XML in Motion from Genome to Drug

Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data representation and exchange over the internet, enabling researchers to aggregate data from various heterogeneous data resources. The present article covers a comprehensive idea of the integration of XML on particular type of biological databases mainly dealing with sequence-structure-function relationship and its application towards drug discovery. This e-medical science approach should be applied to other scientific domains and the latest trend in semantic web applications is also highlighted

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

A Shared Ontology Approach to Semantic Representation of BIM Data

Architecture, engineering, construction and facility management (AEC-FM) projects involve a large number of participants that must exchange information and combine their knowledge for successful completion of a project. Currently, most of the AEC-FM domains store their information about a project in text documents or use XML, relational, or object-oriented formats that make information integration difficult. The AEC-FM industry is not taking advantage of the full potential of the Semantic Web for streamlining sharing, connecting, and combining information from different domains. The Semantic Web is designed to solve the information integration problem by creating a web of structured and connected data that can be processed by machines. It allows combining information from different sources with different underlying schemas distributed over the Internet. In the Semantic Web, all data instances and data schema are stored in a graph data store, which makes it easy to merge data from different sources. This paper presents a shared ontology approach to semantic representation of building information. The semantic representation of building information facilitates finding and integrating building information distributed in several knowledge bases. A case study demonstrates the development of a semantic based building design knowledge base

Modeling views in the layered view model for XML using UML

In data engineering, view formalisms are used to provide flexibility to users and user applications by allowing them to extract and elaborate data from the stored data sources. Conversely, since the introduction of Extensible Markup Language (XML), it is fast emerging as the dominant standard for storing, describing, and interchanging data among various web and heterogeneous data sources. In combination with XML Schema, XML provides rich facilities for defining and constraining user-defined data semantics and properties, a feature that is unique to XML. In this context, it is interesting to investigate traditional database features, such as view models and view design techniques for XML. However, traditional view formalisms are strongly coupled to the data language and its syntax, thus it proves to be a difficult task to support views in the case of semi-structured data models. Therefore, in this paper we propose a Layered View Model (LVM) for XML with conceptual and schemata extensions. Here our work is three-fold; first we propose an approach to separate the implementation and conceptual aspects of the views that provides a clear separation of concerns, thus, allowing analysis and design of views to be separated from their implementation. Secondly, we define representations to express and construct these views at the conceptual level. Thirdly, we define a view transformation methodology for XML views in the LVM, which carries out automated transformation to a view schema and a view query expression in an appropriate query language. Also, to validate and apply the LVM concepts, methods and transformations developed, we propose a view-driven application development framework with the flexibility to develop web and database applications for XML, at varying levels of abstraction

Intelligent XML Tag Classification Techniques for XML Encryption Improvement

Flexibility, friendliness, and adaptability have been key components to use XML to exchange information across different networks providing the needed common syntax for various messaging systems. However excess usage of XML as a communication medium shed the light on security standards used to protect exchanged messages achieving data confidentiality and privacy. This research presents a novel approach to secure XML messages being used in various systems with efficiency providing high security measures and high performance. system model is based on two major modules, the first to classify XML messages and define which parts of the messages to be secured assigning an importance level for each tag presented in XML message and then using XML encryption standard proposed earlier by W3C [3] to perform a partial encryption on selected parts defined in classification stage. As a result, study aims to improve both the performance of XML encryption process and bulk message handling to achieve data cleansing efficiently

Planets: Integrated Services for Digital Preservation

The Planets Project is developing services and technology to address core challenges in digital preservation. This article introduces the motivation for this work, describes the extensible technical architecture and places the Planets approach into the context of the Open Archival Information System (OAIS) Reference Model. It also provides a scenario demonstrating Planets’ usefulness in solving real-life digital preservation problems and an overview of the project’s progress to date