Global data for local science: Assessing the scale of data infrastructures in biological and biomedical research

publication-status: Acceptedtypes: ArticleThe use of online databases to collect and disseminate data is typically portrayed as crucial to the management of ‘big science’. At the same time, databases are not deemed successful unless they facilitate the re-use of data towards new scientific discoveries, which often involves engaging with several highly diverse and inherently unstable research communities. This paper examines the tensions encountered by database developers in their efforts to foster both the global circulation and the local adoption of data. I focus on two prominent attempts to build data infrastructures in the fields of plant science and cancer research over the last decade: The Arabidopsis Information Resource and the Cancer Biomedical Informatics Grid. I show how curators’ experience of the diverse and dynamic nature of biological research led them to envision databases as catering primarily for local, rather than global, science; and to structure them as platforms where methodological and epistemic diversity can be expressed and explored, rather than denied or overcome. I conclude that one way to define the scale of data infrastructure is to consider the range and scope of the biological and biomedical questions which it helps to address; and that within this perspective, databases have a larger scale than the science that they serve, which tends to remain fragmented into a wide variety of specialised projects

Towards Interoperable Research Infrastructures for Environmental and Earth Sciences

This open access book summarises the latest developments on data management in the EU H2020 ENVRIplus project, which brought together more than 20 environmental and Earth science research infrastructures into a single community. It provides readers with a systematic overview of the common challenges faced by research infrastructures and how a ‘reference model guided’ engineering approach can be used to achieve greater interoperability among such infrastructures in the environmental and earth sciences. The 20 contributions in this book are structured in 5 parts on the design, development, deployment, operation and use of research infrastructures. Part one provides an overview of the state of the art of research infrastructure and relevant e-Infrastructure technologies, part two discusses the reference model guided engineering approach, the third part presents the software and tools developed for common data management challenges, the fourth part demonstrates the software via several use cases, and the last part discusses the sustainability and future directions

Security-oriented data grids for microarray expression profiles

Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results

From Sensor to Observation Web with Environmental Enablers in the Future Internet

This paper outlines the grand challenges in global sustainability research and the objectives of the FP7 Future Internet PPP program within the Digital Agenda for Europe. Large user communities are generating significant amounts of valuable environmental observations at local and regional scales using the devices and services of the Future Internet. These communities’ environmental observations represent a wealth of information which is currently hardly used or used only in isolation and therefore in need of integration with other information sources. Indeed, this very integration will lead to a paradigm shift from a mere Sensor Web to an Observation Web with semantically enriched content emanating from sensors, environmental simulations and citizens. The paper also describes the research challenges to realize the Observation Web and the associated environmental enablers for the Future Internet. Such an environmental enabler could for instance be an electronic sensing device, a web-service application, or even a social networking group affording or facilitating the capability of the Future Internet applications to consume, produce, and use environmental observations in cross-domain applications. The term ?envirofied? Future Internet is coined to describe this overall target that forms a cornerstone of work in the Environmental Usage Area within the Future Internet PPP program. Relevant trends described in the paper are the usage of ubiquitous sensors (anywhere), the provision and generation of information by citizens, and the convergence of real and virtual realities to convey understanding of environmental observations. The paper addresses the technical challenges in the Environmental Usage Area and the need for designing multi-style service oriented architecture. Key topics are the mapping of requirements to capabilities, providing scalability and robustness with implementing context aware information retrieval. Another essential research topic is handling data fusion and model based computation, and the related propagation of information uncertainty. Approaches to security, standardization and harmonization, all essential for sustainable solutions, are summarized from the perspective of the Environmental Usage Area. The paper concludes with an overview of emerging, high impact applications in the environmental areas concerning land ecosystems (biodiversity), air quality (atmospheric conditions) and water ecosystems (marine asset management)

The Bari Manifesto : An interoperability framework for essential biodiversity variables

Essential Biodiversity Variables (EBV) are fundamental variables that can be used for assessing biodiversity change over time, for determining adherence to biodiversity policy, for monitoring progress towards sustainable development goals, and for tracking biodiversity responses to disturbances and management interventions. Data from observations or models that provide measured or estimated EBV values, which we refer to as EBV data products, can help to capture the above processes and trends and can serve as a coherent framework for documenting trends in biodiversity. Using primary biodiversity records and other raw data as sources to produce EBV data products depends on cooperation and interoperability among multiple stakeholders, including those collecting and mobilising data for EBVs and those producing, publishing and preserving EBV data products. Here, we encapsulate ten principles for the current best practice in EBV-focused biodiversity informatics as 'The Bari Manifesto', serving as implementation guidelines for data and research infrastructure providers to support the emerging EBV operational framework based on trans-national and cross-infrastructure scientific workflows. The principles provide guidance on how to contribute towards the production of EBV data products that are globally oriented, while remaining appropriate to the producer's own mission, vision and goals. These ten principles cover: data management planning; data structure; metadata; services; data quality; workflows; provenance; ontologies/vocabularies; data preservation; and accessibility. For each principle, desired outcomes and goals have been formulated. Some specific actions related to fulfilling the Bari Manifesto principles are highlighted in the context of each of four groups of organizations contributing to enabling data interoperability - data standards bodies, research data infrastructures, the pertinent research communities, and funders. The Bari Manifesto provides a roadmap enabling support for routine generation of EBV data products, and increases the likelihood of success for a global EBV framework.Peer reviewe

3rd EGEE User Forum

We have organized this book in a sequence of chapters, each chapter associated with an application or technical theme introduced by an overview of the contents, and a summary of the main conclusions coming from the Forum for the chapter topic. The first chapter gathers all the plenary session keynote addresses, and following this there is a sequence of chapters covering the application flavoured sessions. These are followed by chapters with the flavour of Computer Science and Grid Technology. The final chapter covers the important number of practical demonstrations and posters exhibited at the Forum. Much of the work presented has a direct link to specific areas of Science, and so we have created a Science Index, presented below. In addition, at the end of this book, we provide a complete list of the institutes and countries involved in the User Forum