Databases and Systems

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database the class Map refers to the genetic map of the chromosome. To facilitate the
composition of queries, John McCarthy, Gary Aochi and Aarun Aggarval added to
the Acedb graphic interface two helpful tools, Query-builder and Query-by-example
which prompt the user for the correct fields and the correct syntax. Once written, the
queries can be named, saved, reused and may contain positional runtime parameters.
This language, which acts like a SQL Select statement, is complemented by Table-
Maker, a graphical tool that leads the user through the steps of creating a tabular view
of a portion of the database. Table-Maker allows the gathering of data from multiple
object classes into a summary report for the purposes of visualization or data
exportation. The table definition can then be saved and reused. In graphic mode, the
complete table must be held in memory, and on normal machines this limits the
length of the returned table to a few thousand lines. But after several rounds of
optimization, the current acedb_4.5 release can export in text-only mode arbitrarily
long tables without using much memory. Release 4.7 will incorporate a fuzzy logic
layer which greatly accelerates the selection of rare objects and is the result of many
years of discussions with Otto Ritter.
The present system is efficient, expressive and well tested, but it is non-standard,
and the table definitions are hard to compose outside of the graphic interface. In the
meantime, the 02 group has developed the object query language OQL[5] which was
adopted as a standard by the Object Definition Management Group ODMG. OQL is
a large system, with nice features like the dynamic construction of new objects, but it
is often clumsy; for example the syntax of a query differs if a field is single or
multivalued, and OQL does not support well the recursivity of the Acedb schema.
Other proposals, like Lorel [6], are closer to Acedb. Following those ideas, Richard
Durbin started last year the design of a new query language for Acedb, which may be
available by the end of 1998. This should simplify the querying of the database from
external clients and allow more general questions.
Client server
Acedb is mostly used as a standalone single user program, and indeed it runs well
even on a low-end system. For example, the full C. elegans database is very useable
even on a 133 MHz PC laptop running Linux. However, we have also developed a
TCP/IP-based client/server architecture intended for heavy multi-user applications
and Web-based interfaces. The server runs as a Unix network daemon, listening for
requests from incoming clients, and replying with textual or graphical representations
of objects (the latter are returned as binary GIF images). Data can be imported into
the server locally or remotely in the form of .ace files, or bulk-loaded from FASTA
files (nucleotide and protein sequences only).
Several clients are defined: a simple dialog interface called aceclient, which has a
very small overhead and is convenient to use interactively over a slow network or to
embed within a shell script; a simplified restricted interface called jade2ace, which
we use to communicate with Java clients, a complete Perl interface called AcePerl
which is convenient for scripting, and finally a fully graphic client called xclient,