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FlyBase:About
2015-04-21T08:20:24Z
<p>Sjm41: /* FlyBase Consortium */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Giulia Antonazzo<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Alix Rey<br />
Nicole Staudt<br />
Ray Stefancsik<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2015'''<br />
<br />
:Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)<br />
: '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2014/11/14/nar.gku1099.abstract 10.1093/nar/gku1099]<br />
<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Representing kidney development using the gene ontology.'''<br />
: PLoS One. 9(6):e99864. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099864 10.1371/journal.pone.0099864]<br />
<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)<br />
: '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2014/11/14/nar.gku1099.abstract 10.1093/nar/gku1099]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
<br />
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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Harriet Platero<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Susan Tweedie<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Positions&diff=131447
FlyBase:FlyBase Positions
2015-03-18T09:51:22Z
<p>Sjm41: </p>
<hr />
<div>'''Genome Database Curator'''<br />
<br />
'''FlyBase, Harvard University'''<br />
<br />
FlyBase seeks a full-time scientific curator/annotator to join our team at the Gelbart Lab in the Department for Molecular and Cellular Biology, Harvard. Curational responsibilities at the Harvard site include the scanning and abstracting of scientific literature on the molecular biology of Drosophila, annotation and analysis of Drosophila genome(s), coordination of the inclusion of high-throughput molecular data sets into FlyBase, and design of improved interfaces for providing molecular data to users. Curators work as a part of a team, interacting with biologists at other FlyBase sites, and coordinating with software engineers to develop and improve software. Curators also interface with the scientific community, assisting users on line and at research conference workshops. FlyBase is constantly evolving, seeking both to improve and to expand its role within the Drosophila and wider scientific communities. This position is grant-funded.<br />
<br />
'''Basic Qualifications''': Ph.D. in molecular biology or genetics. Minimum three years experience with molecular genetics and Drosophila biology.<br />
<br />
'''Additional Qualifications''': Extensive Drosophilia research experience. Excellent communication skills in the English language, both written and oral. Enthusiasm, expertise and ideas concerning emerging directions in Drosophila biology and genomic/proteomic analysis. Familiarity with managing databases or spreadsheets and standardized formats (for example, GFF3, FASTA).<br />
<br />
'''To Apply''': Apply for this position at ASPIRE, the Harvard Recruitment Management System: https://jobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=34261BR<br />
<br />
In addition, please contact William Gelbart (gelbart<at>morgan.harvard.edu), and include a CV, a description of research experience and names of three references. Please cc your communication to senior curator Lynn Crosby (crosby<at>morgan.harvard.edu) and to the project administrative assistant, Carol Sutherland (casuther<at>fas.harvard.edu). <br />
<br />
<br />
<br />
Note: This page is for FlyBase positions only. If you would like to post a job opening, please use the [http://flybase.org/forums/viewforum.php?f=8 Job Postings] section withing our [http://flybase.org/forums/ FlyBase Forum]<br />
<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Positions&diff=131434
FlyBase:FlyBase Positions
2015-02-13T14:48:46Z
<p>Sjm41: </p>
<hr />
<div>'''Genome Database Curator'''<br />
<br />
'''FlyBase, Harvard University'''<br />
<br />
FlyBase seeks a full-time scientific curator/annotator to join our team at the Gelbart Lab in the Department for Molecular and Cellular Biology, Harvard. Curational responsibilities at the Harvard site include the scanning and abstracting of scientific literature on the molecular biology of Drosophila, annotation and analysis of Drosophila genome(s), coordination of the inclusion of high-throughput molecular data sets into FlyBase, and design of improved interfaces for providing molecular data to users. Curators work as a part of a team, interacting with biologists at other FlyBase sites, and coordinating with software engineers to develop and improve software. Curators also interface with the scientific community, assisting users on line and at research conference workshops. FlyBase is constantly evolving, seeking both to improve and to expand its role within the Drosophila and wider scientific communities. This position is grant-funded.<br />
<br />
'''Basic Qualifications''': Ph.D. in molecular biology or genetics. Minimum three years experience with molecular genetics and Drosophila biology.<br />
<br />
'''Additional Qualifications''': Extensive Drosophilia research experience. Excellent communication skills in the English language, both written and oral. Enthusiasm, expertise and ideas concerning emerging directions in Drosophila biology and genomic/proteomic analysis. Familiarity with managing databases or spreadsheets and standardized formats (for example, GFF3, FASTA).<br />
<br />
'''To Apply''': Apply for this position at ASPIRE, the Harvard Recruitment Management System: https://jobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=34261BR<br />
<br />
In addition, please contact William Gelbart (gelbart<at>morgan.harvard.edu), and include a CV, a description of research experience and names of three references. Please cc your communication to senior curator Lynn Crosby (crosby<at>morgan.harvard.edu) and to the project administrative assistant, Carol Sutherland (casuther<at>fas.harvard.edu). <br />
<br />
<br />
<br />
<br />
<br />
<br />
'''Drosophila Literature Analyst (part-time)'''<br />
<br />
'''FlyBase, University of Cambridge, UK'''<br />
<br />
FlyBase seeks a part-time (50-75%) literature analyst to join our group at the University of Cambridge, UK (www.gen.cam.ac.uk/research/flybase.html). This is an office-based post away from the bench, assisting fruit fly (Drosophila) research by contributing to the FlyBase database of genetic and genomic data.<br />
<br />
The primary aim of FlyBase-Cambridge is to identify biological data from scientific articles concerning Drosophila and to record these data in a systematic manner. Curated data are subsequently integrated into the FlyBase database and website to aid the international research community. The successful applicant will contribute to this effort in one or more ways, depending on their expertise. Possible roles include: rapid reading of Drosophila review articles to record genes mentioned therein; recording information about Drosophila models of human disease; focused analysis and annotation of sets of related genes: or contributing to revisions of existing data in the database.<br />
<br />
Essential skills/experience include:<br />
* a biological sciences degree<br />
* research experience using Drosophila<br />
* strong organizational skills and the ability to work with attention to detail<br />
* good communication skills<br />
* excellent English<br />
* strong self-motivation as well as the ability to work in a team<br />
<br />
Useful skills/experience include:<br />
* familiarity with databases<br />
* programming<br />
* annotation/curation experience<br />
<br />
<br />
Please see full advert here:<br />
http://www.jobs.cam.ac.uk/job/6158/<br />
<br />
<br />
<br />
<br />
Note: This page is for FlyBase positions only. If you would like to post a job opening, please use the [http://flybase.org/forums/viewforum.php?f=8 Job Postings] section withing our [http://flybase.org/forums/ FlyBase Forum]<br />
<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=131424
FlyBase:About
2015-01-14T10:48:29Z
<p>Sjm41: /* Citing FlyBase */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2015'''<br />
<br />
:Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)<br />
: '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2014/11/14/nar.gku1099.abstract 10.1093/nar/gku1099]<br />
<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Representing kidney development using the gene ontology.'''<br />
: PLoS One. 9(6):e99864. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099864 10.1371/journal.pone.0099864]<br />
<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)<br />
: '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2014/11/14/nar.gku1099.abstract 10.1093/nar/gku1099]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
<br />
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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Harriet Platero<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Susan Tweedie<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=131423
FlyBase:About
2015-01-14T10:45:14Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2015'''<br />
<br />
:Dos Santos G, Schroeder AJ, Goodman JL, Strelets VB, Crosby MA, Thurmond J, Emmert DB, Gelbart WM; the FlyBase Consortium. (2015)<br />
: '''FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2014/11/14/nar.gku1099.abstract 10.1093/nar/gku1099]<br />
<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Representing kidney development using the gene ontology.'''<br />
: PLoS One. 9(6):e99864. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099864 10.1371/journal.pone.0099864]<br />
<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
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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.<br />
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Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Harriet Platero<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Susan Tweedie<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
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<p>Sjm41: Adding FB-Cam 'Gene function analyst' advert</p>
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<div>'''Genome Database Curator'''<br />
<br />
'''FlyBase, Harvard University'''<br />
<br />
FlyBase seeks a full-time scientific curator/annotator to join our team at the Gelbart Lab in the Department for Molecular and Cellular Biology, Harvard. Curational responsibilities at the Harvard site include the scanning and abstracting of scientific literature on the molecular biology of Drosophila, annotation and analysis of Drosophila genome(s), coordination of the inclusion of high-throughput molecular data sets into FlyBase, and design of improved interfaces for providing molecular data to users. Curators work as a part of a team, interacting with biologists at other FlyBase sites, and coordinating with software engineers to develop and improve software. Curators also interface with the scientific community, assisting users on line and at research conference workshops. FlyBase is constantly evolving, seeking both to improve and to expand its role within the Drosophila and wider scientific communities. This position is grant-funded.<br />
<br />
'''Basic Qualifications''': Ph.D. in molecular biology or genetics. Minimum three years experience with molecular genetics and Drosophila biology.<br />
<br />
'''Additional Qualifications''': Extensive Drosophilia research experience. Excellent communication skills in the English language, both written and oral. Enthusiasm, expertise and ideas concerning emerging directions in Drosophila biology and genomic/proteomic analysis. Familiarity with managing databases or spreadsheets and standardized formats (for example, GFF3, FASTA).<br />
<br />
'''To Apply''': Apply for this position at ASPIRE, the Harvard Recruitment Management System: https://jobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=34261BR<br />
<br />
In addition, please contact William Gelbart (gelbart<at>morgan.harvard.edu), and include a CV, a description of research experience and names of three references. Please cc your communication to senior curator Lynn Crosby (crosby<at>morgan.harvard.edu) and to the project administrative assistant, Carol Sutherland (casuther<at>fas.harvard.edu). <br />
<br />
<br />
<br />
<br />
<br />
'''Gene Function Analyst'''<br />
<br />
'''FlyBase, University of Cambridge, UK'''<br />
<br />
FlyBase seeks a research assistant/associate to join our group at the University of Cambridge, UK. This is a fly-related post away from the bench, assisting Drosophila research by contributing to the FlyBase database of genetic and genomic data. If you have been frustrated by the lack of simple summaries of fly gene function in the FlyBase gene reports, here is your opportunity to fix that, by soliciting, editing and writing such summaries.<br />
<br />
The primary aim of FlyBase-Cambridge is to identify biological data from scientific articles concerning Drosophila and to record these data in a systematic manner. Curated data are subsequently integrated into the FlyBase database and website to aid the international research community. The successful applicant will contribute to this effort by editing and writing short gene function summaries, and also making sure these functions are represented with the standardized terms of Gene Ontology annotation (http://www.geneontology.org). Liaison with other members of the Gene Ontology consortium will ensure accurate and up to date annotations.<br />
<br />
Depending on their previous experience, the successful applicant may also highlight sets of genes involved in a pathway or function, or liaise with the Drosophila research community and FlyBase's software developers to improve the display and searching of Gene Function and Gene Ontology annotations in FlyBase.<br />
<br />
Please see full advert here:<br />
http://www.jobs.cam.ac.uk/job/5805/<br />
<br />
<br />
<br />
Note: This page is for FlyBase positions only. If you would like to post a job opening, please use the [http://flybase.org/forums/viewforum.php?f=8 Job Postings] section withing our [http://flybase.org/forums/ FlyBase Forum]<br />
<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=131394
FlyBase:About
2014-12-17T08:42:58Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Representing kidney development using the gene ontology.'''<br />
: PLoS One. 9(6):e99864. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099864 10.1371/journal.pone.0099864]<br />
<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
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<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Harriet Platero<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Susan Tweedie<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=131388
FlyBase:About
2014-12-08T09:22:50Z
<p>Sjm41: /* FlyBase Alumni */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
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William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
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L. Sian Gramates<br />
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<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
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:UK<br />
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<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
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Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
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The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Harriet Platero<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Susan Tweedie<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=131387
FlyBase:About
2014-12-08T09:22:10Z
<p>Sjm41: /* FlyBase Consortium */ removed Susan Tweedie from FB-Cam list</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
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<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Harriet Platero<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=131366
FlyBase:Nomenclature
2014-12-02T07:30:17Z
<p>Sjm41: Removed section 2.6.9 - no need for 'genes encoding ribosomal proteins' to be listed as a special nomenclature case.</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Reference to genomic location.''' Reference to a gene's genomic sequence coordinates (e.g. 'Chr2L:4.35M' or '3R:415067') in its symbol or name is prohibited. Reference to a gene's cytological location (e.g. '36E' or '88B7') or chromosomal location (e.g. '2' or 'chr2L') in its symbol or name is discouraged.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. lncRNA genes.''' Genes encoding long non-coding RNAs have symbols of the format 'lncRNA-N', where N is a unique identifier.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase (also see [http://flybase.org/reports/FBrf0225080 Pfeiffer, 2014]):<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! AA change compared to FLPG5<br />
! Primary reference<br />
|-<br />
| FLPG5<br />
| -<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPD5<br />
| G5D<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| G5D, K82Y, V226A<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| G5D, R281Y<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| G5D, A36T, T50A, K82Y, G109N, E150G, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| G5D, A36T, T50A, K82Y, G109N, T176A, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| P2S, G5D, L33S, Y108N, S294P<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| G5D, F70L<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=131111
FlyBase:About
2014-09-19T06:44:51Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
: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)<br />
: '''Overview of the gene ontology task at BioCreative IV.'''<br />
: Database 2014. bau086 doi: [http://database.oxfordjournals.org/content/2014/bau086.long 10.1093/database/bau086]<br />
<br />
<br />
: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)<br />
: '''BC4GO: a full-text corpus for the BioCreative IV GO Task.'''<br />
: Database 2014. bau074 doi: [http://database.oxfordjournals.org/content/2014/bau074.long 10.1093/database/bau074]<br />
<br />
<br />
:Cejuela, JM, McQuilton P, Ponting L, Marygold, SJ, Stefancsik R, Millburn GH, Rost B, and the FlyBase Consortium (2014)<br />
: '''tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.'''<br />
: Database 2014. bau033 doi: [http://database.oxfordjournals.org/content/2014/bau033.full 10.1093/database/bau033]<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: '''The Drosophila anatomy ontology.'''<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: '''The Drosophila phenotype ontology.'''<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: '''On the reproducibility of science: unique identification of research resources in the biomedical literature.'''<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: '''FlyBase: improvements to the bibliography.''' <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: '''Systematic analysis of experimental phenotype data reveals gene functions.''' <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: '''Gene Ontology annotations and resources.''' <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: '''Opportunities for text mining in the FlyBase genetic literature curation workflow.''' <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: '''Directly e-mailing authors of newly published papers encourages community curation.''' <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: '''FlyBase 101 – the basics of navigating FlyBase.''' <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: '''Automatic categorization of diverse experimental information in the bioscience literature.'''<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: '''The Gene Ontology: enhancements for 2011.'''<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: '''Toward an interactive article: integrating journals and biological databases.'''<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: '''The representation of heart development in the gene ontology.'''<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: '''The Gene Ontology in 2010: extensions and refinements.'''<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: '''FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.'''<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: '''Inside FlyBase (Biocuration as a career).'''<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: '''The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.'''<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: '''FlyBase: enhancing Drosophila Gene Ontology annotations.'''<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: '''The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.'''<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: '''FlyBase : a database for the Drosophila research community.'''<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: '''Big data: The future of biocuration.'''<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: '''Natural language processing in aid of FlyBase curators.'''<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: '''FlyBase: integration and improvements to query tools.'''<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: '''FlyBase: genomes by the dozen.'''<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: '''Evolution of genes and genomes on the Drosophila phylogeny.'''<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: '''Integrating natural language processing with FlyBase curation.'''<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: '''Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.'''<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: '''A Chado case study: an ontology-based modular schema for representing genome-associated biological information.'''<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: '''Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.'''<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: '''FlyBase: anatomical data, images and queries.'''<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: '''FlyBase : Genes and gene models.'''<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: '''Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.'''<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: '''Using chado to store genome annotation data.'''<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: '''The Drosophila melanogaster genome sequencing and annotation projects: A status report.'''<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: '''An integrated computational pipeline and database to support whole-genome sequence annotation.'''<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: '''Apollo: a sequence annotation editor.'''<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: '''Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.'''<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: '''Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.'''<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: '''Phenotypic data in FlyBase.'''<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: '''FlyBase: Genomic and post-genomic viewpoints.'''<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: '''The FlyBase Database of the Drosophila Genome Projects and community literature.'''<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: '''FlyBase - A Drosophila database.'''<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: '''Proposed genetic nomenclature for Drosophila melanogaster.'''<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: '''FlyBase - The Drosophila database.'''<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: '''FlyBase - The Drosophila genetic database.'''<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: '''FlyBase.'''<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
: '''FlyBase 102 - advanced approaches to interrogating FlyBase.'''<br />
: Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
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===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
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"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Kathy Matthews<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Susan St. Pierre<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]<br />
[[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=131097
FlyBase:Nomenclature
2014-09-16T08:32:20Z
<p>Sjm41: d</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Reference to genomic location.''' Reference to a gene's genomic sequence coordinates (e.g. 'Chr2L:4.35M' or '3R:415067') in its symbol or name is prohibited. Reference to a gene's cytological location (e.g. '36E' or '88B7') or chromosomal location (e.g. '2' or 'chr2L') in its symbol or name is discouraged.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. lncRNA genes.''' Genes encoding long non-coding RNAs have symbols of the format 'lncRNA-N', where N is a unique identifier.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
