.2021.648481][https://{{flybaseorg}}/reports/FBrf0248570 FBrf0248570]
  
  
−
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013).
+
:The Gene Ontology Consortium (2021)
−
:Systematic analysis of experimental phenotype data reveals gene functions.  
+
:   '''The Gene Ontology resource: enriching a GOld mine.'''
−
:PLoS One. 8(4):e60847. PMID: 23626672
+
:   Nucleic Acids Res. 49(D1) D325–D334 [https://doi.org/10.1093/nar/gkaa1113 DOI:10.1093/nar/gkaa1113] [https://{{flybaseorg}}/reports/FBrf0247877 FBrf0247877]
  
  
−
:McQuilton P and the FlyBase Consortium (2012).
+
:Larkin A, Marygold SJ, Antonazzo G, Attrill H, dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J and the FlyBase Consortium (2021)
−
:Opportunities for text mining in the FlyBase genetic literature curation workflow.  
+
:   '''FlyBase: updates to the Drosophila melanogaster knowledge base.'''
−
:Database 2012:bas039. [FBrf0219955]
+
:   Nucleic Acids Res. 49(D1) D899–D907 [https://doi.org/10.1093/nar/gkaa1026 DOI:10.1093/nar/gkaa1026] [https://{{flybaseorg}}/reports/FBrf0247700 FBrf0247700]
  
  
−
:Gene Ontology Consortium (2012).
+
:RNAcentral Consortium (2021)
−
:Gene Ontology annotations and resources.  
+
:   '''RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.'''
−
:Nucleic Acids Res. 41(Database issue):D530-5. doi: 10.1093/nar/gks1050. PubMed PMID: 23161678; PubMed Central PMCID: PMC3531070.
+
:   Nucleic Acids Res. 49(D1) D212–D220 [https://doi.org/10.1093/nar/gkaa921 DOI:10.1093/nar/gkaa921]
  
  
−
:S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).
+
:'''2020'''
−
:Directly e-mailing authors of newly published papers encourages community curation.
 
−
:Database 2012; doi: 10.1093/database/bas024. [FBrf0218522]
 
  
 +
:Marygold SJ, Alic N, Gilmour DS, Grewal SS (2020)
 +
:    '''In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits.'''
 +
:    MicroPubl Biol. 000320 [https://doi.org/10.17912/micropub.biology.000320 DOI:10.17912/micropub.biology.000320] [https://{{flybaseorg}}/reports/FBrf0247389 FBrf0247389]
 +
 +
 +
:Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM and Mungall CJ (2020)
 +
:    '''Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.'''
 +
:    Open Biol 10(9) 200149 [https://doi.org/10.1098/rsob.200149 DOI:10.1098/rsob.200149]
 +
 +
 +
:Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, the Alliance of Genome Resources (2020)
 +
:    '''Automated generation of gene summaries at the Alliance of Genome Resources.'''
 +
:    Database 2020 baaa037 [https://doi.org/10.1093/database/baaa037 DOI:10.1093/database/baaa037]
 +
 +
 +
:Antonazzo G, Urbano JM, Marygold SJ, Millburn GH and Brown NH (2020)
 +
:    '''Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.'''
 +
:    Database 2020 baz152 [https://doi.org/10.1093/database/baz152 DOI:10.1093/database/baz152] [https://{{flybaseorg}}/reports/FBrf0244633 FBrf0244633]
 +
 +
 +
:Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y and Yamaguchi M (2020)
 +
:    '''The DNA polymerases of Drosophila melanogaster.'''
 +
:    Fly 14(1-4) 49-61 [https://doi.org/10.1080/19336934.2019.1710076 DOI:10.1080/19336934.2019.1710076] [https://{{flybaseorg}}/reports/FBrf0245686 FBrf0245686]
 +
 +
 +
:The Alliance of Genome Resources Consortium (2020)
 +
:    '''Alliance of Genome Resources Portal: unified model organism research platform.'''
 +
:    Nucleic Acids Res 48(D1) D650–D658 [https://doi.org/10.1093/nar/gkz813 DOI:10.1093/nar/gkz813] [https://{{flybaseorg}}/reports/FBrf0245774 FBrf0245774]
 +
 +
 +
:'''2019'''
 +
 +
:The Alliance of Genome Resources (2019)
 +
:    '''Building a Modern Data Ecosystem for Model Organism Databases.'''
 +
:    Genetics 213(4):1189-1196 [https://doi.org/10.1534/genetics.119.302523 DOI:10.1534/genetics.119.302523] [https://{{flybaseorg}}/reports/FBrf0244239 FBrf0244239]
 +
 +
 +
:Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. (2019)
 +
:    '''Annotation of gene product function from high-throughput studies using the Gene Ontology.'''
 +
:    Database 2019 baz007 [https://doi.org/10.1093/database/baz007 DOI:10.1093/database/baz007]
 +
 +
 +
:Garapati  PV, Zhang J, Rey AJ and Marygold SJ (2019)
 +
:    '''Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase'''
 +
:    Database 2019 bay144 [https://doi.org/10.1093/database/bay144 DOI:10.1093/database/bay144] [http://{{flybaseorg}}/reports/FBrf0241253.html FBrf0241253]
 +
 +
 +
:Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR and the FlyBase Consortium. (2019)
 +
:    '''FlyBase 2.0: the next generation.'''
 +
:    Nucleic Acids Res. 47(D1) D759–D765 [https://doi.org/10.1093/nar/gky1003 DOI:10.1093/nar/gky1003] [http://{{flybaseorg}}/reports/FBrf0241170.html FBrf0241170]
 +
 +
 +
:The RNAcentral Consortium (2019)
 +
:    '''RNAcentral: a hub of information for non-coding RNA sequences.'''
 +
:    Nucleic Acids Res. 47(D1) D221–D229 [https://doi.org/10.1093/nar/gky1034 DOI:10.1093/nar/gky1034]
 +
 +
 +
:The Gene Ontology Consortium (2019)
 +
:    '''The Gene Ontology Resource: 20 years and still GOing strong.'''
 +
:    Nucleic Acids Res. 47(D1) D330–D338 [https://doi.org/10.1093/nar/gky1055 DOI:10.1093/nar/gky1055]
 +
 +
 +
:'''2018'''
 +
 +
:Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE and Smith C. (2018)
 +
:    '''Model organism data evolving in support of translational medicine.'''
 +
:    Lab Anim (NY) 47:277-289 [https://doi.org/10.1038/s41684-018-0150-4 DOI:10.1038/s41684-018-0150-4] [http://{{flybaseorg}}/reports/FBrf0241113.html FBrf0241113]
 +
 +
 +
:Rey AJ, Attrill H, Marygold SJ and The FlyBase Consortium. (2018)
 +
:    '''Using FlyBase to Find Functionally Related Drosophila Genes.'''
 +
:    Eukaryotic Genomic Databases: Methods and Protocols (M. Kollmar, ed.) pp. 493-512. Springer, New York [https://doi.org/10.1007%2F978-1-4939-7737-6_16 DOI:10.1007%2F978-1-4939-7737-6_16] [http://{{flybaseorg}}/reports/FBrf0238904.html FBrf0238904]
 +
 +
 +
:'''2017'''
 +
 +
:Hu Y, Comjean A, Mohr SE; FlyBase Consortium, Perrimon N. (2017)
 +
:    '''Gene2Function: An Integrated Online Resource for Gene Function Discovery.'''
 +
:    G3 (Bethesda) 7(8):2855-2858 [https://doi.org/10.1534/g3.117.043885 DOI:10.1534/g3.117.043885] [http://{{flybaseorg}}/reports/FBrf0236248.html FBrf0236248]
 +
 +
 +
:The Gene Ontology Consortium. (2017)
 +
:    '''Expansion of the Gene Ontology knowledgebase and resources'''
 +
:    Nucleic Acids Res. 45(D1):D331-D338 [https://doi.org/10.1093/nar/gkw1108 DOI:10.1093/nar/gkw1108]
 +
 +
 +
:Gramates LS, Marygold SJ, dos Santos G, Urbano J-M, Antonazzo G, Matthews BB, Rey AJ, Tabone CJ, Crosby MA, Emmert DB, Falls K, Goodman JL, Hu Y, Ponting L, Schroeder AJ, Strelets VB, Thurmond J, Zhou P and the FlyBase Consortium. (2017)
 +
:    '''FlyBase at 25: looking to the future.'''
 +
:    Nucleic Acids Res. 45(D1):D663-D671 [https://doi.org/10.1093/nar/gkw1016 DOI:10.1093/nar/gkw1016] [http://{{flybaseorg}}/reports/FBrf0234415.html FBrf0234415]
 +
 +
 +
:Marygold SJ, Attrill H, Lasko P. (2017)
 +
:    '''The Translation Factors of Drosophila melanogaster.'''
 +
:    Fly 11(1):65-74 [https://doi.org/10.1080/19336934.2016.1220464 DOI:10.1080/19336934.2016.1220464] [http://{{flybaseorg}}/reports/FBrf0233552.html FBrf0233552]
 +
 +
 +
:'''2016'''
 +
 +
:Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)
 +
:    '''Exploring FlyBase Data Using QuickSearch.'''
 +
:    Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23 [https://doi.org/10.1002/cpbi.19 DOI:10.1002/cpbi.19] [http://{{flybaseorg}}/reports/FBrf0234167.html FBrf0234167]
 +
 +
 +
:Marygold SJ, Crosby MA, Goodman JL and The FlyBase Consortium. (2016)
 +
:    '''Using FlyBase, a Database of Drosophila Genes and Genomes.'''
 +
:    Drosophila: Methods and Protocols, Second edition, vol. 1478 (C. Dahmann, ed.) pp. 1-31. Springer, New York [https://doi.org/10.1007/978-1-4939-6371-3_1 DOI:10.1007/978-1-4939-6371-3_1] [http://{{flybaseorg}}/reports/FBrf0233766.html FBrf0233766)]
 +
 +
 +
:Kahsai L, Millburn GH, Cook KR. (2016)
 +
:    '''Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.'''
 +
:    G3 (Bethesda). 6(8):2665-2670 [https://doi.org/10.1534/g3.116.030940 DOI:10.1534/g3.116.030940] [http://{{flybaseorg}}/reports/FBrf0233125.html FBrf0233125]
 +
 +
 +
:Millburn GH, Crosby MA, Gramates LS, Tweedie S; FlyBase Consortium. (2016)
 +
:    '''FlyBase portals to human disease research using Drosophila models.'''
 +
:    Dis. Model Mech. 9(3):245-252 [https://doi.org/10.1242/dmm.023317 DOI:10.1242/dmm.023317] [http://{{flybaseorg}}/reports/FBrf0231138.html FBrf0231138]
 +
 +
 +
:Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ; the FlyBase Consortium. (2016)
 +
:    '''FlyBase: establishing a Gene Group resource for Drosophila melanogaster.'''
 +
:    Nucleic Acids Res. 44(D1):D786-D792 [https://doi.org/10.1093/nar/gkv1046 DOI:10.1093/nar/gkv1046] [http://{{flybaseorg}}/reports/FBrf0230602.html FBrf0230602]
 +
 +
 +
:'''2015'''
 +
 +
:Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
 +
:    '''The aminoacyl-tRNA synthetases of Drosophila melanogaster.'''
 +
:    Fly 9(2):53-61 [http://dx.doi.org/10.1080/19336934.2015.1101196 DOI:10.1080/19336934.2015.1101196] [http://{{flybaseorg}}/reports/FBrf0230668.html FBrf0230668]
 +
 +
 +
:Matthews BB, dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM, and the FlyBase Consortium. (2015)
 +
:    '''Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.'''
 +
:    G3 (Bethesda) 5:1721-1736 [http://dx.doi.org/10.1534/g3.115.018929 DOI:10.1534/g3.115.018929] [http://{{flybaseorg}}/reports/FBrf0229216.html FBrf0229216]
 +
 +
 +
:Crosby MA, Gramates LS, dos Santos G, Matthews BB, St Pierre SE, Zhou P, Schroeder AJ, Falls K, Emmert DB, Russo SM, Gelbart WM., and the FlyBase Consortium. (2015)
 +
:    '''Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.'''
 +
:    G3 (Bethesda) 5:1737-1749 [http://dx.doi.org/10.1534/g3.115.018937 DOI:10.1534/g3.115.018937] [http://{{flybaseorg}}/reports/FBrf0229217.html FBrf0229217]
 +
 +
 +
: Gene Ontology Consortium. (2015)
 +
:    '''Gene Ontology Consortium: going forward.'''
 +
:    Nucleic Acids Res. 43(Database issue):D1049-56 [http://dx.doi.org/10.1093/nar/gku1179 DOI:10.1093/nar/gku1179]
 +
 +
 +
:Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)
 +
:    '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''
 +
:    Nucleic Acids Res. 43(Database issue): D690-D697 [http://dx.doi.org/10.1093/nar/gku1099 DOI:10.1093/nar/gku1099] [http://{{flybaseorg}}/reports/FBrf0227324.html FBrf0227324]
 +
 +
 +
:'''2014'''
 +
 +
:Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. (2014)
 +
:    '''Representing kidney development using the gene ontology.'''
 +
:    PLoS One. 9(6):e99864 [http://dx.doi.org/10.1371/journal.pone.0099864 DOI:10.1371/journal.pone.0099864]
 +
 +
 +
:Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. (2014)
 +
:    '''Overview of the gene ontology task at BioCreative IV.'''
 +
:    Database 2014. bau086 [http://dx.doi.org/10.1093/database/bau086 DOI:10.1093/database/bau086]
 +
 +
 +
:Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z (2014)
 +
:    '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''
 +
:    Database 2014. bau074 [http://dx.doi.org/10.1093/database/bau074 DOI:10.1093/database/bau074]
 +
 +
 +
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)
 +
:    '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''
 +
:    Database 2014. bau033 [http://dx.doi.org/10.1093/database/bau033 DOI:10.1093/database/bau033]
 +
 +
 +
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)
 +
:    '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''
 +
:    Nucleic Acids Res. 42(Database issue):D780-8 [http://dx.doi.org/10.1093/nar/gkt1092 DOI:10.1093/nar/gkt1092] [http://{{flybaseorg}}/reports/FBrf0223749.html FBrf0223749]
 +
 +
 +
:'''2013'''
 +
 +
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
 +
:    '''The Drosophila anatomy ontology.'''
 +
:    J. Biomed. Semantics 4(1):32 [http://dx.doi.org/10.1186/2041-1480-4-32 DOI:10.1186/2041-1480-4-32] [http://{{flybaseorg}}/reports/FBrf0223849.html FBrf0223849]
 +
 +
 +
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV. (2013)
 +
:    '''The Drosophila phenotype ontology.'''
 +
:    J. Biomed. Semantics 4(1):30 [http://dx.doi.org/10.1186/2041-1480-4-30 DOI:10.1186/2041-1480-4-30] [http://{{flybaseorg}}/reports/FBrf0223876.html FBrf0223876]
 +
 +
 +
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)
 +
:    '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''
 +
:    PeerJ. 1:e148 [http://dx.doi.org/10.7717/peerj.148 DOI:10.7717/peerj.148] [http://{{flybaseorg}}/reports/FBrf0222712.html FBrf0222712]
 +
 +
 +
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)
 +
:    '''FlyBase: improvements to the bibliography.'''
 +
:    Nucleic Acids Res. 41(Database issue):D751-D757 [http://dx.doi.org/10.1093/nar/gks1024 DOI:10.1093/nar/gks1024] [http://{{flybaseorg}}/reports/FBrf0220350.html FBrf0220350]
 +
 +
 +
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)
 +
:    '''Systematic analysis of experimental phenotype data reveals gene functions.'''
 +
:    PLoS One. 8(4):e60847 [http://dx.doi.org/10.1371/journal.pone.0060847 DOI:10.1371/journal.pone.0060847] [http://{{flybaseorg}}/reports/FBrf0221415.html FBrf0221415]
 +
 +
 +
:Gene Ontology Consortium (2013)
 +
:    '''Gene Ontology annotations and resources.'''
 +
:    Nucleic Acids Res. 41(Database issue):D530-5. [http://dx.doi.org/10.1093/nar/gks1050 DOI:10.1093/nar/gks1050]
 +
 +
 +
:'''2012'''
 +
 +
:McQuilton P and the FlyBase Consortium (2012)
 +
:    '''Opportunities for text mining in the FlyBase genetic literature curation workflow.'''
 +
:    Database 2012:bas039 [http://dx.doi.org/10.1093/database/bas039 DOI:10.1093/database/bas039] [http://{{flybaseorg}}/reports/FBrf0219955.html FBrf0219955]
 +
 +
 +
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)
 +
:    '''Directly e-mailing authors of newly published papers encourages community curation.'''
 +
:    Database 2012:bas024 [http://dx.doi.org/10.1093/database/bas024 DOI:10.1093/database/bas024] [http://{{flybaseorg}}/reports/FBrf0218522.html FBrf0218522]
 +
 +
 +
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)
 +
:    '''FlyBase 101 – the basics of navigating FlyBase.'''
 +
:    Nucleic Acids Res. 40 (Database issue):D706-14 [http://dx.doi.org/10.1093/nar/gkr1030 DOI:10.1093/nar/gkr1030] [http://{{flybaseorg}}/reports/FBrf0217108.html FBrf0217108]
 +
 +
 +
:Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold S, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW (2012)
 +
:    '''Automatic categorization of diverse experimental information in the bioscience literature.'''
 +
:    BMC Bioinformatics. 13(1):16 [http://dx.doi.org/10.1186/1471-2105-13-16 DOI:10.1186/1471-2105-13-1] [http://{{flybaseorg}}/reports/FBrf0218533.html FBrf0218533]
 +
 +
 +
:Gene Ontology Consortium (2012)
 +
:    '''The Gene Ontology: enhancements for 2011.'''
 +
:    Nucleic Acids Res. 40(Database issue):D559-64 [http://dx.doi.org/10.1093/nar/gkr1028 DOI:10.1093/nar/gkr1028]
 +
 +
 +
:'''2011'''
 +
 +
:Rangarajan A, Schedl T, Yook K, Chan J, Haenel S, Otis L, Faelten S, DePellegrin‑Connelly T, Isaacson R, Skrzypek MS, Marygold SJ, Stefancsik R, Cherry JM, Sternberg PW and Müller H-M (2011)
 +
:    '''Toward an interactive article: integrating journals and biological databases.'''
 +
:    BMC Bioinformatics 12:175 [http://dx.doi.org/10.1186/1471-2105-12-175 DOI:10.1186/1471-2105-12-175] [http://{{flybaseorg}}/reports/FBrf0214821.html FBrf0214821]
 +
 +
 +
:Daines, B., Wang, H., Wang, L., Li, Y., Han, Y., Emmert, D., Gelbart, W., Wang, X., Li, W., Gibbs, R., Chen, R. (2011).
 +
:    '''The Drosophila melanogaster transcriptome by paired-end RNA sequencing.'''
 +
:    Genome Res. 21(2): 315--324 [http://dx.doi.org/10.1101/gr.107854.110 DOI:10.1101/gr.107854.110] [http://{{flybaseorg}}/reports/FBrf0213064.html FBrf0213064]
 +
 +
 +
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)
 +
:    '''The representation of heart development in the gene ontology.'''
 +
:    Dev Biol. 354(1):9-17 [http://dx.doi.org/10.1016/j.ydbio.2011.03.011 DOI:10.1016/j.ydbio.2011.03.011]
  
