Lightweight XML-based query, integration and visualization of distributed, multimodality brain imaging data

A need of many neuroimaging researchers is to integrate multimodality brain data that may be stored in separate databases. To address this need we have developed a framework that provides a uniform XML-based query interface across multiple online data sources. The development of this framework is driven by the need to integrate neurosurgical and neuroimaging data related to language. The data sources for the language studies are 1) a web-accessible relational database of neurosurgical cortical stimulation mapping data (CSM) that includes patient-specific 3-D coordinates of each stimulation site mapped to an MRI reconstruction of the patient brain surface; and 2) an XML database of fMRI and structural MRI data and analysis results, created automatically by a batch program we have embedded in SPM. To make these sources available for querying each is wrapped as an XML view embedded in a web service. A top level web application accepts distributed XQueries over the sources, which are dispatched to the underlying web services. Returned results can be displayed as XML, HTML, CSV (Excel format), a 2-D schematic of a parcellated brain, or a 3-D brain visualization. In the latter case the CSM patient-specific coordinates returned by the query are sent to a transformation web-service for conversion to normalized space, after which they are sent to our 3-D visualization program MindSeer, which is accessed via Java WebStart through a generated link. The anatomical distribution of pooled CSM sites can then be visualized using various surfaces derived from brain atlases. As this framework is further developed and generalized we believe it will have appeal for researchers who wish to query, integrate and visualize results across their own databases as well as those of collaborators

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

Information Integration - the process of integration, evolution and versioning

At present, many information sources are available wherever you are. Most of the time, the information needed is spread across several of those information sources. Gathering this information is a tedious and time consuming job. Automating this process would assist the user in its task. Integration of the information sources provides a global information source with all information needed present. All of these information sources also change over time. With each change of the information source, the schema of this source can be changed as well. The data contained in the information source, however, cannot be changed every time, due to the huge amount of data that would have to be converted in order to conform to the most recent schema.\ud In this report we describe the current methods to information integration, evolution and versioning. We distinguish between integration of schemas and integration of the actual data. We also show some key issues when integrating XML data sources

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

Heterogeneous data source integration for smart grid ecosystems based on metadata mining

The arrival of new technologies related to smart grids and the resulting ecosystem of applications andmanagement systems pose many new problems. The databases of the traditional grid and the variousinitiatives related to new technologies have given rise to many different management systems with several formats and different architectures. A heterogeneous data source integration system is necessary toupdate these systems for the new smart grid reality. Additionally, it is necessary to take advantage of theinformation smart grids provide. In this paper, the authors propose a heterogeneous data source integration based on IEC standards and metadata mining. Additionally, an automatic data mining framework isapplied to model the integrated information.Ministerio de Economía y Competitividad TEC2013-40767-

Qualitative Effects of Knowledge Rules in Probabilistic Data Integration

One of the problems in data integration is data overlap: the fact that different data sources have data on the same real world entities. Much development time in data integration projects is devoted to entity resolution. Often advanced similarity measurement techniques are used to remove semantic duplicates from the integration result or solve other semantic conflicts, but it proofs impossible to get rid of all semantic problems in data integration. An often-used rule of thumb states that about 90% of the development effort is devoted to solving the remaining 10% hard cases. In an attempt to significantly decrease human effort at data integration time, we have proposed an approach that stores any remaining semantic uncertainty and conflicts in a probabilistic database enabling it to already be meaningfully used. The main development effort in our approach is devoted to defining and tuning knowledge rules and thresholds. Rules and thresholds directly impact the size and quality of the integration result. We measure integration quality indirectly by measuring the quality of answers to queries on the integrated data set in an information retrieval-like way. The main contribution of this report is an experimental investigation of the effects and sensitivity of rule definition and threshold tuning on the integration quality. This proves that our approach indeed reduces development effort — and not merely shifts the effort to rule definition and threshold tuning — by showing that setting rough safe thresholds and defining only a few rules suffices to produce a ‘good enough’ integration that can be meaningfully used