'''<span id="2.6.9">2.6.9</span>. Ribosomal protein genes.''' Genes encoding ribosomal proteins are named based on orthology to their mammalian counterparts. Genes encoding cytoplasmic ribosomal proteins have symbols of the format 'RpSn' or 'RpLn', where S denotes a gene encoding a protein of the small subunit and L a gene encoding a protein of the large subunit, and n is a number reflecting orthology, e.g., [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0261592.html ''RpS6'']. Genes encoding mitochondrial ribosomal proteins have symbols of a similar format and are prefixed with 'm', e.g., [http://flybase.org/reports/FBgn0037566.html ''mRpL1''], [http://flybase.org/reports/FBgn0031639.html ''mRpS2'']. Some ribosomal proteins are encoded by duplicate genes; these are distinguished by using a a or b suffix, e.g., [http://flybase.org/reports/FBgn0004403.html ''RpS14a''] and [http://flybase.org/reports/FBgn0004404.html ''RpS14b'']. Some ribosomal protein genes were originally named after a mutant phenotype, e.g. [http://flybase.org/reports/FBgn0003714.html ''tko'']; these have been retained as the approved gene symbols/names in FlyBase.<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase (also see [http://flybase.org/reports/FBrf0225080 Pfeiffer, 2014]):<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! AA change compared to FLPG5<br />
! Primary reference<br />
|-<br />
| FLPG5<br />
| -<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPD5<br />
| G5D<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| G5D, K82Y, V226A<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| G5D, R281Y<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| G5D, A36T, T50A, K82Y, G109N, E150G, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| G5D, A36T, T50A, K82Y, G109N, T176A, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| P2S, G5D, L33S, Y108N, S294P<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| G5D, F70L<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=131096
FlyBase:Nomenclature
2014-09-16T08:00:07Z
<p>Sjm41: Added section 2.6.6 with basic 'lncRNA' nomenclature convention.</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Italicization.''' All gene symbols and names should be italicized.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. lncRNA genes.''' Genes encoding long non-coding RNAs have symbols of the format 'lncRNA-N', where N is a unique identifier.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
'''<span id="2.6.9">2.6.9</span>. Ribosomal protein genes.''' Genes encoding ribosomal proteins are named based on orthology to their mammalian counterparts. Genes encoding cytoplasmic ribosomal proteins have symbols of the format 'RpSn' or 'RpLn', where S denotes a gene encoding a protein of the small subunit and L a gene encoding a protein of the large subunit, and n is a number reflecting orthology, e.g., [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0261592.html ''RpS6'']. Genes encoding mitochondrial ribosomal proteins have symbols of a similar format and are prefixed with 'm', e.g., [http://flybase.org/reports/FBgn0037566.html ''mRpL1''], [http://flybase.org/reports/FBgn0031639.html ''mRpS2'']. Some ribosomal proteins are encoded by duplicate genes; these are distinguished by using a a or b suffix, e.g., [http://flybase.org/reports/FBgn0004403.html ''RpS14a''] and [http://flybase.org/reports/FBgn0004404.html ''RpS14b'']. Some ribosomal protein genes were originally named after a mutant phenotype, e.g. [http://flybase.org/reports/FBgn0003714.html ''tko'']; these have been retained as the approved gene symbols/names in FlyBase.<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase (also see [http://flybase.org/reports/FBrf0225080 Pfeiffer, 2014]):<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! AA change compared to FLPG5<br />
! Primary reference<br />
|-<br />
| FLPG5<br />
| -<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPD5<br />
| G5D<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| G5D, K82Y, V226A<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| G5D, R281Y<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| G5D, A36T, T50A, K82Y, G109N, E150G, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| G5D, A36T, T50A, K82Y, G109N, T176A, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| P2S, G5D, L33S, Y108N, S294P<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| G5D, F70L<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=125580
FlyBase:Nomenclature
2014-05-27T06:46:41Z
<p>Sjm41: /* FLPase construct symbols. */</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Italicization.''' All gene symbols and names should be italicized.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Ribosomal protein genes.''' Genes encoding ribosomal proteins are named based on orthology to their mammalian counterparts. Genes encoding cytoplasmic ribosomal proteins have symbols of the format 'RpSn' or 'RpLn', where S denotes a gene encoding a protein of the small subunit and L a gene encoding a protein of the large subunit, and n is a number reflecting orthology, e.g., [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0261592.html ''RpS6'']. Genes encoding mitochondrial ribosomal proteins have symbols of a similar format and are prefixed with 'm', e.g., [http://flybase.org/reports/FBgn0037566.html ''mRpL1''], [http://flybase.org/reports/FBgn0031639.html ''mRpS2'']. Some ribosomal proteins are encoded by duplicate genes; these are distinguished by using a a or b suffix, e.g., [http://flybase.org/reports/FBgn0004403.html ''RpS14a''] and [http://flybase.org/reports/FBgn0004404.html ''RpS14b'']. Some ribosomal protein genes were originally named after a mutant phenotype, e.g. [http://flybase.org/reports/FBgn0004867.html ''sop''] or [http://flybase.org/reports/FBgn0003714.html ''tko'']; these have been retained as the approved gene symbols/names in FlyBase.<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase (also see [http://flybase.org/reports/FBrf0225080 Pfeiffer, 2014]):<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! AA change compared to FLPG5<br />
! Primary reference<br />
|-<br />
| FLPG5<br />
| -<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPD5<br />
| G5D<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| G5D, K82Y, V226A<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| G5D, R281Y<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| G5D, A36T, T50A, K82Y, G109N, E150G, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| G5D, A36T, T50A, K82Y, G109N, T176A, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| P2S, G5D, L33S, Y108N, S294P<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| G5D, F70L<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=125579
FlyBase:Nomenclature
2014-05-20T09:58:06Z
<p>Sjm41: /* FLPase construct symbols. */</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Italicization.''' All gene symbols and names should be italicized.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Ribosomal protein genes.''' Genes encoding ribosomal proteins are named based on orthology to their mammalian counterparts. Genes encoding cytoplasmic ribosomal proteins have symbols of the format 'RpSn' or 'RpLn', where S denotes a gene encoding a protein of the small subunit and L a gene encoding a protein of the large subunit, and n is a number reflecting orthology, e.g., [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0261592.html ''RpS6'']. Genes encoding mitochondrial ribosomal proteins have symbols of a similar format and are prefixed with 'm', e.g., [http://flybase.org/reports/FBgn0037566.html ''mRpL1''], [http://flybase.org/reports/FBgn0031639.html ''mRpS2'']. Some ribosomal proteins are encoded by duplicate genes; these are distinguished by using a a or b suffix, e.g., [http://flybase.org/reports/FBgn0004403.html ''RpS14a''] and [http://flybase.org/reports/FBgn0004404.html ''RpS14b'']. Some ribosomal protein genes were originally named after a mutant phenotype, e.g. [http://flybase.org/reports/FBgn0004867.html ''sop''] or [http://flybase.org/reports/FBgn0003714.html ''tko'']; these have been retained as the approved gene symbols/names in FlyBase.<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase (also see [Pfeiffer, 2014]):<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! AA change compared to FLPG5<br />
! Primary reference<br />
|-<br />
| FLPG5<br />
| -<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPD5<br />
| G5D<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| G5D, K82Y, V226A<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| G5D, R281Y<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| G5D, A36T, T50A, K82Y, G109N, E150G, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| G5D, A36T, T50A, K82Y, G109N, T176A, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| P2S, G5D, L33S, Y108N, S294P<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| G5D, F70L<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=125578
FlyBase:Nomenclature
2014-05-20T09:37:54Z
<p>Sjm41: /* FLPase construct symbols. */ Adding amino acid changes</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Italicization.''' All gene symbols and names should be italicized.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Ribosomal protein genes.''' Genes encoding ribosomal proteins are named based on orthology to their mammalian counterparts. Genes encoding cytoplasmic ribosomal proteins have symbols of the format 'RpSn' or 'RpLn', where S denotes a gene encoding a protein of the small subunit and L a gene encoding a protein of the large subunit, and n is a number reflecting orthology, e.g., [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0261592.html ''RpS6'']. Genes encoding mitochondrial ribosomal proteins have symbols of a similar format and are prefixed with 'm', e.g., [http://flybase.org/reports/FBgn0037566.html ''mRpL1''], [http://flybase.org/reports/FBgn0031639.html ''mRpS2'']. Some ribosomal proteins are encoded by duplicate genes; these are distinguished by using a a or b suffix, e.g., [http://flybase.org/reports/FBgn0004403.html ''RpS14a''] and [http://flybase.org/reports/FBgn0004404.html ''RpS14b'']. Some ribosomal protein genes were originally named after a mutant phenotype, e.g. [http://flybase.org/reports/FBgn0004867.html ''sop''] or [http://flybase.org/reports/FBgn0003714.html ''tko'']; these have been retained as the approved gene symbols/names in FlyBase.<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase:<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! AA change compared to FLPG5<br />
! Primary reference<br />
|-<br />
| FLPG5<br />
| -<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPD5<br />
| G5D<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| G5D, K82Y, V226A<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| G5D, R281Y<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| G5D, A36T, T50A, K82Y, G109N, E150G, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| G5D, A36T, T50A, K82Y, G109N, T176A, R281V<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| P2S, G5D, L33S, Y108N, S294P<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| G5D, F70L<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Nomenclature&diff=125577
FlyBase:Nomenclature
2014-05-20T09:14:43Z
<p>Sjm41: /* Transposons and Transgene Constructs */ Added new section 4.5 on FLPase construct nomenclature</p>
<hr />
<div><br />
<br />
'''<big><big>Preamble</big></big>'''<br />
<br />
The nomenclature guidelines below explain how FlyBase assigns canonical symbols and names to its genetic objects (genes, alleles, transposons, insertions, aberrations and balancers). We encourage the community and journals to adhere to FlyBase-approved symbols/names for consistency in published datasets. While these guidelines cover most circumstances, there may be exceptional cases not clearly covered here. Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact FlyBase] to discuss such cases or any other aspect of the nomenclature.<br />
<br />
==Policy for establishing FlyBase-approved gene symbols and names ==<br />
<br />
===Justification for unique approved symbols/names. === <br />
It is of great value to the research community that there is a single officially sanctioned (approved) symbol and name for each gene in FlyBase. Use of unique symbols/names, together with corresponding unique identifiers (e.g., FBgn numbers) minimizes ambiguity in referring to these genes in the scientific literature.<br />
<br />
===Assigning approved symbols/names.===<br />
It is inevitable that multiple synonyms for a gene arise in the literature, typically as a result of publications on the same gene by multiple laboratories or the realization that genes previously thought to be independent are actually part of the same genetic unit. In such cases, FlyBase adheres to the following rules for establishing or changing the approved gene symbol/name.<br />
<br />
'''<span id="1.2.1">1.2.1</span>. Chronological precedence.''' Approved gene symbols/names are normally established by the earliest date of publication of the proposed symbol/name in a peer-reviewed primary research paper. (No other form of publication is relevant to chronological precedence.)<br />
<br />
'''<span id="1.2.2">1.2.2</span>. Selection of lower or upper case of initial letter.''' Gene symbols/names begin with a lowercase letter if the gene is FIRST named for the phenotype of a recessive mutant allele, and begin with an uppercase letter if they are FIRST named for the phenotype of a dominant mutant allele. Gene symbols/names also begin with an uppercase letter if they are FIRST named for an aspect of the wild-type molecular function or activity of the gene product, which includes genes named after an ortholog or paralog.<br />
<br />
'''<span id="1.2.3">1.2.3</span>. Community usage.''' The chronological precedence and capitalization rules can be overridden in favor of an alternative gene symbol/name that is clearly favored by the research community. This can be on a gene-by-gene basis or to rationalize the nomenclature for an entire gene family or other functional grouping.<br />
<br />
'''<span id="1.2.4">1.2.4</span>. Placeholders.''' Certain classes of generic gene symbols/names are placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) and are subject to replacement by a more meaningful symbol/name according to the rules of [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.5|1.2.5]]. However, generic symbols/names based on a phenotype shall be retained by FlyBase if they are re-used by the first peer-reviewed research paper to characterize that gene and/or are clearly favored by the research community.<br />
<br />
'''<span id="1.2.5">1.2.5</span>. Validity criteria.''' Authors' preferred symbols/names will be used as the FlyBase-approved gene symbols/names whenever possible. However, the validity criteria set out in section [[FlyBase:Nomenclature#Requirements of FlyBase-approved Drosophila gene symbols and names.|2.2]] must be adhered to, and FlyBase will modify authors' preferred gene symbols/names where necessary.<br />
<br />
==Gene symbols and names ==<br />
<br />
===Symbols versus names.===<br />
The gene ''symbol'' is typically an abbreviation of the full ''gene name'' and as such, should ordinarily consist of a minimal number of characters. The gene symbol and name should use comparable capitalization and character sets.<br />
<br />
===Requirements of FlyBase-approved Drosophila gene symbols and names.===<br />
<br />
'''<span id="2.2.1">2.2.1</span>. Uniqueness.''' Each approved gene symbol and name must be unique amongst all FlyBase-approved symbols and names.<br />
<br />
'''<span id="2.2.2">2.2.2</span>. Relevance.''' The name should allude to the gene's function, mutant phenotype or other relevant characteristic.<br />
<br />
'''<span id="2.2.3">2.2.3</span>. Restricted and non-permissible characters.''' There are several characters which have specific meanings in a genotype string. Use of these characters in a gene symbol would complicate interpretation of genotypes. Therefore, approved gene symbols shall adhere to the following rules:<br />
<br />
'''<span id="2.2.3.1">2.2.3.1</span>.''' Approved symbols shall not contain the following characters: /, \, {, }, <, >, [, ], ;, *.<br />
<br />
'''<span id="2.2.3.2">2.2.3.2</span>. Approved symbols shall not contain spaces.''' Where a separator is needed to keep characters from losing meaning by running together, a hyphen "-" should be used.<br />
<br />
'''<span id="2.2.3.3">2.2.3.3</span>.''' Approved symbols shall not contain letters from any character sets other than English or Greek.<br />
<br />
'''<span id="2.2.3.4">2.2.3.4</span>.''' Colons ":" shall only be used in the approved symbols of certain classes of non-protein-coding genes, genes encoded in the mitochondrial genome, and synthetic fusion genes, as described in section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
'''<span id="2.2.3.5">2.2.3.5</span>.''' Round brackets "( )" shall only be used in certain classes of approved gene symbols as separators to designate a chromosome or an allele whose phenotype is modified by the gene in question.<br />
<br />
'''<span id="2.2.4">2.2.4</span>. Capitalization.''' The rules governing the capitalization of the initial letter of gene symbols/names are described in sections [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.3|1.2.3]] Subsequent letters are normally lowercase.<br />
<br />
'''<span id="2.2.5">2.2.5</span>. Superscripts and subscripts.''' Gene symbols and names should not normally contain superscripts or subscripts. The only exception is when an allele name is an integral part of a gene symbol or name, e.g., [http://flybase.org/reports/FBgn0003638.html ''su(w<sup>a</sup>)''].<br />
<br />
'''<span id="2.2.6">2.2.6</span>. Italicization.''' All gene symbols and names should be italicized.<br />
<br />
'''<span id="2.2.7">2.2.7</span>. Genus/species prefixes.''' Genes from all species, except ''D. melanogaster'', automatically get a unique species abbreviation prefix appended to their FlyBase-approved symbol (see section [[FlyBase:Nomenclature#2.5.1|2.5.1]]). Any different/additional indication of a gene's origin (e.g. D, Dro or Dm) is redundant and/or ambiguous and will not form part of the FlyBase-approved gene symbol/name.<br />
<br />
'''<span id="2.2.8">2.2.8</span>.''' Symbols and names must be inoffensive.<br />
<br />
===Common prefixes===<br />
<br />
'''<span id="2.3.1">2.3.1</span>. Prefixes based on phenotype, EST or STS.''' Several generic gene symbol/name prefixes have been used for genes sharing a common mutant phenotype or originally identified by virtue of an EST or STS. A non-exhaustive list is shown below: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Class<br />
! Prefix used in gene symbol *<br />
|-<br />
| anonymous gene<br />
| ''anon-''<br />
|-<br />
| Berkeley Drosophila Genome Project<br />
| ''BEST:''<br />
|-<br />
| EST cluster-based gene<br />
| <br />
|-<br />
| enhancer<br />
| ''e(a)m, E(a)m''<br />
|-<br />
| European Drosophila Genome Project STS-based gene<br />
| ''ESTS:''<br />
|-<br />
| female sterile<br />
| ''fs(n)m, Fs(n)m''<br />
|-<br />
| lethal<br />
| ''l(n)m'' <br />
|-<br />
| male sterile<br />
| ''ms(n)m, Ms(n)m''<br />
|-<br />
| male & female sterile<br />
| ''mfs(n)m, Mfs(n)m''<br />
|-<br />
| maternal<br />
| ''mat(n)m, Mat(n)m''<br />
|-<br />
| meiotic mutant<br />
| ''mei-''<br />
|-<br />
| Minute <br />
| ''M(n)m''<br />
|-<br />
| mitotic mutant<br />
| ''mit(n)m, Mit(n)m''<br />
|-<br />
| mutagen sensitive<br />
| ''mus''<br />
|-<br />
| NIDDK EST Project-based gene <br />
| ''NEST:''<br />
|-<br />
| resistance <br />
| ''rst(n)m, Rst(n)m''<br />
|-<br />
| suppressor <br />
| ''su(a)m, Su(a)m''<br />
|-<br />
| 'tumor' <br />
| ''tu(n)m, Tu(n)m''<br />
|- <br />
|}<br />
''*'' ''n'' designates the chromosome, ''m'' a distinguishing symbol, and ''a'' a gene whose phenotype is modified by an enhancer or suppressor <br />
<br />
Gene symbols/names using these generic prefixes are placeholders and are subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]]. <br />
<br />
'''<span id="2.3.2">2.3.2</span>. Prefixes based on common molecular function.''' Genes encoding products of similar molecular function may be given symbols/names with identical prefixes and unique suffixes. This is to be encouraged and FlyBase will rationalize the nomenclature for an entire gene family or other functional grouping if favored by the research community. Historically, the unique suffix may refer to a gene's cytological location (e.g. [http://flybase.org/reports/FBgn0000042.html ''Actin-5C''], [http://flybase.org/reports/FBgn0000043.html ''Actin-42A''], [http://flybase.org/reports/FBgn0000044.html ''Actin-57B''] etc). More recently, the unique suffix may simply be an incremental numerical value (e.g. [http://flybase.org/reports/FBgn0067861.html ''Sdic1''], [http://flybase.org/reports/FBgn0053497.html ''Sdic2''], [http://flybase.org/reports/FBgn0052823.html ''Sdic3''] etc.), or reflect some other distinguishing feature, such as orthology with a reference data set (e.g. [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0003279.html ''RpL4''], [http://flybase.org/reports/FBgn0064225.html ''RpL5''] etc.). Also see section [[FlyBase:Nomenclature#Special cases.|2.6]].<br />
<br />
===Annotation IDs.===<br />
Gene annotation IDs, which are distinct from gene symbols, exist for all molecularly defined gene models in the 12 sequenced species of Drosophila.<br />
<br />
'''<span id="2.4.1">2.4.1</span>. Format.''' Annotation IDs are represented in a common way: a species-specific 2 letter prefix followed by a four or five digit integer. For historical reasons, there are two 2-letter prefixes for ''D. melanogaster'': CG for protein-coding genes and CR for non-protein-coding-genes. For all other species, there is a single two-letter code to be used for gene models, regardless of which class of gene they identify. <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Prefix<br />
! Species<br />
|-<br />
| CG, CR <br />
| ''Drosophila melanogaster'' <br />
|-<br />
| GA<br />
| ''Drosophila pseudoobscura pseudoobscura''<br />
|-<br />
| GD<br />
| ''Drosophila simulans''<br />
|-<br />
| GE<br />
| ''Drosophila yakuba''<br />
|-<br />
| GF<br />
| ''Drosophila ananassae''<br />
|-<br />
| GG<br />
| ''Drosophila erecta''<br />
|-<br />
| GH<br />
| ''Drosophila grimshawi''<br />
|-<br />
| GI<br />
| ''Drosophila mojavensis''<br />
|-<br />
| GJ<br />
| ''Drosophila virilis''<br />
|-<br />
| GK<br />
| ''Drosophila willistoni''<br />
|-<br />
| GL<br />
| ''Drosophila persimilis'' <br />
|-<br />
| GM<br />
| ''Drosophila sechellia'' <br />
|-<br />
|}<br />
<br />
'''<span id="2.4.2">2.4.2</span>. Use as approved gene symbols.''' In the absence of other information, the annotation ID is used as a placeholder for the gene symbol (while the gene name field is left blank) and is subject to replacement by a more meaningful symbol/name according to the rules set out in sections [[FlyBase:Nomenclature#1.2.1|1.2.1]], [[FlyBase:Nomenclature#1.2.2|1.2.2]] and [[FlyBase:Nomenclature#1.2.4|1.2.4]].<br />
<br />
===Approved gene symbols/names for non-''D. melanogaster'' genes.===<br />
FlyBase includes genes from all species of Drosophilidae plus genes from other species that have been introduced into Drosophila.<br />
<br />
'''<span id="2.5.1">2.5.1</span>. Species abbreviation prefixes.''' For species other than ''Drosophila melanogaster'', the FlyBase-approved gene symbol follows a species abbreviation indicating the species of origin. The prefix has the form 'Nnnn\', where N is the initial letter of the genus and nnn is a unique code for a given species of that genus, usually the first three letters of the species name. (For example, Dsim is the species abbreviation for ''Drosophila simulans''.) A complete list of valid abbreviations is available on the [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] page. By convention, a 'Dmel' prefix is not used for ''D. melanogaster'' gene symbols in FlyBase (unless this is important in context). Gene names are not prefixed with species information.<br />
<br />
'''<span id="2.5.2">2.5.2</span>. Approved gene symbols/names.''' The FlyBase-approved gene symbols/names may correspond to the meaningful symbol/name of the ''D. melanogaster'' orthologs, distinguished by the relevant species prefix (as described in [[FlyBase:Nomenclature#2.5.1|2.5.1]]). (It should be noted that the assignment of orthology can be problematic in the absence of whole genome sequence information.) ''D. melanogaster'' gene symbols/names that are defined as placeholders (see sections [[FlyBase:Nomenclature#2.3.1|2.3.1]] and [[FlyBase:Nomenclature#Annotation IDs.|2.4]]) or contain ''D. melanogaster''-specific cytological information should not be used as the symbols/names of orthologs in other species.<br />
<br />
===Special cases.===<br />
<br />
