FlyBase: anatomical data, images and queries

Abstract

FlyBase (http://flybase.org/) is a database of genetic and genomic data on the model organism Drosophila melanogaster and the entire insect family Drosophilidae. The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain. Access to the data is provided through graphical and textual user interfaces tailored to particular types of data. FlyBase data types include maps at the cytological, genetic and sequence levels, genes and alleles including their products, functions, expression patterns, mutant phenotypes and genetic interactions as well as aberrant chromosomes, annotated genomes, genetic stock collections, transposons, transgene constructs and insertions, anatomy and images, bibliographic data, and community contact information.

Figure 1

The FlyBase ‘Synopsis’ gene report (). Following the links in the highlighted subreports and subsection leads to reports that contain fly anatomy and development CV terms used in the curation of phenotype and expression pattern data (see also Figure 2).

Figure 2

The ‘Expression pattern’ and ‘Summary of Allele Phenotypes’ sections of the ‘Expression and Phenotypes’ subreport (). The linked terms in the ‘Tissue/Position’ fields describe the expression pattern of the transcript in the ‘Source’ column at particular points in time and lead to ‘CV term’ reports. Similarly, the linked terms in the ‘Phenotype manifest in’ fields describe the phenotype of the particular allele in the ‘Allele’ column and lead to ‘CV term’ reports. The terms in this example show the wide variety of fly biology that can be described using the Anatomy and Development ontologies.

Figure 3

The FlyBase ‘CV term’ report for the CV term ‘arista’ (). This report shows fields that describe the term, displays the location of the term in a subset of the term hierarchy and has links to other objects in FlyBase that are associated with this term.

Figure 4

The anatomical ‘Image’ report for an image that graphically represents the arista (). Fields in this report describe the image and show all the terms used to annotate the image. If subcomponents of the image have been demarcated, the area of the image that corresponds to a given term and the term in the ‘Anatomy Terms’ field will simultaneously be highlighted when the cursor rolls over either of them. This creates the equivalent of a figure legend with annotation that has been normalized to the CV used by FlyBase.