A Query Integrator and Manager for the Query Web

Brinkley, James F and Detwiler, Landon T. (2012) A Query Integrator and Manager for the Query Web. Journal of Biomedical Informatics, 45 (5). pp. 975-991. ISSN 15320464

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Abstract

Received 16 November 2011 Accepted 31 March 2012 Available online 17 April 2012 Keywords: Ontologies Data integration Semantic web Query Web 1. Introduction In recent years researchers spend as much or more time at their computers as they do in the wet lab. A significant component of this time is spent managing experimental or clinical research data with the aid of spreadsheets, local databases, or small-scale web- based databases [1–4]. In addition, with the worldwide increase in web-accessible databases at levels ranging from chemicals to public health [5–25] researchers tend to spend significant time searching these databases for information that is available about, for example, a particular gene, protein or disease of interest. In fact more often than not researchers first consult the online databases before doing experiments, often in order to develop hypotheses that can be tested in the lab. However, because most databases are designed independently, with different data models and (generally web-based) user inter- faces, it has become an increasingly significant effort for research- ers to access and combine data from different sources. In a 2002 paper [26] Stein likened the situation to a nation of city-states, ⇑ Corresponding author. Address: Department of Biological Structure, University of Washington, Box 357420, Seattle, WA 98195, United States. Fax: +1 206 543 1524. E-mail addresses: brinkley@u.washington.edu (J.F. Brinkley), det@u.washington. edu (L.T. Detwiler). 1532-0464/$ - see front matter Ó 2012 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.jbi.2012.03.008 abstract 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, XQue- ry); 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 appro- priate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontol- ogy 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.

Item Type: Article
Subjects: All Projects > Query Integrator
Divisions: University of Washington > Department of Biological Structure
Depositing User: Jim Brinkley
Date Deposited: 02 May 2019 18:45
Last Modified: 09 May 2019 23:45
URI: http://sigpubs.si.washington.edu/id/eprint/364

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