Databases and Systems

203
In the remainder of this chapter, we describe the complex type model underlying
BioKleisli, and a query language for manipulating these types called the “Collection
Programming Language” (CPL). We then briefly describe the use of BioKleisli
through an example of a parameterized view. We close by summarizing how
BioKleisli compares with other systems in use within bioinformatics, in particular
OPM and CORBA.
The Complex Type Model
The type system underlying BioKleisli goes well beyond the “sets of records” type
system of the relational model and allows complex types – arbitrarily nested records,
sets, lists, bags and variants. Recall that a bag (also called a multi-set) is a set in
which duplicates may occur, and that a list is a bag with order.
As an example of a complex type, consider the Publication type shown below,
which has been taken from the ASN. 1 citation literature (1). Note the nesting of a set
of keywords (strings) within the keywd record field of the Publication type, the
nesting of author records within the authors record field, and the use of a variant or
“tagged union” type within the journal field representing that publications are either
controlled journal entries (also a variant type), or uncontrolled entries containing the
name of the person who performed the data entry.
Publication = SET{
RCD{ title: string,
authors: LIST{ RCD{ name: string, initial: string}}