Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning

Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies

Achieving excellence in design research: a case study of research and education framework at Northumbria University

This paper discusses the case study of the new research and education framework applied at the School of Design at Northumbria University that aims at building an integrated sustainable design research community. This community concerns itself with developing design value propositions (new methods, new knowledge and new design IDEAS or applications) by combining the three broad domains of the discipline (forms of practice); practice through collaboration (new methods), discovery through research (new knowledge), and new solutions through engagement (new products, and services). In both academic and commercial context, this also culminates into a purposeful learning for all stakeholders. The authors explain that the methodological gap between design ‘doers’ and design scholars in an academic context makes the process of design leadership very difficult. This paper discusses the paradox that design in the academia needs to respond to the conflict between learning through doing (design) and learning through research of design. Additionally, this paper highlights the challenges that the School of Design at Northumbria came across while establishing this research community and also discusses everyday challenges of maintaining this community

Applying knowledge management in education : teaching database normalization : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Information Science at Massey University

In tertiary education, Information Science has been attracting more attention in both teaching and learning. However, along the course on the database design theory, learners always find it hard to grasp the knowledge on database normalisation and hard to apply different levels of the normal forms while designing a database. This results poor database construction and difficulties in database maintenance. In regard to this teaching and learning dilemma, academic teaching staff should, on the one hand, pay more attention to organising different teaching resources on database normalisation concepts and making the best use of the existing and newly developed resources so as to make the teaching environment more adaptive and more sharable. and on the other hand, apply different teaching methods to different students according to their knowledge levels by understanding the nature of each learner's behaviour, interests and preferences concerning the existing learning resources. However, at present there is no effective Information Technology tool to use in considering the dynamic nature of knowledge discovery, creation, transfer utilisation and reuse in this area. This provides an opportunity to examine the potentiality of applying knowledge management in education with the focus on teaching database normalisation, in terms of knowledge discovering, sharing, utilisation and reuse. This thesis contains a review of knowledge management and web mining technologies in the education environment, presents a dynamic knowledge management framework for better utilising teaching resource in the area of database normalisation and diagnoses the students' learning patterns and behaviours to assist effective teaching and learning. It is argued that knowledge management-supported education can work as a value-added process which supports the different needs of teachers and learners

Extracting Maximum Benefits from Web-Based Searching

With huge amounts of information connected to the Internet, efficient and effective discovery of resource and knowledge using the Internet has become an imminent research issue. A vast array of networks services is growing up around the Internet and massive amounts of information is added everyday. Users can now access massive amounts of information in various forms, thereby creating an equally massive problem. This rapid growth in data volume, user base, and data diversity render Internet-accessible information increasingly difficult to be used effectively. Therefore, search for a specific information on this massive and exploding Internet information resource base becomes highly critical. In this paper we discuss the issues involved in the application of machine learning techniques to the problem of Internet-based information overload. We present a general architecture and describe how it has been instantiated in a functional system we developed. The system attempts to concurrently maximize and optimize the resource/knowledge discovery, and custimize the information to individual users. We discuss the design issues involved in the attempt to develop an evolvable architecture which can easily and inexpensively accommodate future generations of web-based systems and technologies

Allosteric modulation of protein oligomerization: an emerging approach to drug design

Many disease-related proteins are in equilibrium between different oligomeric forms. The regulation of this equilibrium plays a central role in maintaining the activity of these proteins in vitro and in vivo. Modulation of the oligomerization equilibrium of proteins by molecules that bind preferentially to a specific oligomeric state is emerging as a potential therapeutic strategy that can be applied to many biological systems such as cancer and viral infections. The target proteins for such compounds are diverse in structure and sequence, and may require different approaches for shifting their oligomerization equilibrium. The discovery of such oligomerization-modulating compounds is thus achieved based on existing structural knowledge about the specific target proteins, as well as on their interactions with partner proteins or with ligands. In silico design and combinatorial tools such as peptide arrays and phage display are also used for discovering compounds that modulate protein oligomerization. The current review highlights some of the recent developments in the design of compounds aimed at modulating the oligomerization equilibrium of proteins, including the shiftides approach developed in our lab

