Databases - Bioinformatics Computing - page 75

separate text document, researchers can simply work with the gene object.

Although the object-oriented approach holds great promise in bioinformatics, it still lags far behind
relational technology in the global database market. In addition, because of the flexibility and power
of the relational design, many of the object-oriented DBMS products on the market are based on
extensions of commercial relational database packages. Because of the added overhead, the
performance of these hybrid object-oriented systems is necessarily less than that of either a pure
relational or an object-oriented system.

In addition to object-oriented models built on relational model technology, a variety of other models
that are optimum for bioinformatics work can be constructed from relational technology. For
example, the deductive model is an extension of the relational database with a logic programming
interface based on the principles of logic programming. The logic programming interface is composed
of rules, facts, and queries, using the relational database infrastructure to contain the facts.

The database is termed deductive because from the set of rules and the facts it is possible to derive
new facts not contained in the original set of facts. Unlike logic programming languages such as
PROLOG, which search for a single answer to a query using a top-down search, deductive databases
search from bottom-up, starting from the facts to find all answers to a query.

For example, using the format "patient (Patient ID, Sex, Mother Carrier, Father Trait)," data in the
deductive database describing a sex-linked recessive gene such as red-green color blindness could be
represented in a relational table as in Table 2-6 .

Table 2-6. Data for a Deductive Database. Columns, from left to right,
represent Patient ID, Sex, Mother Carrier, and Father Trait.

Patient ID Sex Mother Carrier Father Trait

001 Male Yes Yes

002 Female Yes No

003 Male No Yes

004 Female No Yes

005 Male Yes No

006 Male No No

007 Female Yes Yes

A relevant rule in a deductive database would be:

Potential Carrier (Sex = Female) AND (Mother Carrier = Yes)

That is, the patient is a potential carrier if the sex of the patient is female and the patient's mother is
a known carrier. Males with the gene exhibit the disease, or red-green color blindness. However,
because the gene involved in color blindness is maternal, then the state of the father's color acuity is
irrelevant.

The query: