Databases and Systems

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Creation of External Database Links
FlyBase receives daily updates of GenBank/EMBL/DDBJ records of the family
Drosophilidae, and captures the links to valid FlyBase gene symbols and identifers.
Tables of these links are shared with the sequence databanks. Similar procedures are
used with regard to links to other sequence databases, particularly SwissProt. Links
from the literature to “homologs” in other species are selective, and are based upon
stated sequence similarities in papers. Based on these statements, FlyBase captures
the valid gene symbol and identifier for the declared “homolog” in the foreign
community database. The BDGP and EDGP use sequence similarities as one aspect
of gene prediction, and capture and maintain links to the strongest BLAST
similarities in GenBank/EMBL/DDBJ, focusing on the major genetic systems
wherever possible.
Data Coordination within FlyBase
It will be obvious from the above that there are many data objects in FlyBase that are
common to the genome projects and the literature (the latter being the product of the
entire Drosophila research community). In order to bring these data into a single
structure, we will need to integrate and homogenize the data in a stepwise process.
All FlyBase data will move, as a first step into either of two databases: one being
an integrated Genome Project database and the other an integrated Literature
database. (The integrated Literature database is already in production use; the
integrated Genome Project database will be implemented soon.) At this step,
considerable data validation and homogenization occurs. The next step will be to
interrelate and homogenize literature-derived and genome project data of the same
class. This has been done successfully as an experiment for selected data classes,
such as transposon insertions. Based on this experience, expert annotators will need
to examine the data to ensure that identical objects with variant names are being
recognized as identical, and valid symbols will need to be agreed upon and
propagated to all of the relevant working and intermediary databases. Based on
FlyBase’s experience with the integrated Literature database, procedures will be
established such that new data objects at each site will receive valid symbols and
interconnections to other valid objects as they are introduced into the database. The
final step will be to map field identities between the integrated Literature and
integrated Genome Project databases and thereby permit the data to be housed in one
structure.