−
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012).
 
−
:FlyBase 101 – the basics of navigating FlyBase.
 
−
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108]
 
−
   
 
  
−
:Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold S, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW (2012).
+
:'''2010'''
−
:    Automatic categorization of diverse experimental information in the bioscience literature.
 
−
:    BMC Bioinformatics. 13(1):16. [FBrf0218533]
 
−
   
 
  
−
:Gene Ontology Consortium (2012).
+
:Gene Ontology Consortium (2010)
−
:    The Gene Ontology: enhancements for 2011.
+
:    '''The Gene Ontology in 2010: extensions and refinements.'''
−
:    Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568; PubMed Central PMCID: PMC3245151.
+
:    Nucleic Acids Res. 38(Database issue):D331-5 [http://dx.doi.org/10.1093/nar/gkp1018 DOI:10.1093/nar/gkp1018]
−
   
 
  
−
:A. Rangarajan, T. Schedl, K. Yook, J. Chan, S. Haenel, L. Otis, S. Faelten, T. DePellegrin‑Connelly, R. Isaacson, M.S. Skrzypek, S.J. Marygold, R. Stefancsik, J.M. Cherry, P.W. Sternberg, H‑M. Müller (2011).
 
−
:    Toward an interactive article: integrating journals and biological databases.
 
−
:    BMC Bioinformatics 2011, 12:175. [FBrf0214821]
 
  
 +
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)
 +
:    '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''
 +
:    Nucleic Acids Res. 38(Database issue):D443-7 [http://dx.doi.org/10.1093/nar/gkp910 DOI:10.1093/nar/gkp910] [http://{{flybaseorg}}/reports/FBrf0209611.html FBrf0209611]
  
−
:    Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).
 
−
:    The representation of heart development in the gene ontology.
 
−
:    Dev Biol. 354(1):9-17. doi: 10.1016/j.ydbio.2011.03.011. PubMed PMID: 21419760; PubMed Central PMCID: PMC3302178.
 
  
 +
:'''2009'''
 
      
 
      
−
:Gene Ontology Consortium (2009).
+
:St. Pierre S and McQuilton P (2009)
−
:    The Gene Ontology in 2010: extensions and refinements.
+
:    '''Inside FlyBase (Biocuration as a career).'''
−
:    Nucleic Acids Res. 38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. PubMed PMID: 19920128; PubMed Central PMCID: PMC2808930.
+
:    Fly 3(1):112-114 [http://dx.doi.org/10.4161/fly.3.1.7769 DOI:10.4161/fly.3.1.7769] [http://{{flybaseorg}}/reports/FBrf0213427.html FBrf0213427]
  
 
      
 
      
−
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).
+
:Reference Genome Group of the Gene Ontology Consortium (2009)
−
:    FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
+
:    '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''
−
:    Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132; PubMed Central PMCID: PMC2808907. [FBrf0209611]
+
:    PLoS Comput Biol. 5(7):e1000431 [http://dx.doi.org/10.1371/journal.pcbi.1000431 DOI:10.1371/journal.pcbi.1000431]
  
 
      
 
      
−
:S. St. Pierre, P. McQuilton (2009).
+
:Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi‑Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium (2009)
−
:    Inside FlyBase (Biocuration as a career).
+
:    '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''
−
:    Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427]
+
:    Nucleic Acids Res. 37(Database issue):D555-D559 [http://dx.doi.org/10.1093/nar/gkn788 DOI:10.1093/nar/gkn788] [http://{{flybaseorg}}/reports/FBrf0206621.html FBrf0206621]
 +
   
  
 +
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)
 +
:    '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''
 +
:    BMC Bioinformatics. 10:59 [http://dx.doi.org/10.1186/1471-2105-10-59 DOI:10.1186/1471-2105-10-59] [http://{{flybaseorg}}/reports/FBrf0207486.html FBrf0207486]
 
      
 
      
−
:Reference Genome Group of the Gene Ontology Consortium (2009).
 
