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FlyBase (RRID:SCR_006549)


http://flybase.org/

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.


Keywords

mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae

Resource ID

SCR_006549

Alternate IDs

nif-0000-00558, OMICS_01649

Website Status

Last checked up

Abbreviation(s)

FB

Species

drosophila

Resource Type

Resource, topical portal, organism-related portal, analysis service resource, database, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resource

Funding Information

NHGRI |

Used By

NIF Data Federation, Resource Identification Portal, Monarch Initiative, PhenoGO, Integrated Animals, Drososhare

Availability

Free, Acknowledgement requested, Non-commercial, Commercial use requires permission, The community can contribute to this resource

Synonym(s)

FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FlyBase: A Database of Drosophila Genes and Genomes, FB, FlyBase: A Database of Drosophila Genes and Genomes

Other resources frequently mentioned in the literature with this resource

SciCrunch Registry

Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch are assigned RRIDs which are used to cite resources in scientific manuscripts.

Phenotypic data in FlyBase.

  • Drysdale R
  • Brief. Bioinformatics
  • 2001 Mar 23

Phenotypic analysis combined with molecular genetics is a powerful tool for mapping gene function onto the genome. Phenotypic data are, by their nature, descriptive, and as varied as the range of mutant phenotypes that can be presented by the organism under study. This paper discusses the mechanisms FlyBase has implemented to systematise published phenotypic data about Drosophila, and provides an introduction to the query tools available for the mining of the data. Though FlyBase is specific to Drosophila, the issues faced in devising protocols for capturing, storing and reporting data are the same issues faced by any database with an interest in using phenotypic data to maximise the potential of genomic analysis.

FlyBase--the Drosophila database. The FlyBase Consortium.

  • Nucleic Acids Res.
  • 1994 Sep 8

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is available from the ftp.bio.indiana.edu Gopher server. The scope of FlyBase includes: genes, alleles, aberrations, pointers to sequence data, stock lists, Drosophila workers and bibliographic references.

The FlyBase database of the Drosophila genome projects and community literature.

  • FlyBase Consortium
  • Nucleic Acids Res.
  • 2003 Jan 1

FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. FlyBase has primary responsibility for the continual reannotation of the D. melanogaster genome. The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. A complete revision of the annotations of the now-finished euchromatic genomic sequence has been completed. There are many points of entry to the genome within FlyBase, most notably through maps, gene products and ontologies, structured phenotypic and gene expression data, and anatomy.

FlyBase: a Drosophila database. The FlyBase consortium.

  • Gelbart WM
  • Nucleic Acids Res.
  • 1997 Jan 1

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, transposons, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. The Encyclopedia of Drosophila is a joint effort between FlyBase and the Berkeley Drosophila Genome Project which integrates FlyBase data with those from the BDGP.

FlyBase: a Drosophila database.

  • FlyBase Consortium
  • Nucleic Acids Res.
  • 1998 Jan 1

FlyBase (http://flybase.bio.indiana.edu/) is a comprehensive database of genetic and molecular data concerning Drosophila . FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (with phenotypes), aberrations, transposons, pointers to sequence data, gene products, maps, clones, stock lists, Drosophila workers and bibliographic references.

FlyBase--the Drosophila genetic database.

  • Ashburner M
  • Development
  • 1994 Jul 1

The FlyBase database of the Drosophila Genome Projects and community literature.

  • FlyBase Consortium
  • Nucleic Acids Res.
  • 1999 Jan 1

The FlyBase Drosophila genetics database and the public interfaces of the Berkeley Drosophila Genome Project (BDGP) and European Drosophila Genome Project (EDGP) are in the process of integrating. At present, the data of these projects are available from independent, but hyperlinked, WWW sites (FlyBase URL, http://flybase. bio.indiana.edu/; BDGP URL, http://fruitfly.berkeley.edu/; EDGP URL, http://edgp.ebi.ac.uk/ ). Because of the considerable overlap of data classes between the contributions of the Drosophila genome projects and the Drosophila community, the new and enlarged FlyBase consortium views the implementation of a single integrated Drosophila genomics/genetics server as essential to the scientific community. This integration will occur in a stepwise fashion over the next 1-2 years. In this report, the salient features of the current databases and how to interrogate and navigate the extensive data sets are discussed.

FlyBase: a virtual Drosophila cornucopia.

  • Bellen HJ
  • Trends Genet.
  • 1995 Nov 8

FlyBase: the Drosophila database.

  • Flybase Consortium
  • Nucleic Acids Res.
  • 1996 Jan 1

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase). The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. FlyBase is also available on CD-ROM for Macintosh systems (Encyclopaedia of Drosophila).

The FlyBase database of the Drosophila genome projects and community literature.

  • FlyBase Consortium
  • Nucleic Acids Res.
  • 2002 Jan 1

FlyBase (http://flybase.bio.indiana.edu/) provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species. Following on the success of the Drosophila genome project, FlyBase has primary responsibility for the continual reannotation of the D.melanogaster genome. The ultimate goal of the reannotation effort is to decorate the euchromatic sequence of the genome with as much biological information as is available from the community and from the major genome project centers. The current cycle of reannotation focuses on establishing a comprehensive data set of gene models (i.e. transcription units and CDSs). There are many points of entry to the genome within FlyBase, most notably through maps, gene ontologies, structured phenotypic and gene expression data, and anatomy.

