Cytoscape: Hands-down Winner for Large-scale Graph Visualization I still never cease to be amazed at how wonderful and powerful tools are so often and easily overlooked. The most recent example is Cytoscape, a winner in our recent review of more than 25 tools for large-scale RDF graph visualization. We began this review because the UMBEL subject concept “backbone” ontology will involve literally thousands of concepts. Graph visualization software suitable to very large graphs would aid UMBEL’s construction and refinement. Cytoscape describes itself as a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Cytoscape is partially based on GINY and Piccolo, among other open-source toolkits. Cytoscape was first brought to our attention by François Belleau of Bio2RDF.org. Requirements We had a number of requirements and items on our wish list prior to beginning our review. Features and Attractions Other Cytoscape Resources Plugins Initial Use Tips
eumedis approach Supports the development of information society in the Mediterranean Partner Countries, through promoting information and communication technologies Algeria, Egypt, Israel, Jordan, Lebanon, Morocco, Occupied Palestinian Territory, Syria, Tunisia, Turkey Timeframe: 1999-2007 Budget: €65 million (MEDA) Objectives It aims at contributing towards the development and modernisation of the Euro-Mediterranean Information Society, and thus bring about economic development, improve quality of life and promote understanding. The Euro-Mediterranean Information Society Initiative (EUMEDIS) project focuses on the modernisation of the most strategic sectors and reinforces support tools and methodologies. What does it do? It has also funded regional pilot Information Society projects in five priority sectors, namely healthcare networks, electronic commerce, tourism and cultural heritage, industry, research and innovation and education. What's next? Actions in brief
eVa in 3-color For a whole number of reasons, I am currently looking into the visualisation of large-scale graphs and ontologies and to that end, I have made some notes concerning tools and concepts which might be useful for others. Here they are: Visualisation by Node-Link and Tree jOWL: jQuery Plugin for the navigation and visualisation of OWL ontologies and RDFS documents. OntoViz: Plugin into Protege…at the moment supports Protege 3.4 and doesn’t seem to work with Protege 4. IsaViz: Much the same as OntoViz really. NeOn Toolkit: The Neon toolkit also has some visualisation capability, but not independent of the editor. OntoTrack: OntoTrack is a graphical OWL editor and as such has visualisation capabilities. Cone Trees: Cone trees are three-dimensional extensions of 2D tree structures and have been designed to allow for a greater amount odf information to be visualised and navigated. Welkin: Standalone application for the visualisation of RDF graphs. Three-Dimensional Visualisation Like this:
RelFinder - Visual Data Web Are you interested in how things are related with each other? The RelFinder helps to get an overview: It extracts and visualizes relationships between given objects in RDF data and makes these relationships interactively explorable. Highlighting and filtering features support visual analysis both on a global and detailed level. Check out the following links for some examples: The RelFinder can easily be configured to work with different RDF datasets. The RelFinder can also be more deeply integrated with your project: Integrating the RelFinder See the following examples of how the RelFinder is integrated into other projects: Ontotext applies the RelFinder to enable an exploration of relationships in the biomedical domain. The RelFinder is readily configured to access RDF data of the DBpedia project and only requires a Flash Player plugin to be executed (which is usually already installed in web browsers). All tools on this website are research prototypes that might contain errors.
Triplestore Much like a relational database, one stores information in a triplestore and retrieves it via a query language. Unlike a relational database, a triplestore is optimized for the storage and retrieval of triples. In addition to queries, triples can usually be imported/exported using Resource Description Framework (RDF) and other formats. Some triplestores can store billions of triples.[2] Implementation[edit] Some triplestores have been built as database engines from scratch, while others have been built on top of existing commercial relational database engines (i.e. List of implementations[edit] Technical overview[edit] The following table is an overview of available triplestores, their technical implementation, support for the SPARQL World Wide Web Consortium (W3C) recommendations, and available application programming interfaces (API). See also[edit] Freebase uses a triplestore called graphd[citation needed]Named graph a.k.a. References[edit] External links[edit]
med forum par Javier Cisneros Coordonnateur de Projets de Coopération MED Forum Présentation Introduction à la coopération dans la Méditerranée 1. A. 1. B. 4. C. 6. 4. Présentation du programme «Coopération Méditerranéenne» de MED Forum 1. A. 4. Je voudrais, en premier lieu, souhaiter la bienvenue à tous les assistants au V Forum Environnemental de la Méditerranée (Barcelone, 19 et 20 novembre 1998) et remercier la présence de nos illustres invités. Un des objectifs de ce V Forum est d’établir les bases du programme de «Coopération Méditerranéenne» afin d’impulser un codéveloppement soutenable de l’ensemble du bassin méditerranéen. D’après le programme prévu, nous allons démarrer la séance à travers une petite introduction sur ce que nous comprenons par «coopération méditerranéenne», puis nous essayerons d’ébaucher les particularités propres à la réalisation d’une tâche aussi vaste que la coopération au développement lorsque nous la limitons au domaine méditerranéen. 1. - 1966. 2. 3. A. A. 1.