−
:    The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
 
−
:    PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431; PubMed Central PMCID: PMC2699109.
 
  
 +
:'''2008'''
 +
 +
:Drysdale R, and The FlyBase Consortium, (2008)
 +
:    '''FlyBase : a database for the Drosophila research community.'''
 +
:    Methods Mol. Biol. 420: 45-59 [http://dx.doi.org/10.1007/978-1-59745-583-1_3 DOI:10.1007/978-1-59745-583-1_3] [http://{{flybaseorg}}/reports/FBrf0205804.html FBrf0205804]
 
      
 
      
−
:S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi‑Sutherland, A. Schroeder, R. Seal, H. Zhang, and The FlyBase Consortium, (2009).
+
 
−
:    FlyBase: enhancing Drosophila Gene Ontology annotations.
+
:Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY (2008)
−
:    Nucleic Acids Res. 37: D555-D559; doi:10.1093/nar/gkn788. [FBrf0206621]
+
:    '''Big data: The future of biocuration.'''
 +
:    Nature 455(7209):47-50 [http://dx.doi.org/10.1038/455047a DOI:10.1038/455047a]
  
 
      
 
      
−
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).
+
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)
−
:    The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
+
:    '''Natural language processing in aid of FlyBase curators.'''
−
:    BMC Bioinformatics. 10:59. doi: 10.1186/1471-2105-10-59. PubMed PMID: 19210778; PubMed Central PMCID: PMC2648944. [FBrf0207486]
+
:    BMC Bioinformatics 9:193 [http://dx.doi.org/10.1186/1471-2105-9-193 DOI:10.1186/1471-2105-9-193] [http://{{flybaseorg}}/reports/FBrf0206381.html FBrf0206381]
  
 
      
 
      
−
:R. Drysdale, and The FlyBase Consortium, (2008).
+
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)
−
:    FlyBase : a database for the Drosophila research community.
+
:    '''FlyBase: integration and improvements to query tools.'''
−
:    Methods Molec. Biol. 420: 45-59. [FBrf0205804]
+
:    Nucleic Acids Res. 36:D588-D593 [http://dx.doi.org/10.1093/nar/gkm930 DOI:10.1093/nar/gkm930] [http://{{flybaseorg}}/reports/FBrf0203012.html FBrf0203012]
 +
   
  
 +
:'''2007'''
 +
 +
:Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR (2017)
 +
:    '''The ribosomal protein genes and Minute loci of Drosophila melanogaster.'''
 +
: Genome Biol. 2007;8(10):R216. [http://dx.doi.org/10.1186/gb-2007-8-10-r216 DOI:10.1186/gb-2007-8-10-r216] [http://{{flybaseorg}}/reports/FBrf0205398.html FBrf0205398]
 +
 +
 +
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)
 +
:    '''FlyBase: genomes by the dozen.'''
 +
:    Nucleic Acids Res. 35:D486-D491 [http://dx.doi.org/10.1093/nar/gkl827 DOI:10.1093/nar/gkl827] [http://{{flybaseorg}}/reports/FBrf0194786.html FBrf0194786]
 
      
 
      
−
:Howe, Doug; Costanzo, Maria; Fey, Petra; Gojobori, Takashi; Hannick, Linda; Hide, Winston; Hill, David P.; Kania, Renate; Schaeffer, Mary; St Pierre, Susan; Twigger, Simon; White, Owen; Yon Rhee, Seung (2008).
+
 
−
:    Big data: The future of biocuration.
+
:Drosophila 12 Genomes Consortium. (2007)
−
:    Nature. 455(7209):47-50. doi: 10.1038/455047a. PubMed PMID: 19182544; PubMed Central PMCID: PMC2819144. [FBrf0213427]
+
:    '''Evolution of genes and genomes on the Drosophila phylogeny.'''
 +
:    Nature 450(7167):203-218 [http://dx.doi.org/10.1038/nature06341 DOI:10.1038/nature06341] [http://{{flybaseorg}}/reports/FBrf0200326.html FBrf0200326]
  
 
      
 
      
−
:N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).
+
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)
−
:    Natural language processing in aid of FlyBase curators.
+
:    '''Integrating natural language processing with FlyBase curation.'''
−
:    BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381]
+
:    Pac Symp Biocomput. 2007:245-56 [http://{{flybaseorg}}/reports/FBrf0206379.html FBrf0206379]
 +
   
  
 +
:Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.. (2007)
 +
:    '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''
 +
:    Genome Res. 17(12):1823-1836 [http://dx.doi.org/10.1101/gr.6679507 DOI:10.1101/gr.6679507] [http://{{flybaseorg}}/reports/FBrf0202906.html FBrf0202906]
 
      
 
      
−
:R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).
 
−
:    FlyBase: integration and improvements to query tools.
 
−
:    Nucleic Acids Res. 36: D588-D593; doi:10.1093/nar/gkm930. [FBrf0203012]
 
  
 +
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)
 +
:    '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''
 +
:    Bioinformatics 23(13):i337-346 [http://dx.doi.org/10.1093/bioinformatics/btm189 DOI:10.1093/bioinformatics/btm189] [http://{{flybaseorg}}/reports/FBrf0201050.html FBrf0201050]
 
      
 
      
−
:M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).
 
−
:    FlyBase: genomes by the dozen.
 
−
:    Nucleic Acids Res. 35: D486-D491; doi:10.1093/nar/gkl827. [FBrf0194786]
 
  
 +
:Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M (2007)
 +
:    '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''
 +
:    Nature 450(7167):219-232 [http://dx.doi.org/10.1038/nature06340 DOI:10.1038/nature06340] [http://{{flybaseorg}}/reports/FBrf0200674.html FBrf0200674]
 
      
 
      
−
:Drosophila 12 Genomes Consortium., (2007).
 
−
:    Evolution of genes and genomes on the Drosophila phylogeny.
 
−
:    Nature 450: 203-218. [FBrf0200326]
 
  
 +
:'''2006'''
 +
 +
:Grumbling G, Strelets V and The FlyBase Consortium (2006)
 +
:    '''FlyBase: anatomical data, images and queries.'''
 +
:    Nucleic Acids Res. 34:D484-D488 [http://dx.doi.org/10.1093/nar/gkj068 DOI:10.1093/nar/gkj068] [http://{{flybaseorg}}/reports/FBrf0191339.html FBrf0191339]
 +
 +
 +
:'''2005'''
 +
 +
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
 +
:    '''FlyBase : Genes and gene models.'''
 +
:    Nucleic Acids Res., 33: D390-D395 [http://dx.doi.org/10.1093/nar/gki046 DOI:10.1093/nar/gki046] [http://{{flybaseorg}}/reports/FBrf0184221.html FBrf0184221]
 +
 +
   
 +
:Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. (2005)
 +
:    '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''
 +
:    Genome Res. 15(1):1-18 [http://dx.doi.org/10.1101/gr.3059305 DOI:10.1101/gr.3059305] [http://{{flybaseorg}}/reports/FBrf0184012.html FBrf0184012]
 
      
 
      
−
:N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).
 
−
:    Integrating natural language processing with FlyBase curation.
 
−
:    Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]
 
  
 +
:Zhou P, Emmert D, Zhang P (2005)
 +
:    '''Using chado to store genome annotation data.'''
 +
:    Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [http://dx.doi.org/10.1002/0471250953.bi0906s12 DOI:10.1002/0471250953.bi0906s12] [http://{{flybaseorg}}/reports/FBrf0206380.html FBrf0206380]
 
      
 
      
−
:M.F. Lin, et al., (2007).
 
−
:    Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
 
−
:    Genome Res 17: 1823-1836. [FBrf0202906]
 
  
−
   
+
:'''2003'''
−
:C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).
 
−
:    A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
 
−
:    Bioinformatics 23: i337-346. [FBrf0201050]
 
  
−
   
+
:The FlyBase Consortium, (2003)
−
:A. Stark et al., (2007).
+
:    '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''
−
:    Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
+
:    Nucleic Acids Res. 31:172-175 [http://dx.doi.org/10.1093/nar/gkg094 DOI:10.1093/nar/gkg094] [http://{{flybaseorg}}/reports/FBrf0159266.html FBrf0159266]
−
:    Nature 450: 219-232. [FBrf0200674]
 
  
 
      
 
      
−
:G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).
+
:Drysdale R (2003)
−
:    FlyBase: anatomical data, images and queries.
+
:    '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''
−
:    Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]
+
:    Briefings in Functional Genomics and Proteomics 2(2):128--134 [http://dx.doi.org/10.1093/bfgp/2.2.128 DOI:10.1093/bfgp/2.2.128] [http://{{flybaseorg}}/reports/FBrf0167361.html FBrf0167361]
  
−
   
 
−
:R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).
 
−
:    FlyBase : Genes and gene models.
 
−
:    Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]
 
−
: (Reproduced with permission from NAR Online )
 
  
−
   
+
:'''2002'''
−
:S. Richards et al., (2005).
+
 
−
:    Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
+
:Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM and Lewis SE. (2002)
−
:    Genome Res., 15: 1-18. [FBrf0184012]
+
:    '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''
 +
:    Genome Biol. 3:research0081 [http://dx.doi.org/10.1186/gb-2002-3-12-research0081 DOI:10.1186/gb-2002-3-12-research0081] [http://{{flybaseorg}}/reports/FBrf0155825.html FBrf0155825]
 +
  
 +
:Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ and Clamp ME. (2002)
 +
:    '''Apollo: a sequence annotation editor.'''
 +
:    Genome Biol. 3(12):research0082 [http://dx.doi.org/10.1186/gb-2002-3-12-research0082 DOI:10.1186/gb-2002-3-12-research0082] [http://{{flybaseorg}}/reports/FBrf0155826.html FBrf0155826]
 
      
 
      
−
:P. Zhou, D. Emmert, P. Zhang, (2005).
 
−
:    Using chado to store genome annotation data.
 
−
:    Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]
 
  
 +
:Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfield EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey ADNJ, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM and Lewis SE. (2002)
 +
:    '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''
 +
:    Genome Biol. 3:research0083 [http://dx.doi.org/10.1186/gb-2002-3-12-research0083 DOI:10.1186/gb-2002-3-12-research0083] [http://{{flybaseorg}}/reports/FBrf0155827.html FBrf0155827]
 
      
 
      
−
:The FlyBase Consortium, (2003).
 
−
:    The FlyBase Database of the Drosophila Genome Projects and community literature.
 
