eXamine: a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

In the quest of specific-domain ontology components for the semantic web

This paper describes an approach we have been using to identify specific-domain ontology components by using Self-Organizing Maps. These components are clustered together in a natural way according to their similarity. The knowledge maps, as we call them, show colored regions containing knowledge components that may be used to populate an specific-domain ontology. Later, these ontology may be used by software agents to carry out basic reasoning task on our behalf. In particular, we deal with the issue of not constructing the ontology from scratch, our approach helps us to speed up the ontology creation process

Specification and implementation of mapping rule visualization and editing : MapVOWL and the RMLEditor

Visual tools are implemented to help users in defining how to generate Linked Data from raw data. This is possible thanks to mapping languages which enable detaching mapping rules from the implementation that executes them. However, no thorough research has been conducted so far on how to visualize such mapping rules, especially if they become large and require considering multiple heterogeneous raw data sources and transformed data values. In the past, we proposed the RMLEditor, a visual graph-based user interface, which allows users to easily create mapping rules for generating Linked Data from raw data. In this paper, we build on top of our existing work: we (i) specify a visual notation for graph visualizations used to represent mapping rules, (ii) introduce an approach for manipulating rules when large visualizations emerge, and (iii) propose an approach to uniformly visualize data fraction of raw data sources combined with an interactive interface for uniform data fraction transformations. We perform two additional comparative user studies. The first one compares the use of the visual notation to present mapping rules to the use of a mapping language directly, which reveals that the visual notation is preferred. The second one compares the use of the graph-based RMLEditor for creating mapping rules to the form-based RMLx Visual Editor, which reveals that graph-based visualizations are preferred to create mapping rules through the use of our proposed visual notation and uniform representation of heterogeneous data sources and data values. (C) 2018 Elsevier B.V. All rights reserved

Concept Relation Discovery and Innovation Enabling Technology (CORDIET)

Concept Relation Discovery and Innovation Enabling Technology (CORDIET), is a toolbox for gaining new knowledge from unstructured text data. At the core of CORDIET is the C-K theory which captures the essential elements of innovation. The tool uses Formal Concept Analysis (FCA), Emergent Self Organizing Maps (ESOM) and Hidden Markov Models (HMM) as main artifacts in the analysis process. The user can define temporal, text mining and compound attributes. The text mining attributes are used to analyze the unstructured text in documents, the temporal attributes use these document's timestamps for analysis. The compound attributes are XML rules based on text mining and temporal attributes. The user can cluster objects with object-cluster rules and can chop the data in pieces with segmentation rules. The artifacts are optimized for efficient data analysis; object labels in the FCA lattice and ESOM map contain an URL on which the user can click to open the selected document

Geovisual Analytics Environment for Supporting the Resilience of Maritime Surveillance System

International audienceThis paper presents an original approach for supporting the resilience in Maritime Domain Awareness, based on geovisual analytics. While many research projects focus on developing rules for detecting anomalies at by automated means, there is no support to visual exploration led by human operators. We investigate the use of visual methods for analyzing mobility data of ships. Behaviors of interest can be known (modeled) or unknown, asking for various ways of visualizing and studying the information. We assume that supporting the use of geovisual analytics will make the exploration and the analysis process easier, reducing the cognitive load of the tasks led by the actors of maritime surveillance. The detection and the identification of threats at sea are improved by using adequate visualization methods, regarding the context of use. Our suggested framework is based on ontologies for maritime domain awareness and geovisual analytics environments, coupled to rules