Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs

Linked data in the library & OpenRefine

Session on linked data and OpenRefine in Stay Savvy with Scholarly Communication Brown Bag Lunch at the University of Central Florida Libraries. It covers the following topics: Why does linked data matter? How can libraries and librarians embrace linked data? Linked Data in the Library and the Web (Cases, Standards and Vocabularies); Linked Data Design Principles, Building Blocks & Creation; Current Digital Repositories and Linked Data; Data Editing Tool: OpenRefine (Features, Examples); Possible Ways to Get Involved

Evaluating FAIR Digital Object and Linked Data as distributed object systems

FAIR Digital Object (FDO) is an emerging concept that is highlighted by European Open Science Cloud (EOSC) as a potential candidate for building a ecosystem of machine-actionable research outputs. In this work we systematically evaluate FDO and its implementations as a global distributed object system, by using five different conceptual frameworks that cover interoperability, middleware, FAIR principles, EOSC requirements and FDO guidelines themself. We compare the FDO approach with established Linked Data practices and the existing Web architecture, and provide a brief history of the Semantic Web while discussing why these technologies may have been difficult to adopt for FDO purposes. We conclude with recommendations for both Linked Data and FDO communities to further their adaptation and alignment.Comment: 40 pages, submitted to PeerJ C

Linked Research on the Decentralised Web

This thesis is about research communication in the context of the Web. I analyse literature which reveals how researchers are making use of Web technologies for knowledge dissemination, as well as how individuals are disempowered by the centralisation of certain systems, such as academic publishing platforms and social media. I share my findings on the feasibility of a decentralised and interoperable information space where researchers can control their identifiers whilst fulfilling the core functions of scientific communication: registration, awareness, certification, and archiving. The contemporary research communication paradigm operates under a diverse set of sociotechnical constraints, which influence how units of research information and personal data are created and exchanged. Economic forces and non-interoperable system designs mean that researcher identifiers and research contributions are largely shaped and controlled by third-party entities; participation requires the use of proprietary systems. From a technical standpoint, this thesis takes a deep look at semantic structure of research artifacts, and how they can be stored, linked and shared in a way that is controlled by individual researchers, or delegated to trusted parties. Further, I find that the ecosystem was lacking a technical Web standard able to fulfill the awareness function of research communication. Thus, I contribute a new communication protocol, Linked Data Notifications (published as a W3C Recommendation) which enables decentralised notifications on the Web, and provide implementations pertinent to the academic publishing use case. So far we have seen decentralised notifications applied in research dissemination or collaboration scenarios, as well as for archival activities and scientific experiments. Another core contribution of this work is a Web standards-based implementation of a clientside tool, dokieli, for decentralised article publishing, annotations and social interactions. dokieli can be used to fulfill the scholarly functions of registration, awareness, certification, and archiving, all in a decentralised manner, returning control of research contributions and discourse to individual researchers. The overarching conclusion of the thesis is that Web technologies can be used to create a fully functioning ecosystem for research communication. Using the framework of Web architecture, and loosely coupling the four functions, an accessible and inclusive ecosystem can be realised whereby users are able to use and switch between interoperable applications without interfering with existing data. Technical solutions alone do not suffice of course, so this thesis also takes into account the need for a change in the traditional mode of thinking amongst scholars, and presents the Linked Research initiative as an ongoing effort toward researcher autonomy in a social system, and universal access to human- and machine-readable information. Outcomes of this outreach work so far include an increase in the number of individuals self-hosting their research artifacts, workshops publishing accessible proceedings on the Web, in-the-wild experiments with open and public peer-review, and semantic graphs of contributions to conference proceedings and journals (the Linked Open Research Cloud). Some of the future challenges include: addressing the social implications of decentralised Web publishing, as well as the design of ethically grounded interoperable mechanisms; cultivating privacy aware information spaces; personal or community-controlled on-demand archiving services; and further design of decentralised applications that are aware of the core functions of scientific communication

A Complex Web: Upgrading to Linked Data in Digital Repositories

As libraries, archives, and museums (“LAMs”) adopt linked data for purposes of enhancing their bibliographic and authority metadata, the technologies around digital repositories also are similarly changing course to model digital objects using linked data standards such as RDF. This study explores the digital repository community's engagement and perceptions of linked data modeling. The study is split into two phases consisting of a web survey and semi-structured interviews. Qualitative analysis of the data summarizes key characteristics of the community of practice, and open problems in transitioning to linked data in the redesign of the Fedora storage and preservation architecture commonly used in digital repositories. Other areas of discussion include the perceived concerns in cross-walking MODS to RDF, as well as the community’s recommended implementation of the Portland Common Data Model (PCDM).Master of Science in Information Scienc

Rule-based Programming of User Agents for Linked Data

While current Semantic Web languages and technologies are well-suited for accessing and integrating static data, methods and technologies for the handling of dynamic aspects – required in many modern web environments – are largely missing. We propose to use Abstract State Machines (ASMs) as the formal basis for dealing with changes in Linked Data, which is the combination of the Resource Description Framework (RDF) with the Hypertext Transfer Protocol (HTTP). We provide a synthesis of ASMs and Linked Data and show how the combination aligns with the relevant specifications such as the Request/Response communication in HTTP, the guidelines for updating resource state in the Linked Data Platform (LDP) specification, and the formal grounding of RDF in model theory. Based on the formalisation of Linked Data resources that change state over time, we present the syntax and operational semantics of a small rule-based language to specify user agents that use HTTP to interact with Linked Data as the interface to the environment. We show the feasibility of the approach in an evaluation involving the specification of automation in a Smart Building scenario, where the presented approach serves as a theoretical foundation

Methodology to sustain common information spaces for research collaborations

Information and knowledge sharing collaborations are essential for scientific research and innovation. They provide opportunities to pool expertise and resources. They are required to draw on today’s wealth of data to address pressing societal challenges. Establishing effective collaborations depends on the alignment of intellectual and technical capital. In this thesis we investigate implications and influences of socio-technical aspects of research collaborations to identify methods of facilitating their formation and sustained success. We draw on our experience acquired in an international federated seismological context, and in a large research infrastructure for solid-Earth sciences. We recognise the centrality of the users and propose a strategy to sustain their engagement as actors participating in the collaboration. Our approach promotes and enables their active contribution in the construction and maintenance of Common Information Spaces (CISs). These are shaped by conceptual agreements that are captured and maintained to facilitate mutual understanding and to underpin their collaborative work. A user-driven approach shapes the evolution of a CIS based on the requirements of the communities involved in the collaboration. Active users’ engagement is pursued by partitioning concerns and by targeting their interests. For instance, application domain experts focus on scientific and conceptual aspects; data and information experts address knowledge representation issues; and architects and engineers build the infrastructure that populates the common space. We introduce a methodology to sustain CIS and a conceptual framework that has its foundations on a set of agreed Core Concepts forming a Canonical Core (CC). A representation of such a CC is also introduced that leverages and promotes reuse of existing standards: EPOS-DCAT-AP. The application of our methodology shows promising results with a good uptake and adoption by the targeted communities. This encourages us to continue applying and evaluating such a strategy in the future