−
:    Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]
 
−
:    (Reproduced with permission from NAR Online )
 
  
−
   
+
:The FlyBase Consortium (2002)
−
:Rachel Drysdale, (2003).
+
:    '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''
−
:    The Drosophila melanogaster genome sequencing and annotation projects: A status report.
+
:    Nucleic Acids Res. 30:106-108 [http://dx.doi.org/10.1093/nar/30.1.106 DOI:10.1093/nar/30.1.106] [http://{{flybaseorg}}/reports/FBrf0141697.html FBrf0141697]
−
:    Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]
 
−
:    (Reproduced with permission from Briefings in Functional Genomics and Proteomics)
 
  
  
−
:'''Genome Annotation, (2002)'''
+
:'''2001'''
  
−
 
+
:Matthews K and Cook K (2001)
−
::CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin and SE Lewis. (2002).
+
:   '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''
−
::   An integrated computational pipeline and database to support whole-genome sequence annotation.
+
:    In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [http://{{flybaseorg}}/reports/FBrf0185967.html FBrf0185967]
−
::    Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]
+
   
  
 +
:Drysdale R (2001)
 +
:    '''Phenotypic data in FlyBase.'''
 +
:    Brief. Bioinform. 2(1):68-80 [http://dx.doi.org/10.1093/bib/2.1.68. DOI:10.1093/bib/2.1.68] [http://{{flybaseorg}}/reports/FBrf0137187.html FBrf0137187]
 
    
 
    
−
::SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall and ME Clamp. (2002).
 
−
::    Apollo: a sequence annotation editor.
 
−
::    Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]
 
  
 +
:'''1999'''
 +
 +
:FlyBase (1999)
 +
:    '''FlyBase: Genomic and post-genomic viewpoints.'''
 +
:    In S. Letovsky (Ed.) Bioinformatics: Databases and Systems 141-150 [http://{{flybaseorg}}/reports/FBrf0111589.html FBrf0111589]
 
      
 
      
−
::S Misra, MA Crosby, CJ Mungall, BB Matthews, KS Campbell, P Hradecky, Y Huang, JS Kaminker, GH Millburn, SE Prochnik, CD Smith, JL Tupy, EJ Whitfield, L Bayraktaroglu, BP Berman, BR Bettencourt, SE Celniker, ADNJ de Grey, RA Drysdale, NL Harris, J Richter, S Russo, AJ Schroeder, SQ Shu, M Stapleton, C Yamada, M Ashburner, WM Gelbart, GM Rubin and SE Lewis. (2002).
+
 
−
::    Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
+
:The FlyBase Consortium, (1999)
−
::    Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]
+
:    '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''
 +
:    Nucleic Acids Res. 27:85-88 [http://dx.doi.org/10.1093/nar/27.1.85 DOI:10.1093/nar/27.1.85] [http://{{flybaseorg}}/reports/FBrf0107356.html FBrf0107356]
  
 
      
 
      
−
:The FlyBase Consortium, (2002).
+
:'''1998'''
−
:    The FlyBase Database of the Drosophila Genome Projects and community literature.
 
−
:    Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]
 
−
:    (Reproduced with permission from NAR Online )
 
  
 +
:The FlyBase Consortium (1998)
 +
:    '''FlyBase - A Drosophila database.'''
 +
:    Nucleic Acids Res. 26:85-88 [http://dx.doi.org/10.1093/nar/26.1.85 DOI:10.1093/nar/26.1.85] [http://{{flybaseorg}}/reports/FBrf0100346.html FBrf0100346]
 
      
 
      
−
:K. Matthews and K. Cook (2001).
 
−
:    Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.
 
−
:    In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]
 
  
 +
:'''1997'''
 +
 +
:The FlyBase Consortium (1997)
 +
:    '''FlyBase - A Drosophila database.'''
 +
:    Nucleic Acids Res. 25:63-66 [http://dx.doi.org/10.1093/nar/25.1.63 DOI:10.1093/nar/25.1.63] [http://{{flybaseorg}}/reports/FBrf0093096.html FBrf0093096]
 
      
 
      
−
:Rachel Drysdale, (2001).
 
−
:    Phenotypic data in FlyBase.
 
−
:    Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]
 
−
:    (Reproduced with permission from Briefings in Bioinformatics)
 
−
 
 
−
 
 
−
:FlyBase (1999).
 
−
:    FlyBase: Genomic and post-genomic viewpoints.
 
−
:    In S. Letovsky (Ed.)
 
−
:    Bioinformatics: Databases and Systems 141--150. [FBrf0111589]
 
  
 +
:'''1996'''
 +
 +
:The FlyBase Consortium (1996)
 +
:    '''FlyBase - The Drosophila database.'''
 +
:    Nucleic Acids Res. 24:53-56 [http://dx.doi.org/10.1093/nar/24.1.53 DOI:10.1093/nar/24.1.53] [http://{{flybaseorg}}/reports/FBrf0085043.html FBrf0085043]
 
      
 
      
−
:The FlyBase Consortium, (1999).
 
−
:    The FlyBase Database of the Drosophila Genome Projects and community literature.
 
−
:    Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]
 
−
:    (Reproduced with permission from NAR Online )
 
  
−
   
+
:'''1995'''
−
:The FlyBase Consortium (1998).
+
 
−
:    FlyBase - A Drosophila database.
+
:The FlyBase Consortium (1995)
−
:    Nucleic Acids Res., 26:85-88 [FBrf0100346]
+
:    '''Proposed genetic nomenclature for Drosophila melanogaster.'''
 +
:    Trends in Genetics: Genetic Nomenclature Guide 26-29. [http://{{flybaseorg}}/reports/FBrf0078422.html FBrf0078422]
 +
 
 +
 
 +
:'''1994'''
 +
 
 +
:The FlyBase Consortium (1994)
 +
:    '''FlyBase - The Drosophila database.'''
 +
:    Nucleic Acids Res. 22(17):3456-3458 [http://dx.doi.org/10.1093/nar/22.17.3456 DOI:10.1093/nar/22.17.3456] [http://{{flybaseorg}}/reports/FBrf0077015.html FBrf0077015]
 +
 
 +
 
 +
:Ashburner M and Drysdale R (1994)
 +
:    '''FlyBase - The Drosophila genetic database.'''
 +
:    Development 120:2077-2079 [http://{{flybaseorg}}/reports/FBrf0072526.html FBrf0072526]
 +
 
  
−
   
+
:'''1993'''
−
:The FlyBase Consortium (1997).
 
−
:    FlyBase - A Drosophila database.
 
−
:    Nucleic Acids Res., 25:63-66 [FBrf0093096]
 
  
−
   
+
:Ashburner M (1993)
−
:The FlyBase Consortium (1996).
+
:    '''FlyBase.'''
−
:    FlyBase - The Drosophila database.
+
:    GNome News 13:19-20 [http://{{flybaseorg}}/reports/FBrf0058642.html FBrf0058642]
−
:    Nucleic Acids Res., 24:53-56 [FBrf0085043]
 
  
−
   
+
==FlyBase Mission Statement==
−
:The FlyBase Consortium (1995).
+
The aim of the FlyBase project is to provide an openly accessible centralized resource for Drosophila genetic, genomic and functional data.
−
:    Proposed genetic nomenclature for Drosophila melanogaster.
 
−
:    Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]
 
  
−
   
+
==FlyBase Licenses and Availability==
−
:The FlyBase Consortium (1994).
 
−
:    FlyBase - The Drosophila database.
 
−
:    Nucleic Acids Res., 22:3456-3458 [FBrf0077015]
 
  
−
   
+
FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://ftp.flybase.org/>.
−
:M. Ashburner and R. Drysdale (1994).
 
−
:    FlyBase - The Drosophila genetic database.
 
−
:    Development 120:2077-2079 [FBrf0072526]
 
  
−
   
+
FlyBase software is made available under either the [https://en.wikipedia.org/wiki/MIT_License MIT License] (Expat) or the [https://opensource.org/licenses/BSD-3-Clause BSD 3-Clause].  
−
:M. Ashburner (1993).
 
−
:   FlyBase.
 
−
:    GNome News 13:19-20. [FBrf0058642]
 
  
−
==Citing FlyBase==
+
All annotations and data produced by FlyBase that are accessible from flybase.org are distributed under a [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International License] (CC BY 4.0). Different licensing and copyright terms may apply for data provided by these resources that are not distributed by FlyBase.
−
We suggest FlyBase be referenced in publications in the following manner:
 
−
:S.J. Marygold, P.C. Leyland, R.L. Seal, J.L. Goodman, J.R. Thurmond, V.B. Strelets, R.J. Wilson and the FlyBase Consortium (2013). FlyBase: improvements to the bibliography. Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350]:
 
−
==FlyBase Copyright==
 
−
===The Copyright of FlyBase===
 
−
Copyright ©1993-2006 by The Genetics Society of America.
 
−
All Rights Reserved.
 
  
−
FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://flybase.net/flybase/>.
+
FlyBase adheres to the principle of full and unfettered data access to FlyBase data for the entire scientific community, and is a member of [https://fairsharing.org/FAIRsharing.wrvze3 FAIRsharing].  FlyBase is also is registered at the [https://www.re3data.org/repository/r3d100010591 re3data.org repository] and is an [https://elixiruknode.org/news/2021/elixir-uk-announces-seven-new-services/ ELIXIR-UK service].
  
−
This publication may be copied for non-commercial, scientific uses by individuals or organizations (including for-profit organizations). FlyBase is freely distributed to the scientific community on the understanding that it will not be used for commercial gain by any organization. Any commercial use of this publication, or any parts thereof, is expressly prohibited without permission in writing from the FlyBase consortium.
+
We are now members of the [https://globalbiodata.org/ Global Biodata Coalition] and our application is under review with [https://www.coretrustseal.org/about/ Core Trust Seal].
  
−
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.
+
The primary means of disseminating FlyBase data is through our web site (http://flybase.org)  which provides an interface with many options for browsing, interrogating and manipulating FlyBase data according to the needs of the user. In addition, the web site links to our ftp site containing all FlyBase data in a variety of formats, including various sequence formats, archival data, and the entire FlyBase Chado database.
−
Warranty
+
 +
All FlyBase data are available for download to other resources without restriction. In addition to our web site, FlyBase shares data with other major genetic / genomic resources. Most notable among these are NCBI and UniProt. FlyBase is the authority source for data on D. melanogaster and provides files (including whole genome annotation GenBank submissions to NCBI) that are used to generate reference files such as RefSeq. D. melanogaster GenBank/RefSeq submissions are updated annually, and power users are encouraged to use these stable annotation sets in their analyses.
 +
 +
===Warranty===
  
 
FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement.
 
FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement.
Line 329: Line 689:
  
 
By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information.
 
By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information.
−
Disclaimer
 
  
−
Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.
+
===Disclaimer===
  
−
===BIOSIS Copyright===
+
Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.
−
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:
 
−
 
 
−
"This database is copyrighted by Biological Abstracts Inc. (BIOSIS®). All rights reserved. No part of the information may be reproduced in hard copy, machine-readable form or other form without advance written permission from BIOSIS. Information has been obtained from public sources believed to be reliable. BIOSIS makes a diligent effort to provide complete and accurate representation of the bioscientific and other literature in its publications and services. However, BIOSIS does not guarantee the accuracy, adequacy, or completeness of any information and BIOSIS makes no warranties or representations of any kind, express or implied, including but not limited to warranties of merchantability or fitness for particular purpose. BIOSIS disclaims all liability for errors or omissions that may exist and shall not be liable for any incidental, consequential or other damages (whether resulting from negligence or otherwise) including, without limitation, exemplary damages or lost profits arising out of or in connection with the use of this database. Errors or omissions may be reported to Biological Abstracts Inc., 2100 Arch Street, Philadelphia, PA 19103-1399."
 
