Mediated data integration and transformation for web service-based software architectures

Service-oriented architecture using XML-based web services has been widely accepted by many organisations as the standard infrastructure to integrate heterogeneous and autonomous data sources. As a result, many Web service providers are built up on top of the data sources to share the data by supporting provided and required interfaces and methods of data access in a unified manner. In the context of data integration, problems arise when Web services are assembled to deliver an integrated view of data, adaptable to the specific needs of individual clients and providers. Traditional approaches of data integration and transformation are not suitable to automate the construction of connectors dedicated to connect selected Web services to render integrated and tailored views of data. We propose a declarative approach that addresses the oftenneglected data integration and adaptivity aspects of serviceoriented architecture

Data integration through service-based mediation for web-enabled information systems

The Web and its underlying platform technologies have often been used to integrate existing software and information systems. Traditional techniques for data representation and transformations between documents are not sufficient to support a flexible and maintainable data integration solution that meets the requirements of modern complex Web-enabled software and information systems. The difficulty arises from the high degree of complexity of data structures, for example in business and technology applications, and from the constant change of data and its representation. In the Web context, where the Web platform is used to integrate different organisations or software systems, additionally the problem of heterogeneity arises. We introduce a specific data integration solution for Web applications such as Web-enabled information systems. Our contribution is an integration technology framework for Web-enabled information systems comprising, firstly, a data integration technique based on the declarative specification of transformation rules and the construction of connectors that handle the integration and, secondly, a mediator architecture based on information services and the constructed connectors to handle the integration process

Annotation of SBML Models Through Rule-Based Semantic Integration

*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.
*Results:* We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.
*Availability:* Detailed information including download and mapping of the ontologies as well as integration results is available from "http://www.cisban.ac.uk/RBM":http://www.cisban.ac.uk/RB

Building XML data warehouse based on frequent patterns in user queries

[Abstract]: With the proliferation of XML-based data sources available across the Internet, it is increasingly important to provide users with a data warehouse of XML data sources to facilitate decision-making processes. Due to the extremely large amount of XML data available on web, unguided warehousing of XML data turns out to be highly costly and usually cannot well accommodate the users’ needs in XML data acquirement. In this paper, we propose an approach to materialize XML data warehouses based on frequent query patterns discovered from historical queries issued by users. The schemas of integrated XML documents in the warehouse are built using these frequent query patterns represented as Frequent Query Pattern Trees (FreqQPTs). Using hierarchical clustering technique, the integration approach in the data warehouse is flexible with respect to obtaining and maintaining XML documents. Experiments show that the overall processing of the same queries issued against the global schema become much efficient by using the XML data warehouse built than by directly searching the multiple data sources

Pattern Reification as the Basis for Description-Driven Systems

One of the main factors driving object-oriented software development for information systems is the requirement for systems to be tolerant to change. To address this issue in designing systems, this paper proposes a pattern-based, object-oriented, description-driven system (DDS) architecture as an extension to the standard UML four-layer meta-model. A DDS architecture is proposed in which aspects of both static and dynamic systems behavior can be captured via descriptive models and meta-models. The proposed architecture embodies four main elements - firstly, the adoption of a multi-layered meta-modeling architecture and reflective meta-level architecture, secondly the identification of four data modeling relationships that can be made explicit such that they can be modified dynamically, thirdly the identification of five design patterns which have emerged from practice and have proved essential in providing reusable building blocks for data management, and fourthly the encoding of the structural properties of the five design patterns by means of one fundamental pattern, the Graph pattern. A practical example of this philosophy, the CRISTAL project, is used to demonstrate the use of description-driven data objects to handle system evolution.Comment: 20 pages, 10 figure

Specialization in the Presence of Trade and Financial Integration: Explorations of the Integration-Specialization Nexus

In this paper we investigate the economic integration - industrial specialization nexus and unravel the relationship between trade and financial openness and industrial specialization. For a panel of 31 countries over the period 1970 to 2005, we find that trade integration relates negatively to specialization, while financial integration relates positively tospecialization. Furthermore, the relationship between trade (financial) integration and specialization is further deepened by the level of financial (trade) integration. Lastly, trade integration has a stronger connection to industrial specialization in countries with a high degree of intra-industry trade, whereas financial integration has a stronger connectionto specialization in countries with a relatively underdeveloped financial system. Our findings are robust to various measures and alternative model specifications.financial economics and financial management ;

Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

Integrating Genomic Knowledge Sources through an Anatomy Ontology

Modern genomic research has access to a plethora of knowledge sources. Often, it is imperative that researchers combine and integrate knowledge from multiple perspectives. Although some technology exists for connecting data and knowledge bases, these methods are only just begin-ning to be successfully applied to research in modern cell biology. In this paper, we argue that one way to integrate multiple knowledge sources is through anatomy—both generic cellular anatomy, as well as anatomic knowledge about the tissues and organs that may be studied via microarray gene expression experiments. We present two examples where we have combined a large ontology of human anatomy (the FMA) with other genomic knowledge sources: the gene ontology (GO) and the mouse genomic databases (MGD) of the Jackson Labs. These two initial examples of knowledge integration provide a proof of concept that anatomy can act as a hub through which we can usefully combine a variety of genomic knowledge and data