Graphical Database Architecture For Clinical Trials

The general area of the research is Health Informatics. The research focuses on creating an innovative and novel solution to manage and analyze clinical trials data. It constructs a Graphical Database Architecture (GDA) for Clinical Trials (CT) using New Technology for Java (Neo4j) as a robust, a scalable and a high-performance database. The purpose of the research project is to develop concepts and techniques based on architecture to accelerate the processing time of clinical data navigation at lower cost. The research design uses a positivist approach to empirical research. The research is significant because it proposes a new approach of clinical trials through graph theory and designs a responsive structure of clinical data that can be deployed across all the health informatics landscape. It uniquely contributes to scholarly literature of the phenomena of Not only SQL (NoSQL) graph databases, mainly Neo4j in CT, for future research of clinical informatics. A prototype is created and examined to validate the concepts, taking advantage of Neo4j’s high availability, scalability, and powerful graph query language (Cypher). This research study finds that integration of search methodologies and information retrieval with the graphical database provides a solid starting point to manage, query, and analyze the clinical trials data, furthermore the design and the development of a prototype demonstrate the conceptual model of this study. Likewise the proposed clinical trials ontology (CTO) incorporates all data elements of a standard clinical study which facilitate a heuristic overview of treatments, interventions, and outcome results of these studies

Integration of Heterogeneous Databases: Discovery of Meta-Information and Maintenance of Schema-Restructuring Views

In today\u27s networked world, information is widely distributed across many independent databases in heterogeneous formats. Integrating such information is a difficult task and has been adressed by several projects. However, previous integration solutions, such as the EVE-Project, have several shortcomings. Database contents and structure change frequently, and users often have incomplete information about the data content and structure of the databases they use. When information from several such insufficiently described sources is to be extracted and integrated, two problems have to be solved: How can we discover the structure and contents of and interrelationships among unknown databases, and how can we provide durable integration views over several such databases? In this dissertation, we have developed solutions for those key problems in information integration. The first part of the dissertation addresses the fact that knowledge about the interrelationships between databases is essential for any attempt at solving the information integration problem. We are presenting an algorithm called FIND2 based on the clique-finding problem in graphs and k-uniform hypergraphs to discover redundancy relationships between two relations. Furthermore, the algorithm is enhanced by heuristics that significantly reduce the search space when necessary. Extensive experimental studies on the algorithm both with and without heuristics illustrate its effectiveness on a variety of real-world data sets. The second part of the dissertation addresses the durable view problem and presents the first algorithm for incremental view maintenance in schema-restructuring views. Such views are essential for the integration of heterogeneous databases. They are typically defined in schema-restructuring query languages like SchemaSQL, which can transform schema into data and vice versa, making traditional view maintenance based on differential queries impossible. Based on an existing algebra for SchemaSQL, we present an update propagation algorithm that propagates updates along the query algebra tree and prove its correctness. We also propose optimizations on our algorithm and present experimental results showing its benefits over view recomputation

Comparison of Graph Databases and Relational Databases When Handling Large-Scale Social Data

Over the past few years, with the rapid development of mobile technology, more people use mobile social applications, such as Facebook, Twitter and Weibo, in their daily lives, and there is an increasing amount of social data. Thus, finding a suitable storage approach to store and process the social data, especially for the large-scale social data, should be important for the social network companies. Traditionally, a relational database, which represents data in terms of tables, is widely used in the legacy applications. However, a graph database, which is a kind of NoSQL databases, is in a rapid development to handle the growing amount of unstructured or semi-structured data. The two kinds of storage approaches have their own advantages. For example, a relational database should be a more mature storage approach, and a graph database can handle graph-like data in an easier way. In this research, a comparison of capabilities for storing and processing large-scale social data between relational databases and graph databases is applied. Two kinds of analysis, the quantitative research analysis of storage cost and executing time and the qualitative analysis of five criteria, including maturity, ease of programming, flexibility, security and data visualization, are taken into the comparison to evaluate the performance of relational databases and graph databases when handling large-scale social data. Also, a simple mobile social application is developed for experiments. The comparison is used to figure out which kind of database is more suitable for handling large-scale social data, and it can compare more graph database models with real-world social data sets in the future research

Flexibility in Data Management

With the ongoing expansion of information technology, new fields of application requiring data management emerge virtually every day. In our knowledge culture increasing amounts of data and work force organized in more creativity-oriented ways also radically change traditional fields of application and question established assumptions about data management. For instance, investigative analytics and agile software development move towards a very agile and flexible handling of data. As the primary facilitators of data management, database systems have to reflect and support these developments. However, traditional database management technology, in particular relational database systems, is built on assumptions of relatively stable application domains. The need to model all data up front in a prescriptive database schema earned relational database management systems the reputation among developers of being inflexible, dated, and cumbersome to work with. Nevertheless, relational systems still dominate the database market. They are a proven, standardized, and interoperable technology, well-known in IT departments with a work force of experienced and trained developers and administrators. This thesis aims at resolving the growing contradiction between the popularity and omnipresence of relational systems in companies and their increasingly bad reputation among developers. It adapts relational database technology towards more agility and flexibility. We envision a descriptive schema-comes-second relational database system, which is entity-oriented instead of schema-oriented; descriptive rather than prescriptive. The thesis provides four main contributions: (1)~a flexible relational data model, which frees relational data management from having a prescriptive schema; (2)~autonomous physical entity domains, which partition self-descriptive data according to their schema properties for better query performance; (3)~a freely adjustable storage engine, which allows adapting the physical data layout used to properties of the data and of the workload; and (4)~a self-managed indexing infrastructure, which autonomously collects and adapts index information under the presence of dynamic workloads and evolving schemas. The flexible relational data model is the thesis\' central contribution. It describes the functional appearance of the descriptive schema-comes-second relational database system. The other three contributions improve components in the architecture of database management systems to increase the query performance and the manageability of descriptive schema-comes-second relational database systems. We are confident that these four contributions can help paving the way to a more flexible future for relational database management technology

Exploiting Latent Features of Text and Graphs

As the size and scope of online data continues to grow, new machine learning techniques become necessary to best capitalize on the wealth of available information. However, the models that help convert data into knowledge require nontrivial processes to make sense of large collections of text and massive online graphs. In both scenarios, modern machine learning pipelines produce embeddings --- semantically rich vectors of latent features --- to convert human constructs for machine understanding. In this dissertation we focus on information available within biomedical science, including human-written abstracts of scientific papers, as well as machine-generated graphs of biomedical entity relationships. We present the Moliere system, and our method for identifying new discoveries through the use of natural language processing and graph mining algorithms. We propose heuristically-based ranking criteria to augment Moliere, and leverage this ranking to identify a new gene-treatment target for HIV-associated Neurodegenerative Disorders. We additionally focus on the latent features of graphs, and propose a new bipartite graph embedding technique. Using our graph embedding, we advance the state-of-the-art in hypergraph partitioning quality. Having newfound intuition of graph embeddings, we present Agatha, a deep-learning approach to hypothesis generation. This system learns a data-driven ranking criteria derived from the embeddings of our large proposed biomedical semantic graph. To produce human-readable results, we additionally propose CBAG, a technique for conditional biomedical abstract generation

Equivalence of Queries with Nested Aggregation

Query equivalence is a fundamental problem within database theory. The correctness of all forms of logical query rewriting—join minimization, view flattening, rewriting over materialized views, various semantic optimizations that exploit schema dependencies, federated query processing and other forms of data integration—requires proving that the final executed query is equivalent to the original user query. Hence, advances in the theory of query equivalence enable advances in query processing and optimization. In this thesis we address the problem of deciding query equivalence between conjunctive SQL queries containing aggregation operators that may be nested. Our focus is on understanding the interaction between nested aggregation operators and the other parts of the query body, and so we model aggregation functions simply as abstract collection constructors. Hence, the precise language that we study is a conjunctive algebraic language that constructs complex objects from databases of flat relations. Using an encoding of complex objects as flat relations, we reduce the query equivalence problem for this algebraic language to deciding equivalence between relational encodings output by traditional conjunctive queries (not containing aggregation). This encoding-equivalence cleanly unifies and generalizes previous results for deciding equivalence of conjunctive queries evaluated under various processing semantics. As part of our study of aggregation operators that can construct empty sub-collections—so-called “scalar” aggregation—we consider query equivalence for conjunctive queries extended with a left outer join operator, a very practical class of queries for which the general equivalence problem has never before been analyzed. Although we do not completely solve the equivalence problem for queries with outer joins or with scalar aggregation, we do propose useful sufficient conditions that generalize previously known results for restricted classes of queries. Overall, this thesis offers new insight into the fundamental principles governing the behaviour of nested aggregation

Reconciling Schema Matching Networks

Depto. de Mineralogía y PetrologíaFac. de Ciencias GeológicasTRUEpu

Flexibility in Data Management

With the ongoing expansion of information technology, new fields of application requiring data management emerge virtually every day. In our knowledge culture increasing amounts of data and work force organized in more creativity-oriented ways also radically change traditional fields of application and question established assumptions about data management. For instance, investigative analytics and agile software development move towards a very agile and flexible handling of data. As the primary facilitators of data management, database systems have to reflect and support these developments. However, traditional database management technology, in particular relational database systems, is built on assumptions of relatively stable application domains. The need to model all data up front in a prescriptive database schema earned relational database management systems the reputation among developers of being inflexible, dated, and cumbersome to work with. Nevertheless, relational systems still dominate the database market. They are a proven, standardized, and interoperable technology, well-known in IT departments with a work force of experienced and trained developers and administrators. This thesis aims at resolving the growing contradiction between the popularity and omnipresence of relational systems in companies and their increasingly bad reputation among developers. It adapts relational database technology towards more agility and flexibility. We envision a descriptive schema-comes-second relational database system, which is entity-oriented instead of schema-oriented; descriptive rather than prescriptive. The thesis provides four main contributions: (1)~a flexible relational data model, which frees relational data management from having a prescriptive schema; (2)~autonomous physical entity domains, which partition self-descriptive data according to their schema properties for better query performance; (3)~a freely adjustable storage engine, which allows adapting the physical data layout used to properties of the data and of the workload; and (4)~a self-managed indexing infrastructure, which autonomously collects and adapts index information under the presence of dynamic workloads and evolving schemas. The flexible relational data model is the thesis\' central contribution. It describes the functional appearance of the descriptive schema-comes-second relational database system. The other three contributions improve components in the architecture of database management systems to increase the query performance and the manageability of descriptive schema-comes-second relational database systems. We are confident that these four contributions can help paving the way to a more flexible future for relational database management technology

AuRUS: explaining the validation of UML/OCL conceptual schemas

The validation and the verification of conceptual schemas have attracted a lot of interest during the last years, and several tools have been developed to automate this process as much as possible. This is achieved, in general, by assessing whether the schema satisfies different kinds of desirable properties which ensure that the schema is correct. In this paper we describe AuRUS, a tool we have developed to analyze UML/OCL conceptual schemas and to explain their (in)correctness. When a property is satisfied, AuRUS provides a sample instantiation of the schema showing a particular situation where the property holds. When it is not, AuRUS provides an explanation for such unsatisfiability, i.e., a set of integrity constraints which is in contradiction with the property.Peer ReviewedPostprint (author’s final draft