'''<span id="2.6.1">2.6.1</span>. rRNA genes.''' Genes encoding ribosomal RNAs have symbols of the format 'nSrRNA', where n denotes the respective rRNA's sedimentation rate in Svedberg units, e.g., [http://flybase.org/reports/FBgn0061474.html ''28SrRNA'']. By historical convention, the locus containing the genes encoding the 5.8SrRNA, 18SrRNA and 28SrRNA is called [http://flybase.org/reports/FBgn0000164.html ''bobbed (bb)''].<br />
<br />
'''<span id="2.6.2">2.6.2</span>. tRNA genes.''' Genes encoding transfer RNAs have symbols of the format 'tRNA:Xn:m', where X is the 1-letter amino-acid code (in upper-case); n is a number signifying the particular isoform; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish between functionally similar tRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0011984.html ''tRNA:S7:23Ea''].<br />
<br />
'''<span id="2.6.3">2.6.3</span>. snRNA genes.''' Genes encoding small nuclear RNAs have symbols of the format 'snRNA:XX:ma', where XX is the type of snRNA; m is the cytogenetic map position of the gene; and a (if used) is a lower-case letter to distinguish functionally similar snRNA genes mapping to the same location, e.g., [http://flybase.org/reports/FBgn0004188.html ''snRNA:U6:96Aa''].<br />
<br />
'''<span id="2.6.4">2.6.4</span>. snoRNA genes.''' Genes encoding small nucleolar RNAs have symbols of the format 'snoRNA:X'. X usually represents the type of modification catalyzed and/or the substrate, e.g. [http://flybase.org/reports/FBgn0065057.html ''snoRNA:MeU2-C28''], which encodes a snoRNA that guides methylation of nucleotide C28 of the U2 snRNA; or [http://flybase.org/reports/FBgn0082953.html ''snoRNA:Ψ28S-612''], which encodes a snoRNA that guides pseudouridylation of nucleotide 612 of the 28S rRNA. If the substrate is unknown, then 'Or' is used in the symbol to indicate that it encodes an 'Orphan' snoRNA. A suffix is used where necessary to distinguish functionally similar snoRNA genes, e.g., [http://flybase.org/reports/FBgn0086054.html ''snoRNA:Me18S-G1358b''], or [http://flybase.org/reports/FBgn0065046.html ''snoRNA:U3:9B''] (where the suffix is based on cytogenetic position).<br />
<br />
'''<span id="2.6.5">2.6.5</span>. miRNA genes.''' Genes encoding microRNAs have symbols of the format 'mir-N', where N is simply a sequential number according to the conventions outlined in [http://flybase.org/reports/FBrf0205585.html Ambros, Bartel, et. al. 2003] e.g., [http://flybase.org/reports/FBgn0262456.html ''mir-125''].<br />
<br />
'''<span id="2.6.6">2.6.6</span>. Pseudogenes.''' Pseudogenes have symbols of the format ''symbol_of_parental_gene-psX'', where X (if used) is a number to distinguish between multiple pseudogene copies of a particular parental gene. If only one pseudogene copy of a particular gene has been found, it should be given the suffix ''-ps1''.<br />
<br />
'''<span id="2.6.7">2.6.7</span>. Mitochondrial genes.''' Genes encoded by the mitochondrial genome have symbols prefixed with 'mt:', e.g., [http://flybase.org/reports/FBgn0262952.html ''mt:ND4''].<br />
<br />
'''<span id="2.6.8">2.6.8</span>. Ribosomal protein genes.''' Genes encoding ribosomal proteins are named based on orthology to their mammalian counterparts. Genes encoding cytoplasmic ribosomal proteins have symbols of the format 'RpSn' or 'RpLn', where S denotes a gene encoding a protein of the small subunit and L a gene encoding a protein of the large subunit, and n is a number reflecting orthology, e.g., [http://flybase.org/reports/FBgn0020910.html ''RpL3''], [http://flybase.org/reports/FBgn0261592.html ''RpS6'']. Genes encoding mitochondrial ribosomal proteins have symbols of a similar format and are prefixed with 'm', e.g., [http://flybase.org/reports/FBgn0037566.html ''mRpL1''], [http://flybase.org/reports/FBgn0031639.html ''mRpS2'']. Some ribosomal proteins are encoded by duplicate genes; these are distinguished by using a a or b suffix, e.g., [http://flybase.org/reports/FBgn0004403.html ''RpS14a''] and [http://flybase.org/reports/FBgn0004404.html ''RpS14b'']. Some ribosomal protein genes were originally named after a mutant phenotype, e.g. [http://flybase.org/reports/FBgn0004867.html ''sop''] or [http://flybase.org/reports/FBgn0003714.html ''tko'']; these have been retained as the approved gene symbols/names in FlyBase.<br />
<br />
==Allele symbols and names==<br />
<br />
===Superscripts.===<br />
Alleles at a particular gene are designated by the same name and symbol and are differentiated by distinguishing superscripts. In written text the allele designation may be separated from that of the gene by a hyphen, e.g., [http://flybase.org/reports/FBal0018195.html ''white-apricot'']. <br />
<br />
===Symbols.===<br />
Allele symbols should be short, preferably no more than three characters long, and cannot contain spaces, superscripts, or subscripts. Whenever possible superscript characters should be limited to the following set:<br />
<br />
a-z A-Z 0-9 - + : . <br />
<br />
The + symbol is reserved for the wild-type allele. Consecutive allele numbers should be used wherever possible.<br />
<br />
Greek characters may be used but are discouraged.<br />
<br />
The character \ is reserved in all gene symbol contexts for species identification.<br />
<br />
The character / is reserved as a homologue separator in genotypes and cannot be used in allele symbols.<br />
<br />
In text in which superscripting is not possible, such as ASCII files, superscripted text should be enclosed between the characters [ and ].<br />
<br />
FlyBase makes exceptions to the brevity rule when recording ''in vitro'' mutagenesis constructs that are represented with alleles. Where these are not otherwise named FlyBase confers symbols according to a system including the initial of the last name of the first author of the first paper in which the allele was initially reported ('I' in the following examples). The most frequently used classes include:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Meaning<br />
|-<br />
| cIa<br />
| for 'construct a of Author-lastname'<br />
|-<br />
| Scer\UAS.cIa<br />
| for 'S. cerevisiae UAS construct a of Author-lastname' <br />
|-<br />
| tIa<br />
| for 'transgene a of Author-lastname' <br />
|-<br />
| mIa<br />
| for 'minigene a of Author-lastname' <br />
|-<br />
| hs.PI<br />
| for 'heat shock construct of Author-lastname' <br />
|-<br />
| gene_symbol.PI <br />
| for 'gene promoter fusion of Author-lastname' <br />
|}<br />
<br />
In addition, exceptions have been required for some large series of alleles and collections of mutations. Nevertheless, brevity of allele symbols is very much to be encouraged.<br />
<br />
'''<span id="3.2.1">3.2.1</span>.''' It is unacceptable to use, as a superscripted allele symbol, elements of the genotype in which the allele arose, since such a designation implies something more than a trivial connection between allele and element. Alleles that are revertants of a pre-existing allele are an exception to this rule. <br />
<br />
'''<span id="3.2.2">3.2.2</span>.''' While historically, the numeral ''1'' has been the implied superscript of nonsuperscripted symbols, this practice has created considerable ambiguity and is now discouraged. As with all other alleles, the numeral ''1'' should be explicitly designated (e.g., [http://flybase.org/reports/FBal0015189.html ''sc<sup>1</sup>''], not [http://flybase.org/reports/FBgn0004170.html ''sc'']).<br />
<br />
'''<span id="3.2.3">3.2.3</span>.''' For a recessive allele of a gene named as a dominant, or a dominant allele of a gene named as a recessive, the superscripts ''r'' and ''D'', respectively, may be used; e.g., [http://flybase.org/reports/FBal0005503.html ''Hn<sup>r</sup>''], [http://flybase.org/reports/FBal0005504.html ''Hn<sup>r2</sup>''], and [http://flybase.org/reports/FBal0001651.html ''ci<sup>D</sup>''].<br />
<br />
'''<span id="3.2.4">3.2.4</span>.''' For a wild-type allele, a superscripted plus character may be used; e.g., b<sup>+</sup> or B<sup>+</sup>. The plus symbol alone implies the normal (wild-type) allele or alleles in any context, such as [http://flybase.org/reports/FBal0018607.html ''y<sup>1</sup>]''/+.<br />
<br />
It may be necessary to distinguish among more than one 'wild-type' allele. In such cases the different wild-type alleles should be given a distinguishing number, which would follow the + character in the superscript, e.g., [http://flybase.org/reports/FBal0014891.html ''ry<sup>+3</sup>''].<br />
<br />
'''<span id="3.2.5">3.2.5</span>.''' Absence of a particular locus may informally be noted by use of a superscript minus character with the symbol; e.g., ''bb<sup>-</sup>''. This is not acceptable as a designation of a ''particular'' allele.<br />
<br />
'''<span id="3.2.6">3.2.6</span>.''' Revertants or partial revertants of mutant alleles are designated by the superscript rv followed by a distinguishing number; these are placed after the allele designator, e.g., [http://flybase.org/reports/FBal0029140.html ''D''<sup>4rv32</sup>], the 32nd revertant of [http://flybase.org/reports/FBal0002213.html ''D''<sup>4</sup>]. Revertants of dominant mutations that are deficiencies are treated not as alleles but as deficiencies and are accordingly not superscripted but listed with the distinguishing number, e.g., [http://flybase.org/reports/FBab0001553.html ''Df(2L)Sco<sup>rv4</sup>''].<br />
<br />
'''<span id="3.2.7">3.2.7</span>.''' Alleles specifying the absence of a particular enzyme or other protein are designated by the superscript ''n'' (null) followed by a distinguishing number or letter, e.g., [http://flybase.org/reports/FBal0000332.html ''Adh<sup>n1</sup>''], or, where lack of function is inviable, by ''l'' (lethal), followed by a distinguishing number, e.g., [http://flybase.org/reports/FBal0013167.html ''Nrg<sup>l2</sup>'']. <br />
<br />
'''<span id="3.2.8">3.2.8</span>.''' An allele known to be mutant but whose specific identity is unknown is given an asterisk as an allele designation, e.g., ''w<sup>*</sup>''.<br />
<br />
==Transposons and Transgene Constructs==<br />
<br />
Transposons or transgene constructs integrated into the Drosophila genome, if they cause a mutant phenotype, are both alleles and aberrations (similar to other classes of aberrations that are associated with mutant phenotypes). Where such insertions produce no mutant phenotype, they are named purely according to aberration conventions. Where transposon/transgene insertions produce a mutant phenotype by disrupting an endogenous gene, they are given names both as an allele of the mutated endogenous gene and as an aberration. The name of the allele follows conventions outlined in section 2. Rules for naming natural transposons and transgene constructs and their insertion into the genome follow.<br />
<br />
Generic naturally occurring transposons are symbolized as ''ends{}'', where ''ends'' stands for the symbol of a given transposon, such as ''P'' for ''P-element''. ''Doc{}'', ''copia{}'' and ''P{}'' are examples. A defined natural variant of the transposon family can be named by including a symbol for that name inside the brackets. A specific insertion of a given transposon is described by including an additional unique symbol following the brackets.<br />
<br />
Insertions of natural transposons annotated as genome sequence features also have synonyms of the form TEnnnnn, for example, [http://flybase.org/reports/FBti0020021.html copia{}910] has the synonym TE20021.<br />
<br />
Symbols for constructed transposons, or transgene constructs, must always include a construct symbol, which defines a particular construct. A '''full transgene construct genotype''' consists of the source of transposon ends, included genes, construct symbol, and insertion identifier, in the form ''ends{genes=construct-symbol}''. Once defined, ''ends{construct-symbol}'' (or less formally, ''construct-symbol'' alone) can be used in most circumstances to refer to a specific transgene construct. The symbol for a '''specific insertion''' of a given transgene construct has the form ''ends{construct-symbol}insertion-identifier''. Further details are given in the sections that follow.<br />
<br />
Some examples:<br />
<br />
[http://flybase.org/reports/FBtp0000359.html ''P{w<sup>+mC</sup> ovo<sup>D1-18</sup>=ovoD1-18}'']<br />
<br />
:the full genotype of the P-element transgene construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBti0002104.html ''P{ovoD1-18}13X6'']<br />
<br />
:a viable insertion of the construct [http://flybase.org/reports/FBtp0000359.html ''P{ovoD1-18}'']<br />
<br />
[http://flybase.org/reports/FBtp0000352.html P{Scer\GAL4<sup>wB>/sup> w<sup>+mW.hs</sup> ''Ecol\ampR Ecol\ori=GawB}'']<br />
<br />
:the full genotype of the transgene construct [http://flybase.org/reports/FBtp0000352.html ''P{GawB}'']<br />
<br />
[http://flybase.org/reports/FBti0002095.html ''P{GawB}h<sup>1J3</sup>'']<br />
<br />
:an insertion of the construct [http://flybase.org/reports/FBti0002095.html P{GawB}] that disrupts the [http://flybase.org/reports/FBgn0001168.html ''h''] gene<br />
<br />
[http://flybase.org/reports/FBtp0000910.html ''H{w<sup>+mC</sup> Ecol\ori Tn\kanR Ecol\lacZ<sup>HZ50a</sup>=Lw2}'']<br />
<br />
:the full genotype of the hobo transgene construct [http://flybase.org/reports/FBtp0000910.html ''H{Lw2}'']<br />
<br />
[http://flybase.org/reports/FBti0002564.html ''H{Lw2}dpp<sup>151H</sup>'']<br />
<br />
:an insertion of the transgene construct [http://flybase.org/reports/FBtp0000910.html H{Lw2}] that disrupts the [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene<br />
<br />
This nomenclature is formally similar to that used for aberrations, where the ends{symbol} prefix is similar to the Df(n), Dp(n;m), etc., prefixes of aberrations, and the identifier suffix is similar to the gene-allele suffix of aberrations with associated alleles, or the alphanumeric string suffix of other aberrations. Specific rules for assembling the components of a transgene construct genotype follow.<br />
<br />
===Transposon ends.===<br />
Pairs of terminal repeats which together form a transposon are symbolized by opposing braces, {}. The source of the transposon ends is indicated outside the braces, at the left end of the string by a symbol derived from the name of the transposon family: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Transposon ends<br />
!<br />
! Transposon family<br />
|-<br />
| ''P''<br />
| =<br />
| P-element<br />
|-<br />
| ''H''<br />
| =<br />
| H-element (hobo) <br />
|-<br />
| ''I''<br />
| =<br />
| I-element <br />
|-<br />
| ''M''<br />
| =<br />
| mariner-element <br />
|-<br />
| ''Mi''<br />
| =<br />
| Minos-element <br />
|}<br />
<br />
<span id="4.1.1"></span><br />
'''4.1.1.''' Isolated terminal repeats are indicated with the family symbol followed by 3' or 5', e.g., P5' represents the isolated 5' end of a ''P{}'' transposon.<br />
<br />
<span id="4.1.2"></span><br />
'''4.1.2.''' Multiple sets of matched transposon ends are indicated by nesting ''ends{}'' symbols, e.g., [http://flybase.org/reports/FBtp0005038.html ''P{I{neo[RT<nowiki>]</nowiki>W[+<nowiki>]</nowiki>}}'']. A ''P'' transgene construct containing [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] and an isolated ''hobo'' terminal repeat from the 5' end of a ''hobo'' element would be described as ''P{ry+t7.2 H5'}''.<br />
<br />
Formally, this system can be extended to any insertion of mobile DNA, for example, the ''copia'', ''gypsy'' and ''FB'' elements. Thus, the [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] mutation, caused by the insertion of a gypsy element, is called ''gypsy{}ct<sup>MR2</sup>''. When a mobile element inserts into a mutant gene already carrying a mobile element, it is the new insertion that is named. For example, a jockey insertion into [http://flybase.org/reports/FBal0002042.html ''ct<sup>MR2</sup>''] generates [http://flybase.org/reports/FBal0030987.html ''ct<sup>MRpD</sup>''], this is called ''jockey{}ct<sup>MRpD</sup>''. The name describes the new insertion which has caused the new phenotype. A full genotype description, including all sets of transposable element ends, is only provided when the progenitor allele is also fully described.<br />
<br />
FlyBase uses this nomenclature not only because of its rigor, but also because its more general use may be needed if such elements are engineered.<br />
<br />
===Included genes.=== <br />
A full transgene construct description lists within the braces all functional genes, including non-Drosophila genes such as antibiotic resistance genes, bacterial and phage origins of replication, and the ''FLP1'' recombination target (''FRT''), separated by spaces. The left-right order of these elements reflect their 5' to 3' order (with respect to the transposon ends) within the construct. If the order of a gene is unknown, it is placed at one end of the list, followed or preceded by a comma.<br />
<br />
<span id="4.2.1"></span><br />
'''4.2.1. Drosophila melanogaster genes.''' Valid gene symbols are used to name ''D. melanogaster'' genes. Wild-type alleles of intact genes are indicated by a superscripted '+t' followed by an identifier, e.g., [http://flybase.org/reports/FBal0039845.html ''ry<sup>+t7.2</sup>''] or [http://flybase.org/reports/FBal0038104.html ''Adh<sup>+t3.2</sup>'']. A convenient identifier (used in these examples) is the size of the genomic fragment carrying the wild-type gene. Transgene-construct-borne genes that do not confer wild-type function are given unique allele designations without the preceding '+t', e.g., [http://flybase.org/reports/FBal0034664.html ''ftz<sup>B</sup>''] or [http://flybase.org/reports/FBal0036042.html ''y<sup>D225</sup>'']. Replacement of promoter or other control sequences can be indicated in the allele designation: [http://flybase.org/reports/FBal0049436.html ''dpp<sup>hs.PP</sup>''], e.g., for a [http://flybase.org/reports/FBgn0000490.html ''dpp''] gene controlled by a heat shock promoter.<br />
<br />
<span id="4.2.2"></span><br />
'''4.2.2. Species of origin.''' Species of origin is indicated for non-''melanogaster'' Drosophila genes present in transgene constructs. A species code composed of the first letter of the genus (capitalized) and a three letter code, usually the first three letters of the species (lower case) is added to the gene symbol with a separating backslash, e.g., ''Dvir\Dfd<sup>+t7.6</sup>'' for the wild-type Deformed gene from Drosophila ''virilis'' (see paragraph [[FlyBase:Nomenclature#2.2.7|2.2.7]].).<br />
<br />
For genes from species other than those of Drosophila the valid gene symbols are used following a four-letter symbol, as above, indicating the species of origin, e.g., ''Hsap'', for humans, ''Gdom'', for chicken, ''Hsim'', for Herpes simplex, ''Ecol'' for E. coli etc. For viruses, the name or abbreviation, e.g., ''Abelson'', ''Adeno5'', ''Cmeg'', or symbolic name, e.g., ''T4'', ''M13'', the greek symbol lambda, is sometimes used instead of a genus-species-derived four-letter symbol. In all cases, these symbols are separated from the gene symbol by a backslash \. A file of these [http://flybase.org/static_pages/docs/abbreviations.html species abbreviations] is available on FlyBase.<br />
<br />
FlyBase considers transposable elements, the mitochondrial DNA and other similar entities to be species (this is because each can contain several different genes). It is for this reason that, for example, the ''P-element Transposase'' has the symbol P\T in constructs.<br />
<br />
<span id="4.2.3"></span><br />
'''4.2.3. Fusion genes.''' Fusion genes are defined (by FlyBase) as the fusion of protein coding regions of distinct genes constructed by ''in vitro'' mutagenesis. They are named using the gene symbols of their component parts, separated by a double colon, e.g., ''[http://flybase.org/reports/FBgn0012038.html Antp::Scr]'' or [http://flybase.org/reports/FBgn0026604.html ''Act88F::Scer\act1''] .<br />
<br />
The order of gene symbols stated in the fusion gene will be alphabetical. The complexity of these constructs is such that were each to be named according to its molecular composition, for example in the 5' to 3' direction, the number of named fusion genes would rapidly become impractical.<br />
<br />
An exception to the 'alphabetical order' rule will be made for cases where the fusion is between a ''D. melanogaster'' and a non- ''melanogaster'' gene. In such cases the ''melanogaster'' gene symbol will be stated first, e.g., [http://flybase.org/reports/FBgn0025729.html ''tra2::Hsap\SFRS2''].<br />
<br />
For historic reasons, some promoter fusions involving reporter genes such as [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ''], though technically protein fusions, are simply treated as alleles of [http://flybase.org/reports/FBgn0014447.html ''Ecol\lacZ'']. The symbol for the additional gene(s) contributing to the fusion indicated as part of a superscript, e.g., [http://flybase.org/reports/FBal0043886.html ''Ecol\lacZ<sup>P\T.A92</sup>'']. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name. <br />
<br />
<span id="4.2.4"></span><br />
'''4.2.4. Modified genes.''' Modified genes, cDNAs and ''in vitro'' mutagenized sequences are treated as alleles, and will be curated by FlyBase as such. They should be named, therefore, by the same conventions used to name classical alleles. The following allele symbols have been assigned by FlyBase to the commonly used modified genes of ''D. melanogaster'': <br />
<br />
<br />
[http://flybase.org/reports/FBal0028610.html ''w<sup>+mC</sup>'']<br />
<br />
:The mini-white gene constructed by Pirrotta (1988) by deleting the ''Hin dIII- Xba I'' fragment from the long 5'-intron of the ''w<sup>+</sup>'' gene. Carried by Casper plasmids and their derivatives.<br />
<br />
[http://flybase.org/reports/FBal0028611.html ''w<sup>+mW.hs</sup>'']<br />
<br />
:The mini-white gene constructed by Klemenz ''et al''. (1987). Carried by the W6, W8 family of plasmids and their derivatives. <br />
<br />
<br />
Genes modified by the addition of a tag allowing the product to be identified, marked or purified represents a special class of modified genes. Tags are used to mark a transcript, e.g., with a piece of M13 DNA allowing the transcript to be identified by ''in situ'' hybridization. Tags are also be used to mark a protein, for purposes of purification (e.g., (His)<sub>6</sub>), for purposes of identification (epitope tags) or for purposes of targeting to a cellular compartment (nls tags). FlyBase considers as tags constructs designed for these purposes and curates these modified genes as alleles of the tagged gene. Tagged genes have symbols with the format ''T:y'' where ''T'' stands for Tag and ''y'' is the species\gene symbol of the tag, e.g., [http://flybase.org/reports/FBgn0015310.html ''T:Hsap\Myc''], [http://flybase.org/reports/FBgn0015306.html ''T:Ivir\HA1''], [http://flybase.org/reports/FBgn0015313.html ''T:Hsap\p53''], [http://flybase.org/reports/FBgn0015307.html ''T:Zzzz\His6''] (the Zzzz 'species' prefix is used when the tag is artificial).<br />
<br />
A complete list of tagged gene symbols and their definitions is available from FlyBase through [http://flybase.org/ QuickSearch]. Change the 'Species' option from the default 'Dmel' to 'All species'. Ensure the 'Search' option is set as 'ID/Symbol/Name' and 'genes' is selected as the 'Data Class'. Type 'T:*' (don't use the quotation marks) in the 'Enter text' field and submit the query.<br />
<br />
===Construct symbol.===<br />
Every construct must be assigned a symbol which, in conjunction with the description of the terminal repeats, uniquely describes a transgene construct, for example, [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''], [http://flybase.org/reports/FBtp0001399.html ''H{PDelta2-3}'']. Symbols must be unique, but should be kept as short as possible.<br />
<br />
<span id="4.3.1"></span><br />
'''4.3.1. Full genotype.''' In the full genotype of a transgene construct, the construct symbol is the final entry within the braces, separated from the final gene symbol by the equal sign, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacZ<sup>P\T.W</sup> w<sup>+mC</sup> ampR ori=lacW}''] is the full genotype of [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''].<br />
<br />
<span id="4.3.2"></span><br />
'''4.3.2. Short form and partial genotypes.''' Once defined, a transgene construct can be referred to by either the transgene symbol, e.g., [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] (or, less formally, [http://flybase.org/reports/FBtp0000204.html ''lacW'']), or the symbol plus insertion identifier (see below) in most contexts. Additional components can be added as needed for clarity. For example, in stock genotypes it is preferable to include the visible markers, as in [http://flybase.org/reports/FBti0005620.html ''P{w<sup>+mC</sup>=lacW}th<sup>j5C8</sup>''] or [http://flybase.org/reports/FBti0001477.html ''P{w<sup>+t11.7</sup> ry<sup>+t7.2</sup>= wA}3-1''], to avoid misunderstandings about the expected phenotypes of the flies.<br />
<br />
===Insertion identifier.===<br />
The right-most position of the transgene symbol, outside the outer-most bracket, is reserved for a string that identifies a specific insertion into the genome of the defined construct. There are four cases to consider for naming insertions.<br />
<br />
<span id="4.4.1"></span><br />
