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. Visualisations mainly as trees, navigation bars.
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. Last stable version 2004 and does not seem to see active development.
NeOn Toolkit: The Neon toolkit also has some visualisation capability, but not independent of the editor. Under active development with a growing user base.
OntoTrack: OntoTrack is a graphical OWL editor and as such has visualisation capabilities. Meager though and it does not seem to be supported or developed anymore either…the current version seems about 5 years old.
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. Not found any software for download at the moment, but the idea is so interesting that we should bear it in mind. Examples are here, here and the key reference is Robertson, George G. and Mackinlay, Jock D. and Card, Stuart K., Cone Trees: animated 3D visualizations of hierarchical information, CHI ’91: Proceedings of the SIGCHI conference on Human factors in computing systems, 1991, ISBN = 0-89791-383-3, pp.189-194. (DOI here)
Welkin: Standalone application for the visualisation of RDF graphs. Allows dynamic filtering, colour coding of resources etc…
Ontosphere3D: Visualisation of ontologies on 3D spheres. Does not seem to be supported anymore and requires Java 3D, which is just a bad nightmare in itself.
Cone Trees (see above) with their extension of Disc Trees (for an example of disc trees, see here
3D Hyperbolic Tree as exemplified by the Walrus software. Originally developed for website visualisation, results in stunnign images. Not under active development anymore, but source code available for download.
Cytoscape: The 1000 pound gorilla in the room of large-scale graph visualization. There are several plugins available for interaction with the Gene Ontology, such as BiNGO and ClueGO. Both tools consider the ontologies as annotation rather than a knowledgebase of its own and can be used for the identification of GO terms, which are overrepresented in a cluster/network. In terms of visualisation of ontologies themselves, there is there is the RDFScape plugin, which can visualize ontologies.
Jamabalaya – Protege Plugin, but can also run as a browser applet. Uses Shrimp to visualise class hierarchies in ontologies and arrows between boxes to represent relationships.
CropCircles (link is to the paper describing it): CropCircles have been implemented in the SWOOP ontology editor which is not under active development anymore, but where the source code is available.
Information Landscapes – again, no software, just papers.