Co-mentions heatmap

Load a heatmap of the top 20 resources that share the most co-mentions with this resource in the literature.


Flybase: Genotypes

FlyBase is a database of genetic and molecular data for D. melanogaster and other Drosophila species. Flybase:Genotypes are the curated details of genetic variant flies, laboratory strains, and relevant publications.

Flybase: Phenotypes

FlyBase is a database of genetic and molecular data for D. melanogaster and other Drosophila species. The Phenotypes view shows the curated links for phenotypes of the flies of a specified genotype, in a specified environment, attributed to a publication.

License Information:
We suggest FlyBase be referenced in publications in the following manner: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014). FlyBase 102 - advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42(D1):D780-D788. doi: 10.1093/nar/gkt1092 [FBrf0223749] ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Citing FlyBase We suggest FlyBase be referenced in publications in the following manner: St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014). FlyBase 102 - advanced approaches to interrogating FlyBase. Nucleic Acids Res. doi: 10.1093/nar/gkt1092 FlyBase Copyright The Copyright of FlyBase Copyright ©1993-2006 by The Genetics Society of America. All Rights Reserved. FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address . 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. Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase. Warranty FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement. The information contained in this publication is subject to change without notice. By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information. Disclaimer Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it. BIOSIS Copyright The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS: "This database is copyrighted by Biological Abstracts Inc. (BIOSIS®). All rights reserved. No part of the information may be reproduced in hard copy, machine-readable form or other form without advance written permission from BIOSIS. Information has been obtained from public sources believed to be reliable. BIOSIS makes a diligent effort to provide complete and accurate representation of the bioscientific and other literature in its publications and services. However, BIOSIS does not guarantee the accuracy, adequacy, or completeness of any information and BIOSIS makes no warranties or representations of any kind, express or implied, including but not limited to warranties of merchantability or fitness for particular purpose. BIOSIS disclaims all liability for errors or omissions that may exist and shall not be liable for any incidental, consequential or other damages (whether resulting from negligence or otherwise) including, without limitation, exemplary damages or lost profits arising out of or in connection with the use of this database. Errors or omissions may be reported to Biological Abstracts Inc., 2100 Arch Street, Philadelphia, PA 19103-1399." Herskowitz's Bibliography Copyright The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography: "Bibliography on the genetics of Drosophila: Part 5, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1969 by Macmillan Publishing Company. " "Bibliography on the genetics of Drosophila: Part 6, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1974 by Macmillan Publishing Company." Lindsley and Zimm (1992) Lindsley and Zimm (1992) - The New Redbook The Genome of Drosophila melanogaster Dan L. Lindsley & Georgianna G. Zimm Copyright 1992 By Academic Press, Inc. All Rights Reserved. ISBN 0-12-450990-8 Academic Press, Inc. 1250 Sixth Avenue, San Diego, California 92101-4311 FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- How do I cite the Drosophila phylogeny? The Drosophila phylogeny shown on FlyBase is a compilation of information that can be found in: A Powell, J.R. 1997 Progress and Prospects in Evolutionary Biology: The Drosophila Model. Oxford University Press, Inc. New York BIOSIS ID: 1102964 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- GO Usage Policy
The GO Consortium gives permission for any of its products to be used without license for any purpose under three conditions:
* That the Gene Ontology Consortium is clearly acknowledged as the source of the product;
* That any GO Consortium file(s) displayed publicly include the date(s) and/or version number(s) of the relevant GO file(s) (the GO is evolving and changes will occur with time);
* That neither the content of the GO file(s) nor the logical relationships embedded within the GO file(s) be altered in any way.

This policy covers the GO ontology, the GO database and the annotations provided by GO Consortium members. The software developed by the GO project, including the ontology editor OBO-Edit, the AmiGO web interface, and the go-dev software utilities are also freely available to the public under the terms stated above; please check the documentation provided with the software for any additional conditions.

Please address any questions about this policy to the GO helpdesk.

Cite GO
To reference the Gene Ontology project, please cite this paper:
The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet.. May 2000;25(1):25-9. [abstract | full text (PDF) | read online at Nature Genetics]

GO Data
If you wish to cite data provided by the Gene Ontology project, either from AmiGO or the files downloaded from the GO website, please state the release date and/or version number of the data. Both annotation and ontology data may change over time, and to reproduce the results of an analysis, it is important that the same initial GO data is used.

Ontology files: Metadata is stored at the top of the ontology file; please state the date of the file and the CVS revision number.

Gene Association files: Please cite the GOC validation date and the CVS revision number, both of which can be found in the first few lines of a gene association file.

Database: Release information can be found in the instance_data table in the database. Please state both the release date and the release type.

Data from AmiGO: The database release can be found in the page footer on the right-hand side.

To cite the annotations of individual database groups please see the GO publications list.

Website Disclaimer
All information on this website is copyright 1999- Tuesday, 07-Feb-2012 12:42:33 PST Gene Ontology Consortium. Permission to use the information contained in this database was given by the researchers and institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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