myTea: Connecting the Web to Digital Science on the Desktop

Bioinformaticians regularly access the hundreds of databases and tools that are available to them on the Web. None of these tools communicate with each other, causing the scientist to copy results manually from a Web site into a spreadsheet or word processor. myGrids' Taverna has made it possible to create templates (workflows) that automatically run searches using these databases and tools, cutting down what previously took days of work into hours, and enabling the automated capture of experimental details. What is still missing in the capture process, however, is the details of work done on that material once it moves from the Web to the desktop: if a scientist runs a process on some data, there is nothing to record why that action was taken; it is likewise not easy to publish a record of this process back to the community on the Web. In this paper, we present a novel interaction framework, built on Semantic Web technologies, and grounded in usability design practice, in particular the Making Tea method. Through this work, we introduce a new model of practice designed specifically to (1) support the scientists' interactions with data from the Web to the desktop, (2) provide automatic annotation of process to capture what has previously been lost and (3) associate provenance services automatically with that data in order to enable meaningful interrogation of the process and controlled sharing of the results

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

Provenance-based trust for grid computing: Position Paper

Current evolutions of Internet technology such as Web Services, ebXML, peer-to-peer and Grid computing all point to the development of large-scale open networks of diverse computing systems interacting with one another to perform tasks. Grid systems (and Web Services) are exemplary in this respect and are perhaps some of the first large-scale open computing systems to see widespread use - making them an important testing ground for problems in trust management which are likely to arise. From this perspective, today's grid architectures suffer from limitations, such as lack of a mechanism to trace results and lack of infrastructure to build up trust networks. These are important concerns in open grids, in which "community resources" are owned and managed by multiple stakeholders, and are dynamically organised in virtual organisations. Provenance enables users to trace how a particular result has been arrived at by identifying the individual services and the aggregation of services that produced such a particular output. Against this background, we present a research agenda to design, conceive and implement an industrial-strength open provenance architecture for grid systems. We motivate its use with three complex grid applications, namely aerospace engineering, organ transplant management and bioinformatics. Industrial-strength provenance support includes a scalable and secure architecture, an open proposal for standardising the protocols and data structures, a set of tools for configuring and using the provenance architecture, an open source reference implementation, and a deployment and validation in industrial context. The provision of such facilities will enrich grid capabilities by including new functionalities required for solving complex problems such as provenance data to provide complete audit trails of process execution and third-party analysis and auditing. As a result, we anticipate that a larger uptake of grid technology is likely to occur, since unprecedented possibilities will be offered to users and will give them a competitive edge

NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies. It also can be customized to fit the needs of different scenarios. Ontology Recommender 2.0 combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available.Comment: 29 pages, 8 figures, 11 table

A Semantic Web Annotation Tool for a Web-Based Audio Sequencer

Music and sound have a rich semantic structure which is so clear to the composer and the listener, but that remains mostly hidden to computing machinery. Nevertheless, in recent years, the introduction of software tools for music production have enabled new opportunities for migrating this knowledge from humans to machines. A new generation of these tools may exploit sound samples and semantic information coupling for the creation not only of a musical, but also of a "semantic" composition. In this paper we describe an ontology driven content annotation framework for a web-based audio editing tool. In a supervised approach, during the editing process, the graphical web interface allows the user to annotate any part of the composition with concepts from publicly available ontologies. As a test case, we developed a collaborative web-based audio sequencer that provides users with the functionality to remix the audio samples from the Freesound website and subsequently annotate them. The annotation tool can load any ontology and thus gives users the opportunity to augment the work with annotations on the structure of the composition, the musical materials, and the creator's reasoning and intentions. We believe this approach will provide several novel ways to make not only the final audio product, but also the creative process, first class citizens of the Semantic We

