Contorsion: A Semantic XPath Processor

AbstractThis work describes the architecture of Contorsion, a semantic XPath processor that acts over an RDF mapping of XML. It contributes to a recent research trend that defines an XML-to-RDF mapping allowing XML documents interoperate at the semantic level. We use a model-mapping approach to represent instances of XML and XML Schema in RDF. This representation retains the node order, in contrast with the usual structure-mapping approach. The processor can be fed with an unlimited set of XML schemas and/or RDFS/OWL ontologies. The queries are resolved taking in consideration the structural and semantic connections descrived in the schemas and ontologies. Such behaviour, schema-awareness and semantic integration, can be useful for exploiting schema and ontology hierarchies in XPath queries

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Automated syntactic mediation for Web service integration

As the Web Services and Grid community adopt Semantic Web technology, we observe a shift towards higher-level workflow composition and service discovery practices. While this provides excellent functionality to non-expert users, more sophisticated middleware is required to hide the details of service invocation and service integration. An investigation of a common Bioinformatics use case reveals that the execution of high-level workflow designs requires additional processing to harmonise syntactically incompatible service interfaces. In this paper, we present an architecture to support the automatic reconciliation of data formats in such Web Service worklflows. The mediation of data is driven by ontologies that encapsulate the information contained in heterogeneous data structures supplying a common, conceptual data representation. Data conversion is carried out by a Configurable Mediator component, consuming mappings between \xml schemas and \owl ontologies. We describe our system and give examples of our mapping language against the background of a Bioinformatics use case

Bioinformatics service reconciliation by heterogeneous schema transformation

This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services

Integrated management of hierarchical levels: towards a CAPE tool

The integration of decision-making procedures usually assigned to different hierarchical production systems requires the use of complex mathematical models and high computational efforts, in addition to the need of an extensive management of data and knowledge within the production systems. This work addresses this integration problem and proposes a comprehensive solution approach, as well as guidelines for Computer Aided Process Engineering (CAPE) tools managing the corresponding cyberinfrastructure. This study presents a methodology based on a domain ontology which is used as the connector between the introduced data, the different available formulations developed to solve the decision-making problem, and the necessary information to build the finally required problem instance. The methodology has demonstrated its capability to help exploiting different available decision-making problem formulations in complex cases, leading to new applications and/or extensions of these available formulations in a robust and flexible way.Peer ReviewedPostprint (author's final draft