  
 
===Herskowitz's Bibliography Copyright===
 
===Herskowitz's Bibliography Copyright===
Line 356: Line 712:
 
1250 Sixth Avenue, San Diego, California 92101-4311
 
1250 Sixth Avenue, San Diego, California 92101-4311
  
−
FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.  
+
FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.
 +
 
 
==FlyBase Data Sources==
 
==FlyBase Data Sources==
  
−
The Red Book
+
'''The Red Book'''
 +
 
 +
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster
 +
 
 +
'''Bibliographies'''
  
−
Bibliographies
+
The major sources that have been incorporated into the FlyBase Bibliography:
  
−
External Databases
+
:Bibliography from The Genetics of Drosophila. T. H. Morgan, C. B. Bridges and A. H. Sturtevant, 1925. Bibliographica Genetica II: 1-262. 'S-Gravenhage, Martinus Nijhoff.
 +
:
 +
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939. Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952. Commonwealth Agricultural Bureaux. Slough: Farnham Royal.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958. Indiana University Publications.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963. McGraw-Hill Book Company, Inc.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969. Macmillan Publishing Company, Inc.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974. Macmillan Publishing Company, Inc.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976. Drosophila Information Service 51: 159-193.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977. Drosophila Information Service 52:186-226.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978. Drosophila Information Service 53: 219-244.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980. Drosophila Information Service 55: 218-262.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981. Drosophila Information Service 56: 199-210.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982. Drosophila Information Service 58: 227-270.
 +
:
 +
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983. Drosophila Information Service 59: 163-207.
 +
:
 +
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).
 +
:
 +
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965. Drosophila Information Service 40: 105-126.
 +
:
 +
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982. Drosophila Information Service: 58: 215-226.
 +
:
 +
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987. Drosophila Information Service 66: 198-208.
 +
:
 +
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991. Drosophila Information Service 70: 110-117.
 +
:
 +
:Bibliography on Drosophila ananassae. B. N. Singh, 1991. Drosophila Information Service 70: 205-211.
 +
:
 +
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988. Dowden, Hutchinson and Ross Publications, Inc.
 +
:
 +
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86). M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293. In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988. Blackie Publications. Glasgow, Scotland.
 +
:
 +
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.
 +
:
 +
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich). January 1993 with regular subsequent updates.
 +
:
 +
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.
 +
:
 +
:Japan Scientific Societies Press and Karger, Tokyo and Basel.
 +
:
 +
:References from the Environmental Mutagen Information Center (EMIC) database.
 +
:
 +
:MEDLINE (National Library of Medicine, Washington). Searching all fields with the text word DROSOPHIL* or MELANOGASTER. Searched from 1966 to date.
 +
:
 +
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.
 +
:
 +
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.
 +
:
 +
:References from John Merriam's Genevent database of molecular data.
 +
:
 +
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.
 +
:
 +
:Jeff Hall's bibliography on neurogenetics of Drosophila.
  
−
Journal Articles and Books
+
'''External Databases'''
  
−
Drosophila Conference Abstracts
+
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)
 +
UniProtKB
 +
InterPro
  
−
Personal Communications to FlyBase
+
'''Journal Articles and Books'''
  
−
Direct Submission of High-Throughput Data
+
Publications relevant to Drosophila from various journals and books.
  
−
Insertion Collection Data
+
'''Drosophila Conference Abstracts'''
  
−
Stock Lists Submitted to FlyBase
+
The following abstracts were curated until 2008:
 +
GSA Annual Drosophila Research Conference Abstracts
 +
European Drosophila Research Conference Abstracts
  
−
People
+
'''Personal Communications to FlyBase'''
 +
 
 +
Information and observations provided by the Fly Community
 +
 
 +
'''Direct Submission of High-Throughput Data'''
 +
 
 +
:'''Proteomics data'''
 +
:
 +
:Center for Model Organism Proteomes --
 +
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)
 +
:
 +
:'''Microarrays''' (Oligos, cDNAs)
 +
:
 +
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)
 +
:
 +
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)
 +
:
 +
:'''Tiling BACs'''
 +
:
 +
:Berkeley Drosophila Genome Project
 +
:
 +
'''Insertion Collection Data'''
 +
 +
:'''Transgene insertion data'''
 +
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)
 +
:
 +
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)
 +
:
 +
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)
 +
:
 +
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)
 +
:
 +
:P{GawB} Project, GETDB, Japan (2002 - 2004)
 +
:
 +
:NCI lethals (2002 - 2004)(Oh et. al., 2003)
 +
:
 +
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004)
 +
:
 +
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)
 +
:
 +
:'''Natural transposon insertion data'''
 +
:
 +
:[http://{{flybaseorg}}/reports/FBrf0155828.html Kaminker J. et al. 2002]
 +
:
 +
:[http://{{flybaseorg}}/reports/FBrf0184336.html Quesneville H. et al. 2005]
 +
 
 +
'''Stock Lists Submitted to FlyBase'''
 +
 
 +
Bloomington Drosophila Stock Center
 +
 
 +
Drosophila Genetic Resource Center
 +
 
 +
UC San Diego Drosophila Species Stock Center
 +
 
 +
Exelixis Drosophila Stock Collection at Harvard Medical School
 +
 
 +
Nusslein-Volhard laboratory
 +
 
 +
Garcia-Bellido laboratory
 +
 
 +
Carpenter laboratory
 +
 
 +
'''People'''
 +
 +
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.
 +
 
 +
An e-mail address list compiled and maintained by Dr. John Haynie (1992)
 +
 
 +
Records of the Bloomington Drosophila Stock Center (1992)
 +
 
 +
The distribution list of Drosophila Information Newsletter (1992)
 +
 
 +
A subset of the Genetics Society of America's mailing and membership list (1992)
 +
 
 +
The mailing list for the European Drosophila Research Conference (1992)
  
 
==FlyBase Alumni==
 
==FlyBase Alumni==
 
FlyBase thanks these former members of the FlyBase consortium for their contribution:
 
FlyBase thanks these former members of the FlyBase consortium for their contribution:
  
 +
    Boris Adryan
 +
    Julie Agapite
 
     Manish Anand
 
     Manish Anand
 
     Michael Ashburner
 
     Michael Ashburner
 +
    Phill Baker
 
     Leyla Bayraktaroglu
 
     Leyla Bayraktaroglu
 
     Ben Berman
 
     Ben Berman
Line 394: Line 900:
 
     Russell Collins
 
     Russell Collins
 
     Kim Cook
 
     Kim Cook
 +
    Marta Costa
 +
    Bryon Czoch
 
     Anthony DeAngelo
 
     Anthony DeAngelo
 
     Aubrey de Grey
 
     Aubrey de Grey
 
     Rachel Drysdale
 
     Rachel Drysdale
 +
    David Emmert
 +
    Kathleen Falls
 +
    Silvie Fexova
 
     Helen Field
 
     Helen Field
 
     Rebecca Foulger
 
     Rebecca Foulger
 
     Erwin Frise
 
     Erwin Frise
 +
    Phani Garapati
 +
    William Gelbart
 
     Mark Gibson
 
     Mark Gibson
 
     Don Gilbert
 
     Don Gilbert
 +
    Gary Grumbling
 
     Janet Gulotta
 
     Janet Gulotta
 
     Cyrus Harmon
 
     Cyrus Harmon
 
     Nomi Harris
 
     Nomi Harris
 
     Gregg Helt
 
     Gregg Helt
 +
    Alex Holmes
 
     Pavel Hradecky
 
     Pavel Hradecky
 
     Yanmei Huang
 
     Yanmei Huang
 +
    Tamsin Jones
 
     Josh Kaminker
 
     Josh Kaminker
 +
    Thomas Kaufman
 
     Kerry Knight
 
     Kerry Knight
 
     Sophia Kossida
 
     Sophia Kossida
 +
    Pravija Krishna
 
     Rob Kulathinal
 
     Rob Kulathinal
 
     Julia Lamenza
 
     Julia Lamenza
Line 419: Line 937:
 
     Guo-chun Liao
 
     Guo-chun Liao
 
     Anne Loraine
 
     Anne Loraine
 +
    Kathy Matthews
 
     Glenn McAlpine
 
     Glenn McAlpine
 +
    Peter McQuilton
 
     John Merriam
 
     John Merriam
 
     Sima Misra
 
     Sima Misra
Line 428: Line 948:
 
     David Osumi-Sutherland
 
     David Osumi-Sutherland
 
     Dawn Palmer
 
     Dawn Palmer
 +
    Harriet Platero
 +
    Laura Ponting
 +
    Sinzi Pop
 
     Simon Prochnik
 
     Simon Prochnik
 
     Simon Reeve
 
     Simon Reeve
 +
    Alix Rey
 
     John Richter
 
     John Richter
 
     Wayne Rindone
 
     Wayne Rindone
 
     Margo Roark
 
     Margo Roark
 
     Gerry Rubin
 
     Gerry Rubin
 +
    Susan St. Pierre
 +
    Andrew Schroeder
 
     Ruth Seal
 
     Ruth Seal
 +
    Jolene Seme
 
     Carolyn Shemen
 
     Carolyn Shemen
 
     Hardik Sheth
 
     Hardik Sheth
Line 442: Line 969:
 
     Chris Smith
 
     Chris Smith
 
     Frank Smutniak
 
     Frank Smutniak
 +
    Nicole Staudt
 +
    Ray Stefancsik
 +
    Vitor Trovisco
 
     Jon Tupy
 
     Jon Tupy
 +
    Susan Tweedie
 +
    Jose Maria Urbano
 
     Edwin Wang
 
     Edwin Wang
 
     Eddy Wellbourne
 
     Eddy Wellbourne
 +
    Maggie Werner-Washburne
 
     Eleanor Whitfield
 
     Eleanor Whitfield
 
     Colin Wiel
 
     Colin Wiel
Line 455: Line 988:
 
     Peili Zhang
 
     Peili Zhang
  
−
==FlyBase Support==
+
==Grants Supporting FlyBase==
−
FlyBase is supported by a grant from the National Human Genome Research Institute at the
+
 
−
U.S. National Institutes of Health #P41 HG000739.
+
1.  "FlyBase: A Drosophila Genomic and Genetic Database"
 +
NHGRI Award #: [https://reporter.nih.gov/project-details/U24HG013300 U24HG013300]
 +
 
 +
2.  "GO annotation: maximizing the potential of Drosophila research to benefit human health"
 +
UK Medical Research Council Award #: [https://gtr.ukri.org/projects?ref=MR%2FW024233%2F1 MR/W024233/1]
 +
 
 +
3.  "BBSRC-NSF/BIO: Integrative analysis and Visualisation of Fly Cell Atlas datasets to enable cross-species comparisons" 
 +
NSF Award #: [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2035515&HistoricalAwards=false 2035515]
 +
BBSRC Award #: [https://gtr.ukri.org/projects?ref=BB%2FT014008%2F1 BB/T014008/1]
 +
 
 +
4.  “Virtual Fly Brain”
 +
Wellcome Trust Award #: [https://wellcome.org/grant-funding/people-and-projects/grants-awarded/virtual-fly-brain-0 PLM13398]
 +
 
 +
5.  "Sustaining FlyBase: The Drosophila genomic and genetic database.“
 +
NSF Award #: [https://www.nsf.gov/awardsearch/showAward?AWD_ID=2039324&HistoricalAwards=false 2039324]
 +
 
 +
6.  "Alliance Central:  A Platform for sustainable development of next generation genome knowledgebases"
 +
NHGRI Award #: [https://reporter.nih.gov/project-details/9856160 U24HG010859]
  
−
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.
+
7.  "Investigating metabolic responses to high sugar diets and the onset of diabetic phenotypes"
 +
NIDDK Award #: [https://reporter.nih.gov/project-details/1R01DK136945-01 1R01DK136945-01]
  
−
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.
+
8. [[FlyBase:List_of_Contributors|FlyBase Users]] all over the world
  
 
[[Category:FlyBase]]
 
[[Category:FlyBase]]
 +
[[Category:DONE]]

Latest revision as of 14:17, 15 October 2024

FlyBase Consortium

The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.

