Databases and Systems

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For 20 years, this information was held in very organized format by a single curator,
Dr. Barbara Bachmann, but in the form of cross-referencing filecard catalogs,
notebooks containing pedigree diagrams, genotype descriptions, gene and gene
function tables and allele information, and also, informal notes and human memory.
Because of its role in tracking genes and alleles, the stock center has also taken on
the task of registering alleles and of publishing the linkage map for E. coli K-12 since
1976 (e.g., 1-4). Converting this information to electronic form was a task begun in
1989 as a two-phase development that was functional, in terms of software and
essential data entry, in early 1990. A major imperative for this was the need to
ensure the continuity of the stock center into the future, and the crucial need to
modernize the records as part of this process had been recognized by program and
division officers at the supporting agency, the National Science Foundation, for some
time. The structured and generally consistent nature of the record-keeping that had
evolved during those 20 years, the clear mission of the stock center, the observable
patterns of usage of the various types of data, and the absence of a pressing deadline
for completion facilitated a user's needs and dataflow analysis that led to conceptual
and data models. We wanted the robustness of a commercial relational database
management system and eventually chose Sybase from among those available, while
keeping the model itself 'object-oriented'. Some schema modifications occurred
during the implementation phases (with Stan Letovsky the sole software developer
for a rapid development and testing process), but the resultant database bore a
striking, perhaps surprising, resemblance to the early plans.
Several aspects of the conceptual data model had either not been included in models
of other databases or were distinctly different from other treatments. Any segment of
the canonical (wildtype) chromosome was modeled as a "Site" (alias locus). This
includes genes, control regions, intergenic and intragenic regions, groups of genes,
including operons, segments of the chromosome that were deleted, inserted, or
inverted in structural mutations. Every site has a left endpoint and a right endpoint.
Thus overlaps between the end of one gene and the beginning of another or inclusion
of a regulatory region within an adjacent gene could be described and detected in
searches. The coordinates for these points can have multiple values, reflecting
different map versions, with the current version, of course, setting coordinates
according to completed nucleotide sequence for E. coli K-12 (5). Sites can have
"subsites"; e.g., all the genes carried on a deleted or inverted segment are subsites of
the segment, and genes within an operon are subsites of the operon, with each subsite
also being represented as an independent site. Since there was a single isolate of K-
12 that is considered to be THE "wildtype", the structure and sequence of this
wildtype chromosome can be used to define the standard chromosome (genome), and
deviations from this structure can be described as mutations of the wildtype. Only
mutations need be described in presenting the genotype of a strain; this is the
convention followed by geneticists since the earliest days of the field. It is important
in the database structure, since properties that belong to the gene itself can be