Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

TGF-beta signaling proteins and the Protein Ontology

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses

Robot Consciousness: Physics and Metaphysics Here and Abroad

Interest has been renewed in the study of consciousness, both theoretical and applied, following developments in 20th and early 21st-century logic, metamathematics, computer science, and the brain sciences. In this evolving narrative, I explore several theoretical questions about the types of artificial intelligence and offer several conjectures about how they affect possible future developments in this exceptionally transformative field of research. I also address the practical significance of the advances in artificial intelligence in view of the cautions issued by prominent scientists, politicians, and ethicists about the possible dangers of such sufficiently advanced general intelligence, including by implication the search for extraterrestrial intelligence

Evolutionary intelligent agents for e-commerce: Generic preference detection with feature analysis

Product recommendation and preference tracking systems have been adopted extensively in e-commerce businesses. However, the heterogeneity of product attributes results in undesired impediment for an efficient yet personalized e-commerce product brokering. Amid the assortment of product attributes, there are some intrinsic generic attributes having significant relation to a customer’s generic preference. This paper proposes a novel approach in the detection of generic product attributes through feature analysis. The objective is to provide an insight to the understanding of customers’ generic preference. Furthermore, a genetic algorithm is used to find the suitable feature weight set, hence reducing the rate of misclassification. A prototype has been implemented and the experimental results are promising

Constraint capture and maintenance in engineering design

The Designers' Workbench is a system, developed by the Advanced Knowledge Technologies (AKT) consortium to support designers in large organizations, such as Rolls-Royce, to ensure that the design is consistent with the specification for the particular design as well as with the company's design rule book(s). In the principal application discussed here, the evolving design is described against a jet engine ontology. Design rules are expressed as constraints over the domain ontology. Currently, to capture the constraint information, a domain expert (design engineer) has to work with a knowledge engineer to identify the constraints, and it is then the task of the knowledge engineer to encode these into the Workbench's knowledge base (KB). This is an error prone and time consuming task. It is highly desirable to relieve the knowledge engineer of this task, and so we have developed a system, ConEditor+ that enables domain experts themselves to capture and maintain these constraints. Further we hypothesize that in order to appropriately apply, maintain and reuse constraints, it is necessary to understand the underlying assumptions and context in which each constraint is applicable. We refer to them as “application conditions” and these form a part of the rationale associated with the constraint. We propose a methodology to capture the application conditions associated with a constraint and demonstrate that an explicit representation (machine interpretable format) of application conditions (rationales) together with the corresponding constraints and the domain ontology can be used by a machine to support maintenance of constraints. Support for the maintenance of constraints includes detecting inconsistencies, subsumption, redundancy, fusion between constraints and suggesting appropriate refinements. The proposed methodology provides immediate benefits to the designers and hence should encourage them to input the application conditions (rationales)

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

A framework for integrating syntax, semantics and pragmatics for computer-aided professional practice: With application of costing in construction industry

Producing a bill of quantity is a knowledge-based, dynamic and collaborative process, and evolves with variances and current evidence. However, within the context of information system practice in BIM, knowledge of cost estimation has not been represented, nor has it been integrated into the processes based on BIM. This paper intends to establish an innovative means of taking data from the BIM linked to a project, and using it to create the necessary items for a bill of quantity that will enable cost estimation to be undertaken for the project. Our framework is founded upon the belief that three components are necessary to gain a full awareness of the domain which is being computerised; the information type which is to be assessed for compatibility (syntax), the definition for the pricing domain (semantics), and the precise implementation environment for the standards being taken into account (pragmatics). In order to achieve this, a prototype is created that allows a cost item for the bill of quantity to be spontaneously generated, by means of the semantic web ontology and a forward chain algorithm. Within this paper, ‘cost items’ signify the elements included in a bill of quantity, including details of their description, quantity and price. As a means of authenticating the process being developed, the authors of this work effectively implemented it in the production of cost items. In addition, the items created were contrasted with those produced by specialists. For this reason, this innovative framework introduces the possibility of a new means of applying semantic web ontology and forward chain algorithm to construction professional practice resulting in automatic cost estimation. These key outcomes demonstrate that, decoupling the professional practice into three key components of syntax, semantics and pragmatics can provide tangible benefits to domain use

Ways of Applying Artificial Intelligence in Software Engineering

As Artificial Intelligence (AI) techniques have become more powerful and easier to use they are increasingly deployed as key components of modern software systems. While this enables new functionality and often allows better adaptation to user needs it also creates additional problems for software engineers and exposes companies to new risks. Some work has been done to better understand the interaction between Software Engineering and AI but we lack methods to classify ways of applying AI in software systems and to analyse and understand the risks this poses. Only by doing so can we devise tools and solutions to help mitigate them. This paper presents the AI in SE Application Levels (AI-SEAL) taxonomy that categorises applications according to their point of AI application, the type of AI technology used and the automation level allowed. We show the usefulness of this taxonomy by classifying 15 papers from previous editions of the RAISE workshop. Results show that the taxonomy allows classification of distinct AI applications and provides insights concerning the risks associated with them. We argue that this will be important for companies in deciding how to apply AI in their software applications and to create strategies for its use