Please use the contact FlyBase form to write to us.

FlyBase-Harvard
Biological Laboratories, Harvard University
16 Divinity Avenue
Cambridge, Massachusetts 02138
USA
   Norbert Perrimon (PI)
   Susan Russo Gelbart (PD)
   Kris Broll
   Lynn Crosby
   Gil dos Santos
   L. Sian Gramates
   Victoria Jenkins
   Ian Longden
   Beverley Matthews
   Carol Sutherland
   Christopher J. Tabone
   Pinglei Zhou
   Mark Zytkovicz
FlyBase-Cambridge
Department of Physiology, Development and Neuroscience, University of Cambridge
Downing Street, Cambridge CB2 3DY
UK
   Nick Brown (Co-PI)
   Giulia Antonazzo
   Helen Attrill
   Damien Goutte-Gattat
   Aoife Larkin
   Steven Marygold
   Alex McLachlan
   Gillian Millburn
   Arzu Öztürk-Çolak
   Clare Pilgrim
   Rossana Zaru
FlyBase-Indiana
Department of Biology, Indiana University
1001 East 3rd Street
Bloomington, Indiana 47405-7005
USA
   Brian Calvi (Co-PI)
   Seth Campbell
   Josh Goodman
   Victor Strelets
   Jim Thurmond
FlyBase-New Mexico
Department of Biology, Castetter Hall - Room 200
University of New Mexico,
Albuquerque, New Mexico 87131
USA
   Richard Cripps (Co-PI)
   TyAnna Lovato

FlyBase Publications

2024
Antonazzo G, Gaudet P, Lovering RC, Attrill H (2024)
Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.
RNA Biol. 21(1) 36–48 DOI:10.1080/15476286.2024.2408523


Marygold SJ (2024)
The alpha-ketoacid dehydrogenase complexes of Drosophila melanogaster.
MicroPubl Biol. 001209 DOI:10.17912/micropub.biology.001209 FBrf0259508


Alliance of Genome Resources Consortium (2024)
Updates to the Alliance of Genome Resources Central Infrastructure.
Genetics 227(1) iyae049 DOI:10.1093/genetics/iyae049 FBrf0259417


Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold SJ, Novoa EM, Motorin Y, Roignant JY (2024)
Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster.
Nucleic Acids Res 52(6) 2848-2864 DOI:10.1093/nar/gkae139 FBrf0259352


Öztürk-Çolak A, Marygold SJ, Antonazzo G, Attrill H, Goutte-Gattat D, Jenkins VK, Matthews BB, Millburn G, dos Santos G, Tabone CJ, the FlyBase Consortium (2024)
FlyBase: updates to the Drosophila genes and genomes database.
Genetics 227(1) iyad211 DOI:10.1093/genetics/iyad211 FBrf0259457


Attrill H, Antonazzo G, Goodman JL, Thurmond J, Strelets VB, Brown NH; FlyBase Consortium (2024)
A new experimental evidence-weighted signaling pathway resource in FlyBase.
Development 151(3) dev202255 DOI:10.1242/dev.202255 FBrf0258673


2023
Attrill H (2023)
Comparing the history of signalling pathway research using the research publication record of representative genes.
MicroPubl Biol. 000998 DOI:10.17912/micropub.biology.000998 FBrf0258056


Gene Ontology Consortium (2023)
The Gene Ontology knowledgebase in 2023.
Genetics 224(1) iyad031. DOI:10.1093/genetics/iyad031


Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Chen W, Li F, Chao T, Mohr SE, Brown NH, Perrimon N. (2023)
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms.
Nucleic Acids Res 51(W1) W419--WW426. DOI:10.1093/nar/gkad331 FBrf0256969


Marygold SJ and the FlyBase Consortium (2023)
Exploring FlyBase Data Using QuickSearch (Updated protocol)
Current Protocols 3:e731. DOI:10.1002/cpz1.731 FBrf0256232


Court R, Costa M, Pilgrim C, Millburn G, Holmes A, McLachlan A, Larkin A, Matentzoglu N, Kir H, Parkinson H, Brown NH, O'Kane CJ, Armstrong JD, Jefferis GSXE, Osumi-Sutherland D. (2023)
Virtual Fly Brain-An interactive atlas of the Drosophila nervous system.
Front Physiol. 14:1076533. DOI:10.3389/fphys.2023.1076533 FBrf0255719


2022
Jenkins VK, Larkin A, Thurmond J; FlyBase Consortium. (2022)
Using FlyBase: A Database of Drosophila Genes and Genetics.
Methods Mol Biol. 2540:1-34. DOI:10.1007/978-1-0716-2541-5_1 FBrf0254317


Trovisco V (2022)
Featured Resource: FlyBase.
The Node: Resources


Marygold SJ, Chan PP, Lowe TM (2022)
Systematic identification of tRNA genes in Drosophila melanogaster.
MicroPubl Biol. 000560 DOI:10.17912/micropub.biology.000560 FBrf0253514


Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby MA, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews BB, Millburn G, Strelets VB and the FlyBase Consortium (2022)
FlyBase: A guided tour of highlighted features.
Genetics 220(4) iyac035 DOI:10.1093/genetics/iyac035 FBrf0253076


Alliance of Genome Resources Consortium (2022)
Harmonizing model organism data in the Alliance of Genome Resources.
Genetics 220(4) iyac022 DOI:10.1093/genetics/iyac022 FBrf0253213


Liu Y, Li JSS, Rodiger J, Comjean A, Attrill H, Antonazzo G, Brown NH, Hu Y, Perrimon N (2022)
FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila.
Genetics 220(3) iyab235 DOI:10.1093/genetics/iyab235 FBrf0252867


2021
Meyer H, Buhr A, Callaerts P, Schiemann R, Wolfner MF, Marygold SJ (2021)
Identification and bioinformatic analysis of neprilysin and neprilysin-like metalloendopeptidases in Drosophila melanogaster.
MicroPubl Biol. 000410 DOI:10.17912/micropub.biology.000410 FBrf0249415


Hu Y, Tattikota SG, Liu Y, Comjean A, Gao Y, Forman C, Kim G, Rodiger J, Papatheodorou I, Dos Santos G, Mohr SE, Perrimon N (2021)
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.
Comput Struct Biotechnol J 19:2018-2026. DOI:10.1016/j.csbj.2021.04.021FBrf0249044


Ahn SJ and Marygold SJ (2021)
The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis.
Front Physiol 12 648481 DOI:10.3389/fphys.2021.648481FBrf0248570


The Gene Ontology Consortium (2021)
The Gene Ontology resource: enriching a GOld mine.
Nucleic Acids Res. 49(D1) D325–D334 DOI:10.1093/nar/gkaa1113 FBrf0247877


Larkin A, Marygold SJ, Antonazzo G, Attrill H, dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J and the FlyBase Consortium (2021)
FlyBase: updates to the Drosophila melanogaster knowledge base.
Nucleic Acids Res. 49(D1) D899–D907 DOI:10.1093/nar/gkaa1026 FBrf0247700


RNAcentral Consortium (2021)
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
Nucleic Acids Res. 49(D1) D212–D220 DOI:10.1093/nar/gkaa921


2020
Marygold SJ, Alic N, Gilmour DS, Grewal SS (2020)
In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits.
MicroPubl Biol. 000320 DOI:10.17912/micropub.biology.000320 FBrf0247389


Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM and Mungall CJ (2020)
Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.
Open Biol 10(9) 200149 DOI:10.1098/rsob.200149


Kishore R, Arnaboldi V, Van Slyke CE, Chan J, Nash RS, Urbano JM, Dolan ME, Engel SR, Shimoyama M, Sternberg PW, the Alliance of Genome Resources (2020)
Automated generation of gene summaries at the Alliance of Genome Resources.
Database 2020 baaa037 DOI:10.1093/database/baaa037


Antonazzo G, Urbano JM, Marygold SJ, Millburn GH and Brown NH (2020)
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation.
Database 2020 baz152 DOI:10.1093/database/baz152 FBrf0244633


Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y and Yamaguchi M (2020)
The DNA polymerases of Drosophila melanogaster.
Fly 14(1-4) 49-61 DOI:10.1080/19336934.2019.1710076 FBrf0245686


The Alliance of Genome Resources Consortium (2020)
Alliance of Genome Resources Portal: unified model organism research platform.
Nucleic Acids Res 48(D1) D650–D658 DOI:10.1093/nar/gkz813 FBrf0245774


2019
The Alliance of Genome Resources (2019)
Building a Modern Data Ecosystem for Model Organism Databases.
Genetics 213(4):1189-1196 DOI:10.1534/genetics.119.302523 FBrf0244239


Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. (2019)
Annotation of gene product function from high-throughput studies using the Gene Ontology.
Database 2019 baz007 DOI:10.1093/database/baz007


Garapati PV, Zhang J, Rey AJ and Marygold SJ (2019)
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase
Database 2019 bay144 DOI:10.1093/database/bay144 FBrf0241253


Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR and the FlyBase Consortium. (2019)
FlyBase 2.0: the next generation.
Nucleic Acids Res. 47(D1) D759–D765 DOI:10.1093/nar/gky1003 FBrf0241170


The RNAcentral Consortium (2019)
RNAcentral: a hub of information for non-coding RNA sequences.
Nucleic Acids Res. 47(D1) D221–D229 DOI:10.1093/nar/gky1034


The Gene Ontology Consortium (2019)
The Gene Ontology Resource: 20 years and still GOing strong.
Nucleic Acids Res. 47(D1) D330–D338 DOI:10.1093/nar/gky1055


2018
Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE and Smith C. (2018)
Model organism data evolving in support of translational medicine.
Lab Anim (NY) 47:277-289 DOI:10.1038/s41684-018-0150-4 FBrf0241113


Rey AJ, Attrill H, Marygold SJ and The FlyBase Consortium. (2018)
Using FlyBase to Find Functionally Related Drosophila Genes.
Eukaryotic Genomic Databases: Methods and Protocols (M. Kollmar, ed.) pp. 493-512. Springer, New York DOI:10.1007%2F978-1-4939-7737-6_16 FBrf0238904


2017
Hu Y, Comjean A, Mohr SE; FlyBase Consortium, Perrimon N. (2017)
Gene2Function: An Integrated Online Resource for Gene Function Discovery.
G3 (Bethesda) 7(8):2855-2858 DOI:10.1534/g3.117.043885 FBrf0236248


The Gene Ontology Consortium. (2017)
Expansion of the Gene Ontology knowledgebase and resources
Nucleic Acids Res. 45(D1):D331-D338 DOI:10.1093/nar/gkw1108


Gramates LS, Marygold SJ, dos Santos G, Urbano J-M, Antonazzo G, Matthews BB, Rey AJ, Tabone CJ, Crosby MA, Emmert DB, Falls K, Goodman JL, Hu Y, Ponting L, Schroeder AJ, Strelets VB, Thurmond J, Zhou P and the FlyBase Consortium. (2017)
FlyBase at 25: looking to the future.
Nucleic Acids Res. 45(D1):D663-D671 DOI:10.1093/nar/gkw1016 FBrf0234415


