Databases and Systems

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and returns the translated result to the query execution module for further processing
within the original CPL query.
Non-Human Homolog Search
To illustrate how BioKleisli executes queries, we will walk through an example:
“Find information on the known DNA sequences on human chromosome 22, as well
as information on homologous sequences from other organisms.” The strategy taken
in writing this query will be to combine information from relational GDB and ASN. 1
GenBank. GDB is queried for information about the accession numbers of DNA
sequences known to be within chromosome 22. The NA-Homolog-Summary function
available in the Entrez interface to ASN.l GenBank is then invoked to retrieve
homologous sequences (i.e., sequences with significant similarity to the original).
The homologous sequences are then filtered to retrieve only non-human entries. The
final answer is printed as a nested relation.
The GDB Query.
The GDB query joins three tables – locus, object_genbank_eref, and the portion of
the locus_cyto_location that corresponds to entries on Chromosome 22– over the
locus_symbol field, and projects over the locus_symbol and genbank_ref fields.
Assuming that the function GDB has been registered within BioKleisli to access the
contents of a table whose name must be specified by the query writer, the query is
simply written in CPL as
define Loci22 =
setof rcd { locus-symbol:x, genbank-ref: y}
where rcd{locus-symbol: \x, locus_id ;\a,...} (“locus”),
rcd {genbank_ref : \y, object_id : a, object_class_key: 1, ...}
(“object_genbank_eref”),
rcd{loc_cyto_chrom_num: “22”, locus_cyto_location_id : a, ...}
(“locus_cyto_location”)
Note that we could also have written this query by registering separate functions for
each table accessed (locus, locus_cyto_location and locus_symbol) and that this
would have given query writers an idea of the names available within GDB.
If executed as written, Loci22 would generate three separate SQL queries to GDB,
each of which would extract the contents of a table. The optimizer, however,
improves this by writing the entire function as a single SQL query. In fact, a feature
of the optimizer is that it is capable of moving the largest possible subquery of a CPL
query to an external server for execution. This can be done for a wide variety of
types of data sources (5), including relational and ASN.l-Entrez data sources. The