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

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

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

Is Mindfulness-Based Therapy Effective In Increasing Total Sleep Time In Adults?

Objective: The objective of this selective evidence based medicine review is to determine whether or not mindfulness-based therapy is effective in increasing total sleep time in adults. Study design: Review of three randomized controlled trials published in 2011, 2014 and 2015, all English language. Data source-The three randomized controlled trials that were used in this review were found using PubMed. Outcomes measured: Total sleep time, sleep onset latency, wake after sleep onset, number of awakenings, time in bed, subjective sleep quality, sleep duration, habitual sleep efficiency, sleep disturbances, use of sleep medications, and daytime dysfunction were the main outcomes measured. Results: In the Black et al. study there showed an improvement in the mindful awareness practice group by a mean of 2.8 and a mean of 1.1 in the sleep hygiene education group when comparing Pittsburgh Sleep Index Quotient (PSQI) scores which includes total sleep time from baseline to post intervention. The Gross et al. study showed a baseline mean of total sleep time of 6.34 hours in the mindfulness-based stress reduction group was reduced to 6.21 hours and in the pharmacotherapy group a baseline total sleep time of 6.40 hours increased to 6.95 hours at the end of active treatment. The Ong et al. study showed an increase in the total sleep time of 27.68 minutes in the mindfulness-based stress reduction group and the mindfulness-based therapy for insomnia group showed an increase of 2.5 minutes along with the self-monitoring group that had an increase of 6.53 minutes in the total sleep time. Conclusion: Mindfulness-based therapy (MBT) has not been shown to be as effective in increasing total sleep time as pharmacotherapy in the short term, but was shown to increase total sleep time when compared to sleep hygiene education or self-monitoring. MBT can be used as an adjunctive therapy for those that suffer from insomnia and may be more efficacious when used long term

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

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