Databases and Systems

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In this query "Amber" is a mutation property, and certain properties, such as
constitutivity or nonsense suppressibility (e.g., Amber) are such distinctive properties
that traditionally a symbol is parenthetically appended to the mutation designation.
This convention fortuitously provides a shortcut for this query. It is not necessary to
"subquery" on the Mutation form to specify the property, but only to enter it as part
of the name, "laclZwildcard](Am)". The retrieval on these forms also illustrates
another feature of the database. Some comments (shown as Type Inherited on the
form) are Mutation Comments, inherited by all strains carrying that mutation. Also,
the definition of the Mutation property (Am) is inherited by the Strain form.
Other common queries are for strains that carry a specific mutation with a transposon
or other selectable marker nearby; a strain that carries a mutation and is an Hfr that
transfers that mutation early in a mating; a combination of mutations in two or more
specific genes; or a strain that lacks a specific enzyme. These are easily carried out
by users familiar with the genetics of E. coli.
A current version of the traditional linkage map ("stick-and-tick" representation) can
also be accessed from the web, as drawings of 2-minute segments from the web site,
or as an ordered list of genes and coordinates drawn directly from the database.
Quality Control and Curation
Because we were confronted with so much data entry from paper files, we initially
emphasized triggers and tools that attempted to facilitate and ensure data integrity for
entries and updates, and these have served us well in maintaining quality control and
in the curation process.
We attempted to circumscribe the content of this database, so that the part-time
attention of one or two people could accomplish curation of the "primary data", and
access to important related data would be provided by links to other data