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
Metadata? Thesauri? Taxonomies? Topic Maps! Making sense of it all Abstract To be faced with a document collection and not to be able to find the information you know exists somewhere within it is a problem as old as the existence of document collections. Information Architecture is the discipline dealing with the modern version of this problem: how to organize web sites so that users actually can find what they are looking for. Information architects have so far applied known and well-tried tools from library science to solve this problem, and now topic maps are sailing up as another potential tool for information architects. The paper argues that topic maps go beyond the traditional solutions in the sense that it provides a framework within which they can be represented as they are, but also extended in ways which significantly improve information retrieval. Table of contents 1. The task of an information architect is to create web sites where users can actually find the information they are looking for. 2. 2.1. Metadata 2.2. title
Mapping Social Networks The growth of social networks such as Facebook and MySpace has introduced the idea of the 'social graph' into common parlance. the social graph is Watch this short video describing the proof of concept Vizter social network browser visualisation: Vizter explanatory video. How does vizter allow you to identify friends you have in common with other people? How does vizter help the user identify possible communities in the social graph? If you have a Facebook account, there are several tools that you can use to visualise your friends network on there (requires adding the visulisation as a Facebook application). Touchgraph frinds'n'photos browser;Nexus social graph browser;FriendwheelFacebook Mutual Friend Network Visualization in FlashFriends visulisation in Many Eyes: this application will mine your friends network and produce a data output that will let you visualise your friends network using the Many Eyes network visualisation tool. There are a couple of things to note about this graph.
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]
Ontology (information science) In computer science and information science, an ontology formally represents knowledge as a hierarchy of concepts within a domain, using a shared vocabulary to denote the types, properties and interrelationships of those concepts.[1][2] Ontologies are the structural frameworks for organizing information and are used in artificial intelligence, the Semantic Web, systems engineering, software engineering, biomedical informatics, library science, enterprise bookmarking, and information architecture as a form of knowledge representation about the world or some part of it. The creation of domain ontologies is also fundamental to the definition and use of an enterprise architecture framework. The term ontology has its origin in philosophy and has been applied in many different ways. The word element onto- comes from the Greek ὤν, ὄντος, ("being", "that which is"), present participle of the verb εἰμί ("be"). According to Gruber (1993): Common components of ontologies include:
Hive Plots - Linear Layout for Network Visualization - Visually Interpreting Network Structure and Content Made Possible 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
Vizster: Visualizing Online Social Networks VizsterVisualizing Online Social Networks Jeffrey Heer – jheer@cs.berkeley.edu Professor Marti Hearst InfoSys 247 – Information Visualization University of California, Berkeley Spring Semester, 2004 Vizster is an interactive visualization tool for online social networks, allowing exploration of the community structure of social networking services such as friendster.com [4], tribe.net [12], and orkut [10]. Vizster provides a visualization of such services, providing an interactive sociogram for exploring the links between network members. Vizster currently limits itself to ego-centric social networks, or network views centered on a single individual and her direct linkages. The social network data being visualized is the structure and content of friendster.com [4], the most popular online social networking service. In addition to friendship linkage, the database contains the profile data for each crawled user. The basic Vizster visualization is shown below in Figure 1. Figure 6. 1.
Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization Data Visualization Software | ADVIZOR Solutions Interactive Infographic with SVG and CSS Animations Learn how to build an interactive animated infographic using SVG, CSS and JavaScript. View demo Download source One of the less talked about features of newer browsers is increasing support for the SVG file format. But one of the really cool things that some developers do not realize is that SVG is built on the XML specification, which at the end of the day means that its plain old markup, and can be worked with in a similar manner to HTML. With the right techniques and modern browser support, developers can now produce some pretty impressive animations, effects and interactions using SVG. Preparing an SVG file There are tons of ways to create SVG graphics, and while it is possible to do some SVG coding “by hand”, for more complex graphics we will want to have some type of vector editing software that can export as SVG. Whatever software you choose, it is essential to have the ability to group objects together, and be able to name those groups (assign the id attribute). The HTML The CSS