BACKGROUND: A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. A significant barrier to translational research is the lack of uniformly structured data across related biomedical domains. The Semantic Web is an extension of the current Web that enables navigation and meaningful use of digital resources by automatic processes. It is based on common formats that support aggregation and integration of data drawn from diverse sources. A variety of technologies have been built on this foundation that, together, support identifying, representing, and reasoning across a wide range of biomedical data. The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG), set up within the framework of the World Wide Web Consortium, was launched to explore the application of these technologies in a variety of areas. Subgroups focus on making biomedical data available in RDF, working with biomedical ontologies, prototyping clinical decision support systems, working on drug safety and efficacy communication, and supporting disease researchers navigating and annotating the large amount of potentially relevant literature. RESULTS: We present a scenario that shows the value of the information environment the Semantic Web can support for aiding neuroscience researchers. We then report on several projects by members of the HCLSIG, in the process illustrating the range of Semantic Web technologies that have applications in areas of biomedicine. CONCLUSION: Semantic Web technologies present both promise and challenges. Current tools and standards are already adequate to implement components of the bench-to-bedside vision. On the other hand, these technologies are young. Gaps in standards and implementations still exist and adoption is limited by typical problems with early technology, such as the need for a critical mass of practitioners and installed base, and growing pains as the technology is scaled up. Still, the potential of interoperable knowledge sources for biomedicine, at the scale of the World Wide Web, merits continued work.

The earliest Web browsers focussed on the display of textual information. When graphics were added, essentially only image graphics and image file formats were supported. For a significant range of applications, image graphics has severe limitations, for example in terms of file size, download time and inability to interact with and modify the graphics client‐side. Vector graphics may be more appropriate in these cases, and this has become possible through the introduction of the WebCGM and Scalable Vector Graphics (SVG) formats, both of which are open standards, the former from ISO/IEC and W3C and the latter from W3C. This paper reviews the background to Web graphics, presents the WebCGM file format, and gives a more detailed exposition of the most recent format, SVG. The paper concludes with reflections on the current state of this area and future prospects.

Abstract The usage of SVG (Scaleable Vector Graphics) creates new possibilities as well as new challenges for theaccessibility of Web sites. This paper presents a metadata vocabulary to describe the information content ofan SVG file geared towards accessibility. When used with a suitable tool, this metadata description can helpin generating a textual (``linear'') version of the content, which can be used for users with disabilities or withnon‐visual devices. Although this paper concentrates on SVG, i.e. on graphics on the Web, the metadata approach and vocabularypresented below can be applied in relation to other technologies, too. Indeed, accessibility issues have a muchwider significance, and have an effect on areas like CAD, cartography, or information visualization. Hence, theexperiences of the work presented below may also be useful for practitioners in other areas. ACM CSS: I.3.4 Graphics Utilities—Graphics Packages, I.3.6 Methodology and Techniques—Graphics datastructures and data types, Standards, K.4.2 Social Issues—Assistive technologies for persons with disabilities

Abstract Many applications, from everyday file system browsers to visual programming tools, require the display of network and graph structures. The Graph Visualization Framework (GVF) (available at http://www.cwi.nl/InfoVisu/GVF) is an architecture that supports the tasks common to most graph browsers and editors. This article gives a brief overview of the design of the GVF and focuses on the core classes that are used to represent and manipulate graphs. The design of the core classes is justified by the requirements for navigation and visualization. Copyright © 2001 John Wiley & Sons, Ltd.

GraphXML is a graph description language in XML that can be used as an interchange format for graph drawing and visualization packages. The generality and rich features of XML make it possible to define an interchange format that not only supports the pure, mathematical description of a graph, but also the needs of information visualization applications that use graph-based data structures. These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a survey on graph visualization and navigation techniques, as used in information visualization. Graphs appear in numerous applications such as Web browsing, state-transition diagrams, and data structures. The ability to visualize and to navigate in these potentially large, abstract graphs is often a crucial part of an application. Information visualization has specific requirements, which means that this survey approaches the results of traditional graph drawing from a different perspective.

