Describing and communicating uncertainty within the semantic web

The Semantic Web relies on carefully structured, well defined, data to allow machines to communicate and understand one another. In many domains (e.g. geospatial) the data being described contains some uncertainty, often due to incomplete knowledge; meaningful processing of this data requires these uncertainties to be carefully analysed and integrated into the process chain. Currently, within the SemanticWeb there is no standard mechanism for interoperable description and exchange of uncertain information, which renders the automated processing of such information implausible, particularly where error must be considered and captured as it propagates through a processing sequence. In particular we adopt a Bayesian perspective and focus on the case where the inputs / outputs are naturally treated as random variables. This paper discusses a solution to the problem in the form of the Uncertainty Markup Language (UncertML). UncertML is a conceptual model, realised as an XML schema, that allows uncertainty to be quantified in a variety of ways i.e. realisations, statistics and probability distributions. UncertML is based upon a soft-typed XML schema design that provides a generic framework from which any statistic or distribution may be created. Making extensive use of Geography Markup Language (GML) dictionaries, UncertML provides a collection of definitions for common uncertainty types. Containing both written descriptions and mathematical functions, encoded as MathML, the definitions within these dictionaries provide a robust mechanism for defining any statistic or distribution and can be easily extended. Universal Resource Identifiers (URIs) are used to introduce semantics to the soft-typed elements by linking to these dictionary definitions. The INTAMAP (INTeroperability and Automated MAPping) project provides a use case for UncertML. This paper demonstrates how observation errors can be quantified using UncertML and wrapped within an Observations & Measurements (O&M) Observation. The interpolation service uses the information within these observations to influence the prediction outcome. The output uncertainties may be encoded in a variety of UncertML types, e.g. a series of marginal Gaussian distributions, a set of statistics, such as the first three marginal moments, or a set of realisations from a Monte Carlo treatment. Quantifying and propagating uncertainty in this way allows such interpolation results to be consumed by other services. This could form part of a risk management chain or a decision support system, and ultimately paves the way for complex data processing chains in the Semantic Web.

UncertWeb processing service:making models easer to access on the web

Models are central tools for modern scientists and decision makers, and there are many existing frameworks to support their creation, execution and composition. Many frameworks are based on proprietary interfaces, and do not lend themselves to the integration of models from diverse disciplines. Web based systems, or systems based on web services, such as Taverna and Kepler, allow composition of models based on standard web service technologies. At the same time the Open Geospatial Consortium has been developing their own service stack, which includes the Web Processing Service, designed to facilitate the executing of geospatial processing - including complex environmental models. The current Open Geospatial Consortium service stack employs Extensible Markup Language as a default data exchange standard, and widely-used encodings such as JavaScript Object Notation can often only be used when incorporated with Extensible Markup Language. Similarly, no successful engagement of the Web Processing Service standard with the well-supported technologies of Simple Object Access Protocol and Web Services Description Language has been seen. In this paper we propose a pure Simple Object Access Protocol/Web Services Description Language processing service which addresses some of the issues with the Web Processing Service specication and brings us closer to achieving a degree of interoperability between geospatial models, and thus realising the vision of a useful 'model web'.

PIP-DB:the protein isoelectric point database

A protein's isoelectric point or pI corresponds to the solution pH at which its net surface charge is zero. Since the early days of solution biochemistry, the pI has been recorded and reported, and thus literature reports of pI abound. The Protein Isoelectric Point database (PIP-DB) has collected and collated these data to provide an increasingly comprehensive database for comparison and benchmarking purposes. A web application has been developed to warehouse this database and provide public access to this unique resource. PIP-DB is a web-enabled SQL database with an HTML GUI front-end. PIP-DB is fully searchable across a range of properties.

Design of an information system for metrology contents

Dimensional and form inspections are key to the manufacturing and assembly of products. Product verification can involve a number of different measuring instruments operated using their dedicated software. Typically, each of these instruments with their associated software is more suitable for the verification of a pre-specified quality characteristic of the product than others. The number of different systems and software applications to perform a complete measurement of products and assemblies within a manufacturing organisation is therefore expected to be large. This number becomes even larger as advances in measurement technologies are made. The idea of a universal software application for any instrument still appears to be only a theoretical possibility. A need for information integration is apparent. In this paper, a design of an information system to consistently manage (store, search, retrieve, search, secure) measurement results from various instruments and software applications is introduced. Two of the main ideas underlying the proposed system include abstracting structures and formats of measurement files from the data so that complexity and compatibility between different approaches to measurement data modelling is avoided. Secondly, the information within a file is enriched with meta-information to facilitate its consistent storage and retrieval. To demonstrate the designed information system, a web application is implemented. © Springer-Verlag Berlin Heidelberg 2010.

MEG responses to the perception of global structure within glass patterns

The perception of global form requires integration of local visual cues across space and is the foundation for object recognition. Here we used magnetoencephalography (MEG) to study the location and time course of neuronal activity associated with the perception of global structure from local image features. To minimize neuronal activity to low-level stimulus properties, such as luminance and contrast, the local image features were held constant during all phases of the MEG recording. This allowed us to assess the relative importance of striate (V1) versus extrastriate cortex in global form perception.

Computer aided design and manufacture for three dimensional milling

Advances in both computer technology and the necessary mathematical models capable of capturing the geometry of arbitarily shaped objects has led to the development in this thesis of a surface generation package called 'IBSCURF' aimed at providing a more economically viable solution to free-form surface manufacture. A suit of computer programs written in FORTRAN 77 has been developed to provide computer aids for every aspect of work in designing and machining free-form surfaces. A vector-valued parametric method was used for shape description and a lofting technique employed for the construction of the surface. The development of the package 'IBSCURF' consists of two phases. The first deals with CAD. The design process commences in defining the cross-sections which are represented by uniform B-spline curves as approximations to give polygons. The order of the curve and the position and number of the polygon vertices can be used as parameters for the modification to achieve the required curves. When the definitions of the sectional curves is complete, the surface is interpolated over them by cubic cardinal splines. To use the CAD function of the package to design a mould for a plastic handle, a mathematical model was developed. To facilitate the integration of design and machining using the mathematical representation of the surface, the second phase of the package is concerned with CAM which enables the generation of tool offset positions for ball-nosed cutters and a general post-processor has been developed which automatically generates NC tape programs for any CNC milling machine. The two phases of these programs have been successfully implemented, as a CAD/CAM package for free-form surfaces on the VAX 11/750 super-minicomputer with graphics facilities for displaying drawings interactively on the terminal screen. The development of this package has been beneficial in all aspects of design and machining of free form surfaces.

AKTive Food:semantic web based knowledge conduits for the organic food industry

We present a vision and a proposal for using Semantic Web technologies in the organic food industry. This is a very knowledge intensive industry at every step from the producer, to the caterer or restauranteur, through to the consumer. There is a crucial need for a concept of environmental audit which would allow the various stake holders to know the full environmental impact of their economic choices. This is a di?erent and parallel form of knowledge to that of price. Semantic Web technologies can be used e?ectively for the calculation and transfer of this type of knowledge (together with other forms of multimedia data) which could contribute considerably to the commercial and educational impact of the organic food industry. We outline how this could be achieved as our essential ob jective is to show how advanced technologies could be used to both reduce ecological impact and increase public awareness.

Exploratory database visualisation: the application and assessment of data and dimensionality reduction

This thesis describes the development of a complete data visualisation system for large tabular databases, such as those commonly found in a business environment. A state-of-the-art 'cyberspace cell' data visualisation technique was investigated and a powerful visualisation system using it was implemented. Although allowing databases to be explored and conclusions drawn, it had several drawbacks, the majority of which were due to the three-dimensional nature of the visualisation. A novel two-dimensional generic visualisation system, known as MADEN, was then developed and implemented, based upon a 2-D matrix of 'density plots'. MADEN allows an entire high-dimensional database to be visualised in one window, while permitting close analysis in 'enlargement' windows. Selections of records can be made and examined, and dependencies between fields can be investigated in detail. MADEN was used as a tool for investigating and assessing many data processing algorithms, firstly data-reducing (clustering) methods, then dimensionality-reducing techniques. These included a new 'directed' form of principal components analysis, several novel applications of artificial neural networks, and discriminant analysis techniques which illustrated how groups within a database can be separated. To illustrate the power of the system, MADEN was used to explore customer databases from two financial institutions, resulting in a number of discoveries which would be of interest to a marketing manager. Finally, the database of results from the 1992 UK Research Assessment Exercise was analysed. Using MADEN allowed both universities and disciplines to be graphically compared, and supplied some startling revelations, including empirical evidence of the 'Oxbridge factor'.

Transition of legacy systems to semantically enabled applications:TAO method and tools

Despite expectations being high, the industrial take-up of Semantic Web technologies in developing services and applications has been slower than expected. One of the main reasons is that many legacy systems have been developed without considering the potential of theWeb in integrating services and sharing resources.Without a systematic methodology and proper tool support, the migration from legacy systems to SemanticWeb Service-based systems can be a tedious and expensive process, which carries a significant risk of failure. There is an urgent need to provide strategies, allowing the migration of legacy systems to Semantic Web Services platforms, and also tools to support such strategies. In this paper we propose a methodology and its tool support for transitioning these applications to Semantic Web Services, which allow users to migrate their applications to Semantic Web Services platforms automatically or semi-automatically. The transition of the GATE system is used as a case study. © 2009 - IOS Press and the authors. All rights reserved.

Relation discovery from web data for competency management

In current organizations, valuable enterprise knowledge is often buried under rapidly expanding huge amount of unstructured information in the form of web pages, blogs, and other forms of human text communications. We present a novel unsupervised machine learning method called CORDER (COmmunity Relation Discovery by named Entity Recognition) to turn these unstructured data into structured information for knowledge management in these organizations. CORDER exploits named entity recognition and co-occurrence data to associate individuals in an organization with their expertise and associates. We discuss the problems associated with evaluating unsupervised learners and report our initial evaluation experiments in an expert evaluation, a quantitative benchmarking, and an application of CORDER in a social networking tool called BuddyFinder.

PPD v1.0 - an integrated, web-accessible database of experimentally determined protein pKa values

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pKa archive and as a source of data that allows for the development and improvement of pKa prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information.

The uncertainty enabled model web (UncertWeb)

UncertWeb is a European research project running from 2010-2013 that will realize the uncertainty enabled model web. The assumption is that data services, in order to be useful, need to provide information about the accuracy or uncertainty of the data in a machine-readable form. Models taking these data as imput should understand this and propagate errors through model computations, and quantify and communicate errors or uncertainties generated by the model approximations. The project will develop technology to realize this and provide demonstration case studies.