This paper presents an algebraic approach to optimize
queries in domain-specific database management system
for protein structure data. The approach involves the introduction of
several protein structure specific algebraic operators to query the
complex data stored in an object-oriented database system. The
Protein Algebra provides an extensible set of high-level Genomic
Data Types and Protein Data Types along with a comprehensive
collection of appropriate genomic and protein functions. The paper
also presents a query translator that converts high-level query
specifications in algebra into low-level query specifications in
Protein-QL, a query language designed to query protein structure
data. The query transformation process uses a Protein Ontology that
serves the purpose of a dictionary.
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