'''4.4.1. Insertion hits a known gene.''' When a mutant phenotype associated with a transgene construct insertion is assigned to a known gene, the insertion-induced allele should be named by the normal rules. Since such insertions cause new alleles, the gene-<sup>''allele''</sup> description is used as the identifier of the associated insertion (just as with other alleles identified as aberrations). For example, a [http://flybase.org/reports/FBtp0000204.html ''P{lacW}''] insertion referred to as ''l(2)k05007'' and then shown to be an allele of [http://flybase.org/reports/FBgn0010382.html ''CycE''] becomes [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. Insertion-induced alleles in stock genotypes should include the aberration name of the construct, i.e., [http://flybase.org/reports/FBti0005358.html ''P{lacW}CycE<sup>k05007</sup>'']. In most other circumstances the insertion aberration prefix can be dropped and the mutation referred to in the usual way, in this case, [http://flybase.org/reports/FBal0008524.html ''CycE<sup>k05007</sup>'']. <br />
<br />
'''<span id="4.4.2">4.4.2</span>. Insertion defines a new gene.''' Often insertions cause a phenotype that cannot be associated with any known gene. In that case the insertion defines the first allele of a new gene, which is named by the normal rules, e.g., [http://flybase.org/reports/FBti0003098.html ''P{lacW}Trf<sup>1</sup>'']. <br />
<br />
'''4.4.3. A mapped insertion with no phenotype.''' If an insertion has no phenotype but is mapped to the polytene chromosomes, then it is preferable to use the polytene chromosome subdivision to which it maps as its identifier, e.g., [http://flybase.org/reports/FBti0001967.html ''P{bw<sup>+</sup>L}60B'']. If a similar construct already has this name then that of the new one would be ''P{bw<sup>+</sup>L}60B-2'' or similar.<br />
<br />
If the insertion is not mapped then there is no alternative but to give the insertion an arbitrary number or code, e.g., [http://flybase.org/reports/FBti0009781.html ''P{A92}A45'']. This symbol must be unique and as simple as possible using only characters from the set:<br />
<br />
a-z A-Z 0-9 -<br />
<br />
===FLPase construct symbols.===<br />
There are at least eight specific protein variants of the ''S. cerevisiae FLP1'' ('FLPase') recombinase ([http://flybase.org/reports/FBgn0014444.html ''Scer\FLP1'']) used in transgenes in FlyBase:<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! FLPase variant<br />
! Primary reference<br />
|-<br />
| FLPD5<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPG5<br />
| [http://flybase.org/reports/FBrf0214794.html Nern ''et al.'', 2011]<br />
|-<br />
| FLPm4<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm5<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm6<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPm7<br />
| [http://flybase.org/reports/FBrf0213120.html Hadjieconomou ''et al.'', 2011] <br />
|-<br />
| FLPo<br />
| [http://flybase.org/reports/FBrf0209355.html Hong ''et al.'', 2009] [http://flybase.org/reports/FBrf0210697.html Potter ''et al.'', 2010] <br />
|-<br />
| FLPL<br />
| [http://flybase.org/reports/FBrf0218611.html Pan ''et al.'', 2012] <br />
|}<br />
<br />
<span id="4.5.1"></span><br />
'''4.5.1. General format.''' FLPase-containing construct symbols have the format: ''element_ends{promoter-FLPVARIANT.identifier}''.<br />
<br />
<span id="4.5.2"></span><br />
'''4.5.2. Indication of FLP variant.''' Where the specific FLPase variant is known/specified, this is indicated using the symbols in the table above, ''e.g.'' [http://flybase.org/reports/FBtp0069396.html ''P{hs-FLPG5}'']; where it is unknown/unspecified, a generic 'FLP' symbol is used, ''e.g.'' [http://flybase.org/reports/FBtp0022241.html ''P{Ubx-FLP}''].<br />
<br />
<span id="4.5.3"></span><br />
'''4.5.3. Additional identifier.''' An 'identifier' (such as a tag, or an indication of origin) may be appended after the ''FLPVARIANT'' symbol and a period, especially in cases where it is necessary to distinguish between otherwise similar/identical construct symbols. ''E.g.'' [http://flybase.org/reports/FBtp0018510.html ''P{UAS-FLP.Exel}''], [http://flybase.org/reports/FBtp0010171.html ''P{ey-FLP.B}''].<br />
<br />
<span id="4.5.4"></span><br />
'''4.5.4. Exceptions.''' The [http://flybase.org/reports/FBtp0000267.html ''P{hsFLP}''] and [http://flybase.org/reports/FBtp0001131.html ''P{70FLP}''] construct symbols have been retained because of historical and popular use in the literature.<br />
<br />
==Cytogenetic descriptions==<br />
<br />
Breakpoints should be according to the revised salivary gland chromosome maps published by C. B. and P. N. Bridges (see [http://flybase.org/reports/FBrf0066905.html Lindsley and Zimm, 1992]), except for chromosome 4, where the [http://www.helsinki.fi/~saura/EM/ map of Sorsa] ([http://flybase.org/reports/FBrf0074506.html Chromosome maps of Drosophila Vol. II, CRC Press, 1988]) should be used. <br />
<br />
===Range designations.===<br />
For the location of a single object (breakpoint of aberration, gene position, site of transposon insertion, etc.) the range is given as "(d1)(S1)(b1)-(d2)(S2)(b2)", where: <br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Designation<br />
|-<br />
| d<br />
| =<br />
| numbered division (1 to 102)<br />
|-<br />
| S<br />
| =<br />
| lettered subdivision (A to F) <br />
|-<br />
| b<br />
| =<br />
| band number (1 to n, depending upon the particular subdivision)<br />
|}<br />
<br />
For ranges not known to the accuracy of a band, see paragraph [[FlyBase:Nomenclature#Accuracy of cytological descriptions.|5.5]].<br />
<br />
If the range encompasses two different numbered divisions (''i.e.'', d1 does not equal d2), then the full designations for both the left end and the right end of the range will be used, e.g., 32A3-33A2.<br />
<br />
If the range is within a single numbered division (i.e., d1=d2) but within different subdivisions (''i.e.'', S1 does not equal S2), then the numbered division designation is not repeated to the right of the hyphen, e.g., 32A3-D4.<br />
<br />
If the range is within both the same single numbered division and the same lettered subdivision (''i.e.'', d1S1=d2S2), then neither the division nor the subdivision designation will be repeated, e.g., 32A3-5.<br />
<br />
If a location is known to a single band, then the location will be given as (d1)(S1)(b1) with no hyphen and no repetition of the band location, e.g., 32A3.<br />
<br />
If a location is known to a single doublet, then the location will be given as (d1)(S1)(b1)-(b1+1) where (b1) and (b1+1) represent the two succeeding bands of the doublet, e.g., 32A1-2.<br />
<br />
If only one end of a location range is within a doublet, the location will simply refer to the band number maximizing the range, e.g., 32C1-D5 will be used, not 32C1,2-D5 and 32B4-C2 will be used, not 32B4-C1,2.<br />
<br />
It is sometimes necessary to represent interbands in data curated by FlyBase. Interbands have the same symbol as the immediately preceding band, with the suffix symbol +. The interband between the Bridges' bands 3A4 and 3A5 is, therefore, represented as 3A4+.<br />
<br />
===Telomeres.===<br />
Telomeres are designated by nAt, where n is a chromosome number, A is the chromosome arm, and t indicates the telomere:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
!<br />
! Meaning<br />
|-<br />
| 1Lt<br />
| =<br />
| the telomere of the left arm of X <br />
|-<br />
| 1Rt<br />
| =<br />
| the telomere of the right arm of X <br />
|-<br />
| YLt<br />
| =<br />
| the telomere of the left arm of Y<br />
|-<br />
| YSt<br />
| =<br />
| the telomere of the short arm of Y<br />
|-<br />
| 2Lt<br />
| =<br />
| the telomere of the left arm of 2<br />
|-<br />
| 2Rt<br />
| =<br />
| the telomere of the right arm of 2<br />
|-<br />
| 3Lt<br />
| =<br />
| the telomere of the left arm of 3<br />
|-<br />
| 3Rt<br />
| =<br />
| the telomere of the right arm of 3<br />
|-<br />
| 4Lt<br />
| =<br />
| the telomere of the left arm of 4<br />
|-<br />
| 4Rt<br />
| =<br />
| the telomere of the right arm of 4<br />
|-<br />
| If the telomere is of unknown origin, use:<br />
|-<br />
| ?t<br />
| =<br />
| undefined telomere<br />
|}<br />
<br />
===Centromeres and centric heterochromatin.===<br />
Centromeres are designated as ncen, where n indicates the chromosome, ''i.e.'',1cen, Ycen, 2cen, 3cen and 4cen.<br />
<br />
'''5.3.1.''' Centric heterochromatic blocks will be indicated as hn, where n is a consecutive number.<br />
<br />
===Composite chromosome architecture.===<br />
The designations of the chromosomes, including polytene band ranges, heterochromatic blocks and centromeres are:<br />
<br />
YLt h1 -- h17 Ycen h18 -- h25 YSt<br />
<br />
1Lt 1A1 -- 20F4 h26 -- h32 1cen h33 -- h34 1Rt<br />
<br />
2Lt 21A1 -- 40F7 h35 -- h37 h38L 2cen h38R h39 -- h46 41A1 -- 60F5 2Rt<br />
<br />
3Lt 61A1 --- 80F9 h47 -- h52 h53L 3cen h53R h54 -- h58 81F1 -- 100F5 3Rt<br />
<br />
4Lt h59 -- h61 4cen 101F1 -- 102F8 4Rt<br />
<br />
<br />
Note that the centromeres of chromosomes 2 and 3 lie within heterochromatic bands h38 and h53 respectively. Some heterochromatic bands, (h25, h42) are divided into two (h25A, h25B, h42A, h42B) in some stocks.<br />
<br />
===Accuracy of cytological descriptions.===<br />
In designating cytological position, the level of accuracy of the determination should be reflected in the specificity of the statement.<br />
<br />
Some examples should make these distinctions clear. Note that the polytene subdivision described here, 77B, has 9 bands.<br />
<br />
Case 1 - High level of uncertainty about subdivision location:<br />
:If the observer thinks that the location of a rearrangement breakpoint might be in 77B but could also possibly be in 77A or 77C, then the position should be reported as 77A-C. <br />
Case 2 - Low level of uncertainty about subdivision location:<br />
:If the observer's best estimate is that the true breakpoint position is very likely to be in 77B, then the observer should report the position as 77B.<br />
Case 3 - No uncertainty about subdivision location:<br />
:If the observer is absolutely certain that the location is within 77B, then the location should be reported as 77B1-9.<br />
<br />
==Chromosome aberrations==<br />
<br />
Chromosome aberrations have names that consist of a prefix, indicating the class of aberration, an indication of the chromosome, or chromosomes (or their arms) involved contained within parentheses and a specific designation which identifies the particular rearrangement.<br />
<br />
===General principles for naming aberrations.===<br />
<br />
'''6.1.1.''' Aberrations not named after a gene: The suffix (''i.e.'', the component of the name following the parentheses) should include only letters and digits. There should be no superscripts or subscripts except for the particular cases of synthetic inversions with ''L'' and ''R'' superscripts (see [[FlyBase:Nomenclature#6.4.4|6.4.4]]). They should not contain spaces. The characters ( and ) are only to be used to enclose the designation of a chromosome or chromosome arm.<br />
<br />
'''6.1.2.''' Aberrations named after a gene but not associated with an allele: Here the association with the gene carries circumstantial information about the aberration's breakpoints. The suffix should comprise the gene symbol, followed by a hyphen if needed for clarity, followed by any alphanumeric of the investigator's choosing. There should be no superscripts.<br />
<br />
'''6.1.3.''' If a gene whose symbol appears in an aberration changes its name, e.g., for reasons of newly-discovered allelism, then this name change is propagated to the aberration(s) in question. The old name will become a synonym.<br />
<br />
'''6.1.4.''' Aberrations named for a specific associated allele: Here the suffix should be exactly the same as the allele designation, ''i.e.'' the gene symbol followed by the superscripted allele symbol. If the allele designation (either gene or allele part) changes, that change will be propagated to the aberration.<br />
<br />
===Translocations.===<br />
<br />
'''6.2.1.''' Translocations have the symbol ''T(n1;n2...)m'', where ''n1'', ''n2'' ... indicate the numbers of the chromosomes involved in the translocation.<br />
<br />
When chromosomes are listed within the parenthetical information of a translocation symbol they are listed in the order: ''1'', ''Y'', ''2'', ''3'', ''4''. The numbers of the different chromosomes are separated by semicolons, with no spaces.<br />
<br />
'''6.2.2. The separable components of translocations.'''<br />
<br />
Previous conventions for naming such aneuploid segregants have been difficult to employ and do not contain sufficient information in the derivative name to permit automated recognition of the relationship between aneuploid segregant and euploid progenitor.<br />
<br />
FlyBase will employ the following conventions for different classes of euploid chromosomal aberrations and their aneuploid derivatives. <br />
<br />
'''6.2.2.1. Translocation segregants.''' Translocations, standardly named ''T(n1;n2)m'', consist of two or more translocated chromosomes, each of which can potentially exist as an aneuploid segregant. Such segregants will be named using telomeres of the rearranged chromosomes as landmarks for specific segregants. Two-break translocations are often called reciprocal translocations if two chromosome segments have simply been exchanged.<br />
<br />
The general form of the name of a segregant will be ''Ts(n1Pt;n2Qt)m''. Ts stands for 'Translocation segregant,' ''n1Pt'' and ''n2Qt'' for the designation of the landmark telomere(s) (e.g., 2Lt, 3Rt) and m is the same suffix as the progenitor translocation from which the segregant is derived.<br />
<br />
Example 1: Two-break reciprocal translocation. No ambiguity about the locations of either breakpoint relative to the centromere.<br />
<br />
:[http://flybase.org/reports/FBab0008033.html T(2;3)rg35] (= T(2;3) 27E-F;62C2-D1)<br />
<br />
::The two aneuploid segregants are therefore named:<br />
<br />
:::''Ts(2Lt;3Rt)rg35'' (= 2Lt-27E|62D1-3Rt)<br />
:::''Ts(2Rt;3Lt)rg35'' (= 2Rt-27F|62C2-3Lt)<br />
<br />
Example 2: Three-break reciprocal translocation. No ambiguity about the locations of any breakpoint relative to the centromere.<br />
:[http://flybase.org/reports/FBab0006200.html T(1;2;3)OR9] (= T(1;2;3)19-20;49F;81F)<br />
<br />
::The three aneuploid segregants are accordingly named:<br />
<br />
:::''Ts(1Lt;3Lt)OR9'' (= 1Lt-19|81F-3Lt)<br />
:::''Ts(1Rt;2Rt)OR9'' (= 1Rt-20|49F-2Rt)<br />
:::''Ts(2Lt;3Rt)OR9'' (= 2Lt-49F|81F-3Rt)<br />
<br />
'''6.2.2.2. Complex segregants and recombinants.''' For many complex translocations or inversions with four or more breakpoints, multiple aneuploid segregants or recombinants can potentially occur. It is impossible to invent a naming scheme for these complex cases that would automatically reveal the specific aneuploid chromosome complement. In such instances, resulting aneuploids will be given appropriate names as follows:<br />
<br />
The first duplication or deletion is assigned the unique suffix of the parental euploid rearrangement. The new order of the resulting chromosome must be reported.<br />
<br />
Succeeding duplications or deletions are assigned other unique suffixes. Their new orders must also be reported.<br />
<br />
===Rings.===<br />
Ring chromosomes have the symbol R(n)m , where n indicates the number of the chromosome and m is a specific designation. <br />
<br />
===Inversions.===<br />
<br />
'''<span id="6.4.1">6.4.1</span>.''' Inversions have the symbol ''In(nA)m'', where ''n'' indicates the number of the chromosome involved, ''A'' the arm or arms involved and ''m'' is a specific designator.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.4.2">6.4.2</span>.''' If it is not known whether or not an inversion is paracentric (does not include the centromere) or pericentric (includes the centromere) then the indicator of chromosome arm(s) is omitted, ''i.e.'', ''In(n)m''.<br />
<br />
'''<span id="6.4.3">6.4.3</span>.''' By convention, ''In(1)'' implies ''In(1L)''.<br />
<br />
'''<span id="6.4.4">6.4.4</span>. Recombinant products between two inversions.''' Recombination between similar inversions may produce viable recombinant inversions with the left end of one and the right end of the other. Superscripts ''L'' and ''R'' are used to identify the sources of the two ends; for example; [http://flybase.org/reports/FBab0004411.html ''In(2L)Cy<sup>L</sup>t<sup>R</sup>''].<br />
<br />
===Transpositions.===<br />
Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. Rearrangments that alter the pairing of telomeres are classified as translocations.<br />
<br />
In the case of multiple-break intrachromosomal rearrangements, the distinction between inversions and transpositions often becomes ambiguous. An intrachromosomal rearrangement that can be partitioned into a duplicated and a deficient product by exchange with a normal-sequence chromosome is designated a transposition even though it may carry an inverted segment; otherwise, it is designated an inversion.<br />
<br />
'''<span id="6.5.1">6.5.1</span>.''' Transpositions have the symbol ''Tp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the 'recipient' chromosome and ''m'' a specific designation. For intrachromosomal transpositions ''n1'' = ''n2''.<br />
<br />
'''<span id="6.5.2">6.5.2</span>. Separable components of transpositions.'''<br />
<br />
'''<span id="6.5.2.1">6.5.2.1</span>. Interchromosomal transpositions.''' Segregants of interchromosomal transpositions will continue to be referred to as in the past. For a transposition with the name ''Tp(n1;n2)m'', the chromosome segregant containing the duplicated material will be named ''Dp(n1;n2)m'', and the chromosome containing the deleted material will be named ''Df(n1A)m'', where ''A'' refers to the chromosome arm of the deletion.<br />
<br />
Example: [http://flybase.org/reports/FBab0009961.html ''Tp(3;1)kar<sup>5l</sup>''] (= Tp(3;1)87C7-D1;88E2-3;20)<br />
:The two aneuploid segregants are:<br />
::[http://flybase.org/reports/FBab0010533.html ''Dp(3;1)kar<sup>5l</sup>''] (= 1Lt-20|87D1-88E2|20-1Rt)<br />
::[http://flybase.org/reports/FBab0010532.html ''Df(3R)kar<sup>5l</sup>''] (= 3Lt-87C7|88E3-3Rt)<br />
<br />
'''<span id="6.5.2.2">6.5.2.2</span>. Intrachromosomal transpositions.''' Segregants here are produced by recombination with a structurally normal chromosome, not by chromosome segregation. For transpositions in which the transposed segment is in the uninverted orientation relative to the standard map, there may be two potential duplication and two potential deletion derivatives (one set resulting from recombination events in the region between the deficiency and duplication components of the transposition, and one set resulting from recombination events within the transposed segment). For transpositions of the type ''Tp(n1;n1)m'', the reported duplication segregant will be named ''Dp(n1;n1)m'' and the new order must be reported to eliminate any ambiguity. Similarly, the reported deletion recombinant is referred to as ''Df(n1A)m'', where A refers to the chromosome arm bearing the deletion. In rare cases in which the alternative duplication or deletion recombinant (generated by recombination within the transposed segment) is also reported, it will be given a different suffix from the progenitor transposition and the new order will be reported.<br />
<br />
Example: [http://flybase.org/reports/FBab0010014.html ''Tp(3;3)Dl,sup>II13</sup>''] (= Tp(3;3)88F5-9;91A3-8;92A2)<br />
:The primary aneuploid recombinants would then be:<br />
::''Dp(3;3)Dl<sup>II13</sup>'' (= 3Lt-92A2|88F9-91A3|92A2-3Rt)<br />
::''Df(3R)Dl<sup>II13</sup>'' (= 3Lt-88F5|91A8-3Rt)<br />
<br />
If subsequently, the other deletion or duplication recombinant is generated, it will be given a novel suffix, perhaps completely unrelated to the progenitor, e.g.:<br />
<br />
::''Df(3R)xxx'' (= 3Lt-91A3|92A2-3Rt)<br />
::''Dp(3;3)xxx'' (= 3Lt-88F5|91A8-92A2|88F5-3Rt)<br />
<br />
===Deficiencies (deletions).===<br />
<br />
Deficiencies (deletions) have the symbol ''Df(nA)m'', where ''n'' is the number of the deleted chromosome, ''A'' is the chromosome arm and ''m'' is a specific designator.<br />
<br />
Intragenic deletions are not treated as deficiencies, but as alleles; at least two adjacent loci must be removed or disrupted before a lesion is considered a deletion.<br />
<br />
===Duplications.===<br />
<br />
Duplications have the symbol ''Dp(n1;n2)m'', where ''n1'' is the 'donor' chromosome, ''n2'' the recipient and ''m'' a specific designator; ''n1'' may equal ''n2''.<br />
<br />
Duplications may be: tandem (in direct or inverted order), insertional or free. Direct and inverted tandem duplications are not distinguished by their symbols. Ambiguity must be avoided by explicit description of the new order (see section 7.1 New order).<br />
<br />
'''<span id="6.7.1">6.7.1</span>.''' When the duplicated sequences are carried as a free centric element, the letter ''f'' (free) follows the semicolon within the parentheses, replacing ''n2''; e.g., [http://flybase.org/reports/FBab0003270.html ''Dp(1;f)101''].<br />
<br />
<span id="6.7.2">6.7.2</span>. Higher order repeats. Higher-order repeats are also symbolized ''Dp'', with the number of repeats indicated in the parenthetical chromosomal designation, ''i.e.'', ''Dp(1;1)'' = duplication, ''Dp(1;1;1)'' = triplication, and so forth. <br />
<br />
===Y derivatives.===<br />
<br />
In the past many Y chromosome derivatives (e.g., marked- Y chromosomes) were named in a rather special way, as ''m1Ym2'' , where ''m1'' is a marker (or markers) carried on YL and m2 a marker (or markers) carried on YS. Such chromosomes should be named as duplications, following the normal rules. Thus a ''y''<sup>+</sup>Y is [http://flybase.org/reports/FBab0010476.html ''Dp(1;Y )y<sup>+</sup>''] and Y''mal''<sup>+</sup> is [http://flybase.org/reports/FBab0003199.html ''Dp(1;Y)mal<sup>+</sup>''].<br />
<br />
===Autosynaptic elements.===<br />
A pericentric inversion can be converted to two reciprocal autosynaptic elements by recombination between the inverted segment and a normal homolog. For a pericentric of the type ''In(nLR)m'', the two autosynaptic products are ''LS(n)m'' and ''DS(n)m'', where ''LS'' refers to the product carrying the two left (L = levo) telomeres and ''DS'' to that carrying the two right (D = dextro) telomeres. Chromosome elements of very similar structures to autosynaptic elements can be recovered by other means; by convention, these are also called autosynaptic elements if autosynaptic elements were used in their recovery.<br />
<br />
'''<span id="6.9.1">6.9.1</span>.''' In stocks, autosynaptic elements must be carried as balanced pairs; their symbols are then separated by a double slash thus, ''LS(n)m1//DS(n)m2''. In the special case where the two members of such a balanced pair are reciprocal recombinant products (e.g., ''LS(n)m1//DS(n)m1'') then such a genotype can be called ''AS(n)m1''.<br />
<br />
===Compound chromosomes.===<br />
<br />
Compound chromosomes may be subdivided into two classes, homocompounds, consisting of two copies of the same chromosomal arm attached to a common centromere, and heterocompounds in which two arms from different chromosomes are connected through the centromere of one of them. They are designated by the symbol ''C'' followed parenthetically by the designation of the involved chromosome arm or arms.<br />
<br />
In stock genotypes, the linkage relationship of markers on compound chromosomes is indicated with a colon, e.g., ''C(4)RM-P2'', ''ci<sup>1</sup>'' ''ey<sup>R</sup>'': ''gvl<sup>1</sup>'' ''sv<sup>n</sup>''.<br />
<br />
'''<span id="6.10.1">6.10.1</span>. Homocompounds.''' Homocompound chromosomes are classified according to relative orientation of their arms (''i.e.'', tandem, reversed or ring) and the position of their centromeres (''i.e.'', acrocentric or metacentric): reversed acrocentrics (''C(n)RA''), reversed metacentrics (''C(n)RM''), reversed rings (''C(n)RR''), tandem acrocentrics (''C(n)TA''), tandem metacentrics (''C(n)TM''), and tandem rings (''C(n)TR''), where ''n'' is a the number of a chromosome or chromosome arm. In each case the symbol is followed by a specific designator, separated by a hyphen.<br />
<br />
'''<span id="6.10.1.1">6.10.1.1</span>.''' When the component arms differ in sequence by something other than whole-arm inversion, the tandem or reversed classification becomes ambiguous. Furthermore, when the component arms are separable from each other by a single break, the terms acrocentric and metacentric are descriptive; however, when elements of the two arms become interspersed (as for example by interarm rearrangements), these terms lose meaning. Consequently, the more-complex compounds are given arbitrary symbols.<br />
<br />
===Heterocompounds.=== <br />
Heterocompound chromosomes have the symbol ''C'' followed by the chromosome or arms involved within parentheses, e.g., ''C(1;Y)'', ''C(2L;3R)''. The chromosomal origin of the centromere in such compounds is frequently ambiguous. It is usually necessary to describe the structure of any given heterocompound in some more detail, by its new order. The distinction between some heterocompound chromosomes and whole-arm translocations can be moot. <br />
