Schema architecture and their relationships to transaction processing in distributed database systems

We discuss the different types of schema architectures which could be supported by distributed database systems, making a clear distinction between logical, physical, and federated distribution. We elaborate on the additional mapping information required in architecture based on logical distribution in order to support retrieval as well as update operations. We illustrate the problems in schema integration and data integration in multidatabase systems and discuss their impact on query processing. Finally, we discuss different issues relevant to the cooperation (or noncooperation) of local database systems in a heterogeneous multidatabase system and their relationship to the schema architecture and transaction processing

On incremental global update support in cooperative database systems

OzGateway is a cooperative database system designed for integrating heterogeneous existing information systems into an interoperable environment. It also aims to provide a gatewway for legacy information system migration. This paper summarises the problems and results of multidatabase transaction management research. In supporting global updates in OzGateway in an evolutionary way, we introduce a classification of multidatabase transactions and discuss the problems in each category. The architecture of OzGateway and the design of the global transaction manager and servers are presented

A Framework for Creating Global Schema Using Global Views from Distributed Heterogeneous Relational Databases in Multidatabase System

oai:ojs2.computerresearch.org:article/10000

An Agent Based Transaction Manager for Multidatabase Systems

A multidatabase system (MDBMS) is a facility that allows users to access data located in multiple autonomous database management systems (DBMSs) at different sites. To ensure global atomicity for multidatabase transactions, a reliable global atomic commitment protocol is a possible solution. In this protocol a centralized transaction manager (TM) receives global transactions, submits subtransactions to the appropriate sites via AGENTS. An AGENT is a component of MDBS that runs on each site; AGENTS after receiving subtransactions from the transaction manager perform the transaction and send the results back to TM. We have presented a unique proof-of-concept, a JAVA application for an Agent Based Transaction Manager that preserves global atomicity. It provides a user friendly interface through which reliable atomic commitment protocol for global transaction execution in multidatabase environment can be visualized. We demonstrated with three different test case scenarios how the protocol works. This is useful in further research in this area where atomicity of transactions can be verified for protocol correctness

Global Semantic Integrity Constraint Checking for a System of Databases

In today’s emerging information systems, it is natural to have data distributed across multiple sites. We define a System of Databases (SyDb) as a collection of autonomous and heterogeneous databases. R-SyDb (System of Relational Databases) is a restricted form of SyDb, referring to a collection of relational databases, which are independent. Similarly, X-SyDb (System of XML Databases) refers to a collection of XML databases. Global integrity constraints ensure integrity and consistency of data spanning multiple databases. In this dissertation, we present (i) Constraint Checker, a general framework of a mobile agent based approach for checking global constraints on R-SyDb, and (ii) XConstraint Checker, a general framework for checking global XML constraints on X-SyDb. Furthermore, we formalize multiple efficient algorithms for varying semantic integrity constraints involving both arithmetic and aggregate predicates. The algorithms take as input an update statement, list of all global semantic integrity constraints with arithmetic predicates or aggregate predicates and outputs sub-constraints to be executed on remote sites. The algorithms are efficient since (i) constraint check is carried out at compile time, i.e. before executing update statement; hence we save time and resources by avoiding rollbacks, and (ii) the implementation exploits parallelism. We have also implemented a prototype of systems and algorithms for both R-SyDb and X-SyDb. We also present performance evaluations of the system

BioWarehouse: a bioinformatics database warehouse toolkit

BACKGROUND: This article addresses the problem of interoperation of heterogeneous bioinformatics databases. RESULTS: We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. CONCLUSION: BioWarehouse embodies significant progress on the database integration problem for bioinformatics