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

Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface

Ontology-based domain modelling for consistent content change management

Ontology-based modelling of multi-formatted software application content is a challenging area in content management. When the number of software content unit is huge and in continuous process of change, content change management is important. The management of content in this context requires targeted access and manipulation methods. We present a novel approach to deal with model-driven content-centric information systems and access to their content. At the core of our approach is an ontology-based semantic annotation technique for diversely formatted content that can improve the accuracy of access and systems evolution. Domain ontologies represent domain-specific concepts and conform to metamodels. Different ontologies - from application domain ontologies to software ontologies - capture and model the different properties and perspectives on a software content unit. Interdependencies between domain ontologies, the artifacts and the content are captured through a trace model. The annotation traces are formalised and a graph-based system is selected for the representation of the annotation traces

Semantic web technologies for video surveillance metadata

Video surveillance systems are growing in size and complexity. Such systems typically consist of integrated modules of different vendors to cope with the increasing demands on network and storage capacity, intelligent video analytics, picture quality, and enhanced visual interfaces. Within a surveillance system, relevant information (like technical details on the video sequences, or analysis results of the monitored environment) is described using metadata standards. However, different modules typically use different standards, resulting in metadata interoperability problems. In this paper, we introduce the application of Semantic Web Technologies to overcome such problems. We present a semantic, layered metadata model and integrate it within a video surveillance system. Besides dealing with the metadata interoperability problem, the advantages of using Semantic Web Technologies and the inherent rule support are shown. A practical use case scenario is presented to illustrate the benefits of our novel approach