Satellite-enabled interactive education: scenarios and systems architectures

There are specific sectors of the economy that can benefit from satellite-based tele-education. Areas, such as maritime and agriculture, share common needs for both broadband connectivity at remote geographical areas that cannot otherwise be covered, and for innovative content for tele-education purposes. Furthermore, each area has special requirements with regard to the type of content to be delivered. In this paper we propose a set of architectural designs and case scenarios that will realise such interactive end-to-end education systems based on satellite communications. Services requirements in this setting are also identified and discussed

Context Aware Computing for The Internet of Things: A Survey

As we are moving towards the Internet of Things (IoT), the number of sensors deployed around the world is growing at a rapid pace. Market research has shown a significant growth of sensor deployments over the past decade and has predicted a significant increment of the growth rate in the future. These sensors continuously generate enormous amounts of data. However, in order to add value to raw sensor data we need to understand it. Collection, modelling, reasoning, and distribution of context in relation to sensor data plays critical role in this challenge. Context-aware computing has proven to be successful in understanding sensor data. In this paper, we survey context awareness from an IoT perspective. We present the necessary background by introducing the IoT paradigm and context-aware fundamentals at the beginning. Then we provide an in-depth analysis of context life cycle. We evaluate a subset of projects (50) which represent the majority of research and commercial solutions proposed in the field of context-aware computing conducted over the last decade (2001-2011) based on our own taxonomy. Finally, based on our evaluation, we highlight the lessons to be learnt from the past and some possible directions for future research. The survey addresses a broad range of techniques, methods, models, functionalities, systems, applications, and middleware solutions related to context awareness and IoT. Our goal is not only to analyse, compare and consolidate past research work but also to appreciate their findings and discuss their applicability towards the IoT.Comment: IEEE Communications Surveys & Tutorials Journal, 201

Higher-Order Process Modeling: Product-Lining, Variability Modeling and Beyond

We present a graphical and dynamic framework for binding and execution of business) process models. It is tailored to integrate 1) ad hoc processes modeled graphically, 2) third party services discovered in the (Inter)net, and 3) (dynamically) synthesized process chains that solve situation-specific tasks, with the synthesis taking place not only at design time, but also at runtime. Key to our approach is the introduction of type-safe stacked second-order execution contexts that allow for higher-order process modeling. Tamed by our underlying strict service-oriented notion of abstraction, this approach is tailored also to be used by application experts with little technical knowledge: users can select, modify, construct and then pass (component) processes during process execution as if they were data. We illustrate the impact and essence of our framework along a concrete, realistic (business) process modeling scenario: the development of Springer's browser-based Online Conference Service (OCS). The most advanced feature of our new framework allows one to combine online synthesis with the integration of the synthesized process into the running application. This ability leads to a particularly flexible way of implementing self-adaption, and to a particularly concise and powerful way of achieving variability not only at design time, but also at runtime.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455

The Semantic Grid: A future e-Science infrastructure

e-Science offers a promising vision of how computer and communication technology can support and enhance the scientific process. It does this by enabling scientists to generate, analyse, share and discuss their insights, experiments and results in an effective manner. The underlying computer infrastructure that provides these facilities is commonly referred to as the Grid. At this time, there are a number of grid applications being developed and there is a whole raft of computer technologies that provide fragments of the necessary functionality. However there is currently a major gap between these endeavours and the vision of e-Science in which there is a high degree of easy-to-use and seamless automation and in which there are flexible collaborations and computations on a global scale. To bridge this practice–aspiration divide, this paper presents a research agenda whose aim is to move from the current state of the art in e-Science infrastructure, to the future infrastructure that is needed to support the full richness of the e-Science vision. Here the future e-Science research infrastructure is termed the Semantic Grid (Semantic Grid to Grid is meant to connote a similar relationship to the one that exists between the Semantic Web and the Web). In particular, we present a conceptual architecture for the Semantic Grid. This architecture adopts a service-oriented perspective in which distinct stakeholders in the scientific process, represented as software agents, provide services to one another, under various service level agreements, in various forms of marketplace. We then focus predominantly on the issues concerned with the way that knowledge is acquired and used in such environments since we believe this is the key differentiator between current grid endeavours and those envisioned for the Semantic Grid

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description