THE PALLADIOLIBRARY GEO-MODELS: AN OPEN 3D ARCHIVE TO MANAGE AND VISUALIZE INFORMATION-COMMUNICATION RESOURCES ABOUT PALLADIO

Abstract. The paper describes objectives, methods, procedures and outcomes of the development of the digital archive of Palladio works and documentation: the PALLADIOLibrary of Centro Internazionale di Studi di Architettura Andrea Palladio di Vicenza (CISAAP). The core of the application consists of fifty-one reality-based 3D models usable and navigable within a system grounded on GoogleEarth. This information system, a collaboration of four universities bearers of specific skills returns a comprehensive, structured and coherent semantic interpretation of Palladian landscape through shapes realistically reconstructed from historical sources and surveys and treated for GE with Ambient Occlusion techniques, overcoming the traditional display mode

Building a Disciplinary, World-Wide Data Infrastructure

Sharing scientific data, with the objective of making it fully discoverable, accessible, assessable, intelligible, usable, and interoperable, requires work at the disciplinary level to define in particular how the data should be formatted and described. Each discipline has its own organization and history as a starting point, and this paper explores the way a range of disciplines, namely materials science, crystallography, astronomy, earth sciences, humanities and linguistics get organized at the international level to tackle this question. In each case, the disciplinary culture with respect to data sharing, science drivers, organization and lessons learnt are briefly described, as well as the elements of the specific data infrastructure which are or could be shared with others. Commonalities and differences are assessed. Common key elements for success are identified: data sharing should be science driven; defining the disciplinary part of the interdisciplinary standards is mandatory but challenging; sharing of applications should accompany data sharing. Incentives such as journal and funding agency requirements are also similar. For all, it also appears that social aspects are more challenging than technological ones. Governance is more diverse, and linked to the discipline organization. CODATA, the RDA and the WDS can facilitate the establishment of disciplinary interoperability frameworks. Being problem-driven is also a key factor of success for building bridges to enable interdisciplinary research.Comment: Proceedings of the session "Building a disciplinary, world-wide data infrastructure" of SciDataCon 2016, held in Denver, CO, USA, 12-14 September 2016, to be published in ICSU CODATA Data Science Journal in 201

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. However, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein–protein interaction information can be error-prone and require considerable effort to annotate. Here, we present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score, and accessory information such as protein domains and 3D structures is made available, all within a stable and consistent identifier space. New features in STRING include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org

A Comparison of U. S. and European University-Industry Relations in the Life Sciences

We draw on diverse data sets to compare the institutional organization of upstream life science research across the United States and Europe. Understanding cross-national differences in the organization of innovative labor in the life sciences requires attention to the structure and evolution of biomedical networks involving public research organizations (universities, government laboratories, nonprofit research institutes, and research hospitals), science-based biotechnology firms, and multinational pharmaceutical corporations. We use network visualization methods and correspondence analyses to demonstrate that innovative research in biomedicine has its origins in regional clusters in the United States and in European nations. But the scientific and organizational composition of these regions varies in consequential ways. In the United States, public research organizations and small firms conduct R&D across multiple therapeutic areas and stages of the development process. Ties within and across these regions link small firms and diverse public institutions, contributing to the development of a robust national network. In contrast, the European story is one of regional specialization with a less diverse group of public research organizations working in a smaller number of therapeutic areas. European institutes develop local connections to small firms working on similar scientific problems, while cross-national linkages of European regional clusters typically involve large pharmaceutical corporations. We show that the roles of large and small firms differ in the United States and Europe, arguing that the greater heterogeneity of the U. S. system is based on much closer integration of basic science and clinical development

Augmented Reality and Health Informatics: A Study based on Bibliometric and Content Analysis of Scholarly Communication and Social Media

Healthcare outcomes have been shown to improve when technology is used as part of patient care. Health Informatics (HI) is a multidisciplinary study of the design, development, adoption, and application of IT-based innovations in healthcare services delivery, management, and planning. Augmented Reality (AR) is an emerging technology that enhances the user’s perception and interaction with the real world. This study aims to illuminate the intersection of the field of AR and HI. The domains of AR and HI by themselves are areas of significant research. However, there is a scarcity of research on augmented reality as it applies to health informatics. Given both scholarly research and social media communication having contributed to the domains of AR and HI, research methodologies of bibliometric and content analysis on scholarly research and social media communication were employed to investigate the salient features and research fronts of the field. The study used Scopus data (7360 scholarly publications) to identify the bibliometric features and to perform content analysis of the identified research. The Altmetric database (an aggregator of data sources) was used to determine the social media communication for this field. The findings from this study included Publication Volumes, Top Authors, Affiliations, Subject Areas and Geographical Locations from scholarly publications as well as from a social media perspective. The highest cited 200 documents were used to determine the research fronts in scholarly publications. Content Analysis techniques were employed on the publication abstracts as a secondary technique to determine the research themes of the field. The study found the research frontiers in the scholarly communication included emerging AR technologies such as tracking and computer vision along with Surgical and Learning applications. There was a commonality between social media and scholarly communication themes from an applications perspective. In addition, social media themes included applications of AR in Healthcare Delivery, Clinical Studies and Mental Disorders. Europe as a geographic region dominates the research field with 50% of the articles and North America and Asia tie for second with 20% each. Publication volumes show a steep upward slope indicating continued research. Social Media communication is still in its infancy in terms of data extraction, however aggregators like Altmetric are helping to enhance the outcomes. The findings from the study revealed that the frontier research in AR has made an impact in the surgical and learning applications of HI and has the potential for other applications as new technologies are adopted

MSV3d: database of human MisSense variants mapped to 3D protein structure

The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats

The Cultural Landscape & Heritage Paradox; Protection and Development of the Dutch Archeological-Historical Landscape and its European Dimension

To what extent can we know past and mainly invisible landscapes, and how we can use this still hidden knowledge for actual sustainable management of landscape’s cultural and historical values. It has also been acknowledged that heritage management is increasingly about ‘the management of future change rather than simply protection’. This presents us with a paradox: to preserve our historic environment, we have to collaborate with those who wish to transform it and, in order to apply our expert knowledge, we have to make it suitable for policy and society. The answer presented by the Protection and Development of the Dutch Archaeological-Historical Landscape programme (pdl/bbo) is an integrative landscape approach which applies inter- and transdisciplinarity, establishing links between archaeological-historical heritage and planning, and between research and policy. This is supported by two unifying concepts: ‘biography of landscape’ and ‘action research’. This approach focuses upon the interaction between knowledge, policy and an imagination centered on the public. The European perspective makes us aware of the resourcefulness of the diversity of landscapes, of social and institutional structures, of various sorts of problems, approaches and ways forward. In addition, two related issues stand out: the management of knowledge creation for landscape research and management, and the prospects for the near future. Underlying them is the imperative that we learn from the past ‘through landscape’