Difference between revisions of "FlyBase:About"

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Line 70: Line 70:
:Valerie Wood, Seth Carbon, Midori A. Harris, Antonia Lock, Stacia R. Engel, David P. Hill, Kimberly Van Auken, Helen Attrill, Marc Feuermann, Pascale Gaudet, Ruth C. Lovering, Sylvain Poux, Kim M. Rutherford, Christopher J. Mungall (2020)
: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, Mungall CJ (2020)
:    '''Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.'''
:    '''Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.'''
:    [https://doi.org/10.1101/2020.04.21.045195 bioRxiv]
:    [https://doi.org/10.1101/2020.04.21.045195 bioRxiv]

Revision as of 12:42, 4 May 2020

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.

Biological Laboratories, Harvard University
16 Divinity Avenue
Cambridge, Massachusetts 02138
   Norbert Perrimon (PI)
   Susan Russo Gelbart (PD)
   Julie Agapite
   Kris Broll
   Lynn Crosby
   Gil dos Santos
   Kathleen Falls
   L. Sian Gramates
   Victoria Jenkins
   Ian Longden
   Beverley Matthews
   Carol Sutherland
   Christopher Tabone
   Pinglei Zhou
   Mark Zytkovicz
Department of Physiology, Development and Neuroscience, University of Cambridge
Downing Street, Cambridge CB2 3DY
   Nick Brown (PI)
   Giulia Antonazzo
   Helen Attrill
   Phani Garapati
   Aoife Larkin
   Steven Marygold
   Alex McLachlan
   Gillian Millburn
   Arzu Ozturk-Colak
   Clare Pilgrim
   Vitor Trovisco
Department of Biology, Indiana University
1001 East 3rd Street
Bloomington, Indiana 47405-7005
   Thomas Kaufman (PI)
   Brian Calvi (PI)
   Josh Goodman
   Victor Strelets
   Jim Thurmond
Department of Biology, Castetter Hall - Room 200
University of New Mexico,
Albuquerque, New Mexico 87131
   Maggie Werner-Washburne (PI)
   Richard Cripps (PI)
   Phillip Baker

FlyBase Publications

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, Mungall CJ (2020)
Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns.

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

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.

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

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

Garapati PV, Zhang J, Rey AJ and Marygold SJ (2019)
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase
Database 2019 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 (FBrf0241170)

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

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

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 (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 (FBrf0238904) (PMC5996772)

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 (FBrf0236248)

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

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 (FBrf0234415)

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

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 (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 (FBrf0233766) (PMC5107610)

Kahsai L, Millburn GH, Cook KR. (2016)
Phenotypes Associated with Second Chromosome P Element Insertions in Drosophila melanogaster.
G3 (Bethesda). 6(8):2665-2670 (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 (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 (FBrf0230602)

Lu J, Marygold SJ, Gharib WH and Suter B. (2015)
The aminoacyl-tRNA synthetases of Drosophila melanogaster.
Fly 9(2):53-61 (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 (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 (FBrf0229217)

Gene Ontology Consortium. (2015)
Gene Ontology Consortium: going forward.
Nucleic Acids Res. 43(Database issue):D1049-56

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 (FBrf0227324)

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

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

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

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

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 (FBrf0223749)

Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)
The Drosophila anatomy ontology.
J. Biomed. Semantics 4(1):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 (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 (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 (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 (FBrf0221415)

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

McQuilton P and the FlyBase Consortium (2012)
Opportunities for text mining in the FlyBase genetic literature curation workflow.
Database 2012: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 (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 (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 (FBrf0218533)

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

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 (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 (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

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

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 (FBrf0209611)

St. Pierre S and McQuilton P (2009)
Inside FlyBase (Biocuration as a career).
Fly 3(1):112-114 (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

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 (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 (FBrf0207486)

Drysdale R, and The FlyBase Consortium, (2008)
FlyBase : a database for the Drosophila research community.
Methods Mol. Biol. 420: 45-59 (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

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 (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 (FBrf0203012)

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 (FBrf0194786)

Drosophila 12 Genomes Consortium. (2007)
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450(7167):203-218 (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 (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 (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 (FBrf0200674)

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

Drysdale RA, Crosby MA and the FlyBase Consortium (2005)
FlyBase : Genes and gene models.
Nucleic Acids Res., 33: D390-D395 (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 (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. (FBrf0206380)

The FlyBase Consortium, (2003)
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res. 31:172-175 (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 (FBrf0167361)

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 (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 (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 (FBrf0155827)

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

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 (FBrf0137187)

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 (FBrf0107356)

The FlyBase Consortium (1998)
FlyBase - A Drosophila database.
Nucleic Acids Res. 26:85-88 (FBrf0100346)

The FlyBase Consortium (1997)
FlyBase - A Drosophila database.
Nucleic Acids Res. 25:63-66 (FBrf0093096)

The FlyBase Consortium (1996)
FlyBase - The Drosophila database.
Nucleic Acids Res. 24:53-56 (FBrf0085043)

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

The FlyBase Consortium (1994)
FlyBase - The Drosophila database.
Nucleic Acids Res. 22(17):3456-3458 (FBrf0077015)

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

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

Citing FlyBase

If you have used FlyBase during your research project, we urge you to cite us in your published work. We recommend that you use our latest Nucleic Acids Research:Database issue publication:

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

N.B. You should also state the FlyBase release (e.g. FB2018_06) used for any data obtained/analysed using FlyBase, as data content is updated with each web release. The current release number is found in the header and footer of every FlyBase page.

Information on citing genes or fly lines (alleles, deficiencies, transgenes, insertions) can be found in our Author Guidelines article.

Please see the related video tutorials How to cite FlyBase and Author Guidelines.

FlyBase Copyright

The Copyright of FlyBase

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/>.

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.

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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.

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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.

BIOSIS Copyright

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

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


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).
Searched on the Text Word DROSOPHIL. 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


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)

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

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   Paul Leyland
   Guo-chun Liao
   Anne Loraine
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