In this paper we present a proposal for representing soft constraint satisfaction problems (CSPs) within the Semantic Web architecture. The proposal is motivated by the need for a service-providing agent in a virtual organisation to reason about its commitments as soft constraints. The three essential requirements addressed are: (1) the need to have constraints express commitments in terms of Semantic Web services, (2) the need to associate utility values with constraints, to reflect the relative importance of satisfying them, and (3) the need to make statements about which constraints are satisfied and violated by a given solution. The proposal builds upon previous work in defining a Semantic Web Constraint Interchange Format (CIF), which itself builds on the proposed Semantic Web Rule Language (SWRL). The paper describes an ontology for representing soft CSPs and their solutions, allowing an agent’s set of commitments to be expressed as a collection of soft constraints. The ontology is an open interchange format for soft CSPs, allowing commitment to be communicated and exchanged among the members of a virtual organisation. 1.

Developments in our ability to integrate and analyze data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad hoc queries across multiple data resources and correlating data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous distributed biological databases. Our architecture makes use of the existing search capabilities and indexes of the underlying databases, without infringing on their autonomy. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation, and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in SRS.

Transforming queries for efficient execution is particularly important in federated database systems since a more efficient execution plan can require many fewer data requests to be sent to the component databases. Also, it is important to do as much as possible of the selection and processing close to where the data are stored, making best use of facilities provided by the federation's component database management systems. We address the problem of processing complex queries including quantifiers, which have to be executed against different databases in an expanding heterogeneous federation. This is done by transforming queries within a mediator for global query improvement, and within wrappers to make best use of the query processing capabilities of external databases. Our approach is based on pattern matching and query rewriting. We introduce a high level language for expressing rewrite rules declaratively, and demonstrate the use and flexibility of such rules in improving query performance for existentially quantified subqueries. Extensions to this language that allow generic rewrite rules to be expressed are also presented. The value of performing final transformations within a wrapper for a given remote database is shown in several examples that use AMOS II-an SQLS-like system.

Developments in our ability to integrate and analyse the data held in existing heterogeneous data resources can lead to an increase in our understanding of biological function at all levels. However, supporting ad-hoc queries across multiple data resources and correlating the data retrieved from these is still difficult. To address this, we are building a mediator based on the functional data model database, P/FDM, which integrates access to heterogeneous, distributed biological databases, while making use of existing search engines and indexes, without infringing on the autonomy of the underlying databases. Central to our design philosophy is the use of schemas. We have adopted a federated architecture with a five-level schema, arising from the use of the ANSI-SPARC three-level schema to describe both the existing autonomous data resources and the mediator itself. We describe the use of mapping functions and list comprehensions in query splitting, producing execution plans, code generation and result fusion. We give an example of cross-database querying involving data held locally in P/FDM systems and external data in the Sequence Retrieval System (SRS).

In recent years, research on distributing databases over networks has become increasingly important. In this paper, we concentrate on the issues of the interoperability of heterogeneous DBMSs and enforcing integrity across a multi-database made in this fashion. This has been done through a cooperative project between Aberdeen and Linko/spl uml/ping universities, with database modules distributed between the sites. In the process, we have shown the advantage of using DBMSs based on variants of the functional data model (FDM), which has made it remarkably straightforward to interoperate queries and schema definitions. Further, we have used the constraint transformation facilities of P/FDM (Prolog implementation of FDM) to compile global constraints into active rules installed locally on one or more AMOS (Active Mediators Object System) servers. We present the theory behind this, and the conditions for it to improve performance.

There is unavoidable heterogeneity in the databanks and databases currently used for biological data collections. The authors are aiming to develop a system that will provide uniform access to heterogeneous databases via a single high-level query language or graphical interface and will enable multi-database queries. They have taken an approach in which high-level code in an object-oriented database system (based on the functional data model) is used effectively as a mediator between distributed heterogeneous databases. The resulting system enables one to ask queries that combine, for example, geometric calculations on three-dimensional protein structures stored locally and access to databanks held at the European Bioinformatics Institute, while making use of existing search engines and indexes when accessing remote data.

A procedure for finding clusters of adjacent residues in protein hydrophobic cores--hydrophobic microdomains--has been proposed by Plochocka et al. A program is presented that finds hydrophobic microdomains, making use of protein structure data stored in an object-oriented database and the list-processing features of Prolog. Alternative definitions for hydrophobic microdomains are explored. Results are presented for haemoglobin.

In this paper a query optimiser for use with functional data model databases is described. The system is in use with a large database of protein structures from which examples are taken. The optimiser, which evaluates alternative paths through the object base, is written in Prolog and integrated with a parser for DAPLEX. The constructs of DAPLEX are easily expressed in Prolog, which has also proved suitable for implementing both the parser and rewrite rules. The implementation of the optimiser using rewrite rules is both concise and extensible.

The Perlog system is a Prolog system whose clauses and terms can persist on secondary storege as objects in a database. The unit of commitment is the module, and all atoms indirectly reference their module name, unless they are declared to be global. The module acts as a source of protection and reference to all its clauses, and also provides checks on import/export and on privacy, especially in the case of Abstract Data Types. This paper describes the structure of the module name space and the reasons for the decisions, particularly the use of metacalls to access procedures in other modules, and procedures with multiple definitions in different modules. A method for resolving global name clashes between previously committed modules is described. A model of the interpreter is presented in order to define the semantics of procedure call and assert and consult in a fully modular system. An example is given of a version of assert using B-tree routines in the database for clause storage. The system has been implemented in C and Prolog and PS-Algol under UNIX† on a VAX.‡

A method 1s proposed for accessing Codasyl and Functional 1.

A program generator (ASTRID) has been built which generates Fortran code to access records stored in a Codasyl database which satisfy a query written in a generalised relational algebra. The Join operation can be done either by using coset pointers or else by sort-merge. Also projection and grouping operations will require sorts to find and remove duplicate values if they cannot be accessed in sorted order. A novel method of combining grouping and sorting operations via a sparse array technique is presented. Comparisons are made between this method and separate sorting followed by grouping; timings are given to show the significant advantage in practice. A number of programs have been generated and run using different access paths, with and without sorts. Comparisons between timings and monitored page charges are made and heuristics suggested for predicting the best method. These are shown to be different from those used by Selinger et al. for the System R relational database.