Marygold SJ, Attrill H, Lasko P. (2017)
The Translation Factors of Drosophila melanogaster.
Fly 11(1):65-74 DOI:10.1080/19336934.2016.1220464 FBrf0233552


2016
Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J; FlyBase Consortium. (2016)
Exploring FlyBase Data Using QuickSearch.
Curr. Protoc. Bioinformatics 56:1.31.1-1.31.23 DOI:10.1002/cpbi.19 FBrf0234167


Marygold SJ, Crosby MA, Goodman JL and The FlyBase Consortium. (2016)
Using FlyBase, a Database of Drosophila Genes and Genomes.
Drosophila: Methods and Protocols, Second edition, vol. 1478 (C. Dahmann, ed.) pp. 1-31. Springer, New York DOI:10.1007/978-1-4939-6371-3_1 FBrf0233766)


Kahsai L, Millburn GH, Cook KR. (2016)
Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.
G3 (Bethesda). 6(8):2665-2670 DOI:10.1534/g3.116.030940 FBrf0233125


Millburn GH, Crosby MA, Gramates LS, Tweedie S; FlyBase Consortium. (2016)
FlyBase portals to human disease research using Drosophila models.
Dis. Model Mech. 9(3):245-252 DOI:10.1242/dmm.023317 FBrf0231138


Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ; the FlyBase Consortium. (2016)
FlyBase: establishing a Gene Group resource for Drosophila melanogaster.
Nucleic Acids Res. 44(D1):D786-D792 DOI:10.1093/nar/gkv1046 FBrf0230602


2015
Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
The aminoacyl-tRNA synthetases of Drosophila melanogaster.
Fly 9(2):53-61 DOI:10.1080/19336934.2015.1101196 FBrf0230668


Matthews BB, dos Santos G, Crosby MA, Emmert DB, St Pierre SE, Gramates LS, Zhou P, Schroeder AJ, Falls K, Strelets V, Russo SM, Gelbart WM, and the FlyBase Consortium. (2015)
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.
G3 (Bethesda) 5:1721-1736 DOI:10.1534/g3.115.018929 FBrf0229216


Crosby MA, Gramates LS, dos Santos G, Matthews BB, St Pierre SE, Zhou P, Schroeder AJ, Falls K, Emmert DB, Russo SM, Gelbart WM., and the FlyBase Consortium. (2015)
Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.
G3 (Bethesda) 5:1737-1749 DOI:10.1534/g3.115.018937 FBrf0229217


Gene Ontology Consortium. (2015)
Gene Ontology Consortium: going forward.
Nucleic Acids Res. 43(Database issue):D1049-56 DOI:10.1093/nar/gku1179


Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.
Nucleic Acids Res. 43(Database issue): D690-D697 DOI:10.1093/nar/gku1099 FBrf0227324


2014
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. (2014)
Representing kidney development using the gene ontology.
PLoS One. 9(6):e99864 DOI:10.1371/journal.pone.0099864


Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, Hayman GT, Tweedie S, Schaeffer ML, Laulederkind SJ, Wang SJ, Gobeill J, Ruch P, Luu AT, Kim JJ, Chiang JH, Chen YD, Yang CJ, Liu H, Zhu D, Li Y, Yu H, Emadzadeh E, Gonzalez G, Chen JM, Dai HJ, Lu Z. (2014)
Overview of the gene ontology task at BioCreative IV.
Database 2014. bau086 DOI:10.1093/database/bau086


Van Auken K, Schaeffer ML, McQuilton P, Laulederkind SJ, Li D, Wang SJ, Hayman GT, Tweedie S, Arighi CN, Done J, Müller HM, Sternberg PW, Mao Y, Wei CH, Lu Z (2014)
BC4GO: a full-text corpus for the BioCreative IV GO Task.
Database 2014. bau074 DOI:10.1093/database/bau074


Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.
Database 2014. bau033 DOI:10.1093/database/bau033


St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)
FlyBase 102 - advanced approaches to interrogating FlyBase.
Nucleic Acids Res. 42(Database issue):D780-8 DOI:10.1093/nar/gkt1092 FBrf0223749


2013
Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
The Drosophila anatomy ontology.
J. Biomed. Semantics 4(1):32 DOI:10.1186/2041-1480-4-32 FBrf0223849


Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV. (2013)
The Drosophila phenotype ontology.
J. Biomed. Semantics 4(1):30 DOI:10.1186/2041-1480-4-30 FBrf0223876


Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)
On the reproducibility of science: unique identification of research resources in the biomedical literature.
PeerJ. 1:e148 DOI:10.7717/peerj.148 FBrf0222712


Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)
FlyBase: improvements to the bibliography.
Nucleic Acids Res. 41(Database issue):D751-D757 DOI:10.1093/nar/gks1024 FBrf0220350


Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)
Systematic analysis of experimental phenotype data reveals gene functions.
PLoS One. 8(4):e60847 DOI:10.1371/journal.pone.0060847 FBrf0221415


Gene Ontology Consortium (2013)
Gene Ontology annotations and resources.
Nucleic Acids Res. 41(Database issue):D530-5. DOI:10.1093/nar/gks1050


2012
McQuilton P and the FlyBase Consortium (2012)
Opportunities for text mining in the FlyBase genetic literature curation workflow.
Database 2012:bas039 DOI:10.1093/database/bas039 FBrf0219955


Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)
Directly e-mailing authors of newly published papers encourages community curation.
Database 2012:bas024 DOI:10.1093/database/bas024 FBrf0218522


McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)
FlyBase 101 – the basics of navigating FlyBase.
Nucleic Acids Res. 40 (Database issue):D706-14 DOI:10.1093/nar/gkr1030 FBrf0217108


Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold S, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW (2012)
Automatic categorization of diverse experimental information in the bioscience literature.
BMC Bioinformatics. 13(1):16 DOI:10.1186/1471-2105-13-1 FBrf0218533


Gene Ontology Consortium (2012)
The Gene Ontology: enhancements for 2011.
Nucleic Acids Res. 40(Database issue):D559-64 DOI:10.1093/nar/gkr1028


2011
Rangarajan A, Schedl T, Yook K, Chan J, Haenel S, Otis L, Faelten S, DePellegrin‑Connelly T, Isaacson R, Skrzypek MS, Marygold SJ, Stefancsik R, Cherry JM, Sternberg PW and Müller H-M (2011)
Toward an interactive article: integrating journals and biological databases.
BMC Bioinformatics 12:175 DOI:10.1186/1471-2105-12-175 FBrf0214821


Daines, B., Wang, H., Wang, L., Li, Y., Han, Y., Emmert, D., Gelbart, W., Wang, X., Li, W., Gibbs, R., Chen, R. (2011).
The Drosophila melanogaster transcriptome by paired-end RNA sequencing.
Genome Res. 21(2): 315--324 DOI:10.1101/gr.107854.110 FBrf0213064


Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)
The representation of heart development in the gene ontology.
Dev Biol. 354(1):9-17 DOI:10.1016/j.ydbio.2011.03.011


2010
Gene Ontology Consortium (2010)
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Res. 38(Database issue):D331-5 DOI:10.1093/nar/gkp1018


Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
Nucleic Acids Res. 38(Database issue):D443-7 DOI:10.1093/nar/gkp910 FBrf0209611


2009
St. Pierre S and McQuilton P (2009)
Inside FlyBase (Biocuration as a career).
Fly 3(1):112-114 DOI:10.4161/fly.3.1.7769 FBrf0213427


Reference Genome Group of the Gene Ontology Consortium (2009)
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
PLoS Comput Biol. 5(7):e1000431 DOI:10.1371/journal.pcbi.1000431


Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi‑Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium (2009)
FlyBase: enhancing Drosophila Gene Ontology annotations.
Nucleic Acids Res. 37(Database issue):D555-D559 DOI:10.1093/nar/gkn788 FBrf0206621


Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
BMC Bioinformatics. 10:59 DOI:10.1186/1471-2105-10-59 FBrf0207486


2008
Drysdale R, and The FlyBase Consortium, (2008)
FlyBase : a database for the Drosophila research community.
Methods Mol. Biol. 420: 45-59 DOI:10.1007/978-1-59745-583-1_3 FBrf0205804


Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY (2008)
Big data: The future of biocuration.
Nature 455(7209):47-50 DOI:10.1038/455047a


Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)
Natural language processing in aid of FlyBase curators.
BMC Bioinformatics 9:193 DOI:10.1186/1471-2105-9-193 FBrf0206381


Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)
FlyBase: integration and improvements to query tools.
Nucleic Acids Res. 36:D588-D593 DOI:10.1093/nar/gkm930 FBrf0203012


2007
Marygold SJ, Roote J, Reuter G, Lambertsson A, Ashburner M, Millburn GH, Harrison PM, Yu Z, Kenmochi N, Kaufman TC, Leevers SJ, Cook KR (2017)
The ribosomal protein genes and Minute loci of Drosophila melanogaster.
Genome Biol. 2007;8(10):R216. DOI:10.1186/gb-2007-8-10-r216 FBrf0205398


Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)
FlyBase: genomes by the dozen.
Nucleic Acids Res. 35:D486-D491 DOI:10.1093/nar/gkl827 FBrf0194786


Drosophila 12 Genomes Consortium. (2007)
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450(7167):203-218 DOI:10.1038/nature06341 FBrf0200326


Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)
Integrating natural language processing with FlyBase curation.
Pac Symp Biocomput. 2007:245-56 FBrf0206379


Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.. (2007)
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
Genome Res. 17(12):1823-1836 DOI:10.1101/gr.6679507 FBrf0202906


Mungall CJ, Emmert DB and the FlyBase Consortium (2007)
A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
Bioinformatics 23(13):i337-346 DOI:10.1093/bioinformatics/btm189 FBrf0201050


Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M (2007)
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature 450(7167):219-232 DOI:10.1038/nature06340 FBrf0200674


2006
Grumbling G, Strelets V and The FlyBase Consortium (2006)
FlyBase: anatomical data, images and queries.
Nucleic Acids Res. 34:D484-D488 DOI:10.1093/nar/gkj068 FBrf0191339


2005
Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
FlyBase : Genes and gene models.
Nucleic Acids Res., 33: D390-D395 DOI:10.1093/nar/gki046 FBrf0184221


Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. (2005)
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
Genome Res. 15(1):1-18 DOI:10.1101/gr.3059305 FBrf0184012


Zhou P, Emmert D, Zhang P (2005)
Using chado to store genome annotation data.
Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. DOI:10.1002/0471250953.bi0906s12 FBrf0206380


2003
The FlyBase Consortium, (2003)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 31:172-175 DOI:10.1093/nar/gkg094 FBrf0159266


Drysdale R (2003)
The Drosophila melanogaster genome sequencing and annotation projects: A status report.
Briefings in Functional Genomics and Proteomics 2(2):128--134 DOI:10.1093/bfgp/2.2.128 FBrf0167361


2002
Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM and Lewis SE. (2002)
An integrated computational pipeline and database to support whole-genome sequence annotation.
Genome Biol. 3:research0081 DOI:10.1186/gb-2002-3-12-research0081 FBrf0155825


Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ and Clamp ME. (2002)
Apollo: a sequence annotation editor.
Genome Biol. 3(12):research0082 DOI:10.1186/gb-2002-3-12-research0082 FBrf0155826


Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfield EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey ADNJ, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM and Lewis SE. (2002)
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Genome Biol. 3:research0083 DOI:10.1186/gb-2002-3-12-research0083 FBrf0155827


The FlyBase Consortium (2002)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 30:106-108 DOI:10.1093/nar/30.1.106 FBrf0141697


