A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

Reify Your Collection Queries for Modularity and Speed!

Modularity and efficiency are often contradicting requirements, such that programers have to trade one for the other. We analyze this dilemma in the context of programs operating on collections. Performance-critical code using collections need often to be hand-optimized, leading to non-modular, brittle, and redundant code. In principle, this dilemma could be avoided by automatic collection-specific optimizations, such as fusion of collection traversals, usage of indexing, or reordering of filters. Unfortunately, it is not obvious how to encode such optimizations in terms of ordinary collection APIs, because the program operating on the collections is not reified and hence cannot be analyzed. We propose SQuOpt, the Scala Query Optimizer--a deep embedding of the Scala collections API that allows such analyses and optimizations to be defined and executed within Scala, without relying on external tools or compiler extensions. SQuOpt provides the same "look and feel" (syntax and static typing guarantees) as the standard collections API. We evaluate SQuOpt by re-implementing several code analyses of the Findbugs tool using SQuOpt, show average speedups of 12x with a maximum of 12800x and hence demonstrate that SQuOpt can reconcile modularity and efficiency in real-world applications.Comment: 20 page

Towards an Efficient Evaluation of General Queries

Database applications often require to evaluate queries containing quantifiers or disjunctions, e.g., for handling general integrity constraints. Existing efficient methods for processing quantifiers depart from the relational model as they rely on non-algebraic procedures. Looking at quantified query evaluation from a new angle, we propose an approach to process quantifiers that makes use of relational algebra operators only. Our approach performs in two phases. The first phase normalizes the queries producing a canonical form. This form permits to improve the translation into relational algebra performed during the second phase. The improved translation relies on a new operator - the complement-join - that generalizes the set difference, on algebraic expressions of universal quantifiers that avoid the expensive division operator in many cases, and on a special processing of disjunctions by means of constrained outer-joins. Our method achieves an efficiency at least comparable with that of previous proposals, better in most cases. Furthermore, it is considerably simpler to implement as it completely relies on relational data structures and operators

Automatic generation of simplified weakest preconditions for integrity constraint verification

Given a constraint $c$ assumed to hold on a database $B$ and an update $u$ to be performed on $B$, we address the following question: will $c$ still hold after $u$ is performed? When $B$ is a relational database, we define a confluent terminating rewriting system which, starting from $c$ and $u$, automatically derives a simplified weakest precondition $wp(c,u)$ such that, whenever $B$ satisfies $wp(c,u)$, then the updated database $u(B)$ will satisfy $c$, and moreover $wp(c,u)$ is simplified in the sense that its computation depends only upon the instances of $c$ that may be modified by the update. We then extend the definition of a simplified $wp(c,u)$ to the case of deductive databases; we prove it using fixpoint induction

An engineering approach to automatic programming

An exploratory study of the automatic generation and optimization of symbolic programs using DECOM - a prototypical requirement specification model implemented in pure LISP was undertaken. It was concluded, on the basis of this study, that symbolic processing languages such as LISP can support a style of programming based upon formal transformation and dependent upon the expression of constraints in an object-oriented environment. Such languages can represent all aspects of the software generation process (including heuristic algorithms for effecting parallel search) as dynamic processes since data and program are represented in a uniform format

Database Systems - Present and Future

The database systems have nowadays an increasingly important role in the knowledge-based society, in which computers have penetrated all fields of activity and the Internet tends to develop worldwide. In the current informatics context, the development of the applications with databases is the work of the specialists. Using databases, reach a database from various applications, and also some of related concepts, have become accessible to all categories of IT users. This paper aims to summarize the curricular area regarding the fundamental database systems issues, which are necessary in order to train specialists in economic informatics higher education. The database systems integrate and interfere with several informatics technologies and therefore are more difficult to understand and use. Thus, students should know already a set of minimum, mandatory concepts and their practical implementation: computer systems, programming techniques, programming languages, data structures. The article also presents the actual trends in the evolution of the database systems, in the context of economic informatics.database systems - DBS, database management systems – DBMS, database – DB, programming languages, data models, database design, relational database, object-oriented systems, distributed systems, advanced database systems

Using Ontologies for Semantic Data Integration

While big data analytics is considered as one of the most important paths to competitive advantage of today’s enterprises, data scientists spend a comparatively large amount of time in the data preparation and data integration phase of a big data project. This shows that data integration is still a major challenge in IT applications. Over the past two decades, the idea of using semantics for data integration has become increasingly crucial, and has received much attention in the AI, database, web, and data mining communities. Here, we focus on a specific paradigm for semantic data integration, called Ontology-Based Data Access (OBDA). The goal of this paper is to provide an overview of OBDA, pointing out both the techniques that are at the basis of the paradigm, and the main challenges that remain to be addressed

Deductive Optimization of Relational Data Storage

Optimizing the physical data storage and retrieval of data are two key database management problems. In this paper, we propose a language that can express a wide range of physical database layouts, going well beyond the row- and column-based methods that are widely used in database management systems. We use deductive synthesis to turn a high-level relational representation of a database query into a highly optimized low-level implementation which operates on a specialized layout of the dataset. We build a compiler for this language and conduct experiments using a popular database benchmark, which shows that the performance of these specialized queries is competitive with a state-of-the-art in memory compiled database system