Working Document on Gloss Ontology

This document describes the Gloss Ontology. The ontology and associated class model are organised into several packages. Section 2 describes each package in detail, while Section 3 contains a summary of the whole ontology

Connecting the dots: a multi-pivot approach to data exploration

The purpose of data browsers is to help users identify and query data effectively without being overwhelmed by large complex graphs of data. A proposed solution to identify and query data in graph-based datasets is Pivoting (or set-oriented browsing), a many-to-many graph browsing technique that allows users to navigate the graph by starting from a set of instances followed by navigation through common links. Relying solely on navigation, however, makes it difficult for users to find paths or even see if the element of interest is in the graph when the points of interest may be many vertices apart. Further challenges include finding paths which require combinations of forward and backward links in order to make the necessary connections which further adds to the complexity of pivoting. In order to mitigate the effects of these problems and enhance the strengths of pivoting we present a multi-pivot approach which we embodied in tool called Visor. Visor allows users to explore from multiple points in the graph, helping users connect key points of interest in the graph on the conceptual level, visually occluding the remainder parts of the graph, thus helping create a road-map for navigation. We carried out an user study to demonstrate the viability of our approach

The "Unromantic Pictures" of Quantum Theory

I am concerned with two views of quantum mechanics that John S. Bell called ``unromantic'': spontaneous wave function collapse and Bohmian mechanics. I discuss some of their merits and report about recent progress concerning extensions to quantum field theory and relativity. In the last section, I speculate about an extension of Bohmian mechanics to quantum gravity.Comment: 37 pages LaTeX, no figures; written for special volume of J. Phys. A in honor of G.C. Ghirard

Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery

Motivation: Signaling pathways control a large variety of cellular processes. However, currently, even within the same database signaling pathways are often curated at different levels of detail. This makes comparative and cross-talk analyses difficult. Results: We present SignaLink, a database containing 8 major signaling pathways from Caenorhabditis elegans, Drosophila melanogaster, and humans. Based on 170 review and approx. 800 research articles, we have compiled pathways with semi-automatic searches and uniform, well-documented curation rules. We found that in humans any two of the 8 pathways can cross-talk. We quantified the possible tissue- and cancer-specific activity of cross-talks and found pathway-specific expression profiles. In addition, we identified 327 proteins relevant for drug target discovery. Conclusions: We provide a novel resource for comparative and cross-talk analyses of signaling pathways. The identified multi-pathway and tissue-specific cross-talks contribute to the understanding of the signaling complexity in health and disease and underscore its importance in network-based drug target selection. Availability: http://SignaLink.orgComment: 9 pages, 4 figures, 2 tables and a supplementary info with 5 Figures and 13 Table

Towards a proteomics meta-classification

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins

Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network.

A central question in animal evolution is how multicellular animals evolved from unicellular ancestors. We hypothesize that membrane proteins must be key players in the development of multicellularity because they are well positioned to form the cell-cell contacts and to provide the intercellular communication required for the creation of complex organisms. Here we find that a major mechanism for the necessary increase in membrane protein complexity in the transition from non-metazoan to metazoan life was the new incorporation of domains from soluble proteins. The membrane proteins that have incorporated soluble domains in metazoans are enriched in many of the functions unique to multicellular organisms such as cell-cell adhesion, signaling, immune defense and developmental processes. They also show enhanced protein-protein interaction (PPI) network complexity and centrality, suggesting an important role in the cellular diversification found in complex organisms. Our results expose an evolutionary mechanism that contributed to the development of higher life forms

Ensuring Cyber-Security in Smart Railway Surveillance with SHIELD

Modern railways feature increasingly complex embedded computing systems for surveillance, that are moving towards fully wireless smart-sensors. Those systems are aimed at monitoring system status from a physical-security viewpoint, in order to detect intrusions and other environmental anomalies. However, the same systems used for physical-security surveillance are vulnerable to cyber-security threats, since they feature distributed hardware and software architectures often interconnected by ‘open networks’, like wireless channels and the Internet. In this paper, we show how the integrated approach to Security, Privacy and Dependability (SPD) in embedded systems provided by the SHIELD framework (developed within the EU funded pSHIELD and nSHIELD research projects) can be applied to railway surveillance systems in order to measure and improve their SPD level. SHIELD implements a layered architecture (node, network, middleware and overlay) and orchestrates SPD mechanisms based on ontology models, appropriate metrics and composability. The results of prototypical application to a real-world demonstrator show the effectiveness of SHIELD and justify its practical applicability in industrial settings

Agents in Bioinformatics

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions