A strategy to incorporate prior knowledge into correlation network cutoff selection

Correlation networks are frequently used to statistically extract biological interactions between omics markers. Network edge selection is typically based on the statistical significance of the correlation coefficients. This procedure, however, is not guaranteed to capture biological mechanisms. We here propose an alternative approach for network reconstruction: a cutoff selection algorithm that maximizes the overlap of the inferred network with available prior knowledge. We first evaluate the approach on IgG glycomics data, for which the biochemical pathway is known and well-characterized. Importantly, even in the case of incomplete or incorrect prior knowledge, the optimal network is close to the true optimum. We then demonstrate the generalizability of the approach with applications to untargeted metabolomics and transcriptomics data. For the transcriptomics case, we demonstrate that the optimized network is superior to statistical networks in systematically retrieving interactions that were not included in the biological reference used for optimization

Incorporating Dimensions in XML and DTD

In this paper we investigate various aspects of representing multidimensional information in the frame of the WWW. Multidimensional XML (MXML) is an extension of XML suitable for representing data that assume different facets, having different value or different structure, under different contexts. In Multidimensional XML, elements and attributes may depend on a number of dimensions, that define worlds under which variants of those elements or attributes hold. Moreover, we propose an extension of DTD that takes dimensions into account and is suitable for describing the logical structure of MXML documents. We also present a graph data model for MXML, and show how MXML can be reduced to conventional XML for a given world

A Web-based System for Handling Multidimensional Information through MXML

In this paper we address an issue common in the frame of WWW, namely information entities that present different facets under different contexts (or worlds). Handling such multifacet or multidimensional entities requires a multidimensional paradigm for Web data, which consists of representation, manipulation and presentation issues. For representing multidimensional data we employ Multidimensional XML, a markup language that incorporates dimensions in XML. We discuss the presentation of multidimensional data through multidimensional XSL stylesheets. We describe the design of a system that implements the basic functionality of the multidimensional paradigm, and demonstrates how a user can interact with a multidimensional document and view different variants of the document under different worlds

Towards a Context-Aware Service Directory

Advances in the areas of mobile computing and web services lead to new scenarios of use and innovative applications. Our approach involves mobile devices that act not only as requestors of data, but as data providers as well, providing access to their data through web services

WWW-enabled delivery of interactive multimedia documents

The structure and delivery of Interactive Multimedia Documents (IMDs) has been an issue of intensive research in the last years. In this paper we propose a scenario based structure for IMDS and a mechanism for WWW-enabled delivery of such IMDs. The structure for the IMDs, based on the concept of scenarios, which define the flow of the presentation and the possible user interactions with the IMD. The delivery mechanism consists in a client/server system, which supports the remote presentation of IMDs. The whole framework has been implemented in Java using the Remote Method Invocation (RMI) client server communication protocol and the Java Media Framework (JMF) for handling multimedia objects. The system presents a promising approach for distributed interactive multimedia on the Internet and Intranets

WWW-enabled delivery of interactive multimedia documents

The structure and delivery of Interactive Multimedia Documents (IMDs) has been an issue of intensive research in the last few years. In this paper, we propose a scenario based structure for IMDs and a mechanism for WWW-enabled delivery of such IMDs. The structure for the IMDs, is based on the concept of scenarios, which define the how of the presentation and the possible user interactions with the IMD. The delivery mechanism consists of a client/server system, which supports the remote presentation of IMDs. The whole framework has been implemented in Java using the Remote Method Invocation (RMI) client server communication protocol and the Java Media Framework (JMF) for handing multimedia objects. The system presents a promising approach for distributed interactive multimedia on the Internet and Intranets. (C) 2000 Elsevier Science B.V. All rights reserved