A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax

CHORUS Deliverable 2.1: State of the Art on Multimedia Search Engines

Based on the information provided by European projects and national initiatives related to multimedia search as well as domains experts that participated in the CHORUS Think-thanks and workshops, this document reports on the state of the art related to multimedia content search from, a technical, and socio-economic perspective. The technical perspective includes an up to date view on content based indexing and retrieval technologies, multimedia search in the context of mobile devices and peer-to-peer networks, and an overview of current evaluation and benchmark inititiatives to measure the performance of multimedia search engines. From a socio-economic perspective we inventorize the impact and legal consequences of these technical advances and point out future directions of research

Multi-Dimensional Grid-Based Clustering of Fuzzy Query Results

In usual retrieval processes within large databases, the user formulates a first basic (broad) query to target and filter data and next, she starts browsing the answer looking for precise information. We then propose to perform an offline hierarchical grid-based clustering of the data set in order to quickly provide the user with concise, useful and structured answers as a starting point for an online exploration. Every single answer item describes a subset of the queried data in a user-friendly form using linguistic labels, that is to say it represents a concept that exists within the data. Moreover, answers of a given 'blind' query are nodes of a classification tree and every subtree rooted by an answer offers a 'guided tour' of a data subset to the user. Finally, an experimental study shows that our process is efficient in terms of computational time and achieves high quality clustering schemas of query result

Graph BI & analytics: current state and future challenges

In an increasingly competitive market, making well-informed decisions requires the analysis of a wide range of heterogeneous, large and complex data. This paper focuses on the emerging field of graph warehousing. Graphs are widespread structures that yield a great expressive power. They are used for modeling highly complex and interconnected domains, and efficiently solving emerging big data application. This paper presents the current status and open challenges of graph BI and analytics, and motivates the need for new warehousing frameworks aware of the topological nature of graphs. We survey the topics of graph modeling, management, processing and analysis in graph warehouses. Then we conclude by discussing future research directions and positioning them within a unified architecture of a graph BI and analytics framework.Peer ReviewedPostprint (author's final draft

Doctor of Philosophy

dissertationBiomedical data are a rich source of information and knowledge. Not only are they useful for direct patient care, but they may also offer answers to important population-based questions. Creating an environment where advanced analytics can be performed against biomedical data is nontrivial, however. Biomedical data are currently scattered across multiple systems with heterogeneous data, and integrating these data is a bigger task than humans can realistically do by hand; therefore, automatic biomedical data integration is highly desirable but has never been fully achieved. This dissertation introduces new algorithms that were devised to support automatic and semiautomatic integration of heterogeneous biomedical data. The new algorithms incorporate both data mining and biomedical informatics techniques to create "concept bags" that are used to compute similarity between data elements in the same way that "word bags" are compared in data mining. Concept bags are composed of controlled medical vocabulary concept codes that are extracted from text using named-entity recognition software. To test the new algorithm, three biomedical text similarity use cases were examined: automatically aligning data elements between heterogeneous data sets, determining degrees of similarity between medical terms using a published benchmark, and determining similarity between ICU discharge summaries. The method is highly configurable and 5 different versions were tested. The concept bag method performed particularly well aligning data elements and outperformed the compared algorithms by iv more than 5%. Another configuration that included hierarchical semantics performed particularly well at matching medical terms, meeting or exceeding 30 of 31 other published results using the same benchmark. Results for the third scenario of computing ICU discharge summary similarity were less successful. Correlations between multiple methods were low, including between terminologists. The concept bag algorithms performed consistently and comparatively well and appear to be viable options for multiple scenarios. New applications of the method and ideas for improving the algorithm are being discussed for future work, including several performance enhancements, configuration-based enhancements, and concept vector weighting using the TF-IDF formulas