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

Modeling Temporal Evidence from External Collections

Newsworthy events are broadcast through multiple mediums and prompt the crowds to produce comments on social media. In this paper, we propose to leverage on this behavioral dynamics to estimate the most relevant time periods for an event (i.e., query). Recent advances have shown how to improve the estimation of the temporal relevance of such topics. In this approach, we build on two major novelties. First, we mine temporal evidences from hundreds of external sources into topic-based external collections to improve the robustness of the detection of relevant time periods. Second, we propose a formal retrieval model that generalizes the use of the temporal dimension across different aspects of the retrieval process. In particular, we show that temporal evidence of external collections can be used to (i) infer a topic's temporal relevance, (ii) select the query expansion terms, and (iii) re-rank the final results for improved precision. Experiments with TREC Microblog collections show that the proposed time-aware retrieval model makes an effective and extensive use of the temporal dimension to improve search results over the most recent temporal models. Interestingly, we observe a strong correlation between precision and the temporal distribution of retrieved and relevant documents.Comment: To appear in WSDM 201

Thesaurus-assisted search term selection and query expansion: a review of user-centred studies

This paper provides a review of the literature related to the application of domain-specific thesauri in the search and retrieval process. Focusing on studies which adopt a user-centred approach, the review presents a survey of the methodologies and results from empirical studies undertaken on the use of thesauri as sources of term selection for query formulation and expansion during the search process. It summaries the ways in which domain-specific thesauri from different disciplines have been used by various types of users and how these tools aid users in the selection of search terms. The review consists of two main sections covering, firstly studies on thesaurus-aided search term selection and secondly those dealing with query expansion using thesauri. Both sections are illustrated with case studies that have adopted a user-centred approach

User requirement elicitation for cross-language information retrieval

Who are the users of a cross-language retrieval system? Under what circumstances do they need to perform such multi-language searches? How will the task and the context of use affect successful interaction with the system? Answers to these questions were explored in a user study performed as part of the design stages of Clarity, a EU founded project on cross-language information retrieval. The findings resulted in a rethink of the planned user interface and a consequent expansion of the set of services offered. This paper reports on the methodology and techniques used for the elicitation of user requirements as well as how these were in turn transformed into new design solutions

An adaptive approach for image organisation and retrieval

We propose and evaluate an adaptive approach towards content-based image retrieval (CBIR), which is based on the Ostensive Model of developing information needs. We use ostensive relevance to capture the user's current interest and tailor the retrieval accordingly. Our approach supports content-assisted browsing, by incorporating an adaptive query learning scheme based on implicit feedback from the user. Textual and colour features are employed to characterise images. Evidence from these features are combined using the Dempster-Shafer theory of evidence combination. Results from a user-centred, task-oriented evaluation show that the ostensive interface is preferred over a traditional interface with manual query facilities. Its strengths are considered to lie in its ability to adapt to the user's need, and its very intuitive and fluid way of operation

Observing Users - Designing clarity a case study on the user-centred design of a cross-language information retrieval system

This paper presents a case study of the development of an interface to a novel and complex form of document retrieval: searching for texts written in foreign languages based on native language queries. Although the underlying technology for achieving such a search is relatively well understood, the appropriate interface design is not. A study involving users (with such searching needs) from the start of the design process is described covering initial examination of user needs and tasks; preliminary design and testing of interface components; building, testing, and further refining an interface; before finally conducting usability tests of the system. Lessons are learned at every stage of the process leading to a much more informed view of how such an interface should be built

An adaptive technique for content-based image retrieval

We discuss an adaptive approach towards Content-Based Image Retrieval. It is based on the Ostensive Model of developing information needs—a special kind of relevance feedback model that learns from implicit user feedback and adds a temporal notion to relevance. The ostensive approach supports content-assisted browsing through visualising the interaction by adding user-selected images to a browsing path, which ends with a set of system recommendations. The suggestions are based on an adaptive query learning scheme, in which the query is learnt from previously selected images. Our approach is an adaptation of the original Ostensive Model based on textual features only, to include content-based features to characterise images. In the proposed scheme textual and colour features are combined using the Dempster-Shafer theory of evidence combination. Results from a user-centred, work-task oriented evaluation show that the ostensive interface is preferred over a traditional interface with manual query facilities. This is due to its ability to adapt to the user's need, its intuitiveness and the fluid way in which it operates. Studying and comparing the nature of the underlying information need, it emerges that our approach elicits changes in the user's need based on the interaction, and is successful in adapting the retrieval to match the changes. In addition, a preliminary study of the retrieval performance of the ostensive relevance feedback scheme shows that it can outperform a standard relevance feedback strategy in terms of image recall in category search