The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a `knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.

A major challenge still facing the designers and implementors of database programming languages (DBPLs) is that of query optimisation. We investigate algebraic query optimisation for DBPLs in the context of a purely declarative functional language that supports sets as first-class objects. Since the language is computationally complete issues such as non-termination of expressions and construction of infinite data structures can be investigated, whilst its declarative nature allows the issue of side effects to be avoided and a rich set of equivalences to be developed. The language has a well-defined semantics which permits us to reason formally about the properties of expressions, such as their equivalence with other expressions and their termination. The support of a set bulk data type enables much prior work on the optimisation of relational languages to be utilised. In the paper we first give the syntax of an archetypal DBPL and briefly discuss its semantics. We then de...

The provision of more intelligent support for complex database applications is becoming an important research topic, and declaratively stated integrity constraints are increasingly being seen as a potential source of semantic information for such advanced DBMS's. However, despite much research e#ort, the problem of e#ciently compiling and checking a wide range of complex constraints has not yet been solved. And until it is solved, few database designers will be willing to sacrifice the performance of the every day database usage, in order to provide a complete semantic modelling of their application domain. In this paper, we describe the implementation of a constraint checking architecture and compiler, which have been designed to combine an expressive constraint language with e#cient run-time maintenance. While the current implementation does not yet achieve high e#ciency for all constraints, it has been designed with extensibility in mind and forms a solid platform from which to inv...

Compilers and optimizers for declarative query languages use some form of intermediate language to represent user-level queries. The advent of compositional query languages for orthogonal type systems (e.g. OQL) calls for internal query representations beyond extensions of relational algebra. This work adopts a view of query processing which is greatly influenced by ideas from the functional programming domain. A uniform formal framework is presented which covers all query translation phases, including user-level query language compilation, query optimization, and execution plan generation. We pursue the type-based design - based on initial algebras - of a core functional language which is then developed into an intermediate representation that ts the needs of advanced query processing. Based on the principle of structural recursion we extend the language by monad comprehensions (which provide us with a calculus-style sublanguage that proves to be useful during the optimization of nested...

alexQdcs.kcl.ac.uk A major challenge still facing the designers and implementors of database programming languages (DBPLs) is that of query optimisa-tion. We investigate algebraic query optimi-sation techniques for DBPLs in the context of a purely declarative functional language that supports sets as first-class objects. Since the language is computationally complete issues such as non-termination of expressions and construction of infinite data structures can be investigated, whilst its declarative nature al-lows the issue of side effects to be avoided and a richer set of equivalences to be developed. The support of a set bulk data type enables much prior work on the optimisation of rela-tional languages to be utilised. Finally, the language has a well-defined semantics which permits us to reason formally about the prop erties of expressions, such as their equivalence with other expressions and their termination. 1

. This paper investigates the optimisation of aggregation functions in the context of computationally complete database programming languages and aims to generalise and provide a unifying formal foundation for previous work. We define a `fold' operator OE over collection types in terms of which operations such as selection, projection, join and group-by can be defined, as well as aggregation functions such as sum, max and min. We introduce two equivalences for OE which respectively govern the commuting and coalescing of applications of OE. From these two equivalences we then formally derive equivalences governing the commuting and coalescing of iteration operations over collections, the mapping of aggregation functions over grouped collections, the introduction and elimination of aggregation functions, and the promotion of aggregation functions through iteration operations. We also show how some of these equivalences can be used to optimise comprehensions, a high-level query construct ...

Syntax of Object Comprehensions Es ::= E j E , Es E ::= E union E j E differ E j [ Xs --- E ] j E and E j E or E j not E j E hasClass E j E hasClass E with E j Y E ! Y E j E / E j E . E j I( Es ) j I j K j f Es g j f E : : : E g j E . [ E ] j A E j ( E ) Xs ::= j X j X ; Xs X ::= D j L j E D ::= I / E L ::= I as E Y ::= j some j atleast E j just E j atmost E j every A ::= size ::= set j bag j list ! ::= = j = j ? j ?= j ! j != j == j == / ::= * j / j + j - B Abstract Syntax of Function Arguments F ::= I . E j F ffi F Es ::= E j E, Es E ::= E . E j I( Es ) j E ff E j E ! E j E / E j I j K j ( E ) j Q ff ::= j j : ! ::= = j = j ? j ?= j ! j != / ::= * j / j + j - 22 References ...

This thesis proposes an object-oriented query language that is more powerful than many existing query languages. The language is formally specified and its expressive power is demonstrated by giving four translation schemes from other prominent objectoriented query languages. Further, this query language can be supported by a query algebra and both the query language and query algebra can be optimised using meaning preserving transformation rules. Object-Oriented Query Languages. The functional requirements of high-level objectoriented query languages are identified and they combine as well as supplement features found in existing object-oriented query languages. Effectively they formulate a query model against which existing query languages can be evaluated and compared. An evaluation of four representative query languages chosen from research prototypes and commercial products shows that none satisfies all the requirements. On the basis of the requirements a new query language, obje...

We describe a modular compiler architecture that has been developed for a functional data model DBMS. The architecture allows compilers for new sub-languages to be constructed rapidly, by reusing the components of the existing compiler, and allows new semantics and code generation strategies to be defined for existing language constructs. This point is demonstrated by the construction of a new compiler for an integrity constraint language, which required only two new modules to be added to the system. The most significant advantage of our architecture, however, is that it allows the DBMS itself to use the individual compiler modules, opening up a host of possibilities for run-time manipulation of application code.

The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a `knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model.