Representation and use of chemistry in the global electronic age.

We present an overview of the current state of public semantic chemistry and propose new approaches at a strategic and a detailed level. We show by example how a model for a Chemical Semantic Web can be constructed using machine-processed data and information from journal articles.This manuscript addresses questions of robotic access to data and its automatic re-use, including the role of Open Access archival of data. This is a pre-refereed preprint allowed by the publisher's (Royal Soc. Chemistry) Green policy. The author's preferred manuscript is an HTML hyperdocument with ca. 20 links to images, some of which are JPEgs and some of which are SVG (scalable vector graphics) including animations. There are also links to molecules in CML, for which the Jmol viewer is recommended. We susgeest that readers who wish to see the full glory of the manuscript, download the Zipped version and unpack on their machine. We also supply a PDF and DOC (Word) version which obviously cannot show the animations, but which may be the best palce to start, particularly for those more interested in the text

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Ontology-Based Recommendation of Editorial Products

Major academic publishers need to be able to analyse their vast catalogue of products and select the best items to be marketed in scientific venues. This is a complex exercise that requires characterising with a high precision the topics of thousands of books and matching them with the interests of the relevant communities. In Springer Nature, this task has been traditionally handled manually by publishing editors. However, the rapid growth in the number of scientific publications and the dynamic nature of the Computer Science landscape has made this solution increasingly inefficient. We have addressed this issue by creating Smart Book Recommender (SBR), an ontology-based recommender system developed by The Open University (OU) in collaboration with Springer Nature, which supports their Computer Science editorial team in selecting the products to market at specific venues. SBR recommends books, journals, and conference proceedings relevant to a conference by taking advantage of a semantically enhanced representation of about 27K editorial products. This is based on the Computer Science Ontology, a very large-scale, automatically generated taxonomy of research areas. SBR also allows users to investigate why a certain publication was suggested by the system. It does so by means of an interactive graph view that displays the topic taxonomy of the recommended editorial product and compares it with the topic-centric characterization of the input conference. An evaluation carried out with seven Springer Nature editors and seven OU researchers has confirmed the effectiveness of the solution

The HyperBagGraph DataEdron: An Enriched Browsing Experience of Multimedia Datasets

Traditional verbatim browsers give back information in a linear way according to a ranking performed by a search engine that may not be optimal for the surfer. The latter may need to assess the pertinence of the information retrieved, particularly when s$\cdot$he wants to explore other facets of a multi-facetted information space. For instance, in a multimedia dataset different facets such as keywords, authors, publication category, organisations and figures can be of interest. The facet simultaneous visualisation can help to gain insights on the information retrieved and call for further searches. Facets are co-occurence networks, modeled by HyperBag-Graphs -- families of multisets -- and are in fact linked not only to the publication itself, but to any chosen reference. These references allow to navigate inside the dataset and perform visual queries. We explore here the case of scientific publications based on Arxiv searches.Comment: Extension of the hypergraph framework shortly presented in arXiv:1809.00164 (possible small overlaps); use the theoretical framework of hb-graphs presented in arXiv:1809.0019

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

Safe to Be Open: Study on the Protection of Research Data and Recommendations for Access and Usage

Openness has become a common concept in a growing number of scientific and academic fields. Expressions such as Open Access (OA) or Open Content (OC) are often employed for publications of papers and research results, or are contained as conditions in tenders issued by a number of funding agencies. More recently the concept of Open Data (OD) is of growing interest in some fields, particularly those that produce large amounts of data – which are not usually protected by standard legal tools such as copyright. However, a thorough understanding of the meaning of Openness – especially its legal implications – is usually lacking. Open Access, Public Access, Open Content, Open Data, Public Domain. All these terms are often employed to indicate that a given paper, repository or database does not fall under the traditional “closed” scheme of default copyright rules. However, the differences between all these terms are often largely ignored or misrepresented, especially when the scientist in question is not familiar with the law generally and copyright in particular – a very common situation in all scientific fields. On 17 July 2012 the European Commission published its Communication to the European Parliament and the Council entitled “Towards better access to scientific information: Boosting the benefits of public investments in research”. As the Commission observes, “discussions of the scientific dissemination system have traditionally focused on access to scientific publications – journals and monographs. However, it is becoming increasingly important to improve access to research data (experimental results, observations and computer-generated information), which forms the basis for the quantitative analysis underpinning many scientific publications”. The Commission believes that through more complete and wider access to scientific publications and data, the pace of innovation will accelerate and researchers will collaborate so that duplication of efforts will be avoided. Moreover, open research data will allow other researchers to build on previous research results, as it will allow involvement of citizens and society in the scientific process. In the Communication the Commission makes explicit reference to open access models of publications and dissemination of research results, and the reference is not only to access and use but most significantly to reuse of publications as well as research data. The Communication marks an official new step on the road to open access to publicly funded research results in science and the humanities in Europe. Scientific publications are no longer the only elements of its open access policy: research data upon which publications are based should now also be made available to the public. As noble as the open access goal is, however, the expansion of the open access policy to publicly funded research data raises a number of legal and policy issues that are often distinct from those concerning the publication of scientific articles and monographs. Since open access to research data – rather than publications – is a relatively new policy objective, less attention has been paid to the specific features of research data. An analysis of the legal status of such data, and on how to make it available under the correct licence terms, is therefore the subject of the following sections

Understanding spatial data usability

In recent geographical information science literature, a number of researchers have made passing reference to an apparently new characteristic of spatial data known as 'usability'. While this attribute is well-known to professionals engaged in software engineering and computer interface design and testing, extension of the concept to embrace information would seem to be a new development. Furthermore, while notions such as the use and value of spatial information, and the diffusion of spatial information systems, have been the subject of research since the late-1980s, the current references to usability clearly represent something which extends well beyond that initial research. Accordingly, the purposes of this paper are: (1) to understand what is meant by spatial data usability; (2) to identify the elements that might comprise usability; and (3) to consider what the related research questions might be