Exploring FlyBase Data Using QuickSearch

Overview

Journal Curr Protoc

Specialties Biology
Science

Date 2023 Apr 4

PMID 37014762

Authors

Steven J Marygold

Affiliations

Soon will be listed here.

Abstract

FlyBase (www.flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, means that FlyBase now houses a huge quantity of data. Researchers need to be able to query these data rapidly and intuitively, and the QuickSearch tool has been designed to meet these needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This article describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using the "Search FlyBase" tab of QuickSearch Basic Protocol 2: Using the "Data Class" tab of QuickSearch Basic Protocol 3: Using the "References" tab of QuickSearch Basic Protocol 4: Using the "Gene Groups" tab of QuickSearch Basic Protocol 5: Using the "Pathways" tab of QuickSearch Basic Protocol 6: Using the "GO" tab of QuickSearch Basic Protocol 7: Using the "Protein Domains" tab of QuickSearch Basic Protocol 8: Using the "Expression" tab of QuickSearch Basic Protocol 9: Using the "GAL4 etc" tab of QuickSearch Basic Protocol 10: Using the "Phenotype" tab of QuickSearch Basic Protocol 11: Using the "Human Disease" tab of QuickSearch Basic Protocol 12: Using the "Homologs" tab of QuickSearch Support Protocol 1: Managing FlyBase hit lists.

Citing Articles

The alpha-ketoacid dehydrogenase complexes of .

Marygold S MicroPubl Biol. 2024; 2024.

PMID: 38741935 PMC: 11089389. DOI: 10.17912/micropub.biology.001209.

Finding information about uncharacterized Drosophila melanogaster genes.

Mohr S, Kim A, Hu Y, Perrimon N Genetics. 2023; 225(4).

PMID: 37933691 PMC: 10697813. DOI: 10.1093/genetics/iyad187.

Exploring FlyBase Data Using QuickSearch.

Marygold S Curr Protoc. 2023; 3(4):e731.

PMID: 37014762 PMC: 10088454. DOI: 10.1002/cpz1.731.

References

Thurmond J, Goodman J, Strelets V, Attrill H, Gramates L, Marygold S . FlyBase 2.0: the next generation. Nucleic Acids Res. 2018; 47(D1):D759-D765. PMC: 6323960. DOI: 10.1093/nar/gky1003. View

Marygold S . Exploring FlyBase Data Using QuickSearch. Curr Protoc. 2023; 3(4):e731. PMC: 10088454. DOI: 10.1002/cpz1.731. View

Millburn G, Crosby M, Gramates L, Tweedie S . FlyBase portals to human disease research using Drosophila models. Dis Model Mech. 2016; 9(3):245-52. PMC: 4826978. DOI: 10.1242/dmm.023317. View

Larkin A, Marygold S, Antonazzo G, Attrill H, Dos Santos G, Garapati P . FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res. 2020; 49(D1):D899-D907. PMC: 7779046. DOI: 10.1093/nar/gkaa1026. View

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

Hu Y, Flockhart I, Vinayagam A, Bergwitz C, Berger B, Perrimon N . An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics. 2011; 12:357. PMC: 3179972. DOI: 10.1186/1471-2105-12-357. View

Marygold S, Antonazzo G, Attrill H, Costa M, Crosby M, Dos Santos G . Exploring FlyBase Data Using QuickSearch. Curr Protoc Bioinformatics. 2016; 56:1.31.1-1.31.23. PMC: 5152691. DOI: 10.1002/cpbi.19. View

St Pierre S, Ponting L, Stefancsik R, McQuilton P . FlyBase 102--advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2013; 42(Database issue):D780-8. PMC: 3964969. DOI: 10.1093/nar/gkt1092. View

. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2020; 49(D1):D325-D334. PMC: 7779012. DOI: 10.1093/nar/gkaa1113. View

10.

Binns D, Dimmer E, Huntley R, Barrell D, ODonovan C, Apweiler R . QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics. 2009; 25(22):3045-6. PMC: 2773257. DOI: 10.1093/bioinformatics/btp536. View

11.

Schriml L, Munro J, Schor M, Olley D, McCracken C, Felix V . The Human Disease Ontology 2022 update. Nucleic Acids Res. 2021; 50(D1):D1255-D1261. PMC: 8728220. DOI: 10.1093/nar/gkab1063. View

12.

Amberger J, Bocchini C, Scott A, Hamosh A . OMIM.org: leveraging knowledge across phenotype-gene relationships. Nucleic Acids Res. 2018; 47(D1):D1038-D1043. PMC: 6323937. DOI: 10.1093/nar/gky1151. View

13.

Marygold S, Leyland P, Seal R, Goodman J, Thurmond J, Strelets V . FlyBase: improvements to the bibliography. Nucleic Acids Res. 2012; 41(Database issue):D751-7. PMC: 3531214. DOI: 10.1093/nar/gks1024. View

14.

Carbon S, Ireland A, Mungall C, Shu S, Marshall B, Lewis S . AmiGO: online access to ontology and annotation data. Bioinformatics. 2008; 25(2):288-9. PMC: 2639003. DOI: 10.1093/bioinformatics/btn615. View

15.

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

16.

Attrill H, Falls K, Goodman J, Millburn G, Antonazzo G, Rey A . FlyBase: establishing a Gene Group resource for Drosophila melanogaster. Nucleic Acids Res. 2015; 44(D1):D786-92. PMC: 4702782. DOI: 10.1093/nar/gkv1046. View

17.

Seal R, Braschi B, Gray K, Jones T, Tweedie S, Haim-Vilmovsky L . Genenames.org: the HGNC resources in 2023. Nucleic Acids Res. 2022; 51(D1):D1003-D1009. PMC: 9825485. DOI: 10.1093/nar/gkac888. View

18.

Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S . FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 2008; 37(Database issue):D555-9. PMC: 2686450. DOI: 10.1093/nar/gkn788. View

19.

Gramates L, Agapite J, Attrill H, Calvi B, Crosby M, Dos Santos G . FlyBase: a guided tour of highlighted features. Genetics. 2022; 220(4). PMC: 8982030. DOI: 10.1093/genetics/iyac035. View

20.

Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto B, Salazar G . InterPro in 2022. Nucleic Acids Res. 2022; 51(D1):D418-D427. PMC: 9825450. DOI: 10.1093/nar/gkac993. View