Explorative search of distributed bio-data to answer complex biomedical questions

Background The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions. Results A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at http://www.bioinformatics.deib.polimi.it/bio-seco/seco/. It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions. Conclusions By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is fundamental for Life Science data driven knowledge discovery

Cost-Aware Rank Join with Random and Sorted Access

We address the problem of joining ranked results produced by two or more services on the Web. We consider services endowed with two kinds of access that are often available: i) sorted access, which returns tuples sorted by score; ii) random access, which returns tuples matching a given join attribute value. Rank join operators combine objects of multiple relations and output the K combinations with the highest aggregate score. While the past literature has studied suitable bounding schemes for this setting, we focus on the definition of a pulling strategy, which determines the order of invocation of the joined services. We propose CARS (Cost-Aware with Random and Sorted access), a pulling strategy is derived at compile-time that is oblivious of the query-dependent score distributions. We cast CARS as the solution of an optimization problem based on a few parameters characterizing the joined services. We validate the proposed strategy with experiments on both real and synthetic data sets. We show that CARS outperforms prior proposals and that its overall access cost is always within a very short margin from that of an oracle-based optimal strategy. CARS is also shown to be robust w.r.t. the uncertainty that may characterize the estimated parameters

Rank-aware, Approximate Query Processing on the Semantic Web

Search over the Semantic Web corpus frequently leads to queries having large result sets. So, in order to discover relevant data elements, users must rely on ranking techniques to sort results according to their relevance. At the same time, applications oftentimes deal with information needs, which do not require complete and exact results. In this thesis, we face the problem of how to process queries over Web data in an approximate and rank-aware fashion