From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and intuitive form-based interfaces to facilitate easy querying of the data. These interfaces could be seen as implementing a set of "pre-canned" queries commonly used by the life science researchers that we study. The second approach is based on semantic Web technologies and is knowledge (model) driven. It utilizes a large OWL ontology and same datasets as before but associated as RDF instances of the ontology concepts. An intuitive interface is provided that allows the formulation of RDF triples-based queries. Both these approaches are being used in parallel by a team of cell biologists in their daily research activities, with the objective of gradually replacing the conventional approach with the knowledge-driven one. This provides us with a valuable opportunity to compare and qualitatively evaluate the two approaches. We describe several benefits of the knowledge-driven approach in comparison to the traditional way of accessing data, and highlight a few limitations as well. We believe that our analysis not only explicitly highlights the specific benefits and limitations of semantic Web technologies in our context but also contributes toward effective ways of translating a question in a researcher's mind into precise computational queries with the intent of obtaining effective answers from the data. While researchers often assume the benefits of semantic Web technologies, we explicitly illustrate these in practice

QB2OLAP : enabling OLAP on statistical linked open data

Publication and sharing of multidimensional (MD) data on the Semantic Web (SW) opens new opportunities for the use of On-Line Analytical Processing (OLAP). The RDF Data Cube (QB) vocabulary, the current standard for statistical data publishing, however, lacks key MD concepts such as dimension hierarchies and aggregate functions. QB4OLAP was proposed to remedy this. However, QB4OLAP requires extensive manual annotation and users must still write queries in SPARQL, the standard query language for RDF, which typical OLAP users are not familiar with. In this demo, we present QB2OLAP, a tool for enabling OLAP on existing QB data. Without requiring any RDF, QB(4OLAP), or SPARQL skills, it allows semi-automatic transformation of a QB data set into a QB4OLAP one via enrichment with QB4OLAP semantics, exploration of the enriched schema, and querying with the high-level OLAP language QL that exploits the QB4OLAP semantics and is automatically translated to SPARQL.Peer ReviewedPostprint (author's final draft

Exploring user and system requirements of linked data visualization through a visual dashboard approach

One of the open problems in SemanticWeb research is which tools should be provided to users to explore linked data. This is even more urgent now that massive amount of linked data is being released by governments worldwide. The development of single dedicated visualization applications is increasing, but the problem of exploring unknown linked data to gain a good understanding of what is contained is still open. An effective generic solution must take into account the user’s point of view, their tasks and interaction, as well as the system’s capabilities and the technical constraints the technology imposes. This paper is a first step in understanding the implications of both, user and system by evaluating our dashboard-based approach. Though we observe a high user acceptance of the dashboard approach, our paper also highlights technical challenges arising out of complexities involving current infrastructure that need to be addressed while visualising linked data. In light of the findings, guidelines for the development of linked data visualization (and manipulation) are provided

Science with the Virtual Observatory: the AstroGrid VO Desktop

We introduce a general range of science drivers for using the Virtual Observatory (VO) and identify some common aspects to these as well as the advantages of VO data access. We then illustrate the use of existing VO tools to tackle multi wavelength science problems. We demonstrate the ease of multi mission data access using the VOExplorer resource browser, as provided by AstroGrid (http://www.astrogrid.org) and show how to pass the various results into any VO enabled tool such as TopCat for catalogue correlation. VOExplorer offers a powerful data-centric visualisation for browsing and filtering the entire VO registry using an iTunes type interface. This allows the user to bookmark their own personalised lists of resources and to run tasks on the selected resources as desired. We introduce an example of how more advanced querying can be performed to access existing X-ray cluster of galaxies catalogues and then select extended only X-ray sources as candidate clusters of galaxies in the 2XMMi catalogue. Finally we introduce scripted access to VO resources using python with AstroGrid and demonstrate how the user can pass on the results of such a search and correlate with e.g. optical datasets such as Sloan. Hence we illustrate the power of enabling large scale data mining of multi wavelength resources in an easily reproducible way using the VO.Comment: 8 pages; 7 figures; proceedings of invited talk at "Multi wavelength astronomy and the Virtual Observatory" conference, December 2008, EuroVO-AIDA program, European Space Astronomy Centre, Spai

Continuous client-side query evaluation over dynamic linked data

Existing solutions to query dynamic Linked Data sources extend the SPARQL language, and require continuous server processing for each query. Traditional SPARQL endpoints already accept highly expressive queries, so extending these endpoints for time-sensitive queries increases the server cost even further. To make continuous querying over dynamic Linked Data more affordable, we extend the low-cost Triple Pattern Fragments (TPF) interface with support for time-sensitive queries. In this paper, we introduce the TPF Query Streamer that allows clients to evaluate SPARQL queries with continuously updating results. Our experiments indicate that this extension significantly lowers the server complexity, at the expense of an increase in the execution time per query. We prove that by moving the complexity of continuously evaluating queries over dynamic Linked Data to the clients and thus increasing bandwidth usage, the cost at the server side is significantly reduced. Our results show that this solution makes real-time querying more scalable for a large amount of concurrent clients when compared to the alternatives