<br />
===Free chromosome arms.===<br />
<br />
The term 'free' is used with respect to the left and right arms of the major autosomes, and to the long and short arms of the Y chromosome, when an arm exists as an individual chromosome element. The symbol for a free arm is: ''F(nA)m'', where ''n'' = Y, 2 or 3, A = L, R, or S and ''m'' is a symbol (note that ''L'' indicates ''Left'' for the X chromosome and autosomes, but ''Long'' for the Y chromosome). In practice, all free arms carry some chromosome material from another chromosome arm or element. <br />
<br />
===Complex rearrangements.===<br />
<br />
Occasionally an author must report an aberration whose cytology is either ambiguous or cannot (with existing knowledge) be described within one of the usual classes of aberration. These aberrations should be named according to the format ''Ab(N1;N2;..)identifier'' or, when associated with a named allele, ''Ab(N)geneallele''. ''Ab'' stands for Aberration, ''N'' represents the chromosome(s) or chromosome arm(s) that are known to be involved. If one or more of these cannot be identified then a ? symbol is used. If one break is heterochromatic but no further identification is possible then h is used. Examples are: [http://flybase.org/reports/FBab0023380.html ''Ab(3R)faf<sup>BX9</sup>''] and [http://flybase.org/reports/FBab0023374.html ''Ab(3L;h)ME178''].<br />
<br />
The availability of the ''Ab'' prefix is only for the last resort, and should not be used without very good reason. If further information becomes available allowing a more formal description of a complex aberration then the ''Ab'' symbol should be replaced and relegated to synonymy.<br />
<br />
===Combinations of rearrangements.===<br />
<br />
The elementary categories of chromosome aberrations are not mutually exclusive, and some aberrations combine several of them. In such cases the symbol used should be the one most relevant to the anticipated value of the aberration, such as ''Df'' for a deficient translocation that was generated in a screen for deficiencies. When no preference exists, the symbol used is the one that stands highest in the following ranking: ''T'' > interchromosomal ''Tp'' > ''R'' > ''In'' > intrachromosomal ''Tp'' > ''Dp'' > ''Df''. This is especially so when the components are inseparable.<br />
<br />
FlyBase uses the following verbal definitions for classes of three-break aberrations: <br />
<br />
Deficient translocation<br />
:A translocation in which one of the four broken ends loses a segment before re-joining, e.g., [http://flybase.org/reports/FBab0006433.html ''T(1;3)ct<sup>268-21</sup>''].<br />
<br />
Inversion-cum-translocation<br />
:The first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break, e.g., [http://flybase.org/reports/FBab0005939.html ''T(1;2)C324''].<br />
<br />
Bipartite duplication<br />
:The (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break, e.g., [http://flybase.org/reports/FBab0003131.html ''Dp(1;2)K1''].<br />
<br />
Cyclic translocation<br />
:Three breaks in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third, e.g., [http://flybase.org/reports/FBab0006191.html ''T(1;2;3)OR14''].<br />
<br />
Bipartite inversion<br />
:Three breaks in the same chromosome; both central segments are inverted in place (''i.e.'', they are not transposed), e.g., [http://flybase.org/reports/FBab0005373.html ''In(3LR)BTD7''].<br />
<br />
Uninverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0003079.html ''Dp(1;1)hdp-b2''].<br />
<br />
Uninverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments, e.g., [http://flybase.org/reports/FBab0009060.html ''Tp(1;1)B<sup>263-48</sup>''].<br />
<br />
Inverted insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0003109.html ''Dp(1;1)y<sup>bl</sup>''].<br />
<br />
Inverted insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments, e.g., [http://flybase.org/reports/FBab0004956.html ''In(2R)C72']'.<br />
<br />
Unoriented insertional duplication<br />
:A copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0003081.html ''Dp(1;1)hdp-b4''].<br />
<br />
Unoriented insertional transposition<br />
:The segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded, e.g., [http://flybase.org/reports/FBab0009492.html ''Tp(1;2)v<sup>+</sup>75d''].<br />
<br />
'''<span id="6.14.1">6.14.1</span>.''' A complicated rearrangement may be separable genetically into its simpler component aberrations, which are usually sufficiently designated with the distinguishing symbol of the original aberration. When, however, the original is named after a phenotype associated with one of the component aberrations, designation of the other component with the symbol of the mutant is inappropriate.<br />
<br />
'''<span id="6.14.2">6.14.2</span>.''' A rearrangement superimposed upon another rearrangement may be given a name, which more often than not refers to the entire complex since the newly induced aberration is likely to be inseparable from the original; e.g., [http://flybase.org/reports/FBab0004815.html ''In(2LR)SM1''] is a large pericentric inversion superimposed upon [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy] [http://flybase.org/reports/FBab0004960.html In(2R)Cy''].<br />
<br />
===Balancers===<br />
<br />
Balancers can be described in one of three ways: by a complete genotype, by a short genotype or by a single symbol. For FlyBase purposes a single symbol is needed for every balancer variant. If a symbol is not reported for a new balancer variant FlyBase will assign one.<br />
<br />
Balancer symbols should be concise, contain no spaces and should contain characters from the following set:<br />
<br />
a-z A-Z 0-9 : - ( ) {}<br />
<br />
Marked variants of classical balancers should be named beginning with the symbol of the parental variant followed by a hyphen followed by a concise distinguishing string, e.g., [http://flybase.org/reports/FBba0000105.html ''TM3-DZ''].<br />
<br />
Where new balancer variants are reported in the literature the authors' symbol for the variant, if provided, is used by FlyBase. Commas used by authors in publications may be transmuted into hyphens by FlyBase for purposes of making use of a genotype-like string that almost qualifies as a symbol. Likewise, when authors use [] to denote limits of an element insertion, these are transmuted into {} by FlyBase, to maintain consistency with other sections of the database. The use of invalid gene symbols and complete transposable element construct/insertion symbols in balancer symbols is discouraged.<br />
<br />
As an alternative to the concise balancer symbol, balancers may be reported using balancer short genotypes, which combine the symbol of a classical balancer with new allele, aberration or transgene insertion symbols to define a unique balancer variant, e.g., ''TM3'', ''ry<sup>RK</sup>'' ''Sb<sup>1</sup>'' (= [http://flybase.org/reports/FBba0000046.html ''TM3-vKa'']).<br />
<br />
Balancers may, of course, also be reported using a full balancer genotype that lists all aberration, allele and insertion symbols that comprise the unique balancer variant.<br />
<br />
Any variant reported in the literature or donated to a stock center but not given a symbol by the authors is given the symbol 'parental_variant-vIa' and the name 'parent_variant-variant a of Initial (of first author last name)' by FlyBase, e.g., [http://flybase.org/reports/FBba0000046.html ''TM3-vKa''] for ''TM3-variant a of Karess'' .<br />
<br />
==The cytological description of aberrations==<br />
<br />
For all but the simplest two-break chromosome aberrations the explicit description of the new chromosome order is essential (see paragraph 4.5).<br />
<br />
In descriptions of aberrations the cytological breakpoints of the aberration are listed after the symbol, the different items of chromosomal information being separated by semicolons without spaces. Cytological descriptions of new orders are always in roman type. <br />
<br />
===New order.===<br />
The following conventions for specifying sequences of aberrations are to be adopted. The sequence of each chromosome involved in an aberration is specified from one end to the other according to salivary gland chromosome band terminology. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. Thus, the new order of<br />
<br />
[http://flybase.org/reports/FBab0009822.html ''Tp(2;3)P''] (= Tp(2;3)58E3-F2;60D12-E2;96B5-C1)<br />
:is represented as<br />
<br />
:2Lt-58E3|60E2-2Rt; 3Lt-96B5|60D12-58F2|96C1-3Rt.<br />
<br />
===Ambiguities.===<br />
Were the order of the inserted segment 60D12-58F2 not known, the segment would have been included within parentheses; ''i.e.,''<br />
3Lt-96B5|(58F2-60D14)|96C1-3Rt.<br />
<br />
Hierarchies of ambiguities are represented by parentheses within parentheses.<br />
<br />
===Complex rearrangements.===<br />
Breaks rejoin cyclically to produce chromosome aberrations (e.g., A with B and B with A) and multiple breaks may rejoin in one or more cycles. Thus four breaks may interact to form one four-break rearrangement or two two-break rearrangements. A complex rearrangement consisting of two or more simple cyclic rearrangements is indicated in the descriptive symbol; e.g.<br />
<br />
[http://flybase.org/reports/FBab0006036.html ''T(1;2)OR72''] (= T(1;2)19E;29F + In(2LR)24F;54B)<br />
or<br />
[http://flybase.org/reports/FBab0005938.html ''T(1;2)C314''] (= T(1;2)5D;40-41 + T(1;2)9D;51D + T(1;2)20;56F)<br />
<br />
New symbols are required if any of these components (or any new combination of these components) were to be derived separately.<br />
<br />
===Order of description.===<br />
Information on new order is written as follows: each chromosomal element starts at the free end with the lower value and the elements are listed in ascending order, ''Y'' falling between 20 and 21. <br />
<br />
===Rings.===<br />
Rings are differentiated from rod-shaped chromosomes by vertical bars at the beginning and end of the element; the circle is broken for linear designation at the breakpoint with the lowest numerical value; e.g., |1A4-20 1cen 20F-20A1| for R(1)2.<br />
<br />
===New orders of ''Y'' derivatives.===<br />
The constitution of a ''Y'' fragment may be designated by listing its genetic elements in order with any ambiguities in order enclosed within parentheses, e.g., ''KL(bw<sup>+</sup>--ba<sup>+</sup>)'' ''Ycen bb<sup>+</sup> KS''. When there is a hierarchy of ambiguities in order, a hierarchy of parentheses is used, as in ''((ci<sup>+</sup>--spa<sup>+</sup>)KL) Ycen bb<sup>+</sup>KS''.<br />
<br />
==Naming genotypes==<br />
<br />
===Gene separators.===<br />
In designations of genotypes with several mutant genes, allele symbols of genes on the same chromosome are separated by spaces (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> B<sup>1</sup>)''.<br />
<br />
===Homologue separators.===<br />
Allele symbols of genes on homologous chromosomes are separated by a slash bar (e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/B<sup>1</sup>''). The ''X'' and ''Y'' chromosomes are considered to be homologues for this purpose and the different genotypes of males and females are not usually made explicit. For example, ''Dp(1;Ybb-)B<sup>S</sup>''/ ''y<sup>1</sup> car<sup>1</sup>'' describes a stock in which females are homozygous for the ''y<sup>1</sup> car<sup>1</sup> X'' chromosome, and males are hemizygous for ''y<sup>1</sup> car<sup>1</sup>'' and the ''B<sup>S</sup>''-marked ''Y'' chromosome. If desired, multiple genotypes in a stock can be fully described, using an ampersand (&) to separate the genotypes, e.g., ''y<sup>1</sup> car<sup>1</sup>'' & ''Dp(1;Ybb-)B<sup>S</sup>/ y<sup>1</sup> car<sup>1</sup>''.<br />
<br />
It is convention to list allele symbols only once for a genotype that is homozygous for all of the mutations on a particular chromosome, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup> implies y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>. If, however, any one of these mutations were to be heterozygous, then the mutant genotypes of each chromosome would be given, i.e., y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>/y<sup>1</sup> f<sup>1</sup>.<br />
<br />
It is convention to write genotypes with the maternally contributed chromosomes preceding those paternally contributed. For example, in the cross of ''cn<sup>1</sup>/cn<sup>1</sup>'' females to ''cn<sup>+</sup>/cn<sup>+</sup>'' males, the progeny genotype would be written ''cn<sup>1</sup>/cn<sup>+</sup>''; from the reciprocal cross it would be written ''cn<sup>+</sup>/cn<sup>1</sup>''.<br />
<br />
===Nonhomologue separators.===<br />
Allele symbols of genes on nonhomologous chromosomes are separated by semicolons and spaces (e.g., ''bw<sup>1</sup>; e<sup>s</sup>; ey<sup>1</sup>'').<br />
<br />
===Chromosome descriptions.===<br />
<br />
'''<span id="8.4.1">8.4.1</span>.''' In describing a chromosome, inclusion of several types of information is often desirable; e.g., arrangement and mutant allele content. Such categories are separated by a comma followed by a space; e.g., [http://flybase.org/reports/FBab0003929.html ''In(1)FM7''], [http://flybase.org/reports/FBal0018623.html ''y<sup>31d</sup>''] [http://flybase.org/reports/FBal0018195.html ''w<sup>a</sup>''] [http://flybase.org/reports/FBal0017802.html ''v<sup>Of</sup>''] [http://flybase.org/reports/FBal0000817.html ''B<sup>1</sup>''], which designates an ''X'' chromosome carrying the [http://flybase.org/reports/FBab0003929.html ''FM7''] inversion, the recessive alleles ''yellow-31d'', ''white-apricot'' and ''vermillion-of-Offermann'', and the dominant allele ''Bar-1''. Alleles are listed in the order of the standard genetic map irrespective of their order on the chromosome in question.<br />
<br />
'''<span id="8.4.2">8.4.2</span>.''' Description of the gene content of autosynaptic elements requires particular rules. Mutations mapping distal to the breakpoint are indicated after a comma that follows the name of the element itself; mutations mapping proximal to the breakpoint (''i.e.'' within the heterosynaptic region and necessarily hemizygous) are indicated after a second comma; e.g., ''LS(2)m'', ''b<sup>1</sup>'', ''cn<sup>1</sup>'' would be homozygous for ''b<sup>1</sup>'' but hemizygous for ''cn<sup>1</sup>''. If the status of a particular mutation is unknown, then its symbol is enclosed within ().<br />
<br />
'''<span id="8.4.3">8.4.3</span>.''' Mutant alleles on the different chromosomal components of translocations or interchromosomal transpositions are separated by a colon. The translocated chromosomes are separated from their homologues by a slash. For example: [http://flybase.org/reports/FBab0023070.html ''T(2;3)CyO-TM2''], [http://flybase.org/reports/FBal0002196.html ''Cy<sup>1</sup>] [http://flybase.org/reports/FBal0009190.html l(2)DTS513<sup>1</sup>]: [http://flybase.org/reports/FBal0017400.html Ubx<sup>130</sup>'']/[http://flybase.org/reports/FBal0015108.html ''S<sup>1</sup>''].<br />
<br />
In contrast with past practice the + character is not to be used to indicate the presence of more than one separable aberration on the same chromosome, ''i.e.'', [http://flybase.org/reports/FBab0004410.html ''In(2L)Cy''] [http://flybase.org/reports/FBab0004410.html ''In(2R)Cy''] is used, rather than either ''In(2L+2R)Cy'' or ''In(2L)Cy'' + ''In(2R)Cy''.<br />
<br />
===Cross descriptions.===<br />
It is a convention that when genetic crosses are described the female genotype is written to the left of the ''times'' symbol (x), and the male genotype to the right.<br />
<br />
===Uncertainty.===<br />
Uncertainty of specific alleles, genes, and aberrations are all indicated in genotypes with an asterisk, e.g., w<sup>*</sup> for a mutant allele of ''w'' when the specific allele is unknown, ''l(2)<sup>*</sup>'' for a lethal allele on the second chromosome when the gene is unknown, and C(1)<sup>*</sup> for a compound ''X'' chromosome when the nature of the attachment is unknown.<br />
<br />
===Nicknames.===<br />
In a relatively few cases, FlyBase will support an alternative symbol for a genotype component, a nickname. Nicknames are supported when a simplified symbol is already in use by Drosophila workers and is more widely understood than the rigorous valid symbol. For example, [http://flybase.org/reports/FBab0038612.html ''Dp(2;2)Cam11''] is a valid nickname for [http://flybase.org/reports/FBab0038612.html ''In(2LR)TE35B-226<sup>L</sup>TE35B-4<sup>R</sup>''] and [http://flybase.org/reports/FBal0095147.html ''w<sup>67c23</sup>''] is a valid nickname for [http://flybase.org/reports/FBab0001030.html ''Df(1)w67c23'']. Implementation of nicknames within FlyBase is still in progress and the distinction between nicknames and synonyms may not be evident in FlyBase reports.<br />
<br />
==Cytotype==<br />
<br />
It may be necessary to indicate the cytotype of a stock with respect to one or more systems of hybrid dysgenesis. We suggest that this is done by appending the indication of cytotype to the end of the stock description as a single letter code enclosed within <>. This symbol should be separated by the last component of the genotype by a comma, e.g., ''y<sup>1</sup> w<sup>1</sup> f<sup>1</sup>'', <''P''> would indicate a P-cytotype stock with these three markers. If more than one cytotype needs to be designated then these should be separated by a semi-colon, e.g., <''P;I''>.<br />
<br />
==Representation of gene, allele and aberration names and symbols in text==<br />
<br />
===Italic===<br />
Gene, allele, aberration and transposon/transgene-construct names and symbols are italicized in printed text.<br />
<br />
===Non-italic.===<br />
When a full gene name or gene symbol is used to indicate phenotype, rather than genotype, then that name or symbol is printed in roman (non-italic) type; i.e., ''white'' indicates a genotype and white a phenotype.<br />
<br />
===Superscripts and subscripts.===<br />
In ASCII text the characters [ and ] are used to enclose superscripted characters, and <nowiki>[[ and ]]</nowiki> used to enclose subscripts.<br />
<br />
===Cytogenetic terms.===<br />
Cytogenetic designations are not italicized except when part of an aberration symbol.<br />
<br />
===Reserved characters.===<br />
The following characters are reserved for special use in gene, allele, and aberration names and symbols or in genotypes:<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Symbol<br />
! Use<br />
|-<br />
| \<br />
| reserved for use in symbols of genes from species other than D. melanogaster <br />
|-<br />
| /<br />
| reserved for use as a homologue separator in stock genotypes <br />
|-<br />
| {}<br />
| reserved for use in transposon and transgene construct symbols <br />
|-<br />
| <><br />
| reserved for use in transgene construct names and for cytotype designation in stocks <br />
|-<br />
| []<br />
| reserved for indicating superscripts in ASCII text <br />
|-<br />
| [[]]<br />
| reserved for indicating subscripts in ASCII text<br />
|-<br />
| ()<br />
| reserved for use in compound gene names and symbols (e.g., l(1)) and for aberration symbols, and for the indication of ambiguous genotypes <br />
|-<br />
| ;<br />
| reserved as a separator of chromosome (chromosome arm) numbers in aberration names and symbols, and to separate markers or aberrations on non-homologous chromosomes in stock genotypes <br />
|-<br />
| :<br />
| reserved for use in symbols of defined classes, i.e., transgene constructs, genes encoding special RNAs (tRNAs, snRNAs), fusion genes and mitochondrial genes, and, in stock genotypes, to indicate the association between markers on reciprocol components of translocations, or arms of compound chromosomes. <br />
|}<br />
<br />
==Representation of gene products in text==<br />
<br />
===Proteins.===<br />
Protein product names and symbols should '''not''' be italicized in printed text. Where feasible, proteins that are named for the gene should be further distinguished by capitalizing the initial letter of the gene symbol or name. For example, the protein product(s) of the ''hh'' (''hedgehog'') gene could be correctly denoted as Hh or Hedgehog; the protein product(s) of the ''RpL38'' (''Ribosomal protein L38'') gene could be correctly denoted as RpL38 or Ribosomal protein L38; and the the protein product(s) of the ''AGO1'' (''Argonaute-1'') gene could be correctly denoted as AGO1 or Argonaute-1.<br />
<br />
There are no fixed rules for denotation of proteins not named for the gene.<br />
<br />
===RNAs.===<br />
There is no convention for symbolically designating generic RNA products of genes in text. <br />
<br />
==Updates.==<br />
<br />
Substantive changes made to this document since its presentation at the Atlanta Drosophila meeting in April, 1995, are noted here.<br />
<br />
Version 2.01, April 25, 1995: The rules for naming fusion genes (para 3.2.3) have been changed.<br />
<br />
Version 2.02, May 13, 1995: A new paragraph (7.7) on the naming of ambigous genotypes has been added.<br />
<br />
Version 2.06, November 22, 1995: Corrections have been made to the examples of names of transposons to conform with current FlyBase practice. The list of 'honorary genes' has been updated.<br />
<br />
Version 3.0, March 18, 1996: The symbol for complex aberrations has been changed from ''complex'' to ''Ab''. The placement of the <> symbols indicating orientation of an FRT has been changed to conform with current usage. The colon is introduced as a separator of markers on reciprocal components of translocations and arms of compound chromosomes as a way of clarifying the relationships and expected behaviors of these elements in stocks. The list of 'honorary genes' has been updated. A table of contents has been added. Assorted small changes have been made in the document.<br />
<br />
Version 3.01, March 29, 1996: The rules for naming genes identified by sequencing projects have been changed, and new FlyBase mirror sites have been added.<br />
<br />
Version 3.02, August 7, 1996, corrects the explanation of < and > used to indicate FRT orientation. The list of 'honorary genes' has been removed.<br />
<br />
Version 3.03, August 21, 1996, clarifies what constitutes a transposon symbol.<br />
<br />
Version 4.0, February 19, 1997, includes naming of ''in vitro'' mutagenesis constructs ('''Section 2.2.''') and balancers ('''Section 5.14.''').<br />
<br />
Version 4.1, June 3, 1997, includes modification of rules for naming multiple transposon insertions ('''Section 3.1.2.'''), a clarification of rules for representing proteins in text ('''Section 11.1.'''), and a proposal for naming genes that encode ribosomal proteins ('''Appendix A.''').<br />
<br />
Version 4.2, March 8, 1998, includes modified rules for naming genes identified only by genomic sequencing projects ('''Section 1.1.3''').<br />
<br />
Version 4.3, May 21, 1998, includes minor changes to the Introduction and format of the document.<br />
<br />
Version 4.4, February 9, 1999, includes a change to '''Section 5.13'''. supporting the identification of an unknown breakpoint as heterochromatic.<br />
<br />
Version 5.0, July 6, 1999, all references to 'honorary genes' have been removed (this category is no longer used by FlyBase) and a description of nicknames has been added ('''Section 7.7.''').<br />
<br />
Version 5.01, August 23, 1999, assorted minor corrections were made.<br />
<br />
Version 6.0, November 23, 1999, updates '''Section 9.1.''' to include FlyBase's new policy on the use of sequence accessions to determine precedence of gene names and symbols. Many links have been added and assorted corrections made.<br />
<br />
Version 6.1, December 27, 1999, updates '''Section 1.1.3.''' to include genes identified by Celera.<br />
<br />
Version 6.2, April 5, 2000, updates '''Section 1.1.3.''' with the derivation of anonymous gene symbol prefixes.<br />
<br />
Version 6.3, May 12, 2000, updates '''Section 2.2.''' to clarify the current rules for allele symbols.<br />
<br />
Version 7, August 28, 2000, updates '''Section 11.2.''', eliminating the convention (which was never adopted by Drosophilists) that RNA products of genes are designated in text by the gene symbol in all italic capital letters.<br />
<br />
Version 7.1, April 18, 2001, updates '''Section 1.1.3.''' to make explicit the need for authors to provide the CG gene symbol when renaming a CG-named gene.<br />
<br />
Version 7.2, April 24, 2001, updates '''Section 1.1.3.''' to clarify the on-going assignment of CG names.<br />
<br />
Version 8.0, August 1, 2001, updates '''Sections 1.1.''' to clarify the one-gene:one-valid-symbol rule, '''1.1.1.''' to clarify the case of certain gene symbols, and '''5.15.''' to make explicit the various ways in which balancers can be described.<br />
<br />
Version 8.1, August 28, 2001, updates '''Section 5.13.''' to change 'h?' to 'h' as the symbol for undefined heterochromatic breakpoints in complex aberration symbols.<br />
<br />
Version 8.2, October 25, 2001, updates '''Section 3''' to include foreign gene prefixes in example genotypes.<br />
<br />
Version 8.3, November 26, 2001, rewords '''Section 7''' to clarify that genotypes specify alleles of genes.<br />
<br />
Version 8.4, March 22, 2002, updates cytology in examples in Sections '''5.5.2.2.''' and '''6.2.'''<br />
<br />
Version 9, August 16, 2004, updates sequence annotation nomenclature in '''Section 1.1.3.''' and emphasizes in '''1.7.2.''' and '''10.5.''' the prohibition against use of the character / in gene and other symbols. '''11.''' is slightly modified to clarify that these options apply to generic proteins and transcripts from a given gene.<br />
<br />
Version 10, November 16, 2006, updates the proteins of mitochondrial ribosomes entry in the '''Appendix'''<br />
<br />
Version 10.1, August 23, 2007, clarification of the column heading of the common prefixes table '''Section 1.3'''<br />
<br />
Version 10.2, February 6, 2008, created section '''1.1.4''' and ammended section '''1.1.3''' to specify the annotation prefixes used for genes identified in Drosophila genomic sequencing projects '''Sections 1.1.3''' and '''1.1.4'''<br />
<br />
Version 11, October 17, 2008, The guidelines on gene symbols and names were updated. The Preamble replaced the "Introduction", and the sections '''Policy for establishing FlyBase-approved gene symbols and names''' and '''Gene symbols and names''' were created, while the sections "Gene names and symbols" and "Valid Symbols & Synonyms", and Appendix A "Naming of genes encoding ribosomal proteins" were removed. The sections '''Allele names and symbols''' to '''Cytotype''' were renumbered accordingly.<br />
<br />
[[Category:Help]][[Category:DONE]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125297
FlyBase:About
2014-02-05T07:17:41Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
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<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
: [http://flybase.org/reports/FBrf0223849.html FBrf0223849]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
: [http://flybase.org/reports/FBrf0223876.html FBrf0223876]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125296
FlyBase:About
2014-01-21T08:17:52Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2010'''<br />
<br />
:Gene Ontology Consortium (2010)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2010)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:'''2009'''<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125295
FlyBase:About
2014-01-21T08:14:53Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:Gene Ontology Consortium (2013)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
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The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125294
FlyBase:About
2014-01-16T15:18:37Z
<p>Sjm41: /* Citing FlyBase */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
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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.<br />
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Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125293
FlyBase:About
2014-01-16T15:17:55Z
<p>Sjm41: /* Citing FlyBase */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
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<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
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<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125292
FlyBase:About
2014-01-16T15:17:29Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/42/D1/D780.full 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
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Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
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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.<br />
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The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125291
FlyBase:About
2014-01-16T15:12:42Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
: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)<br />
: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
: Genome Biology, 3:research0081<br />
: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
: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)<br />
: Apollo: a sequence annotation editor.<br />
: Genome Biology, 3:research0082<br />
: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
: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)<br />
: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
: Genome Biology, 3:research0083<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
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The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125290
FlyBase:About
2014-01-16T15:11:09Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila phenotype ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
::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)<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081<br />
:: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
::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)<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082<br />
:: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
::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)<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083<br />
:: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125289
FlyBase:About
2014-01-16T15:09:23Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila Phenotype Ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
::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)<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081<br />
:: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
::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)<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082<br />
:: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
::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)<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083<br />
:: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:'''1998'''<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:'''1997'''<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:'''1996'''<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:'''1995'''<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
<br />
:'''1994'''<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:'''1993'''<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125288
FlyBase:About
2014-01-16T15:07:57Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
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<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
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Gillian Millburn<br />
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<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
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Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
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Gary Grumbling<br />
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Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'2014'<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila Phenotype Ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
::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)<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081<br />
:: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
::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)<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082<br />
:: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
::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)<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083<br />
:: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
<br />
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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125287
FlyBase:About
2014-01-16T15:07:26Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
:'''2014'''<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:'''2013'''<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila Phenotype Ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:'''2012'''<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
:'''2011'''<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:'''2009'''<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:'''2008'''<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:'''2007'''<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:'''2006'''<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:'''2005'''<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:'''2003'''<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''2002'''<br />
<br />
::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)<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081<br />
:: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
::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)<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082<br />
:: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
::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)<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083<br />
:: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:'''2001'''<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:'''1999'''<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125286
FlyBase:About
2014-01-16T15:02:29Z
<p>Sjm41: /* FlyBase Publications */ hyperlinking FBrfs</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014)<br />
: FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
: Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
: [http://flybase.org/reports/FBrf0223749.html FBrf0223749]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
: The Drosophila anatomy ontology.<br />
: J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
: The Drosophila Phenotype Ontology.<br />
: J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013)<br />
: On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
: PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
: [http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013)<br />
: FlyBase: improvements to the bibliography. <br />
: Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
: [http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013)<br />
: Systematic analysis of experimental phenotype data reveals gene functions. <br />
: PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
: [http://flybase.org/reports/FBrf0221415.html FBrf0221415]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012)<br />
: Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
: Database 2012:bas039 doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
: [http://flybase.org/reports/FBrf0219955.html FBrf0219955]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: Gene Ontology annotations and resources. <br />
: Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012)<br />
: Directly e-mailing authors of newly published papers encourages community curation. <br />
: Database 2012:bas024 doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
: [http://flybase.org/reports/FBrf0218522.html FBrf0218522]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012)<br />
: FlyBase 101 – the basics of navigating FlyBase. <br />
: Nucleic Acids Res. 40 (Database issue):D706-14. doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
: [http://flybase.org/reports/FBrf0217108.html FBrf0217108]<br />
<br />
<br />
: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)<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
: [http://flybase.org/reports/FBrf0218533.html FBrf0218533]<br />
<br />
<br />
:Gene Ontology Consortium (2012)<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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)<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
: [http://flybase.org/reports/FBrf0214821.html FBrf0214821]<br />
<br />
<br />
:Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011)<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009)<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009)<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
: [http://flybase.org/reports/FBrf0209611.html FBrf0209611]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009)<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
: [http://flybase.org/reports/FBrf0213427.html FBrf0213427]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009)<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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)<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
: [http://flybase.org/reports/FBrf0206621.html FBrf0206621]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009)<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
: [http://flybase.org/reports/FBrf0207486.html FBrf0207486]<br />
<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008)<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
: [http://flybase.org/reports/FBrf0205804.html FBrf0205804]<br />
<br />
<br />
: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)<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008)<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
: [http://flybase.org/reports/FBrf0206381.html FBrf0206381]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008)<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
: [http://flybase.org/reports/FBrf0203012.html FBrf0203012]<br />
<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007)<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. doi:[http://nar.oxfordjournals.org/content/35/suppl_1/D486.full 10.1093/nar/gkl827]<br />
: [http://flybase.org/reports/FBrf0194786.html FBrf0194786]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium. (2007)<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. []<br />
: [http://flybase.org/reports/FBrf0200326.html FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007)<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56.<br />
: [http://flybase.org/reports/FBrf0206379.html FBrf0206379]<br />
<br />
<br />
:Lin MF et al. (2007)<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res. 17: 1823-1836.<br />
: [http://flybase.org/reports/FBrf0202906.html FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007)<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346.<br />
: [http://flybase.org/reports/FBrf0201050.html FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007)<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232.<br />
: [http://flybase.org/reports/FBrf0200674.html FBrf0200674]<br />
<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium (2006)<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068.<br />
: [http://flybase.org/reports/FBrf0191339.html FBrf0191339]<br />
<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium (2005)<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395<br />
: [http://flybase.org/reports/FBrf0184221.html FBrf0184221]<br />
<br />
<br />
:Richards S et al. (2005)<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18.<br />
: [http://flybase.org/reports/FBrf0184012.html FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005)<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28.<br />
: [http://flybase.org/reports/FBrf0206380.html FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175<br />
: [http://flybase.org/reports/FBrf0159266.html FBrf0159266]<br />
<br />
<br />
:Drysdale R (2003)<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134.<br />
: [http://flybase.org/reports/FBrf0167361.html FBrf0167361]<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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)<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081<br />
:: [http://flybase.org/reports/FBrf0155825.html FBrf0155825]<br />
<br />
<br />
::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)<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082<br />
:: [http://flybase.org/reports/FBrf0155826.html FBrf0155826]<br />
<br />
<br />
::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)<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083<br />
:: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:FlyBase (1999)<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:The FlyBase Consortium (1998)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997)<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995)<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
:The FlyBase Consortium (1994)<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994)<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:Ashburner M (1993)<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
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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.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125285
FlyBase:About
2014-01-16T14:22:51Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
:The Drosophila anatomy ontology.<br />
:J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
:The Drosophila Phenotype Ontology.<br />
:J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013).<br />
:On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
:PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
:[http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013). <br />
:FlyBase: improvements to the bibliography. <br />
:Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
:[http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013). <br />
:Systematic analysis of experimental phenotype data reveals gene functions. <br />
:PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012). <br />
:Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
:Database 2012 [FBrf0219955] doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
<br />
<br />
:Gene Ontology Consortium (2012). <br />
:Gene Ontology annotations and resources. <br />
:Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012).<br />
:Directly e-mailing authors of newly published papers encourages community curation. <br />
:Database 2012 [FBrf0218522] doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012). <br />
:FlyBase 101 – the basics of navigating FlyBase. <br />
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108] doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
<br />
<br />
: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).<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. [FBrf0218533] doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
<br />
<br />
:Gene Ontology Consortium (2012).<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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).<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. [FBrf0214821] doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
<br />
<br />
: Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. PubMed PMID: 21419760. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009).<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. PubMed PMID: 19920128. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132. [FBrf0209611] doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009).<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427] doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009).<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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).<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. [FBrf0206621] doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. PubMed PMID: 19210778. [FBrf0207486] doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008).<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [FBrf0205804] [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
<br />
<br />
: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).<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. PubMed PMID: 18769432. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008).<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381] doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008).<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. [FBrf0203012] doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007).<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. [FBrf0194786] [http://nar.oxfordjournals.org/content/35/suppl_1/D486.full doi:10.1093/nar/gkl827]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium., (2007).<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. [FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007).<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]<br />
<br />
<br />
:Lin MF et al., (2007).<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res 17: 1823-1836. [FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007).<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346. [FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007).<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232. [FBrf0200674]<br />
<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium, (2006).<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]<br />
<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium, (2005).<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Richards S et al. (2005).<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18. [FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005).<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Drysdale R (2003).<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]<br />
: (Reproduced with permission from Briefings in Functional Genomics and Proteomics)<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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).<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]<br />
<br />
<br />
::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).<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]<br />
<br />
<br />
::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).<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083 [html] [PDF] []<br />
: [http://flybase.org/reports/FBrf0155827.html FBrf0155827]<br />
<br />
:The FlyBase Consortium (2002)<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108<br />
: [http://flybase.org/reports/FBrf0141697.html FBrf0141697]<br />
<br />
<br />
:Matthews K and Cook K (2001)<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago.<br />
: [http://flybase.org/reports/FBrf0185967.html FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001)<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80<br />
: [http://flybase.org/reports/FBrf0137187.html FBrf0137187]<br />
<br />
<br />
:FlyBase (1999).<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150.<br />
: [http://flybase.org/reports/FBrf0111589.html FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88<br />
: [http://flybase.org/reports/FBrf0107356.html FBrf0107356]<br />
<br />
<br />
:The FlyBase Consortium (1998).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88<br />
: [http://flybase.org/reports/FBrf0100346.html FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66<br />
: [http://flybase.org/reports/FBrf0093096.html FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56<br />
: [http://flybase.org/reports/FBrf0085043.html FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995).<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29.<br />
: [http://flybase.org/reports/FBrf0078422.html FBrf0078422]<br />
<br />
:The FlyBase Consortium (1994).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458<br />
: [http://flybase.org/reports/FBrf0077015.html FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994).<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079<br />
: [http://flybase.org/reports/FBrf0072526.html FBrf0072526]<br />
<br />
<br />
:Ashburner M (1993).<br />
: FlyBase.<br />
: GNome News 13:19-20.<br />
: [http://flybase.org/reports/FBrf0058642.html FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125284
FlyBase:About
2014-01-16T13:30:13Z
<p>Sjm41: /* FlyBase Publications */ Putting initials in correct place in citation</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
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Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
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Josh Goodman<br />
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Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
:The Drosophila anatomy ontology.<br />
:J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
:The Drosophila Phenotype Ontology.<br />
:J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013).<br />
:On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
:PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
:[http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013). <br />
:FlyBase: improvements to the bibliography. <br />
:Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
:[http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013). <br />
:Systematic analysis of experimental phenotype data reveals gene functions. <br />
:PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012). <br />
:Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
:Database 2012 [FBrf0219955] doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
<br />
<br />
:Gene Ontology Consortium (2012). <br />
:Gene Ontology annotations and resources. <br />
:Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH and the FlyBase Consortium (2012).<br />
