Databases and Systems

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databank feature tables and/or via FlyBase direct user submission tools. Scaling this
effort and obtaining effective community involvement in data capture is an important
challenge for the future.
Maintaining Extensive Hyperlinks between Community Databases
One of the outstanding features of the WWW is the ability to embed cross-links
between related items on different servers. FlyBase maintains extensive tables of
connections to support such cross-links, especially to sequence and community
databases. We recognize, however, that this effort is incomplete and not sustainable
by FlyBase alone. For example, FlyBase reflects statements of “homology” in the
primary literature. Except for fully sequenced organisms, however, these
declarations of “homology” are generally based on incomplete information, and more
similar members of the same protein family may well be identified subsequent to
publication. Further, FlyBase considers papers that involve the identification of a
Drosophila gene with sequence similarity to a gene in another taxon as being in its
literature curation domain, but the converse is not true. Papers in which a Drosophila
sequence is used as a probe to identify related sequences in another organism are
viewed as appropriate for curation by the community database for that organism, if it
exists. There is clearly a need for an independent database of links. at least between
the genomes of the major genetic systems, that these organisms’ community
databases contribute to and use for more systematic interconnections.
Genome, Proteome and Phenome Views of FlyBase
Just as the availability of full genomic sequence has changed the way research is
done, functional genomics — that is, the high throughput analysis of gene products –
will clearly have a similar, if not more dramatic, impact. One tremendous advantage
of genomic information is the increased efficiency of positional cloning and gene
identification. Once the gene is identified, however, researchers are usually
interested in understanding relationships at the level of gene products and their
physical, cellular, developmental or behavioral interactions. Much modern research
exploits the major genetic systems to answer sophisticated questions about the
relationship of the “proteome” (the entire constellation of protein products produced
by a genome) with the “phenome” (the constellation of phenotypes controlled by the
various genetic units of the genome).
We are already seeing this trend in Drosophila research. Much research focuses
on fleshing out pathways through a combination of physical methods to identify
protein-protein, protein-RNA or protein-DNA interactions, together with genetic