Databases and Systems

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Genes, including links via published sequence and functional similarities to other
molecular and community databases.
Gene products: transcripts and proteins, including structural and expression
pattern data.
Integrated gene order maps, incorporating recombinational, cytogenetic and
molecular information.
Annotated molecular maps: reference sequence gene maps; regional physical
maps.
Alleles: wild-type, mutant and engineered.
Chromosomal aberrations.
Engineered and natural transposons and their insertions in the genome.
Fly strains: principally, the publicly-funded stock collections.
Contact information for Drosophila researchers.
FlyBase “literature” is meant broadly, and includes hard copy publications,
sequence databank entries, bulk submitted data, stock lists, textual personal
communications, etc. The principle is that all information in FlyBase is attributed,
and is linked to a hard copy or electronic text. The literature database consists of
records containing a mixture of controlled or structured fields and free text
descriptions to extend the structured information. Extensive internal and external
cross-referencing of related data objects is included. For these controlled fields,
FlyBase has developed extensive controlled vocabularies, e.g., for phenotype,
anatomy, mutagen, function of gene product.
Data Curation Approaches
The data of the BDGP and EDGP consist almost exclusively of structured outputs of
high throughput genomic analyses. There is considerable curational input at such
levels as gene predictions in genomic DNA sequences, and genetic analyses of P
element insertions.
The literature curation aspect of FlyBase began in 1992. It took as a starting
point the compilation of Lindsley and Zimm [1], which was largely current to the
beginning of 1990. The goal was to capture information from the post-1989 primary
literature, and selectively curate earlier material as deemed necessary. Curation of
genetic information occurs shortly after journal publication for those journals
considered to be the major ones used by the Drosophila research community. For
papers with molecular information (e.g., on gene structure, transcripts, proteins,
expression patterns, transposons or their insertions), these receive a second round of
curation with sets of papers relating to the same gene being curated together;
available GenBank/EMBL/DDBJ records are examined at the same time, since a
better picture of these molecular data classes emerges from simultaneous
consideration of a group of related papers. Curated reference annotated sequence
records have recently been added to molecular curation (further discussed in
Sequence Annotation, below).