:Directly e-mailing authors of newly published papers encourages community curation. <br />
:Database 2012 [FBrf0218522] doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012). <br />
:FlyBase 101 – the basics of navigating FlyBase. <br />
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108] doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
<br />
<br />
: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).<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. [FBrf0218533] doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
<br />
<br />
:Gene Ontology Consortium (2012).<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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).<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. [FBrf0214821] doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
<br />
<br />
: Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. PubMed PMID: 21419760. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009).<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. PubMed PMID: 19920128. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132. [FBrf0209611] doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
<br />
<br />
:St. Pierre S and McQuilton P (2009).<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427] doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009).<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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).<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. [FBrf0206621] doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. PubMed PMID: 19210778. [FBrf0207486] doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
<br />
<br />
:Drysdale R, and The FlyBase Consortium, (2008).<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [FBrf0205804] [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
<br />
<br />
: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).<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. PubMed PMID: 18769432. doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T, (2008).<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381] doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
<br />
<br />
:Wilson RJ, Goodman JL, Strelets VB and the FlyBase Consortium (2008).<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. [FBrf0203012] doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
<br />
<br />
:Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM and the FlyBase Consortium (2007).<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. [FBrf0194786] [http://nar.oxfordjournals.org/content/35/suppl_1/D486.full doi:10.1093/nar/gkl827]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium., (2007).<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. [FBrf0200326]<br />
<br />
<br />
:Karamanis N, Lewin L, Seal R, Drysdale R, Briscoe E (2007).<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]<br />
<br />
<br />
:Lin MF et al., (2007).<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res 17: 1823-1836. [FBrf0202906]<br />
<br />
<br />
:Mungall CJ, Emmert DB and the FlyBase Consortium (2007).<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346. [FBrf0201050]<br />
<br />
<br />
:Stark A et al. (2007).<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232. [FBrf0200674]<br />
<br />
<br />
:Grumbling G, Strelets V and The FlyBase Consortium, (2006).<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]<br />
<br />
<br />
:Drysdale RA, Crosby MA and the FlyBase Consortium, (2005).<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Richards S et al. (2005).<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18. [FBrf0184012]<br />
<br />
<br />
:Zhou P, Emmert D, Zhang P (2005).<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Drysdale R (2003).<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]<br />
: (Reproduced with permission from Briefings in Functional Genomics and Proteomics)<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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).<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]<br />
<br />
<br />
::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).<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]<br />
<br />
<br />
::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).<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium, (2002).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Matthews K and Cook K (2001).<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]<br />
<br />
<br />
:Drysdale R (2001).<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]<br />
: (Reproduced with permission from Briefings in Bioinformatics)<br />
<br />
<br />
:FlyBase (1999).<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150. [FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:The FlyBase Consortium (1998).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88 [FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66 [FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56 [FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995).<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]<br />
<br />
<br />
:The FlyBase Consortium (1994).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458 [FBrf0077015]<br />
<br />
<br />
:Ashburner M and Drysdale R (1994).<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079 [FBrf0072526]<br />
<br />
<br />
:Ashburner M (1993).<br />
: FlyBase.<br />
: GNome News 13:19-20. [FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
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<br />
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.<br />
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Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125283
FlyBase:About
2014-01-14T12:27:56Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
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<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
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Helen Attrill<br />
Marta Costa<br />
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<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
:The Drosophila anatomy ontology.<br />
:J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
:The Drosophila Phenotype Ontology.<br />
:J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013).<br />
:On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
:PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
:[http://flybase.org/reports/FBrf0222712.html FBrf0222712]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013). <br />
:FlyBase: improvements to the bibliography. <br />
:Nucleic Acids Res. 41(D1):D751-D757. doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
:[http://flybase.org/reports/FBrf0220350.html FBrf0220350]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013). <br />
:Systematic analysis of experimental phenotype data reveals gene functions. <br />
:PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012). <br />
:Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
:Database 2012 [FBrf0219955] doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
<br />
<br />
:Gene Ontology Consortium (2012). <br />
:Gene Ontology annotations and resources. <br />
:Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).<br />
:Directly e-mailing authors of newly published papers encourages community curation. <br />
:Database 2012 [FBrf0218522] doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012). <br />
:FlyBase 101 – the basics of navigating FlyBase. <br />
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108] doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
<br />
<br />
: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).<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. [FBrf0218533] doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
<br />
<br />
:Gene Ontology Consortium (2012).<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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).<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. [FBrf0214821] doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
<br />
<br />
: Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. PubMed PMID: 21419760. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009).<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. PubMed PMID: 19920128. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132. [FBrf0209611] doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
<br />
<br />
:S. St. Pierre, P. McQuilton (2009).<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427] doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009).<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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).<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. [FBrf0206621] doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. PubMed PMID: 19210778. [FBrf0207486] doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
<br />
<br />
:R. Drysdale, and The FlyBase Consortium, (2008).<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [FBrf0205804] [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
<br />
<br />
: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).<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. PubMed PMID: 19182544. [FBrf0213427] doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381] doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
<br />
<br />
:R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. [FBrf0203012] doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
<br />
<br />
:M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. [FBrf0194786] [http://nar.oxfordjournals.org/content/35/suppl_1/D486.full doi:10.1093/nar/gkl827]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium., (2007).<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. [FBrf0200326]<br />
<br />
<br />
:N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]<br />
<br />
<br />
:M.F. Lin, et al., (2007).<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res 17: 1823-1836. [FBrf0202906]<br />
<br />
<br />
:C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346. [FBrf0201050]<br />
<br />
<br />
:A. Stark et al., (2007).<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232. [FBrf0200674]<br />
<br />
<br />
:G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]<br />
<br />
<br />
:R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:S. Richards et al., (2005).<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18. [FBrf0184012]<br />
<br />
<br />
:P. Zhou, D. Emmert, P. Zhang, (2005).<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Rachel Drysdale, (2003).<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]<br />
: (Reproduced with permission from Briefings in Functional Genomics and Proteomics)<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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).<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]<br />
<br />
<br />
::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).<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]<br />
<br />
<br />
::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).<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium, (2002).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:K. Matthews and K. Cook (2001).<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]<br />
<br />
<br />
:Rachel Drysdale, (2001).<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]<br />
: (Reproduced with permission from Briefings in Bioinformatics)<br />
<br />
<br />
:FlyBase (1999).<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150. [FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:The FlyBase Consortium (1998).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88 [FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66 [FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56 [FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995).<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]<br />
<br />
<br />
:The FlyBase Consortium (1994).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458 [FBrf0077015]<br />
<br />
<br />
:M. Ashburner and R. Drysdale (1994).<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079 [FBrf0072526]<br />
<br />
<br />
:M. Ashburner (1993).<br />
: FlyBase.<br />
: GNome News 13:19-20. [FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
<br />
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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125282
FlyBase:About
2014-01-14T12:24:01Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
:The Drosophila anatomy ontology.<br />
:J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
:The Drosophila Phenotype Ontology.<br />
:J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013).<br />
:On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
:PeerJ. 1:e148. FBrf: [http://flybase.org/reports/FBrf0222712.html FBrf0222712] doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
<br />
<br />
:Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013). <br />
:FlyBase: improvements to the bibliography. <br />
:Nucleic Acids Res. 41(D1):D751-D757. FBrf: [http://flybase.org/reports/FBrf0220350.html FBrf0220350] doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013). <br />
:Systematic analysis of experimental phenotype data reveals gene functions. <br />
:PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012). <br />
:Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
:Database 2012 [FBrf0219955] doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
<br />
<br />
:Gene Ontology Consortium (2012). <br />
:Gene Ontology annotations and resources. <br />
:Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).<br />
:Directly e-mailing authors of newly published papers encourages community curation. <br />
:Database 2012 [FBrf0218522] doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012). <br />
:FlyBase 101 – the basics of navigating FlyBase. <br />
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108] doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
<br />
<br />
: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).<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. [FBrf0218533] doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
<br />
<br />
:Gene Ontology Consortium (2012).<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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).<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. [FBrf0214821] doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
<br />
<br />
: Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. PubMed PMID: 21419760. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009).<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. PubMed PMID: 19920128. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132. [FBrf0209611] doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
<br />
<br />
:S. St. Pierre, P. McQuilton (2009).<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427] doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009).<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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).<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. [FBrf0206621] doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. PubMed PMID: 19210778. [FBrf0207486] doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
<br />
<br />
:R. Drysdale, and The FlyBase Consortium, (2008).<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [FBrf0205804] [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
<br />
<br />
: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).<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. PubMed PMID: 19182544. [FBrf0213427] doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381] doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
<br />
<br />
:R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. [FBrf0203012] doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
<br />
<br />
:M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. [FBrf0194786] [http://nar.oxfordjournals.org/content/35/suppl_1/D486.full doi:10.1093/nar/gkl827]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium., (2007).<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. [FBrf0200326]<br />
<br />
<br />
:N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]<br />
<br />
<br />
:M.F. Lin, et al., (2007).<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res 17: 1823-1836. [FBrf0202906]<br />
<br />
<br />
:C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346. [FBrf0201050]<br />
<br />
<br />
:A. Stark et al., (2007).<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232. [FBrf0200674]<br />
<br />
<br />
:G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]<br />
<br />
<br />
:R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:S. Richards et al., (2005).<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18. [FBrf0184012]<br />
<br />
<br />
:P. Zhou, D. Emmert, P. Zhang, (2005).<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Rachel Drysdale, (2003).<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]<br />
: (Reproduced with permission from Briefings in Functional Genomics and Proteomics)<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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).<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]<br />
<br />
<br />
::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).<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]<br />
<br />
<br />
::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).<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium, (2002).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:K. Matthews and K. Cook (2001).<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]<br />
<br />
<br />
:Rachel Drysdale, (2001).<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]<br />
: (Reproduced with permission from Briefings in Bioinformatics)<br />
<br />
<br />
:FlyBase (1999).<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150. [FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:The FlyBase Consortium (1998).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88 [FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66 [FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56 [FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995).<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]<br />
<br />
<br />
:The FlyBase Consortium (1994).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458 [FBrf0077015]<br />
<br />
<br />
:M. Ashburner and R. Drysdale (1994).<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079 [FBrf0072526]<br />
<br />
<br />
:M. Ashburner (1993).<br />
: FlyBase.<br />
: GNome News 13:19-20. [FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
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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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125281
FlyBase:About
2014-01-14T12:17:52Z
<p>Sjm41: /* FlyBase Publications */</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
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Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
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Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
:The Drosophila anatomy ontology.<br />
:J. Biomed. Semantics 4(1):32 doi: [http://www.jbiomedsem.com/content/4/1/32 10.1186/2041-1480-4-32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
:The Drosophila Phenotype Ontology.<br />
:J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013).<br />
:On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
:PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
<br />
<br />
: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). <br />
:FlyBase: improvements to the bibliography. <br />
:Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350] doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013). <br />
:Systematic analysis of experimental phenotype data reveals gene functions. <br />
:PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012). <br />
:Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
:Database 2012 [FBrf0219955] doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
<br />
<br />
:Gene Ontology Consortium (2012). <br />
:Gene Ontology annotations and resources. <br />
:Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).<br />
:Directly e-mailing authors of newly published papers encourages community curation. <br />
:Database 2012 [FBrf0218522] doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012). <br />
:FlyBase 101 – the basics of navigating FlyBase. <br />
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108] doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
<br />
<br />
: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).<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. [FBrf0218533] doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
<br />
<br />
:Gene Ontology Consortium (2012).<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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).<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. [FBrf0214821] doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
<br />
<br />
: Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. PubMed PMID: 21419760. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009).<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. PubMed PMID: 19920128. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132. [FBrf0209611] doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
<br />
<br />
:S. St. Pierre, P. McQuilton (2009).<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427] doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009).<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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).<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. [FBrf0206621] doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. PubMed PMID: 19210778. [FBrf0207486] doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
<br />
<br />
:R. Drysdale, and The FlyBase Consortium, (2008).<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [FBrf0205804] [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
<br />
<br />
: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).<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. PubMed PMID: 19182544. [FBrf0213427] doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381] doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
<br />
<br />
:R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. [FBrf0203012] doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
<br />
<br />
:M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. [FBrf0194786] [http://nar.oxfordjournals.org/content/35/suppl_1/D486.full doi:10.1093/nar/gkl827]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium., (2007).<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. [FBrf0200326]<br />
<br />
<br />
:N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]<br />
<br />
<br />
:M.F. Lin, et al., (2007).<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res 17: 1823-1836. [FBrf0202906]<br />
<br />
<br />
:C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346. [FBrf0201050]<br />
<br />
<br />
:A. Stark et al., (2007).<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232. [FBrf0200674]<br />
<br />
<br />
:G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]<br />
<br />
<br />
:R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:S. Richards et al., (2005).<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18. [FBrf0184012]<br />
<br />
<br />
:P. Zhou, D. Emmert, P. Zhang, (2005).<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Rachel Drysdale, (2003).<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]<br />
: (Reproduced with permission from Briefings in Functional Genomics and Proteomics)<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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).<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]<br />
<br />
<br />
::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).<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]<br />
<br />
<br />
::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).<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium, (2002).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:K. Matthews and K. Cook (2001).<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]<br />
<br />
<br />
:Rachel Drysdale, (2001).<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]<br />
: (Reproduced with permission from Briefings in Bioinformatics)<br />
<br />
<br />
:FlyBase (1999).<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150. [FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:The FlyBase Consortium (1998).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88 [FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66 [FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56 [FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995).<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]<br />
<br />
<br />
:The FlyBase Consortium (1994).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458 [FBrf0077015]<br />
<br />
<br />
:M. Ashburner and R. Drysdale (1994).<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079 [FBrf0072526]<br />
<br />
<br />
:M. Ashburner (1993).<br />
: FlyBase.<br />
: GNome News 13:19-20. [FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
<br />
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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
<br />
[[Category:FlyBase]]</div>
Sjm41
https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:About&diff=125280
FlyBase:About
2014-01-14T12:14:57Z
<p>Sjm41: Added Costa et al, corrected couple of citations.</p>
<hr />
<div>==FlyBase Consortium==<br />
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.<br />
<br />
Please use the contact FlyBase form to write to us.<br />
<br />
:'''FlyBase-Harvard'''<br />
:Biological Laboratories, Harvard University<br />
:16 Divinity Avenue<br />
:Cambridge, Massachusetts 02138<br />
:USA<br />
<br />
William Gelbart (PI)<br />
Kris Broll<br />
Lynn Crosby<br />
Gil dos Santos<br />
David Emmert<br />
L. Sian Gramates<br />
Kathleen Falls<br />
Beverley Matthews<br />
Susan Russo<br />
Andy Schroeder<br />
Susan St. Pierre<br />
Pinglei Zhou<br />
Mark Zytkovicz<br />
<br />
:'''FlyBase-Cambridge'''<br />
:Department of Genetics, University of Cambridge<br />
:Downing Street, Cambridge CB2 3EH<br />
:UK<br />
<br />
Nick Brown (PI)<br />
Boris Adryan<br />
Helen Attrill<br />
Marta Costa<br />
Steven Marygold<br />
Peter McQuilton<br />
Gillian Millburn<br />
Laura Ponting<br />
Ray Stefancsik<br />
Susan Tweedie<br />
<br />
:'''FlyBase-Indiana'''<br />
:Department of Biology, Indiana University<br />
:1001 East 3rd Street<br />
:Bloomington, Indiana 47405-7005<br />
:USA<br />
<br />
Thomas Kaufman (PI)<br />
Kathy Matthews (PI)<br />
Josh Goodman<br />
Gary Grumbling<br />
Victor Strelets<br />
Jim Thurmond<br />
<br />
:'''FlyBase-NewMexico'''<br />
:Department of Biology, Castetter Hall - Room 200<br />
:University of New Mexico,<br />
:Albuquerque, New Mexico 87131<br />
:USA<br />
<br />
Maggie Werner-Washburne (PI)<br />
Richard Cripps (PI)<br />
Harriett Platero<br />
<br />
==FlyBase Publications==<br />
<br />
<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. 42(1):D780-8. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
<br />
:Costa M, Reeve S, Grumbling G, Osumi-Sutherland D. (2013)<br />
:The Drosophila anatomy ontology.<br />
:J. Biomed. Semantics 4(1):32 [http://www.jbiomedsem.com/content/4/1/32]<br />
<br />
<br />
:Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Fall K, Brown NH, Gkoutos GV. (2013)<br />
:The Drosophila Phenotype Ontology.<br />
:J. Biomed. Semantics 4(1):30. doi: [http://www.jbiomedsem.com/content/4/1/30 10.1186/2041-1480-4-30]<br />
<br />
<br />
:Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, Larocca GM, Haendel MA (2013).<br />
:On the reproducibility of science: unique identification of research resources in the biomedical literature.<br />
:PeerJ. 1:e148. doi: [http://peerj.com/articles/148/ 10.7717/peerj.148]<br />
<br />
<br />
: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). <br />
:FlyBase: improvements to the bibliography. <br />
:Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350] doi: [http://nar.oxfordjournals.org/content/41/D1/D751.long 10.1093/nar/gks1024]<br />
<br />
<br />
:Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013). <br />
:Systematic analysis of experimental phenotype data reveals gene functions. <br />
:PLoS One. 8(4):e60847. doi: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060847 10.1371/journal.pone.0060847]<br />
<br />
<br />
:McQuilton P and the FlyBase Consortium (2012). <br />
:Opportunities for text mining in the FlyBase genetic literature curation workflow. <br />
:Database 2012 [FBrf0219955] doi: [http://database.oxfordjournals.org/content/2012/bas039.long 10.1093/database/bas039]<br />
<br />
<br />
:Gene Ontology Consortium (2012). <br />
:Gene Ontology annotations and resources. <br />
:Nucleic Acids Res. 41(Database issue):D530-5. doi: [http://nar.oxfordjournals.org/content/41/D1/D530.full 10.1093/nar/gks1050]<br />
<br />
<br />
:S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).<br />
:Directly e-mailing authors of newly published papers encourages community curation. <br />
:Database 2012 [FBrf0218522] doi: [http://database.oxfordjournals.org/content/2012/bas024.long 10.1093/database/bas024]<br />
<br />
<br />
:McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012). <br />
:FlyBase 101 – the basics of navigating FlyBase. <br />
:Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108] doi: [http://nar.oxfordjournals.org/content/40/D1/D706.long 10.1093/nar/gkr1030]<br />
<br />
<br />
: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).<br />
: Automatic categorization of diverse experimental information in the bioscience literature.<br />
: BMC Bioinformatics. 13(1):16. [FBrf0218533] doi: [http://www.biomedcentral.com/1471-2105/13/16 10.1186/1471-2105-13-16]<br />
<br />
<br />
:Gene Ontology Consortium (2012).<br />
: The Gene Ontology: enhancements for 2011.<br />
: Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568. doi: [http://nar.oxfordjournals.org/content/40/D1/D559.long 10.1093/nar/gkr1028]<br />
<br />
<br />
: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).<br />
: Toward an interactive article: integrating journals and biological databases.<br />
: BMC Bioinformatics 2011, 12:175. [FBrf0214821] doi:[http://www.biomedcentral.com/1471-2105/12/175 10.1186/1471-2105-12-175]<br />
<br />
<br />
: Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).<br />
: The representation of heart development in the gene ontology.<br />
: Dev Biol. 354(1):9-17. PubMed PMID: 21419760. doi: [http://www.sciencedirect.com/science/article/pii/S0012160611001758 10.1016/j.ydbio.2011.03.011]<br />
<br />
<br />
:Gene Ontology Consortium (2009).<br />
: The Gene Ontology in 2010: extensions and refinements.<br />
: Nucleic Acids Res. 38(Database issue):D331-5. PubMed PMID: 19920128. doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D331.long 10.1093/nar/gkp1018]<br />
<br />
<br />
:Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).<br />
: FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.<br />
: Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132. [FBrf0209611] doi: [http://nar.oxfordjournals.org/content/38/suppl_1/D443.long 10.1093/nar/gkp910]<br />
<br />
<br />
:S. St. Pierre, P. McQuilton (2009).<br />
: Inside FlyBase (Biocuration as a career).<br />
: Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427] doi: [http://www.landesbioscience.com/journals/fly/article/7769/ 10.4161/fly.3.1.7769]<br />
<br />
<br />
:Reference Genome Group of the Gene Ontology Consortium (2009).<br />
: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.<br />
: PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431. doi:[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000431 10.1371/journal.pcbi.1000431]<br />
<br />
<br />
: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).<br />
: FlyBase: enhancing Drosophila Gene Ontology annotations.<br />
: Nucleic Acids Res. 37: D555-D559. [FBrf0206621] doi: [http://nar.oxfordjournals.org/content/37/suppl_1/D555.long 10.1093/nar/gkn788]<br />
<br />
<br />
:Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).<br />
: The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.<br />
: BMC Bioinformatics. 10:59. PubMed PMID: 19210778. [FBrf0207486] doi:[http://www.biomedcentral.com/1471-2105/10/59 10.1186/1471-2105-10-59]<br />
<br />
<br />
:R. Drysdale, and The FlyBase Consortium, (2008).<br />
: FlyBase : a database for the Drosophila research community.<br />
: Methods Molec. Biol. 420: 45-59. [FBrf0205804] [http://link.springer.com/protocol/10.1007%2F978-1-59745-583-1_3 Book Chapter.]<br />
<br />
<br />
: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).<br />
: Big data: The future of biocuration.<br />
: Nature. 455(7209):47-50. PubMed PMID: 19182544. [FBrf0213427] doi: [http://www.nature.com/nature/journal/v455/n7209/full/455047a.html 10.1038/455047a]. <br />
<br />
<br />
:N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).<br />
: Natural language processing in aid of FlyBase curators.<br />
: BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381] doi:[http://www.biomedcentral.com/1471-2105/9/193 10.1186/1471-2105-9-193]<br />
<br />
<br />
:R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).<br />
: FlyBase: integration and improvements to query tools.<br />
: Nucleic Acids Res. 36: D588-D593. [FBrf0203012] doi:[http://nar.oxfordjournals.org/content/36/suppl_1/D588.full 10.1093/nar/gkm930]<br />
<br />
<br />
:M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).<br />
: FlyBase: genomes by the dozen.<br />
: Nucleic Acids Res. 35: D486-D491. [FBrf0194786] [http://nar.oxfordjournals.org/content/35/suppl_1/D486.full doi:10.1093/nar/gkl827]<br />
<br />
<br />
:Drosophila 12 Genomes Consortium., (2007).<br />
: Evolution of genes and genomes on the Drosophila phylogeny.<br />
: Nature 450: 203-218. [FBrf0200326]<br />
<br />
<br />
:N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).<br />
: Integrating natural language processing with FlyBase curation.<br />
: Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]<br />
<br />
<br />
:M.F. Lin, et al., (2007).<br />
: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.<br />
: Genome Res 17: 1823-1836. [FBrf0202906]<br />
<br />
<br />
:C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).<br />
: A Chado case study: an ontology-based modular schema for representing genome-associated biological information.<br />
: Bioinformatics 23: i337-346. [FBrf0201050]<br />
<br />
<br />
:A. Stark et al., (2007).<br />
: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.<br />
: Nature 450: 219-232. [FBrf0200674]<br />
<br />
<br />
:G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).<br />
: FlyBase: anatomical data, images and queries.<br />
: Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]<br />
<br />
<br />
:R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).<br />
: FlyBase : Genes and gene models.<br />
: Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:S. Richards et al., (2005).<br />
: Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.<br />
: Genome Res., 15: 1-18. [FBrf0184012]<br />
<br />
<br />
:P. Zhou, D. Emmert, P. Zhang, (2005).<br />
: Using chado to store genome annotation data.<br />
: Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]<br />
<br />
<br />
:The FlyBase Consortium, (2003).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:Rachel Drysdale, (2003).<br />
: The Drosophila melanogaster genome sequencing and annotation projects: A status report.<br />
: Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]<br />
: (Reproduced with permission from Briefings in Functional Genomics and Proteomics)<br />
<br />
<br />
:'''Genome Annotation, (2002)'''<br />
<br />
<br />
::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).<br />
:: An integrated computational pipeline and database to support whole-genome sequence annotation.<br />
:: Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]<br />
<br />
<br />
::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).<br />
:: Apollo: a sequence annotation editor.<br />
:: Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]<br />
<br />
<br />
::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).<br />
:: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.<br />
:: Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]<br />
<br />
<br />
:The FlyBase Consortium, (2002).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:K. Matthews and K. Cook (2001).<br />
: Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.<br />
: In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]<br />
<br />
<br />
:Rachel Drysdale, (2001).<br />
: Phenotypic data in FlyBase.<br />
: Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]<br />
: (Reproduced with permission from Briefings in Bioinformatics)<br />
<br />
<br />
:FlyBase (1999).<br />
: FlyBase: Genomic and post-genomic viewpoints.<br />
: In S. Letovsky (Ed.)<br />
: Bioinformatics: Databases and Systems 141--150. [FBrf0111589]<br />
<br />
<br />
:The FlyBase Consortium, (1999).<br />
: The FlyBase Database of the Drosophila Genome Projects and community literature.<br />
: Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]<br />
: (Reproduced with permission from NAR Online )<br />
<br />
<br />
:The FlyBase Consortium (1998).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 26:85-88 [FBrf0100346]<br />
<br />
<br />
:The FlyBase Consortium (1997).<br />
: FlyBase - A Drosophila database.<br />
: Nucleic Acids Res., 25:63-66 [FBrf0093096]<br />
<br />
<br />
:The FlyBase Consortium (1996).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 24:53-56 [FBrf0085043]<br />
<br />
<br />
:The FlyBase Consortium (1995).<br />
: Proposed genetic nomenclature for Drosophila melanogaster.<br />
: Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]<br />
<br />
<br />
:The FlyBase Consortium (1994).<br />
: FlyBase - The Drosophila database.<br />
: Nucleic Acids Res., 22:3456-3458 [FBrf0077015]<br />
<br />
<br />
:M. Ashburner and R. Drysdale (1994).<br />
: FlyBase - The Drosophila genetic database.<br />
: Development 120:2077-2079 [FBrf0072526]<br />
<br />
<br />
:M. Ashburner (1993).<br />
: FlyBase.<br />
: GNome News 13:19-20. [FBrf0058642]<br />
<br />
==Citing FlyBase==<br />
We suggest FlyBase be referenced in publications in the following manner:<br />
:St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2013).<br />
:FlyBase 102 - advanced approaches to interrogating FlyBase.<br />
:Nucleic Acids Res. doi: [http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1092.long 10.1093/nar/gkt1092]<br />
<br />
==FlyBase Copyright==<br />
===The Copyright of FlyBase===<br />
Copyright ©1993-2006 by The Genetics Society of America.<br />
All Rights Reserved.<br />
<br />
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/>.<br />
<br />
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.<br />
<br />
Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase.<br />
Warranty<br />
<br />
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.<br />
<br />
The information contained in this publication is subject to change without notice.<br />
<br />
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.<br />
Disclaimer<br />
<br />
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. <br />
<br />
===BIOSIS Copyright===<br />
The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:<br />
<br />
"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." <br />
<br />
===Herskowitz's Bibliography Copyright===<br />
The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:<br />
<br />
"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. "<br />
<br />
"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." <br />
<br />
===Lindsley and Zimm (1992)===<br />
Lindsley and Zimm (1992) - The New Redbook<br />
The Genome of Drosophila melanogaster<br />
Dan L. Lindsley & Georgianna G. Zimm<br />
Copyright 1992 By Academic Press, Inc.<br />
All Rights Reserved.<br />
<br />
ISBN 0-12-450990-8<br />
Academic Press, Inc.<br />
1250 Sixth Avenue, San Diego, California 92101-4311<br />
<br />
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. <br />
==FlyBase Data Sources==<br />
<br />
'''The Red Book'''<br />
<br />
Lindsley and Zimm (1992) The Genome of Drosophila melanogaster<br />
<br />
'''Bibliographies'''<br />
<br />
The major sources that have been incorporated into the FlyBase Bibliography:<br />
<br />
: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.<br />
:<br />
:Bibliography on the Genetics of Drosophila. [Part One.] H. J. Muller, 1939.<br />
:Imperial Bureau of Animal Breeding and Genetics. Edinburgh: Oliver and Boyd.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Two. Irwin H. Herskowitz, 1952.<br />
:Commonwealth Agricultural Bureaux. Slough: Farnham Royal.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Three. Irwin H. Herskowitz, 1958.<br />
:Indiana University Publications.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Four. Irwin H. Herskowitz, 1963.<br />
:McGraw-Hill Book Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Five. Irwin H. Herskowitz, 1969.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Six. Irwin H. Herskowitz, 1974.<br />
:Macmillan Publishing Company, Inc.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven A. Irwin H. Herskowitz, 1976.<br />
:Drosophila Information Service 51: 159-193.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven B. Irwin H. Herskowitz, 1977.<br />
:Drosophila Information Service 52:186-226.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven C. Irwin H. Herskowitz, 1978.<br />
:Drosophila Information Service 53: 219-244.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Parts Seven D(I) and D(II). Irwin H. Herskowitz, 1980.<br />
:Drosophila Information Service 55: 218-262.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Seven E. Irwin H. Herskowitz, 1981.<br />
:Drosophila Information Service 56: 199-210.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight A. Irwin H. Herskowitz, 1982.<br />
:Drosophila Information Service 58: 227-270.<br />
:<br />
:Bibliography on the Genetics of Drosophila. Part Eight B. Irwin H. Herskowitz, 1983.<br />
:Drosophila Information Service 59: 163-207.<br />
:<br />
:Contents pages of Drosophila Information Service: volume 50 (1975) to volume 75 (1994).<br />
:<br />
:Bibliography of the biochemical genetics of Drosophila. Morton S. Fuchs, 1965.<br />
:Drosophila Information Service 40: 105-126.<br />
:<br />
:Bibliography of Hawaiian Drosophilidae. Hampton L. Carson and Linden T. Teramoto, 1982.<br />
:Drosophila Information Service: 58: 215-226.<br />
:<br />
:Bibliography on Drosophila hydei. F. M. A. van Breugel, 1987.<br />
:Drosophila Information Service 66: 198-208.<br />
:<br />
:Bibliography on the Drosophila nasuta subgroup. W.-E. Kalisch, 1991.<br />
:Drosophila Information Service 70: 110-117.<br />
:<br />
:Bibliography on Drosophila ananassae. B. N. Singh, 1991.<br />
:Drosophila Information Service 70: 205-211.<br />
:<br />
:The Bibliography of Theoretical Population Genetics. J. Felsenstein, 1988.<br />
:Dowden, Hutchinson and Ross Publications, Inc.<br />
:<br />
:Bibliography: longevity, ageing and parental age effects in Drosophila (1907-86).<br />
:M. Hani Soliman, Frédéric A. Lints, Cécile V. Lints and Pol Bullens. Pages 241-293.<br />
:In: Drosophila as a Model System for Ageing Studies. F.A. Lints and M.H. Soliman (Eds.), 1988.<br />
:Blackie Publications. Glasgow, Scotland.<br />
:<br />
:End of Chapter references from Drosophila: A laboratory handbook and Drosophila: A laboratory manual. Michael Ashburner, 1989. Cold Spring Harbor Laboratory Press.<br />
:<br />
:A bibliography on Drosophila compiled and provided by Dr. G. Baechli (University of Zurich).<br />
:January 1993 with regular subsequent updates.<br />
:<br />
:References from Drosophila ananassae. Genetical and biological aspects. Y.N. Tobari (Editor). 1993.<br />
:<br />
:Japan Scientific Societies Press and Karger, Tokyo and Basel.<br />
:<br />
:References from the Environmental Mutagen Information Center (EMIC) database.<br />
:<br />
:MEDLINE (National Library of Medicine, Washington).<br />
:Searched on the Text Word DROSOPHIL. Searched from 1966 to date.<br />
:<br />
:BIOSIS records searched on the keyword DROSOPHIL from 1982 to 2008.<br />
:<br />
:References from all Drosophila entries in the GenBank, NCBI, EMBL and DDBJ nucleic acid sequence databases and SWISS-PROT and PIR protein sequence databases.<br />
:<br />
:References from John Merriam's Genevent database of molecular data.<br />
:<br />
:Drosophila records from the Zoological Record, volume 115 (1978) to 2008.<br />
:<br />
:Jeff Hall's bibliography on neurogenetics of Drosophila.<br />
<br />
'''External Databases'''<br />
<br />
Nucleic Acid Sequence Databases (GenBank/EMBL/DDBJ)<br />
UniProtKB<br />
InterPro<br />
<br />
'''Journal Articles and Books'''<br />
<br />
Publications relevant to Drosophila from various journals and books.<br />
<br />
'''Drosophila Conference Abstracts''' <br />
<br />
The following abstracts were curated until 2008.<br />
<br />
GSA Annual Drosophila Research Conference Abstracts<br />
<br />
European Drosophila Research Conference Abstracts<br />
<br />
'''Personal Communications to FlyBase'''<br />
<br />
Information and observations provided by the Fly Community<br />
<br />
'''Direct Submission of High-Throughput Data'''<br />
<br />
:'''Proteomics data'''<br />
:<br />
:Center for Model Organism Proteomes --<br />
:(SystemsX and Research Priority Project of the University of Zurich, Switzerland)<br />
:<br />
:'''Microarrays''' (Oligos, cDNAs)<br />
:<br />
:Affymetrix, Santa Clara, CA (Affy v1, Affy v2)<br />
:<br />
:Drosophila Genomics Resource Center, Bloomington, IN (DGRC-1, DGRC-2)<br />
:<br />
:'''Tiling BACs'''<br />
:<br />
:Berkeley Drosophila Genome Project<br />
:<br />
'''Insertion Collection Data'''<br />
<br />
:'''Transgene insertion data'''<br />
:Gene Disruption Project (2005 - present)(Bellen et. al., 2004)<br />
:<br />
:Berkeley Drosophila Genome Project (1998 - 2004)(Spradling et. al., 1999)<br />
:<br />
:DrosDel Project, Cambridge, UK (2003 - 2004)(Ryder et. al., 2004)<br />
:<br />
:P{wHy} Project, Gelbart laboratory, Harvard (2002 - present)(Huet et. al., 2002)<br />
:<br />
:P{GawB} Project, GETDB, Japan (2002 - 2004) <br />
:<br />
:NCI lethals (2002 - 2004)(Oh et. al., 2003)<br />
:<br />
:P{GT1} Project, Ed Ryder, Cambridge, UK (2004) <br />
:<br />
:Schaefer lines, Goettingen, Germany (2004)(Beinert et. al., 2004)<br />
:<br />
:'''Natural transposon insertion data'''<br />
:<br />
:[http://flybase.org/reports/FBrf0155828.html Kaminker J. et al. 2002]<br />
:<br />
:[http://flybase.org/reports/FBrf0184336.html Quesneville H. et al. 2005]<br />
<br />
'''Stock Lists Submitted to FlyBase'''<br />
<br />
Bloomington Drosophila Stock Center<br />
<br />
Drosophila Genetic Resource Center<br />
<br />
UC San Diego Drosophila Species Stock Center<br />
<br />
Exelixis Drosophila Stock Collection at Harvard Medical School<br />
<br />
Nusslein-Volhard laboratory<br />
<br />
Garcia-Bellido laboratory<br />
<br />
Carpenter laboratory<br />
<br />
'''People'''<br />
<br />
The original 1992 data set was compiled from the five sources listed. The data set is now user maintained via addition and correction forms.<br />
<br />
An e-mail address list compiled and maintained by Dr. John Haynie (1992)<br />
<br />
Records of the Bloomington Drosophila Stock Center (1992)<br />
<br />
The distribution list of Drosophila Information Newsletter (1992)<br />
<br />
A subset of the Genetics Society of America's mailing and membership list (1992)<br />
<br />
The mailing list for the European Drosophila Research Conference (1992)<br />
<br />
==FlyBase Alumni==<br />
FlyBase thanks these former members of the FlyBase consortium for their contribution:<br />
<br />
Manish Anand<br />
Michael Ashburner<br />
Leyla Bayraktaroglu<br />
Ben Berman<br />
Brian Bettencourt<br />
Lee Bitsoi<br />
Pete Brokstein<br />
Stephanie Bunt<br />
Heather Butler<br />
Kathy Campbell<br />
Russell Collins<br />
Kim Cook<br />
Anthony DeAngelo<br />
Aubrey de Grey<br />
Rachel Drysdale<br />
Helen Field<br />
Rebecca Foulger<br />
Erwin Frise<br />
Mark Gibson<br />
Don Gilbert<br />
Janet Gulotta<br />
Cyrus Harmon<br />
Nomi Harris<br />
Gregg Helt<br />
Pavel Hradecky<br />
Yanmei Huang<br />
Josh Kaminker<br />
Kerry Knight<br />
Sophia Kossida<br />
Rob Kulathinal<br />
Julia Lamenza<br />
Joe Lemaire<br />
Stan Letovsky<br />
Suzanna Lewis<br />
Paul Leyland<br />
Guo-chun Liao<br />
Anne Loraine<br />
Glenn McAlpine<br />
John Merriam<br />
Sima Misra<br />
Emanuel Mongin<br />
Chris Mungall<br />
Tatiana Murnikova<br />
Catherine Nelson<br />
David Osumi-Sutherland<br />
Dawn Palmer<br />
Simon Prochnik<br />
Simon Reeve<br />
John Richter<br />
Wayne Rindone<br />
Margo Roark<br />
Gerry Rubin<br />
Ruth Seal<br />
Carolyn Shemen<br />
Hardik Sheth<br />
Nihar Sheth<br />
Shengqiang Shu<br />
David Simas<br />
Chris Smith<br />
Frank Smutniak<br />
Jon Tupy<br />
Edwin Wang<br />
Eddy Wellbourne<br />
Eleanor Whitfield<br />
Colin Wiel<br />
Mark Williams<br />
Robert Wilson<br />
J.D. Wong<br />
Chihiro Yamada<br />
Mark Yandell<br />
Haiyan Zhang<br />
Peili Zhang<br />
<br />
==FlyBase Support==<br />
FlyBase is supported by a grant from the National Human Genome Research Institute at the<br />
U.S. National Institutes of Health #P41 HG000739.<br />
<br />
Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.<br />
<br />
Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.<br />
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[[Category:FlyBase]]</div>
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