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

Flattening an object algebra to provide performance

Algebraic transformation and optimization techniques have been the method of choice in relational query execution, but applying them in object-oriented (OO) DBMSs is difficult due to the complexity of OO query languages. This paper demonstrates that the problem can be simplified by mapping an OO data model to the binary relational model implemented by Monet, a state-of-the-art database kernel. We present a generic mapping scheme to flatten data models and study the case of straightforward OO model. We show how flattening enabled us to implement a query algebra, using only a very limited set of simple operations. The required primitives and query execution strategies are discussed, and their performance is evaluated on the 1-GByte TPC-D (Transaction-processing Performance Council's Benchmark D), showing that our divide-and-conquer approach yields excellent result

Moa and the multi-model architecture: a new perspective on XNF2

Advanced non-traditional application domains such as geographic information systems and digital library systems demand advanced data management support. In an effort to cope with this demand, we present the concept of a novel multi-model DBMS architecture which provides evaluation of queries on complexly structured data without sacrificing efficiency. A vital role in this architecture is played by the Moa language featuring a nested relational data model based on XNF2, in which we placed renewed interest. Furthermore, extensibility in Moa avoids optimization obstacles due to black-box treatment of ADTs. The combination of a mapping of queries on complexly structured data to an efficient physical algebra expression via a nested relational algebra, extensibility open to optimization, and the consequently better integration of domain-specific algorithms, makes that the Moa system can efficiently and effectively handle complex queries from non-traditional application domains

The Mirror MMDBMS architecture

Handling large collections of digitized multimedia data, usually referred to as multimedia digital libraries, is a major challenge for information technology. The Mirror DBMS is a research database system that is developed to better understand the kind of data management that is required in the context of multimedia digital libraries (see also URL http://www.cs.utwente.nl/~arjen/mmdb.html). Its main features are an integrated approach to both content management and (traditional) structured data management, and the implementation of an extensible object-oriented logical data model on a binary relational physical data model. The focus of this work is aimed at design for scalability

Object-oriented querying of existing relational databases

In this paper, we present algorithms which allow an object-oriented querying of existing relational databases. Our goal is to provide an improved query interface for relational systems with better query facilities than SQL. This seems to be very important since, in real world applications, relational systems are most commonly used and their dominance will remain in the near future. To overcome the drawbacks of relational systems, especially the poor query facilities of SQL, we propose a schema transformation and a query translation algorithm. The schema transformation algorithm uses additional semantic information to enhance the relational schema and transform it into a corresponding object-oriented schema. If the additional semantic information can be deducted from an underlying entity-relationship design schema, the schema transformation may be done fully automatically. To query the created object-oriented schema, we use the Structured Object Query Language (SOQL) which provides declarative query facilities on objects. SOQL queries using the created object-oriented schema are much shorter, easier to write and understand and more intuitive than corresponding S Q L queries leading to an enhanced usability and an improved querying of the database. The query translation algorithm automatically translates SOQL queries into equivalent SQL queries for the original relational schema

Iris: an Extensible Application for Building and Analyzing Spectral Energy Distributions

Iris is an extensible application that provides astronomers with a user-friendly interface capable of ingesting broad-band data from many different sources in order to build, explore, and model spectral energy distributions (SEDs). Iris takes advantage of the standards defined by the International Virtual Observatory Alliance, but hides the technicalities of such standards by implementing different layers of abstraction on top of them. Such intermediate layers provide hooks that users and developers can exploit in order to extend the capabilities provided by Iris. For instance, custom Python models can be combined in arbitrary ways with the Iris built-in models or with other custom functions. As such, Iris offers a platform for the development and integration of SED data, services, and applications, either from the user's system or from the web. In this paper we describe the built-in features provided by Iris for building and analyzing SEDs. We also explore in some detail the Iris framework and software development kit, showing how astronomers and software developers can plug their code into an integrated SED analysis environment.Comment: 18 pages, 8 figures, accepted for publication in Astronomy & Computin