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

Towards a killer app for the Semantic Web

Killer apps are highly transformative technologies that create new markets and widespread patterns of behaviour. IT generally, and the Web in particular, has benefited from killer apps to create new networks of users and increase its value. The Semantic Web community on the other hand is still awaiting a killer app that proves the superiority of its technologies. There are certain features that distinguish killer apps from other ordinary applications. This paper examines those features in the context of the Semantic Web, in the hope that a better understanding of the characteristics of killer apps might encourage their consideration when developing Semantic Web applications

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

A knowledge representation meta-model for rule-based modelling of signalling networks

The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their literatures and data are consequently fragmented, distributed and sometimes--at least apparently--inconsistent. This makes it extremely difficult to build significant explanatory models with the result that effects in these systems that are brought about by many interacting factors are poorly understood. The rule-based approach to modelling has shown some promise for the representation of the highly combinatorial systems typically found in signalling where many of the proteins are composed of multiple binding domains, capable of simultaneous interactions, and/or peptide motifs controlled by post-translational modifications. However, the rule-based approach requires highly detailed information about the precise conditions for each and every interaction which is rarely available from any one single source. Rather, these conditions must be painstakingly inferred and curated, by hand, from information contained in many papers--each of which contains only part of the story. In this paper, we introduce a graph-based meta-model, attuned to the representation of cellular signalling networks, which aims to ease this massive cognitive burden on the rule-based curation process. This meta-model is a generalization of that used by Kappa and BNGL which allows for the flexible representation of knowledge at various levels of granularity. In particular, it allows us to deal with information which has either too little, or too much, detail with respect to the strict rule-based meta-model. Our approach provides a basis for the gradual aggregation of fragmented biological knowledge extracted from the literature into an instance of the meta-model from which we can define an automated translation into executable Kappa programs.Comment: In Proceedings DCM 2015, arXiv:1603.0053