Exploring FlyBase Data Using QuickSearch

Abstract

FlyBase (flybase.org) is the primary online database of genetic, genomic, and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, 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 unit 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. © 2016 by John Wiley & Sons, Inc.

Keywords: Drosophila melanogaster; FlyBase; QuickSearch; biological database; query tools.

Figure 1

(A) The ‘Simple’ tab of QuickSearch, with the text ‘cadherin’ entered as the search term. (B) The initial results page resulting from running that query.

Figure 2

The ‘Data Class’ tab of QuickSearch, with ‘stocks’ selected from the drop-down menu, ‘ID/Symbol/Name’ selected as the search mode, and ‘dpp*’ entered as the search term. The expanded box shows a subset of the options available from the Data Class menu.

Figure 3

(A) The ‘References’ tab of QuickSearch, with several criteria entered as search terms. (B) The Reference Report for one of the resulting hits.

Figure 4

(A) The ‘Gene Groups’ tab of QuickSearch, with the text ‘Sirtuin’ entered as the search term. Note the link to ‘browse all Gene Groups’. (B) The Gene Group Report for SIRTUIN LYSINE DEACETYLASES.

Figure 5

(A) The ‘Human Disease’ tab of QuickSearch, with the text ‘Alexander’ entered as the search term of the lower ‘Search Disease Ontology’ box. (B) The Term Report for ‘Alexander disease’ showing the link to the associated Human Disease Model Report and to hit-lists of alleles/genes annotated with the term.

Figure 6

(A) The ‘GO’ tab of QuickSearch, with the text ‘axonogenesis’ entered as the search term. (B) The Term Report for ‘axonogenesis’ showing the link to a hit-list of genes annotated with the term.

Figure 7

(A) The ‘Expression’ tab of QuickSearch, with several criteria entered as search terms. (B) The ‘Expression Data’ section of the Gene Report for the AstA gene (one of the resulting hits). The ‘Polypeptide Expression’ subsection is open.

Figure 8

(A) The ‘Phenotype’ tab of QuickSearch, with several criteria entered as search terms within the upper ‘Phenotypic class’ section. (B) The ‘Phenotypic Data’ section of the Allele Report for the polo¹¹ allele (one of the resulting hits).

Figure 9

(A) The ‘Protein Domains’ tab of QuickSearch, with the text ‘SH3 domain’ entered as the search term. (B) The ‘Families, Domains and Molecular Function’ section of the Gene Report for the Abl gene (one of the resulting hits).

Figure 10

(A) The ‘Orthologs’ tab of QuickSearch, searching for orthologs of the Psn gene of D. melanogaster in all organisms in the DIOPT set. (B) The results table from running that query.