silex approach Les données sont une richesse, elles constituent un maillon essentiel de la production scientifique dans un contexte de recherche de plus en plus collaboratif. L'objectif de SILEX est de proposer des méthodes et des outils pour permettre une exploitation efficace et une bonne mutualisation des données en agronomie et environnement. SILEX un méta-projet collaboratif porté par l'UMR MISTEA et impliquant une équipe de développement issue d'unités partenaires avec pour thèmes le phenotypage de plantes, les bio-procédés et la viticulture. SILEX est constitué de composants logiciels mutualisés, de modèles et d'outils. Les collaborateurs UR LBE - Narbonne Virginie Rossard, développeur d'applications et responsable deSilex-LBE UMR LEPSE - Montpellier Vincent Nègre, administrateur des Systèmes d'Information du LEPSEJonathan Mineau, développeur d'applications - responsable du SI PhenoArch Stages 2013 Chaque année, plusieurs étudiants en stages intègrent le projet. Systèmes d'Information et Applications
The Semantic Web: An Introduction This document is designed as being a simple but comprehensive introductory publication for anybody trying to get into the Semantic Web: from beginners through to long time hackers. Recommended pre-reading: the Semantic Web in Breadth. Table Of Contents What Is The Semantic Web? The Semantic Web is a mesh of information linked up in such a way as to be easily processable by machines, on a global scale. The Semantic Web was thought up by Tim Berners-Lee, inventor of the WWW, URIs, HTTP, and HTML. What's the rationale for such a system? So the Semantic Web can be seen as a huge engineering solution... but it is more than that. The Semantic Web is generally built on syntaxes which use URIs to represent data, usually in triples based structures: i.e. many triples of URI data that can be held in databases, or interchanged on the world Wide Web using a set of particular syntaxes developed especially for the task. URI - Uniform Resource Identifier RDF - Resource Description Framework Why RDF? Logic
RDF - Semantic Web Standards Overview RDF is a standard model for data interchange on the Web. RDF has features that facilitate data merging even if the underlying schemas differ, and it specifically supports the evolution of schemas over time without requiring all the data consumers to be changed. RDF extends the linking structure of the Web to use URIs to name the relationship between things as well as the two ends of the link (this is usually referred to as a “triple”). This linking structure forms a directed, labeled graph, where the edges represent the named link between two resources, represented by the graph nodes. Recommended Reading The RDF 1.1 specification consists of a suite of W3C Recommendations and Working Group Notes, published in 2014. A number of textbooks have been published on RDF and on Semantic Web in general. Discussions on a possible next version of RDF W3C has recently set up a new RDF Working Group, whose charter is to make a minor revision of RDF. Last modified and/or added All relevant tools
URL vs. URI vs. URN: The Confusion Continues A year has passsed since my last post on URIs and URLs and it would seem that some of the concepts are still lost on some folks. With that said, I figured I’d throw up another post that I could try and address some of the questions raised in the comments of both posts. URLs and URNs are both URIs This is one point that can’t be stated enough. A URL is a URI and a URN is a URI, plain and simple. It’s really quite challenging to phrase it any other way. Examples of URLs and URNs: People have also suggested that these posts could have been more helpful if I had provided some examples that illustrate the difference between a URL and a URI. Again, all of the examples above are all valid examples of URIs. There’s a very informative page by Tim Berners-Lee that provides a lot of good deails on Uniform Resource Identifiers. “The only thing you can use an identifier for is to refer to an object. When you followed the link to this page, you didn’t have to do anything other than clicking it. No.
Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization