Enabling Web-scale data integration in biomedicine through Linked Open Data

The biomedical data landscape is fragmented with several isolated, heterogeneous data and knowledge sources, which use varying formats, syntaxes, schemas, and entity notations, existing on the Web. Biomedical researchers face severe logistical and technical challenges to query, integrate, analyze, and visualize data from multiple diverse sources in the context of available biomedical knowledge. Semantic Web technologies and Linked Data principles may aid toward Web-scale semantic processing and data integration in biomedicine. The biomedical research community has been one of the earliest adopters of these technologies and principles to publish data and knowledge on the Web as linked graphs and ontologies, hence creating the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we provide our perspective on some opportunities proffered by the use of LSLOD to integrate biomedical data and knowledge in three domains: (1) pharmacology, (2) cancer research, and (3) infectious diseases. We will discuss some of the major challenges that hinder the wide-spread use and consumption of LSLOD by the biomedical research community. Finally, we provide a few technical solutions and insights that can address these challenges. Eventually, LSLOD can enable the development of scalable, intelligent infrastructures that support artificial intelligence methods for augmenting human intelligence to achieve better clinical outcomes for patients, to enhance the quality of biomedical research, and to improve our understanding of living systems

Storage Solutions for Big Data Systems: A Qualitative Study and Comparison

Big data systems development is full of challenges in view of the variety of application areas and domains that this technology promises to serve. Typically, fundamental design decisions involved in big data systems design include choosing appropriate storage and computing infrastructures. In this age of heterogeneous systems that integrate different technologies for optimized solution to a specific real world problem, big data system are not an exception to any such rule. As far as the storage aspect of any big data system is concerned, the primary facet in this regard is a storage infrastructure and NoSQL seems to be the right technology that fulfills its requirements. However, every big data application has variable data characteristics and thus, the corresponding data fits into a different data model. This paper presents feature and use case analysis and comparison of the four main data models namely document oriented, key value, graph and wide column. Moreover, a feature analysis of 80 NoSQL solutions has been provided, elaborating on the criteria and points that a developer must consider while making a possible choice. Typically, big data storage needs to communicate with the execution engine and other processing and visualization technologies to create a comprehensive solution. This brings forth second facet of big data storage, big data file formats, into picture. The second half of the research paper compares the advantages, shortcomings and possible use cases of available big data file formats for Hadoop, which is the foundation for most big data computing technologies. Decentralized storage and blockchain are seen as the next generation of big data storage and its challenges and future prospects have also been discussed

Doctor of Philosophy

dissertationLinked data are the de-facto standard in publishing and sharing data on the web. To date, we have been inundated with large amounts of ever-increasing linked data in constantly evolving structures. The proliferation of the data and the need to access and harvest knowledge from distributed data sources motivate us to revisit several classic problems in query processing and query optimization. The problem of answering queries over views is commonly encountered in a number of settings, including while enforcing security policies to access linked data, or when integrating data from disparate sources. We approach this problem by efficiently rewriting queries over the views to equivalent queries over the underlying linked data, thus avoiding the costs entailed by view materialization and maintenance. An outstanding problem of query rewriting is the number of rewritten queries is exponential to the size of the query and the views, which motivates us to study problem of multiquery optimization in the context of linked data. Our solutions are declarative and make no assumption for the underlying storage, i.e., being store-independent. Unlike relational and XML data, linked data are schema-less. While tracking the evolution of schema for linked data is hard, keyword search is an ideal tool to perform data integration. Existing works make crippling assumptions for the data and hence fall short in handling massive linked data with tens to hundreds of millions of facts. Our study for keyword search on linked data brought together the classical techniques in the literature and our novel ideas, which leads to much better query efficiency and quality of the results. Linked data also contain rich temporal semantics. To cope with the ever-increasing data, we have investigated how to partition and store large temporal or multiversion linked data for distributed and parallel computation, in an effort to achieve load-balancing to support scalable data analytics for massive linked data

HERO: Heterogeneous Embedded Research Platform for Exploring RISC-V Manycore Accelerators on FPGA

Heterogeneous embedded systems on chip (HESoCs) co-integrate a standard host processor with programmable manycore accelerators (PMCAs) to combine general-purpose computing with domain-specific, efficient processing capabilities. While leading companies successfully advance their HESoC products, research lags behind due to the challenges of building a prototyping platform that unites an industry-standard host processor with an open research PMCA architecture. In this work we introduce HERO, an FPGA-based research platform that combines a PMCA composed of clusters of RISC-V cores, implemented as soft cores on an FPGA fabric, with a hard ARM Cortex-A multicore host processor. The PMCA architecture mapped on the FPGA is silicon-proven, scalable, configurable, and fully modifiable. HERO includes a complete software stack that consists of a heterogeneous cross-compilation toolchain with support for OpenMP accelerator programming, a Linux driver, and runtime libraries for both host and PMCA. HERO is designed to facilitate rapid exploration on all software and hardware layers: run-time behavior can be accurately analyzed by tracing events, and modifications can be validated through fully automated hard ware and software builds and executed tests. We demonstrate the usefulness of HERO by means of case studies from our research

Investigating the use of semantic technologies in spatial mapping applications

Semantic Web Technologies are ideally suited to build context-aware information retrieval applications. However, the geospatial aspect of context awareness presents unique challenges such as the semantic modelling of geographical references for efficient handling of spatial queries, the reconciliation of the heterogeneity at the semantic and geo-representation levels, maintaining the quality of service and scalability of communicating, and the efficient rendering of the spatial queries' results. In this paper, we describe the modelling decisions taken to solve these challenges by analysing our implementation of an intelligent planning and recommendation tool that provides location-aware advice for a specific application domain. This paper contributes to the methodology of integrating heterogeneous geo-referenced data into semantic knowledgebases, and also proposes mechanisms for efficient spatial interrogation of the semantic knowledgebase and optimising the rendering of the dynamically retrieved context-relevant information on a web frontend