2001
Matthews K and Cook K (2001)
Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.
In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. FBrf0185967


Drysdale R (2001)
Phenotypic data in FlyBase.
Brief. Bioinform. 2(1):68-80 DOI:10.1093/bib/2.1.68 FBrf0137187


1999
FlyBase (1999)
FlyBase: Genomic and post-genomic viewpoints.
In S. Letovsky (Ed.) Bioinformatics: Databases and Systems 141-150 FBrf0111589


The FlyBase Consortium, (1999)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 27:85-88 DOI:10.1093/nar/27.1.85 FBrf0107356


1998
The FlyBase Consortium (1998)
FlyBase - A Drosophila database.
Nucleic Acids Res. 26:85-88 DOI:10.1093/nar/26.1.85 FBrf0100346


1997
The FlyBase Consortium (1997)
FlyBase - A Drosophila database.
Nucleic Acids Res. 25:63-66 DOI:10.1093/nar/25.1.63 FBrf0093096


1996
The FlyBase Consortium (1996)
FlyBase - The Drosophila database.
Nucleic Acids Res. 24:53-56 DOI:10.1093/nar/24.1.53 FBrf0085043


1995
The FlyBase Consortium (1995)
Proposed genetic nomenclature for Drosophila melanogaster.
Trends in Genetics: Genetic Nomenclature Guide 26-29. FBrf0078422


1994
The FlyBase Consortium (1994)
FlyBase - The Drosophila database.
Nucleic Acids Res. 22(17):3456-3458 DOI:10.1093/nar/22.17.3456 FBrf0077015


Ashburner M and Drysdale R (1994)
FlyBase - The Drosophila genetic database.
Development 120:2077-2079 FBrf0072526


1993
Ashburner M (1993)
FlyBase.
GNome News 13:19-20 FBrf0058642

FlyBase Mission Statement

The aim of the FlyBase project is to provide an openly accessible centralized resource for Drosophila genetic, genomic and functional data.

FlyBase Licenses and Availability

FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://ftp.flybase.org/>.

FlyBase software is made available under either the MIT License (Expat) or the BSD 3-Clause.

All annotations and data produced by FlyBase that are accessible from flybase.org are distributed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). Different licensing and copyright terms may apply for data provided by these resources that are not distributed by FlyBase.

FlyBase adheres to the principle of full and unfettered data access to FlyBase data for the entire scientific community, and is a member of FAIRsharing. FlyBase is also is registered at the re3data.org repository and is an ELIXIR-UK service.

We are now members of the Global Biodata Coalition and our application is under review with Core Trust Seal.

The primary means of disseminating FlyBase data is through our web site (http://flybase.org) which provides an interface with many options for browsing, interrogating and manipulating FlyBase data according to the needs of the user. In addition, the web site links to our ftp site containing all FlyBase data in a variety of formats, including various sequence formats, archival data, and the entire FlyBase Chado database.

All FlyBase data are available for download to other resources without restriction. In addition to our web site, FlyBase shares data with other major genetic / genomic resources. Most notable among these are NCBI and UniProt. FlyBase is the authority source for data on D. melanogaster and provides files (including whole genome annotation GenBank submissions to NCBI) that are used to generate reference files such as RefSeq. D. melanogaster GenBank/RefSeq submissions are updated annually, and power users are encouraged to use these stable annotation sets in their analyses.

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FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement.

The information contained in this publication is subject to change without notice.

By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information.

Disclaimer

Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.

Herskowitz's Bibliography Copyright

The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:

"Bibliography on the genetics of Drosophila: Part 5, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1969 by Macmillan Publishing Company. "

"Bibliography on the genetics of Drosophila: Part 6, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1974 by Macmillan Publishing Company."

Lindsley and Zimm (1992)

Lindsley and Zimm (1992) - The New Redbook The Genome of Drosophila melanogaster Dan L. Lindsley & Georgianna G. Zimm Copyright 1992 By Academic Press, Inc. All Rights Reserved.

ISBN 0-12-450990-8 Academic Press, Inc. 1250 Sixth Avenue, San Diego, California 92101-4311

FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.

FlyBase Data Sources

The Red Book

Lindsley and Zimm (1992) The Genome of Drosophila melanogaster

Bibliographies

The major sources that have been incorporated into the FlyBase Bibliography:

Bibliography from The Genetics of Drosophila. T. H. Morgan, C. B. Bridges and A. H. Sturtevant, 1925. Bibliographica Genetica II: 1-262. 'S-Gravenhage, Martinus Nijhoff.
Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939. Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.
Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952. Commonwealth Agricultural Bureaux. Slough: Farnham Royal.
Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958. Indiana University Publications.
Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963. McGraw-Hill Book Company, Inc.
Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969. Macmillan Publishing Company, Inc.
Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974. Macmillan Publishing Company, Inc.
Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976. Drosophila Information Service 51: 159-193.
Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977. Drosophila Information Service 52:186-226.
Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978. Drosophila Information Service 53: 219-244.
Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980. Drosophila Information Service 55: 218-262.
Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981. Drosophila Information Service 56: 199-210.
Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982. Drosophila Information Service 58: 227-270.
Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983. Drosophila Information Service 59: 163-207.
Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).
Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965. Drosophila Information Service 40: 105-126.
Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982. Drosophila Information Service: 58: 215-226.
Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987. Drosophila Information Service 66: 198-208.
Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991. Drosophila Information Service 70: 110-117.
Bibliography on Drosophila ananassae. B. N. Singh, 1991. Drosophila Information Service 70: 205-211.
The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988. Dowden, Hutchinson and Ross Publications, Inc.
Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86). M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293. In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988. Blackie Publications. Glasgow, Scotland.
End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.
A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich). January 1993 with regular subsequent updates.
References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.
Japan Scientific Societies Press and Karger, Tokyo and Basel.
References from the Environmental Mutagen Information Center (EMIC) database.
MEDLINE (National Library of Medicine, Washington). Searching all fields with the text word DROSOPHIL* or MELANOGASTER. Searched from 1966 to date.
BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.
References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.
References from John Merriam's Genevent database of molecular data.
Drosophila records from the Zoological Record, volume 115 (1978) to 2008.
Jeff Hall's bibliography on neurogenetics of Drosophila.

External Databases

Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ) UniProtKB InterPro

Journal Articles and Books

Publications relevant to Drosophila from various journals and books.

Drosophila Conference Abstracts

The following abstracts were curated until 2008: GSA Annual Drosophila Research Conference Abstracts European Drosophila Research Conference Abstracts

Personal Communications to FlyBase

Information and observations provided by the Fly Community

Direct Submission of High-Throughput Data

Proteomics data
Center for Model Organism Proteomes --
(SystemsX and Research Priority Project of the University of Zurich, Switzerland)
Microarrays (Oligos, cDNAs)
Affymetrix, Santa Clara, CA (Affy v1, Affy v2)
Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)
Tiling BACs
Berkeley Drosophila Genome Project

Insertion Collection Data

Transgene insertion data
Gene Disruption Project (2005 - present)(Bellen et. al., 2004)
Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)
DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)
P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)
P{GawB} Project, GETDB, Japan (2002 - 2004)
NCI lethals (2002 - 2004)(Oh et. al., 2003)
P{GT1} Project, Ed Ryder, Cambridge, UK (2004)
Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)
Natural transposon insertion data
Kaminker J. et al. 2002
Quesneville H. et al. 2005

Stock Lists Submitted to FlyBase

Bloomington Drosophila Stock Center

Drosophila Genetic Resource Center

UC San Diego Drosophila Species Stock Center

Exelixis Drosophila Stock Collection at Harvard Medical School

Nusslein-Volhard laboratory

Garcia-Bellido laboratory

Carpenter laboratory

People

The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.

An e-mail address list compiled and maintained by Dr. John Haynie (1992)

Records of the Bloomington Drosophila Stock Center (1992)

The distribution list of Drosophila Information Newsletter (1992)

A subset of the Genetics Society of America's mailing and membership list (1992)

The mailing list for the European Drosophila Research Conference (1992)

FlyBase Alumni

FlyBase thanks these former members of the FlyBase consortium for their contribution: 

   Boris Adryan
   Julie Agapite
   Manish Anand
   Michael Ashburner
   Phill Baker
   Leyla Bayraktaroglu
   Ben Berman
   Brian Bettencourt
   Lee Bitsoi
   Pete Brokstein
   Stephanie Bunt
   Heather Butler
   Kathy Campbell
   Russell Collins
   Kim Cook
   Marta Costa
   Bryon Czoch
   Anthony DeAngelo
   Aubrey de Grey
   Rachel Drysdale
   David Emmert
   Kathleen Falls
   Silvie Fexova
   Helen Field
   Rebecca Foulger
   Erwin Frise
   Phani Garapati
   William Gelbart
   Mark Gibson
   Don Gilbert
   Gary Grumbling
   Janet Gulotta
   Cyrus Harmon
   Nomi Harris
   Gregg Helt
   Alex Holmes
   Pavel Hradecky
   Yanmei Huang
   Tamsin Jones
   Josh Kaminker
   Thomas Kaufman
   Kerry Knight
   Sophia Kossida
   Pravija Krishna
   Rob Kulathinal
   Julia Lamenza
   Joe Lemaire
   Stan Letovsky
   Suzanna Lewis
   Paul Leyland
   Guo-chun Liao
   Anne Loraine
   Kathy Matthews
   Glenn McAlpine
   Peter McQuilton
   John Merriam
   Sima Misra
   Emanuel Mongin
   Chris Mungall
   Tatiana Murnikova
   Catherine Nelson
   David Osumi-Sutherland
   Dawn Palmer
   Harriet Platero
   Laura Ponting
   Sinzi Pop
   Simon Prochnik
   Simon Reeve
   Alix Rey
   John Richter
   Wayne Rindone
   Margo Roark
   Gerry Rubin
   Susan St. Pierre
   Andrew Schroeder
   Ruth Seal
   Jolene Seme
   Carolyn Shemen
   Hardik Sheth
   Nihar Sheth
   Shengqiang Shu
   David Simas
   Chris Smith
   Frank Smutniak
   Nicole Staudt
   Ray Stefancsik
   Vitor Trovisco
   Jon Tupy
   Susan Tweedie
   Jose Maria Urbano
   Edwin Wang
   Eddy Wellbourne
   Maggie Werner-Washburne
   Eleanor Whitfield
   Colin Wiel
   Mark Williams
   Robert Wilson
   J.D. Wong
   Chihiro Yamada
   Mark Yandell
   Haiyan Zhang
   Peili Zhang

Grants Supporting FlyBase

1. "FlyBase: A Drosophila Genomic and Genetic Database" NHGRI Award #: U24HG013300

2. "GO annotation: maximizing the potential of Drosophila research to benefit human health" UK Medical Research Council Award #: MR/W024233/1

3. "BBSRC-NSF/BIO: Integrative analysis and Visualisation of Fly Cell Atlas datasets to enable cross-species comparisons" NSF Award #: 2035515 BBSRC Award #: BB/T014008/1

4. “Virtual Fly Brain” Wellcome Trust Award #: PLM13398

5. "Sustaining FlyBase: The Drosophila genomic and genetic database.“ NSF Award #: 2039324

6. "Alliance Central: A Platform for sustainable development of next generation genome knowledgebases" NHGRI Award #: U24HG010859

7. "Investigating metabolic responses to high sugar diets and the onset of diabetic phenotypes" NIDDK Award #: 1R01DK136945-01

8. FlyBase Users all over the world

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