Using FlyBase: A Database of Drosophila Genes and Genetics

doi:10.1007/978-1-0716-2541-5_1

. 2022:2540:1-34.

doi: 10.1007/978-1-0716-2541-5_1.

Using FlyBase: A Database of Drosophila Genes and Genetics

Victoria K Jenkins¹, Aoife Larkin², Jim Thurmond³; FlyBase Consortium

Affiliations

¹ The Biological Laboratories, Harvard University, Cambridge, MA, USA. vjenkins@morgan.harvard.edu.
² Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
³ Department of Biology, Indiana University, Bloomington, IN, USA.

PMID: 35980571
DOI: 10.1007/978-1-0716-2541-5_1

Using FlyBase: A Database of Drosophila Genes and Genetics

Victoria K Jenkins et al. Methods Mol Biol. 2022.

. 2022:2540:1-34.

doi: 10.1007/978-1-0716-2541-5_1.

Authors

Victoria K Jenkins¹, Aoife Larkin², Jim Thurmond³; FlyBase Consortium

Affiliations

¹ The Biological Laboratories, Harvard University, Cambridge, MA, USA. vjenkins@morgan.harvard.edu.
² Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
³ Department of Biology, Indiana University, Bloomington, IN, USA.

PMID: 35980571
DOI: 10.1007/978-1-0716-2541-5_1

Abstract

Since 1992, FlyBase has provided a freely available online database of information about the model organism Drosophila melanogaster. Data in FlyBase is curated manually from research papers as well as computationally from a variety of relevant sources, to serve as an information hub that enables and accelerates research discovery. This chapter aims to give users new to the database an overview of the layout and types of data available, as well as introducing some tools with which to access the data. More experienced users will find useful information about recent improvements and descriptions to enable more efficient navigation of the database.

Keywords: Database; Drosophila; Fly; FlyBase; Gene; Genome.

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References

1. Flybase Consortium (1996) FlyBase: the Drosophila database. Nucleic Acids Res 24(1):53–56. https://doi.org/10.1093/nar/24.1.53 - DOI
1. Alliance of Genome Resources Consortium (2020) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res 48(D1):D650–D658. https://doi.org/10.1093/nar/gkz813 - DOI
1. Wilkinson MD, Dumontier M, Sansone SA, da Silva B, Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E (2019) Evaluating FAIR maturity through a scalable, automated, community-governed framework. Sci Data 6(1):174. https://doi.org/10.1038/s41597-019-0184-5 - DOI - PubMed - PMC
1. Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews B, Millburn GH, Strelets V (2022) FlyBase: a guided tour of highlighted features. Genetics 220(4):iyac035. https://doi.org/10.1093/genetics/iyac035
1. Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J, FlyBase Consortium (2016) Exploring FlyBase data using QuickSearch. Curr Protoc Bioinformatics 56:1.31.1-1.31.23. https://doi.org/10.1002/cpbi.19

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[1] Flybase Consortium (1996) FlyBase: the Drosophila database. Nucleic Acids Res 24(1):53–56. https://doi.org/10.1093/nar/24.1.53 - DOI

[2] Flybase Consortium (1996) FlyBase: the Drosophila database. Nucleic Acids Res 24(1):53–56. https://doi.org/10.1093/nar/24.1.53 - DOI

[3] Alliance of Genome Resources Consortium (2020) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res 48(D1):D650–D658. https://doi.org/10.1093/nar/gkz813 - DOI

[4] Alliance of Genome Resources Consortium (2020) Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res 48(D1):D650–D658. https://doi.org/10.1093/nar/gkz813 - DOI

[5] Wilkinson MD, Dumontier M, Sansone SA, da Silva B, Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E (2019) Evaluating FAIR maturity through a scalable, automated, community-governed framework. Sci Data 6(1):174. https://doi.org/10.1038/s41597-019-0184-5 - DOI - PubMed - PMC

[6] Wilkinson MD, Dumontier M, Sansone SA, da Silva B, Santos LO, Prieto M, Batista D, McQuilton P, Kuhn T, Rocca-Serra P, Crosas M, Schultes E (2019) Evaluating FAIR maturity through a scalable, automated, community-governed framework. Sci Data 6(1):174. https://doi.org/10.1038/s41597-019-0184-5 - DOI - PubMed - PMC

[7] Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews B, Millburn GH, Strelets V (2022) FlyBase: a guided tour of highlighted features. Genetics 220(4):iyac035. https://doi.org/10.1093/genetics/iyac035

[8] Gramates LS, Agapite J, Attrill H, Calvi BR, Crosby M, dos Santos G, Goodman JL, Goutte-Gattat D, Jenkins VK, Kaufman T, Larkin A, Matthews B, Millburn GH, Strelets V (2022) FlyBase: a guided tour of highlighted features. Genetics 220(4):iyac035. https://doi.org/10.1093/genetics/iyac035

[9] Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J, FlyBase Consortium (2016) Exploring FlyBase data using QuickSearch. Curr Protoc Bioinformatics 56:1.31.1-1.31.23. https://doi.org/10.1002/cpbi.19

[10] Marygold SJ, Antonazzo G, Attrill H, Costa M, Crosby MA, Dos Santos G, Goodman JL, Gramates LS, Matthews BB, Rey AJ, Thurmond J, FlyBase Consortium (2016) Exploring FlyBase data using QuickSearch. Curr Protoc Bioinformatics 56:1.31.1-1.31.23. https://doi.org/10.1002/cpbi.19

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Using FlyBase: A Database of Drosophila Genes and Genetics

Affiliations

Using FlyBase: A Database of Drosophila Genes and Genetics

Authors

Affiliations

Abstract

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References

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LinkOut - more resources

Full Text Sources

Molecular Biology Databases