Databases and Systems

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nightly. Users are encouraged to connect to local sites for the most rapid response
time. To facilitate development and maintenance of mirrors, the FlyBase WWW
server has developed a series of portability features, including the use of readily
mirrored, nonproprietary software, nightly updating of the mirror sites, and
customized user-selected format preferences. For example, the user preferences
would allow an individual (or an entire mirror site) to connect to the nearest server
for external database links.
Public Server Update Schedule
The FlyBase data classes are updated asynchronously, and this is expected to
continue indefinitely. Considerable editorial work occurs in the batch processing of
records, and for this reason FlyBase has opted against a daily update procedure.
Sequence records need to be the most timely; for this reason, the genome databases
are updated weekly. These updates include the GenBank/EMBL/DDBJ accessions; it
should be noted that all available genomic sequences are posted immediately to the
HTG (high throughput genome) section of the sequence databanks. Public
bibliographic, genetic and molecular data classes are updated monthly, but on
independent schedules.
Genetic nomenclature is in constant flux, sometimes because a group of
laboratories have not yet reached consensus on an appropriate gene name, but other
times because research on seemingly independent genes converge when genetic or
molecular analyses reveals that they are working on the same entity. Because a gene
symbol is part of the name of many related entities -- alleles, transcripts, proteins,
transposons, insertions, etc. – the updating process requires substantial validation,
editing and conflict resolution. In this process, there is significant contact with
authors on specific issues.
Future Issues and Concerns
Sequence Representations in Fly Base
While the first genomic sequence for Drosophila melanogaster will be completed by
the end of 2001, this will in many ways just be the beginning in terms of thorough
genomic analysis of the fly. Thus, there is a need for continual and indefinite
maintenance of the computed and experiment-based annotation of this sequence.
Indeed, it is through such annotation that the genomic sequence becomes meaningful.
Thus, much of FlyBase can be viewed as statements attached directly or indirectly to
the sequence-level annotation features.