907 research outputs found

    A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain

    Get PDF
    Biomedical data are becoming increasingly complex and heterogeneous in nature. The data are stored in distributed information systems, using a variety of data models, and are processed by increasingly more complex tools that analyze and visualize them. We present in this paper our framework for integrating biomedical research data and tools into a unique Web front end. Our framework is applied to the University of Washington’s Human Brain Project. Specifically, we present solutions to four integration tasks: definition of complex mappings from relational sources to XML, distributed XQuery processing, generation of heterogeneous output formats, and the integration of heterogeneous data visualization and analysis tools

    Distributed XQuery

    Get PDF
    XQuery is increasingly being used for ad-hoc integration of heterogeneous data sources that are logically mapped to XML. For example, scientists need to query multiple scientific databases, which are distributed over a large geographic area, and it is possible to use XQuery for that. However, the language currently supports only the data shipping query evaluation model (through the document() function): it fetches all data sources to a single server, then runs the query there. This is a major limitation for many applications, especially when some data sources are very large, or when a data source is only a virtual XML view over some other logical data model. We propose here a simple extension to XQuery that allows query shipping to be expressed in the language, in addition to data shipping

    Constraint-based Query Distribution Framework for an Integrated Global Schema

    Full text link
    Distributed heterogeneous data sources need to be queried uniformly using global schema. Query on global schema is reformulated so that it can be executed on local data sources. Constraints in global schema and mappings are used for source selection, query optimization,and querying partitioned and replicated data sources. The provided system is all XML-based which poses query in XML form, transforms, and integrates local results in an XML document. Contributions include the use of constraints in our existing global schema which help in source selection and query optimization, and a global query distribution framework for querying distributed heterogeneous data sources.Comment: The Proceedings of the 13th INMIC 2009), Dec. 14-15, 2009, Islamabad, Pakistan. Pages 1 - 6 Print ISBN: 978-1-4244-4872-2 INSPEC Accession Number: 11072575 Date of Current Version : 15 January 201

    Lightweight Data Integration Frameworks for Clinical Research

    Get PDF
    Research data from a single clinical study is often spread across multiple applications and systems. We present a reusable, lightweight, secure framework for automatically integrating and querying study data from heterogeneous sources in order to answer routine, operational questions for researchers

    Bioinformatics service reconciliation by heterogeneous schema transformation

    Get PDF
    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

    A Query Integrator and Manager for the Query Web

    Get PDF
    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

    Rule-based information integration

    Get PDF
    In this report, we show the process of information integration. We specifically discuss the language used for integration. We show that integration consists of two phases, the schema mapping phase and the data integration phase. We formally define transformation rules, conversion, evolution and versioning. We further discuss the integration process from a data point of view
    corecore