FlyBase: improvements to the bibliography

Abstract

An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed. Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster. We present an overview of the current content of the bibliography, the pipeline for identifying and adding new references, the presentation of data within Reference Reports and effective methods for searching and retrieving bibliographic data. We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources. Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.

Figure 1.

Bibliography update pipeline. See text for details.

Figure 2.

Example Reference Report pages (from FlyBase release FB2012_05). An example Reference Report is shown on the left; the ‘Genes’ subsection of the ‘Data from Reference’ section is open. The References section from an example Gene Report (Gr5a) is shown on the right (the other sections of the Gene Report are omitted for clarity); note that the number of references of each publication type is given in parentheses in each case. The reciprocal link between the Reference Report and the Gene Report is indicated by the red circle and arrow. (Blue text indicates hyperlinks; green-highlighted text indicates a new reference added in the current FlyBase release.)

Figure 3.

References tab of QuickSearch. See text for details.

Figure 4.

QueryBuilder, a reference hitlist, and frequency analysis (using FB2012_05). A QueryBuilder query for references, excluding reviews, published in the past 10 years that mention the gene Gr5a is shown. Below is the resulting hitlist of the first 12 matches, sorted in reverse chronological order. The ‘Results Analysis/Refinement’ pop-up menu is also shown, together with the frequency analysis of author names from the complete hitlist. (Blue text indicates hyperlinks; a green flag indicates a new reference added in the current FlyBase release; a red flag indicates that new data have been associated with a reference in the current release.)