Swedish LifeWatch ─ a biodiversity infrastructure integrating and reusing data from citizen science, monitoring and research

With continued pressure on biodiversity and ever-growing conflicts with human development, qualified systems for scenario modelling, impact assessment and decision support are urgently needed. Such systems must be able to integrate complex models and information from many sources and do so in a flexible and transparent way. To that end, as well as for other complicated and data-intensive biodiversity research purposes, the concept of LifeWatch has emerged. The idea of LifeWatch is to construct e-infrastructure and virtual laboratories by integrating large data sources, computational capacities, and tools for analysis and modelling in an open, serviceoriented architecture. To be efficient and accurate, a continuous inflow of large quantities of data is essential. However, even with new techniques, government-funded monitoring data and research data will not feed the system with up-to-date species information of sufficient scale and resolution. To fill this void, skilled amateur observers (citizen scientists) can contribute to a very valuable extent. After a preparatory phase, a Swedish LifeWatch (SLW) consortium was initiated in 2011. Swedish LifeWatch developed an infrastructure where all components are accessible through open web services. At the SLW Analysis portal, different formats of species and environmental data can be accessed instantly, and integrated, analysed, visualized and downloaded at selected temporal, spatial or taxonomic scales. Swedish LifeWatch currently provides 46 million species observations from eight different databases, all harmonized according to standardized formats and the Dyntaxa taxonomic backbone database. Almost 40 million of these observations were provided by citizens through the online reporting system named the Species Observation System (SOS) or Artportalen. This paper describes this system, as well as the incentives that make it so successful. The citizen science data in the SOS are accessible, together with data from research and monitoring, in the SLW infrastructure, making the latter a powerful instrument for large-scale data extraction, visualization and analysis

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

Software Infrastructure for Natural Language Processing

We classify and review current approaches to software infrastructure for research, development and delivery of NLP systems. The task is motivated by a discussion of current trends in the field of NLP and Language Engineering. We describe a system called GATE (a General Architecture for Text Engineering) that provides a software infrastructure on top of which heterogeneous NLP processing modules may be evaluated and refined individually, or may be combined into larger application systems. GATE aims to support both researchers and developers working on component technologies (e.g. parsing, tagging, morphological analysis) and those working on developing end-user applications (e.g. information extraction, text summarisation, document generation, machine translation, and second language learning). GATE promotes reuse of component technology, permits specialisation and collaboration in large-scale projects, and allows for the comparison and evaluation of alternative technologies. The first release of GATE is now available - see http://www.dcs.shef.ac.uk/research/groups/nlp/gate/Comment: LaTeX, uses aclap.sty, 8 page

New Methods, Current Trends and Software Infrastructure for NLP

The increasing use of `new methods' in NLP, which the NeMLaP conference series exemplifies, occurs in the context of a wider shift in the nature and concerns of the discipline. This paper begins with a short review of this context and significant trends in the field. The review motivates and leads to a set of requirements for support software of general utility for NLP research and development workers. A freely-available system designed to meet these requirements is described (called GATE - a General Architecture for Text Engineering). Information Extraction (IE), in the sense defined by the Message Understanding Conferences (ARPA \cite{Arp95}), is an NLP application in which many of the new methods have found a home (Hobbs \cite{Hob93}; Jacobs ed. \cite{Jac92}). An IE system based on GATE is also available for research purposes, and this is described. Lastly we review related work.Comment: 12 pages, LaTeX, uses nemlap.sty (included

Building scalable digital library ingestion pipelines using microservices

CORE, a harvesting service offering access to millions of open access research papers from around the world, has shifted its harvesting process from following a monolithic approach to the adoption of a microservices infrastructure. In this paper, we explain how we rearranged and re-scheduled our old ingestion pipeline, present CORE's move to managing microservices and outline the tools we use in a new and optimised ingestion system. In addition, we discuss the ineffciencies of our old harvesting process, the advantages, and challenges of our new ingestion system and our future plans. We conclude that via the adoption of microservices architecture we managed to achieve a scalable and distributed system that would assist with CORE's future performance and evolution

Digital Preservation Services : State of the Art Analysis

Research report funded by the DC-NET project.An overview of the state of the art in service provision for digital preservation and curation. Its focus is on the areas where bridging the gaps is needed between e-Infrastructures and efficient and forward-looking digital preservation services. Based on a desktop study and a rapid analysis of some 190 currently available tools and services for digital preservation, the deliverable provides a high-level view on the range of instruments currently on offer to support various functions within a preservation system.European Commission, FP7peer-reviewe

CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates