Semistructured Data Model Research Articles

NeuroSys: a semistructured laboratory database.

The inherent complexity of traditional relational database systems is a key obstacle to more widespread use of database technology in the neuroscience community. As an alternative to relational technology, we propose a simpler semistructured data model for documenting laboratory procedures and results. The semistructured data model allows researchers to document their data in an organized, regularly formatted, machine-readable, and network accessible manner, without requiring the services of database professionals. We present proof-of-concept software, consisting of an HTML interface that communicates with a remotely located, semistructured database. We also discuss the importance of standardized terminology and the importance of building flexible data description systems that are more easily adapted and reconfigured to conform with standardized terminologies as they evolve.

Representation of Generalized Map Series Using Semi-Structured Data Models

Large cartographic organizations worldwide produce generalized map series (GMS) in order to meet various user requirements. A GMS consists of maps of the same geographic region at different scales. Most of these maps currently are designed in a digital environment, and recently some of them have been distributed through the web. One important issue is the appropriate modeling and handling of cartographic entities composing individual maps in a GMS. Since these entities have rather complex descriptions and may be provided by various agencies, they usually do not conform to a fixed schema (i.e., they do not have a common structure). Hence, their representation in traditional data models, such as the relational or object-oriented, is not always feasible. This paper investigates the use of semi-structured data (SSD) models—an innovative approach recently developed in Information Technology for representing and handling entities in a GMS. Specifically, the Object Exchange Model (OEM), a popular database model for SSD, has been adopted to represent a GMS. How useful information can be extracted from such a representation using the LOREL query language—a popular language for SSD—is also shown.

XML query processing using document type definitions

As eXtensible Markup Language (XML) has become an emerging standard for information exchange on the World Wide Web, it has gained attention in database communities to extract information from XML seen as a database model. Data in XML can be mapped to a semistructured data model based on edge-labeled graph, and queries can be processed against it. Here, we propose new query optimization techniques using document type definitions which have the schema information about XML data. Our techniques reduce the large search space significantly while at the same time requiring less memory compared to the traditional index techniques. Also, as they preserve source database’s structure, they can process many kinds of complex queries. We implemented our techniques and provided preliminary performance results.

An integration platform for heterogeneous bioinformatics software components

Although computer programs and database resources for bioinformatics applications are becoming more widely available, these resources are unstandardized and frequently incompatible. The problem of integrating heterogeneous software is of immense importance to the field, especially because a rapid pace of change and a general scarcity of development resources discourage re-engineering and compel developers to find ways to use legacy resources. In this paper, we describe an approach to the problem of integration of heterogeneous bioinformatics resources that relies on a generalized software platform, written in the JavaTM language, that we call ISYSTM. The ISYS platform employs techniques for interoperation among loosely coupled components, such as brokered service exchange and mediated event exchange, that are increasingly common in software engineering but still not used widely in bioinformatics. In addition, it further promotes loose coupling of independent components through a flexible, semistructured data model that supports run-time association of attributes with objects, and allows different components to maintain different views of the same object. We describe our general approach, the architecture of the system, the mechanics of event and service exchange, and the implementation of the data model. The platform is not restricted in its utility to bioinformatics, and could be useful for any rapidly changing field in which the integration of heterogeneous legacy components is important.

Consistency control for semistructured data

Semistructured data models provide an important tool for studying methods for representing, searching, and processing heterogeneous data in distributed systems with autonomous components (especially, on the WWW). However, the problem of data consistency remains little investigated. In this paper, various approaches to this problem are discussed, and the usability of various mechanisms suggested in the context of databases, including real-time databases, is analyzed. An approach based on the concept of multilevel transactions is presented in detail. In the framework of this approach, commutativity predicates for basic operations on semistructured data are constructed.

Storing semistructured data with STORED

Systems for managing and querying semistructured-data sources often store data in proprietary object repositories or in a tagged-text format. We describe a technique that can use relational database management systems to store and manage semistructured data. Our technique relies on a mapping between the semistructured data model and the relational data model, expressed in a query language called STORED. When a semistructured data instance is given, a STORED mapping can be generated automatically using data-mining techniques. We are interested in applying STORED to XML data, which is an instance of semistructured data. We show how a document-type-descriptor (DTD), when present, can be exploited to further improve performance.

Querying network directories

Heirarchically structured directories have recently proliferated with the growth of the Internet, and are being used to store not only address books and contact information for people, but also personal profiles, network resource information, and network and service policies. These systems provide a means for managing scale and heterogeneity, while allowing for conceptual unity and autonomy across multiple directory servers in the network, in a way for superior to what conventional relational or object-oriented databases offer. Yet, in deployed systems today, much of the data is modeled in an ad hoc manner, and many of the more sophisticated “queries” involve navigational access. In this paper, we develop the core of a formal data model for network directories, and propose a sequence of efficiently computable query languages with increasing expressive power. The directory data model can naturally represent rich forms of heterogeneity exhibited in the real world. Answers to queries expressible in our query languages can exhibit the same kinds of heterogeneity. We present external memory algorithms for the evaluation of queries posed in our directory query languages, and prove the efficiency of each algorithm in terms of its I/O complexity. Our data model and query languages share the flexibility and utility of the recent proposals for semi-structured data models, while at the same time effectively addressing the specific needs of network directory applications, which we demonstrate by means of a representative real-life example.

Your mediators need data conversion!

Due to the development of the World Wide Web, the integration of heterogeneous data sources has become a major concern of the database community. Appropriate architectures and query languages have been proposed. Yet, the problem of data conversion which is essential for the development of mediators/wrappers architectures has remained largely unexplored. In this paper, we present the YAT system for data conversion. This system provides tools for the specification and the implementation of data conversions among heterogeneous data sources. It relies on a middleware model, a declarative language, a customization mechanism and a graphical interface. The model is based on named trees with ordered and labeled nodes. Like semistructured data models, it is simple enough to facilitate the representation of any data. Its main originality is that it allows to reason at various levels of representation. The YAT conversion language (called YATL) is declarative, rule-based and features enhanced pattern matching facilities and powerful restructuring primitives. It allows to preserve or reconstruct the order of collections. The customization mechanism relies on program instantiations: an existing program may be instantiated into a more specific one, and then easily modified. We also present the architecture, implementation and practical use of the YAT prototype, currently under evaluation within the OPAL * project.

Catching the boat with Strudel

The Strudel system applies concepts from database management systems to the process of building Web sites. Strudel's key idea is separating the management of the site's data, the creation and management of the site's structure, and the visual presentation of the site's pages. First, the site builder creates a uniform model of all data available at the site. Second, the builder uses this model to declaratively define the Web site's structure by applying a “site-definition query” to the underlying data. The result of evaluating this query is a “site graph”, which represents both the site's content and structure. Third, the builder specifies the visual presentation of pages in Strudel's HTML-template language. The data model underlying Strudel is a semi-structured model of labeled directed graphs. We describe Strudel's key characteristics, report on our experiences using Strudel, and present the technical problems that arose from our experience. We describe our experience constructing several Web sites with Strudel and discuss the impact of potential users' requirements on Strudel's design. We address two main questions: (1) when does a declarative specification of site structure provide significant benefits, and (2) what are the main advantages provided by the semi-structured data model.