Federated Query Processing over Heterogeneous Data Sources in a Semantic Data Lake

Data provides the basis for emerging scientific and interdisciplinary data-centric applications with the potential of improving the quality of life for citizens. Big Data plays an important role in promoting both manufacturing and scientific development through industrial digitization and emerging interdisciplinary research. Open data initiatives have encouraged the publication of Big Data by exploiting the decentralized nature of the Web, allowing for the availability of heterogeneous data generated and maintained by autonomous data providers. Consequently, the growing volume of data consumed by different applications raise the need for effective data integration approaches able to process a large volume of data that is represented in different format, schema and model, which may also include sensitive data, e.g., financial transactions, medical procedures, or personal data. Data Lakes are composed of heterogeneous data sources in their original format, that reduce the overhead of materialized data integration. Query processing over Data Lakes require the semantic description of data collected from heterogeneous data sources. A Data Lake with such semantic annotations is referred to as a Semantic Data Lake. Transforming Big Data into actionable knowledge demands novel and scalable techniques for enabling not only Big Data ingestion and curation to the Semantic Data Lake, but also for efficient large-scale semantic data integration, exploration, and discovery. Federated query processing techniques utilize source descriptions to find relevant data sources and find efficient execution plan that minimize the total execution time and maximize the completeness of answers. Existing federated query processing engines employ a coarse-grained description model where the semantics encoded in data sources are ignored. Such descriptions may lead to the erroneous selection of data sources for a query and unnecessary retrieval of data, affecting thus the performance of query processing engine. In this thesis, we address the problem of federated query processing against heterogeneous data sources in a Semantic Data Lake. First, we tackle the challenge of knowledge representation and propose a novel source description model, RDF Molecule Templates, that describe knowledge available in a Semantic Data Lake. RDF Molecule Templates (RDF-MTs) describes data sources in terms of an abstract description of entities belonging to the same semantic concept. Then, we propose a technique for data source selection and query decomposition, the MULDER approach, and query planning and optimization techniques, Ontario, that exploit the characteristics of heterogeneous data sources described using RDF-MTs and provide a uniform access to heterogeneous data sources. We then address the challenge of enforcing privacy and access control requirements imposed by data providers. We introduce a privacy-aware federated query technique, BOUNCER, able to enforce privacy and access control regulations during query processing over data sources in a Semantic Data Lake. In particular, BOUNCER exploits RDF-MTs based source descriptions in order to express privacy and access control policies as well as their automatic enforcement during source selection, query decomposition, and planning. Furthermore, BOUNCER implements query decomposition and optimization techniques able to identify query plans over data sources that not only contain the relevant entities to answer a query, but also are regulated by policies that allow for accessing these relevant entities. Finally, we tackle the problem of interest based update propagation and co-evolution of data sources. We present a novel approach for interest-based RDF update propagation that consistently maintains a full or partial replication of large datasets and deal with co-evolution

Heterogeneous biomedical database integration using a hybrid strategy: a p53 cancer research database.

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.)

A unified view of data-intensive flows in business intelligence systems : a survey

Data-intensive flows are central processes in today’s business intelligence (BI) systems, deploying different technologies to deliver data, from a multitude of data sources, in user-preferred and analysis-ready formats. To meet complex requirements of next generation BI systems, we often need an effective combination of the traditionally batched extract-transform-load (ETL) processes that populate a data warehouse (DW) from integrated data sources, and more real-time and operational data flows that integrate source data at runtime. Both academia and industry thus must have a clear understanding of the foundations of data-intensive flows and the challenges of moving towards next generation BI environments. In this paper we present a survey of today’s research on data-intensive flows and the related fundamental fields of database theory. The study is based on a proposed set of dimensions describing the important challenges of data-intensive flows in the next generation BI setting. As a result of this survey, we envision an architecture of a system for managing the lifecycle of data-intensive flows. The results further provide a comprehensive understanding of data-intensive flows, recognizing challenges that still are to be addressed, and how the current solutions can be applied for addressing these challenges.Peer ReviewedPostprint (author's final draft

Identification of Design Principles

This report identifies those design principles for a (possibly new) query and transformation language for the Web supporting inference that are considered essential. Based upon these design principles an initial strawman is selected. Scenarios for querying the Semantic Web illustrate the design principles and their reflection in the initial strawman, i.e., a first draft of the query language to be designed and implemented by the REWERSE working group I4

Towards Knowledge in the Cloud

Knowledge in the form of semantic data is becoming more and more ubiquitous, and the need for scalable, dynamic systems to support collaborative work with such distributed, heterogeneous knowledge arises. We extend the “data in the cloud” approach that is emerging today to “knowledge in the cloud”, with support for handling semantic information, organizing and finding it efficiently and providing reasoning and quality support. Both the life sciences and emergency response fields are identified as strong potential beneficiaries of having ”knowledge in the cloud”

A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain

Biomedical data are becoming increasingly complex and heterogeneous in nature. The data are stored in distributed information systems, using a variety of data models, and are processed by increasingly more complex tools that analyze and visualize them. We present in this paper our framework for integrating biomedical research data and tools into a unique Web front end. Our framework is applied to the University of Washington’s Human Brain Project. Specifically, we present solutions to four integration tasks: definition of complex mappings from relational sources to XML, distributed XQuery processing, generation of heterogeneous output formats, and the integration of heterogeneous data visualization and analysis tools

Ontology-Based Data Access and Integration

An ontology-based data integration (OBDI) system is an information management system consisting of three components: an ontology, a set of data sources, and the mapping between the two. The ontology is a conceptual, formal description of the domain of interest to a given organization (or a community of users), expressed in terms of relevant concepts, attributes of concepts, relationships between concepts, and logical assertions characterizing the domain knowledge. The data sources are the repositories accessible by the organization where data concerning the domain are stored. In the general case, such repositories are numerous, heterogeneous, each one managed and maintained independently from the others. The mapping is a precise specification of the correspondence between the data contained in the data sources and the elements of the ontology. The main purpose of an OBDI system is to allow information consumers to query the data using the elements in the ontology as predicates. In the special case where the organization manages a single data source, the term ontology-based data access (ODBA) system is used