1,102 research outputs found
A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain
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
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
Constraint-based Query Distribution Framework for an Integrated Global Schema
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
State-of-the-art on evolution and reactivity
This report starts by, in Chapter 1, outlining aspects of querying and updating resources on
the Web and on the Semantic Web, including the development of query and update languages
to be carried out within the Rewerse project.
From this outline, it becomes clear that several existing research areas and topics are of
interest for this work in Rewerse. In the remainder of this report we further present state of
the art surveys in a selection of such areas and topics. More precisely: in Chapter 2 we give
an overview of logics for reasoning about state change and updates; Chapter 3 is devoted to briefly describing existing update languages for the Web, and also for updating logic programs;
in Chapter 4 event-condition-action rules, both in the context of active database systems and
in the context of semistructured data, are surveyed; in Chapter 5 we give an overview of some relevant rule-based agents frameworks
Modeling views in the layered view model for XML using UML
In data engineering, view formalisms are used to provide flexibility to users and user applications by allowing them to extract and elaborate data from the stored data sources. Conversely, since the introduction of Extensible Markup Language (XML), it is fast emerging as the dominant standard for storing, describing, and interchanging data among various web and heterogeneous data sources. In combination with XML Schema, XML provides rich facilities for defining and constraining user-defined data semantics and properties, a feature that is unique to XML. In this context, it is interesting to investigate traditional database features, such as view models and view design techniques for XML. However, traditional view formalisms are strongly coupled to the data language and its syntax, thus it proves to be a difficult task to support views in the case of semi-structured data models. Therefore, in this paper we propose a Layered View Model (LVM) for XML with conceptual and schemata extensions. Here our work is three-fold; first we propose an approach to separate the implementation and conceptual aspects of the views that provides a clear separation of concerns, thus, allowing analysis and design of views to be separated from their implementation. Secondly, we define representations to express and construct these views at the conceptual level. Thirdly, we define a view transformation methodology for XML views in the LVM, which carries out automated transformation to a view schema and a view query expression in an appropriate query language. Also, to validate and apply the LVM concepts, methods and transformations developed, we propose a view-driven application development framework with the flexibility to develop web and database applications for XML, at varying levels of abstraction
Feeds as Query Result Serializations
Many Web-based data sources and services are available as feeds, a model that
provides consumers with a loosely coupled way of interacting with providers.
The current feed model is limited in its capabilities, however. Though it is
simple to implement and scales well, it cannot be transferred to a wider range
of application scenarios. This paper conceptualizes feeds as a way to serialize
query results, describes the current hardcoded query semantics of such a
perspective, and surveys the ways in which extensions of this hardcoded model
have been proposed or implemented. Our generalized view of feeds as query
result serializations has implications for the applicability of feeds as a
generic Web service for any collection that is providing access to individual
information items. As one interesting and compelling class of applications, we
describe a simple way in which a query-based approach to feeds can be used to
support location-based services
Use-cases on evolution
This report presents a set of use cases for evolution and reactivity for data in the Web and
Semantic Web. This set is organized around three different case study scenarios, each of them
is related to one of the three different areas of application within Rewerse. Namely, the scenarios
are: “The Rewerse Information System and Portal”, closely related to the work of A3
– Personalised Information Systems; “Organizing Travels”, that may be related to the work
of A1 – Events, Time, and Locations; “Updates and evolution in bioinformatics data sources”
related to the work of A2 – Towards a Bioinformatics Web
Survey over Existing Query and Transformation Languages
A widely acknowledged obstacle for realizing the vision of the Semantic Web is the inability
of many current Semantic Web approaches to cope with data available in such diverging
representation formalisms as XML, RDF, or Topic Maps. A common query language is the first
step to allow transparent access to data in any of these formats. To further the understanding
of the requirements and approaches proposed for query languages in the conventional as well
as the Semantic Web, this report surveys a large number of query languages for accessing
XML, RDF, or Topic Maps. This is the first systematic survey to consider query languages from
all these areas. From the detailed survey of these query languages, a common classification
scheme is derived that is useful for understanding and differentiating languages within and
among all three areas
Efficient Incremental Breadth-Depth XML Event Mining
Many applications log a large amount of events continuously. Extracting
interesting knowledge from logged events is an emerging active research area in
data mining. In this context, we propose an approach for mining frequent events
and association rules from logged events in XML format. This approach is
composed of two-main phases: I) constructing a novel tree structure called
Frequency XML-based Tree (FXT), which contains the frequency of events to be
mined; II) querying the constructed FXT using XQuery to discover frequent
itemsets and association rules. The FXT is constructed with a single-pass over
logged data. We implement the proposed algorithm and study various performance
issues. The performance study shows that the algorithm is efficient, for both
constructing the FXT and discovering association rules
Distributed XQuery-based integration and visualization of multimodality data: Application to brain mapping.
This paper addresses the need for relatively small groups of collaborating investigators to integrate distributed and heterogeneous data about the brain. Although various national efforts facilitate large-scale data sharing, these approaches are generally too “heavyweight” for individual or small groups of investigators, with the result that most data sharing among collaborators continues to be ad hoc. Our approach to this problem is to create a “lightweight” distributed query architecture, in which data sources are accessible via web services that accept arbitrary query languages but return XML results. A Distributed XQuery Processor (DXQP) accepts distributed XQueries in which subqueries are shipped to the remote data sources to be executed, with the resulting XML integrated by DXQP. A web-based application called DXBrain accesses DXQP, allowing a user to create, save and execute distributed XQueries, and to view the results in various formats including a 3-D brain visualization. Example results are presented using distributed brain mapping data sources obtained in studies of language organization in the brain, but any other XML source could be included. The advantage of this approach is that it is very easy to add and query a new source, the tradeoff being that the user needs to understand XQuery and the schemata of the underlying sources. For small numbers of known sources this burden is not onerous for a knowledgeable user, leading to the conclusion that the system helps to fill the gap between ad hoc local methods and large scale but complex national data sharing efforts
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