Imaging Informatics and the Human Brain Project: the Role of Structure, Review

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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

Slisp: A Flexible Software Toolkit for Hybrid, Embedded and Distributed Applications

We describe Slisp (pronounced ‘Ess-Lisp’), a hybrid Lisp–C programming toolkit for the development of scriptable and distributed applications. Computationally expensive operations implemented as separate C-coded modules are selectively compiled into a small Xlisp interpreter, then called as Lisp functions in a Lisp-coded program. The resulting hybrid program may run in several modes: as a stand-alone executable, embedded in a different C program, as a networked server accessed from another Slisp client, or as a networked server accessed from a C-coded client. Five years of experience with Slisp, as well experience with other scripting languages such as Tcl and Perl, are summarized. These experiences suggest that Slisp will be most useful for mid-sized applications in which the kinds of scripting and embeddability features provided by Tcl and Perl can be extended in an efficient manner to larger applications, while maintaining a well-defined standard (Common Lisp) for these extensions. In addition, the generality of Lisp makes Lisp a good candidate for an application-level communication language in distributed environments

Querying Non-Materialized Ontology Views

One approach to simplifying ontologies, for inclusion in a more tractable semantic web, is through the use of non-materialized view queries. View queries define how a simplified “view” or “application” ontology is derived from larger more complex ontologies. In this work we look at a language for specifying view queries over OWL/RDFS sources, and we illustrate some initial ideas for how to execute user queries over our view ontology, without materializing it first

XML-Based Image Annotation: PAIS - a Personal Annotated Image Server

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The Digital Anatomist Foundational Model Server

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Value Sets via Ontology Views

We present a method for defining value sets as queries over ontologies (ontology views), and a mechanism for evaluating such queries. In particular we demonstrate an approach utilizing reusable template queries and parameterized URLs. We illustrate this method using an example from the Ontology of Clinical Research (OCRe)

Profile of On-Line Anatomy Information Resources: Design and Instructional Implications

This study is based on a review of 40 on-line anatomy web resources compiled from sites selected from our own searches as well as sites reviewed and published by an external group (Voiglio et al., 1999, Surg. Radiol. Anat. 21:65-68; Frasca et al., 2000, Surg. Radiol. Anat. 22:107-110). The purpose of our survey was to propose criteria by which anatomy educators could judge the characteristics of the currently available web-based resources for incorporation into the courses they teach. Each site was reviewed and scored based on a survey matrix that included four main categories: 1). site background information, 2). content components, 3). interactivity features, and 4). user interface design components. The average score of the reviewed sites was 3.3 of the total possible score of 10, indicating the limited use of computer-based design features by the majority of sites. We found, however, a number of programs in each of the survey categories that could serve as prototypes for designing future on-line anatomy resources. From the survey we conclude that various design features are less important than the comprehensiveness, depth, and logical organization of content. We suggest that the content should be sufficient for supporting explicitly defined educational objectives, which should target specific end-user populations. The majority of anatomy programs currently accessible on-line fall short of these requirements. There is a need for a coordinated and synergistic effort to generate a comprehensive anatomical information resource that is of sufficient quality and depth to support higher levels of learning beyond the memorization of structure names. Such a resource is a prerequisite for meaningful on-line anatomy education

Semi-automatic Database Design for Neuroscience Experiment Management Systems

Neuroinformatics provides tools for neuroscience researchers to study brain function. In order to handle experiment paradigms that change frequently, we are developing a semiautomatic database design tool that will enable an experiment management system (EMS) to manage data with flexibility while retaining the efficiency of a relational database

Ontology View Query Management

Like views in relational databases, ontology views are expressed as queries, but over source ontologies rather than tables. To enhance the reusability of such views, we are constructing a view Query Manager application. The Query Manager allows queries to be edited, executed, and stored for reuse. View queries are discoverable by searching the Query Manager's metadata catalog. The Query Manager also supports the storage of materialized view results upon which further queries may be issued