The Environmental Dimension of Urban Design: A Point of View

International research on sustainable architecture ascertained the responsibilities of urban forms for buildings’ energy‐environmental performances, highlighting the necessity to broaden the field of intervention in urban design. Furthermore, goals concerning the sustainable city increased design complexity, due to the involvement of different interrelated disciplines, which modified design processes by incorporating external contributions. In particular, environmental analyses are growing in importance and need to be reintegrated into the urban project at the conceptual stage. This ‘environmental awareness’ accompanies the history of the city, and numerous pieces of evidence clearly show the mutual and in‐depth relationship between urban form and local microclimates. Lessons from the ancients constituted the fundamentals in urban design until the Modern Movement, during which knowledge of the past also influenced the work of G. Vinaccia, an Italian pioneer in microclimatic urban design. After the World War II, most of the lessons had been forgotten in favour of technology systems that have since revealed their failures. The current design condition requires a discovery of past abilities, coupling them with contemporary scientific advances. This work introduces a methodology through which to integrate current urban design processes with environmental data and analyses. It is illustrated through a case study and is supported by software

Extracting behavioural patterns from a negotiation game

The work presented focuses not only on the behavioural patterns that influence the outcome of a negotiation, but also on the discovery of ways to predict the type of conflict used in the process and the stress levels of the actors. After setting up an experimental intelligent environment provided with sensors to capture behavioural and contextual information, a set of relevant data was collected and analysed, with the underlying objective of using the behavioural patterns (obtained by statistical/probabilistic methods) as a basis to design and present plans and suggestions to the associated participants. In sooth, these proposals may influence in a positive way the course and outcome of a negotiation task in many aspects. This work highlights the importance of knowledge in negotiation, as in other social forms of interaction, providing also some new insights for informed decision support in situations in which uncertainty and conflict may be present

Reinventing discovery learning: a field-wide research program

© 2017, Springer Science+Business Media B.V., part of Springer Nature. Whereas some educational designers believe that students should learn new concepts through explorative problem solving within dedicated environments that constrain key parameters of their search and then support their progressive appropriation of empowering disciplinary forms, others are critical of the ultimate efficacy of this discovery-based pedagogical philosophy, citing an inherent structural challenge of students constructing historically achieved conceptual structures from their ingenuous notions. This special issue presents six educational research projects that, while adhering to principles of discovery-based learning, are motivated by complementary philosophical stances and theoretical constructs. The editorial introduction frames the set of projects as collectively exemplifying the viability and breadth of discovery-based learning, even as these projects: (a) put to work a span of design heuristics, such as productive failure, surfacing implicit know-how, playing epistemic games, problem posing, or participatory simulation activities; (b) vary in their target content and skills, including building electric circuits, solving algebra problems, driving safely in traffic jams, and performing martial-arts maneuvers; and (c) employ different media, such as interactive computer-based modules for constructing models of scientific phenomena or mathematical problem situations, networked classroom collective “video games,” and intercorporeal master–student training practices. The authors of these papers consider the potential generativity of their design heuristics across domains and contexts

Knowledge data discovery and data mining in a design environment

Designers, in the process of satisfying design requirements, generally encounter difficulties in, firstly, understanding the problem and secondly, finding a solution [Cross 1998]. Often the process of understanding the problem and developing a feasible solution are developed simultaneously by proposing a solution to gauge the extent to which the solution satisfies the specific requirements. Support for future design activities has long been recognised to exist in the form of past design cases, however the varying degrees of similarity and dissimilarity found between previous and current design requirements and solutions has restrained the effectiveness of utilising past design solutions. The knowledge embedded within past designs provides a source of experience with the potential to be utilised in future developments provided that the ability to structure and manipulate that knowledgecan be made a reality. The importance of providing the ability to manipulate past design knowledge, allows the ranging viewpoints experienced by a designer, during a design process, to be reflected and supported. Data Mining systems are gaining acceptance in several domains but to date remain largely unrecognised in terms of the potential to support design activities. It is the focus of this paper to introduce the functionality possessed within the realm of Data Mining tools, and to evaluate the level of support that may be achieved in manipulating and utilising experiential knowledge to satisfy designers' ranging perspectives throughout a product's development

Knowledge transformers : a link between learning and creativity

The purpose of this paper is to investigate whether knowledge transformers which are featured in the learning process, are also present in the creative process. This is achieved by reviewing models and theories of creativity and identifying the existence of the knowledge transformers. The investigation shows that there is some evidence to show that the creative process can be explained through knowledge transformers. Hence, it is suggested that one of links between learning and creativity is through the knowledge transformers