Abstract. Many of the reported experiences in the industrial use of formal methods concern the development of products or product families, where the utility of the method is linked to direct savings in development costs or improved assurance of quality. However, one other area in which formal description techniques make a valuable contribution is in the development and documentation of International Standards, where the cost of using formal methods can be paid off both through increased quality of products that implement a given standard, and through the improved inter-operability of different implementations that comes from having a precise definition of the expected behaviour of a conforming implementation. Standards development, however, has some significant differences from product development, and comes with specific needs and constraints that affect the use of formal description techniques. This paper describes the role that formal methods played in the development of a new standard for distributed multimedia presentation. It describes a number of issues that arose from this experience, and which have longer term importance for formal methods in standards, particularly given the changes that are taking place in the way that standards are developed.

msTRAcT Advmees in hardware, software, and coding stindards for digiti media have now made the defivery of mdtimedia ifiormation a sWdard component of many systems.Unfortunately, the pace of this technologiml development coupled Itith strong commercial competition between leadng vendors, has meant that fittle consensus hx emerged over the dwign of programming interfaces to Wow the creation, maniptiation, ~d presentation of such dab.PREMO &Resentition Environments for Mtitimedia Objeck) is a new MO S*dard, to be pub-~~bed in 1998, that defies a middeware frmework encompassing synchrotiation, the mnagement of distributed media resourcw, and the sdess integration of dab and processw from d~parate appti~tion areas.This paper @ves m ove~ew of the concepts under-l~ting PREMO and the approach by which the shndard ut~ies these concepts to addrws key mpeck of mtitirnedia systems design.1.1

Of the various programming paradigms in use today, object‐orientation is probably the most successful in terms of industrial take‐up and application, particularly in the field of multimedia. It is therefore unsurprising that this technology has been adopted by ISO/IEC JTC1/SC24 as the foundation for a forthcoming International Standard for Multimedia, called PREMO. Two important design aims of PREMO are that it be distributable, and that it provides a set of media‐related services that can be extended in a disciplined way to support the needs of future applications and problem domains. While key aspects of the object‐oriented paradigm provide a sound technical basis for achieving these aims, the need to balance extensibility and a high‐level programming interface against the realities of efficiency and ease of implementation in a distributed setting meant that the task of synthesising a Standard from existing practice was non‐trivial. Indeed, in order to meet the design aims of PREMO is was found necessary to augment the basic object infrastructure with facilities and ideas drawn from other programming paradigms, in particular concepts from constraint management and data flow. This paper describes the important trade‐offs that have affected the development of PREMO and explains how these are addressed through the use of specific programming paradigms.

Information visualisation often requires good navigation aids on large trees, which represent the underlying abstract information. Using trees for information visualisation requires novel user interface techniques, visual clues, and navigational aids. This paper describes a visual clue: using the so‐called Strahler numbers, a map is provided that indicates which parts of the tree are interesting. A second idea is that of “folding” away subtrees that are too “different” in some sense, thereby reducing the visual complexity of the tree. Examples are given demonstrating these techniques, and what the further challenges in this area are.

PREMO is an emerging international standard for the presentations of multimedia objects including computer graphics. Open Inventor™ is a commercially available “de facto” standard for interactive computer graphics packaged as a library of objects. In this paper, we consider whether the concepts and objects of PREMO are sufficient to represent a professional quality system, such as Open Inventor. By comparing PREMO with Open Inventor, we hope to show that PREMO's computer graphics environment model and event model can properly describe Open Inventor's rendering action and event model. The scene graph is very important in Open Inventor. Most Open Inventor functions rely on various operations over scene graphs. The construction, edition and traversal of the scene graphs are implemented as a set of newly defined PREMO objects. Graphics rendering, event handling and scene graphs constitute the fundamental parts of Open Inventor, other Open Inventor functionalities can be constructed from these. We conclude that since these three fundamental parts of Open Inventor can be properly modelled and implemented by means of PREMO, that the concepts and objects of PREMO are sufficient to represent Open Inventor.

PREMO is a major new ISO/IEC standard for graphics and multimedia, which addresses many of the concerns that have been expressed about existing graphics standards. In particular, it addresses the issues of configuration, extension, and interoperation of and between PREMO implementations. This paper gives an overview of PREMO and highlights its most significant features.

Abstract The development of multimedia applications is a complex task. Much of this complexity stems from requirements associated with programming multiple media objects and the control of dependences and inter‐relationships between these media objects and the user(s). It is clearly necessary to have a basic framework on which to build multimedia applications in the face of such complexities. Such a conceptual model is what we have called an object model and it is the main subject of this paper. The MADE object model represents a novel approach to multimedia application programming that is founded on the two principal concepts of active objects and delegation. Although these concepts are not novel in themselves, we believe that their combined use in a multimedia development environment represents a substantial enhancement to more traditional approaches to programming in this area.

Abstract Management of the communications among a set of concurrent processes arises in many applications and is a central concern in parallel computing. In this paper we introduce MANIFOLD: a co‐ordination language whose sole purpose is to describe and manage complex interconnections among independent, concurrent processes. In the underlying paradigm of this language the primary concern is not with what functionality the individual processes in a parallel system provide. Instead, the emphasis is on how these processes are interconnected and how their interaction patterns change during the execution life of the system. This paper also includes an overview of our implementation of MANIFOLD. As an example of the application of MANIFOLD, we present a series of small manifold programs which describe the skeletons of some adaptive recursive algorithms that are of particular interest in computer graphics. Our concern in this paper is to show the expressiveness of MANIFOLD, the feasibility of its implementation and its usefulness in practice. Issues regarding performance and optimization are beyond the scope of this paper.

This paper describes the specification of the GKS input model in Manifold. The aim of the work reported in this paper was two‐fold: first, to review the communication patterns implied by the GKS input model, and second, to evaluate the suitability of the Manifold language as a tool for defining complex dynamic interaction patterns that are common in non‐trivial user interfaces. The GKS input model is also adopted by all more recent ISO graphics standard documents. A more formal scrutiny of the inter‐communication of the components of this model, excluding the implementation details of their functionality, is instructive in itself. It can reveal directions for improvement of its shortcomings and for generalization of its strengths for the ongoing effort to define the functionality of future graphics packages. Manifold is a language for describing inter‐process communications. Processes in Manifold communicate by means of buffered communication links called streams and by reacting to events raised asynchronously by other processes. Our experience shows that Manifold is a promising tool for describing systems of cooperating parallel processes. Our Manifold specification of the GKS input model offers a very flexible way to structure user defined logical input devices. Furthermore, it is simple and modular enough to allow easy extensions to include more functionality by local modifications. As such, it can serve as a basis for possible extensions and enhancements envisioned for future graphics packages. 1987 CR Categories: C.1.2, C.1.3, C.2.m, D.1.3, F.1.2, I.1.3, I.3.6, I.3.4. 1885 Mathematical Subject Classification: 68N99, 68Q10,68U05.

Abstract The modedling clip of the PHIGS ISO Standard is mathematically analysed. The most important result of this analysis is the fact that the projective image of a modding clip body (that is a not necessarily bounded convex body in space) is simply the union of two convex bodies. Furthermore, it will also be proved that in some cases one of these two bodies is empty. This fact makes the implementation of the modelling clip fairly straightforward and makes it also possible to use all already existing results on clipping against general convex bodies without change.

The outline of an extension of traditional 2D graphics systems is given. This extension is aimed at supporting a three dimensional application program, without incorporating full viewing into the general graphics system itself. The resulting system might be very advantageous for large application programs which have their own three dimensional facilities.

Abstract A general formulation for conies and conic arcs for the purpose of computer graphics is given, based on principles and theorems of projective geometry. This approach allows the approximation of these curves by line segments to be postponed in the graphics output pipeline; it results in a more compact storage, faster approximation algorithms and smoother outlook of the curves.

Abstract The modelling clip as proposed for example in PHIGS is mathematically analyzed and a method to perform it is proposed. The method has the particular edvantage of avoiding all possible singularities appearing in the course of a projective transformation. Additionally, further optimizations in the implementation of the whole output pipeline are proposed.

The output pipeline of GKS-3D/PHIGS isexamined to find some possible points where the implementation could be improved to raise efficiency while remaining strictly within the scope of the Standards. Some interesting results are presented in the paper which have led to a 25-30% improvement in speed when compared to a more conservative implementation.

Abstract The fill area primitive is one of the most powerful primitives of GKS and its derivatives (GKS‐3D, PHIGS etc.). Since its specrfication is extremely general, it is important to explore new approaches to achieve higher performance in its implementation. In this paper fast algorithms are presented for special situations, which can be included, together with appropriate tests, into a complete GKS output pipeline. As a result, a speed improvement With a factor of two may be achieved in important practical cases.

General ideas for the creation of a very intelligent graphic terminal are presented; this terminal should know all GKS functionalities, including the future 3D Standard as well. Multiple Workstation concept is maintained and it i s realized by linking it to a multiple context-frame handling.

Abstract A method for generating new device drivers for use in a full GKS implementation is presented. The method is based on conditional compiling techniques making use of the Workstation Description Table, and it has been used in a full GKS to develop several device drivers, which took about 1 week for a novice.