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

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

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)

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

Variation and change in the vowel system of Tyneside English

PhD ThesisThis thesis presents a variationist account of phonological variation and change in the vowel system of Tyneside English. The distributions of the phonetic exponents of five vowel variables are assessed with respect to the social variables sex, age and social class. Using a corpus of conversational and word-list material, for which 32 speakers of Tyneside English were recorded, between 30 and 40 tokens per speaker of the variables (i), (u), (e), (o) and (3) were transcribed impressionistically and subclassified by following phonological context. The results of this analysis are significant on several counts. First, the speakers sampled appear to differentiate themselves within the speech community through the variable use of certain socially marked phonetic variants, which can be correlated with the sex, age and class variables. Secondly, the speakers style shift to a greater or lesser degree according to combinations of the three social factors, such that surface variability is reduced as a function of increased formality. Third, the overall pattern among the sample population seems to be one of increasing uniformity or convergence: it is speculated that social mobility among upper working- and lower-middle class groups may lead to accent levelling, whereby local speech forms are supplanted by supra-local or innovative intermediate ones. That is, the patterns observed here may be indicative of change in progress. Last, a comparison of the results for the (phonologically) paired variables (i u) and (e o) shows a strong tendency for Tyneside speakers to use these 'symmetrically', in that choice of variant in one variable predicts choice of variant in the other. It is suggested that the symmetry in the system is exploited by Tyneside speakers for the purposes of indicating social affiliation and identity, and is in this sense an extra sociolinguistic resource upon which speakers can draw. In addition, the variants of (3) are discussed with reference to the reported merger of this variable with (a); it is suggested that the apparent 'unmerging' of these two classes is unproblematic from a structural point of view, as the putative (3)—(o) merger appears never to have been completed.UK Economic and Social Research Council (award number R00429524350

Distributed Queries for Quality Control Checks in Clinical Trials

Operational Quality Control (QC) checks are standard practice in clinical trials and ensure ongoing compliance with the study protocol, standard operating procedures (SOPs) and Good Clinical Practice (GCP). We present a method for defining QC checks as distributed queries over case report forms (CRF) and clinical imaging data- sources. Our distributed query system can integrate time-sensitive information in order to populate QC checks that can facilitate discrepancy resolution workflow in clinical trials

vSPARQL: A View Definition Language for the Semantic Web

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages

Challenges in Reconciling Different Views of Neuroanatomy in a Reference Ontology of Anatomy

A fundamental requirement for integrating neuroscience data is a well-structured ontology that can incorporate, accommodate and reconcile different neuroanatomical views. Here we describe the challenges in creating such ontology, and, because of its principled design, illustrate the potential of the Foundational Model of Anatomy to be that ontology

Factors associated with geographic variation in cost per episode of care for three medical conditions

Objective: To identify associations between market factors, especially relative reimbursement rates, and the probability of surgery and cost per episode for three medical conditions (cataract, benign prostatic neoplasm, and knee degeneration) with multiple treatment options. Methods: We use 2004–2006 Medicare claims data for elderly beneficiaries from sixty nationally representative communities to estimate multivariate models for the probability of surgery and cost per episode of care as a function local market factors, including Medicare physician reimbursement for surgical versus non-surgical treatment and the availability of primary care and specialty physicians. We used Symmetry’s Episode Treatment Groups (ETG) software to group claims into episodes for the three conditions (n = 540,874 episodes). Results: Higher Medicare reimbursement for surgical episodes and greater availability of the relevant specialists are significantly associated with more surgery and higher cost per episode for all three conditions, while greater availability of primary care physicians is significantly associated with less frequent surgery and lower cost per episode. Conclusion: Relative Medicare reimbursement rates for surgical vs. non-surgical treatments and the availability of both primary care physicians and relevant specialists are associated with the likelihood of surgery and cost per episode

Enabling RadLex with the Foundational Model of Anatomy Ontology to Organize and Integrate Neuro-imaging Data

In this study we focused on empowering RadLex with an ontological framework and additional content derived from the Foundational Model of Anatomy Ontology1 thereby providing RadLex the facility to correlate the different standards used in annotating neuroradiological image data. The objective of this work is to promote data sharing, data harmonization and interoperability between disparate neuroradiological labeling systems