A Semantic-Based Information Management System to Support Innovative Product Design

International competition and the rapidly global economy, unified by improved communication and transportation, offer to the consumers an enormous choice of goods and services. The result is that companies now require quality, value, time to market and innovation to be successful in order to win the increasing competition. In the engineering sector this is traduced in need of optimization of the design process and in maximization of re-use of data and knowledge already existing in the company. The “SIMI-Pro” (Semantic Information Management system for Innovative Product design) system addresses specific deficiencies in the conceptual phase of product design when knowledge management, if applied, is often sectorial. Its main contribution is in allowing easy, fast and centralized collection of data from multiple sources and in supporting the retrieval and re-use of a wide range of data that will help stylists and engineers shortening the production cycle. SIMI-Pro will be one of the first prototypes to base its information management and its knowledge sharing system on process ontology and it will demonstrate how the use of centralized network systems, coupled with Semantic Web technologies, can improve inter-working activities and interdisciplinary knowledge sharing

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

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

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

Linked Data - the story so far

The term “Linked Data” refers to a set of best practices for publishing and connecting structured data on the Web. These best practices have been adopted by an increasing number of data providers over the last three years, leading to the creation of a global data space containing billions of assertions— the Web of Data. In this article, the authors present the concept and technical principles of Linked Data, and situate these within the broader context of related technological developments. They describe progress to date in publishing Linked Data on the Web, review applications that have been developed to exploit the Web of Data, and map out a research agenda for the Linked Data community as it moves forward

Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

Integration with Ontologies

One of today’s hottest IT topics is integration, as bringing together information from different sources and structures is not completely solved. The approach outlined here wants to illustrate how ontologies [Gr93] could help to support the integration process

The design and implementation of an infrastructure for multimedia digital libraries

We develop an infrastructure for managing, indexing and serving multimedia content in digital libraries. This infrastructure follows the model of the Web, and thereby is distributed in nature. We discuss the design of the Librarian, the component that manages meta data about the content. The management of meta data has been separated from the media servers that manage the content itself. Also, the extraction of the meta data is largely independent of the Librarian. We introduce our extensible data model and the daemon paradigm that are the core pieces of this architecture. We evaluate our initial implementation using a relational database. We conclude with a discussion of the lessons we learned in building this system, and proposals for improving the flexibility, reliability, and performance of the syste

Visual Information Retrieval in Digital Libraries

The emergence of information highways and multimedia computing has resulted in redefining the concept of libraries. It is widely believed that in the next few years, a significant portion of information in libraries will be in the form of multimedia electronic documents. Many approaches are being proposed for storing, retrieving, assimilating, harvesting, and prospecting information from these multimedia documents. Digital libraries are expected to allow users to access information independent of the locations and types of data sources and will provide a unified picture of information. In this paper, we discuss requirements of these emerging information systems and present query methods and data models for these systems. Finally, we briefly present a few examples of approaches that provide a preview of how things will be done in the digital libraries in the near future.published or submitted for publicatio