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Linked Research on the Decentralised Web Linked Research on the Decentralised Web Dissertation zur Erlangung des Doktorgrades (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Sarven Capadisli aus Istanbul, Turkey Bonn, 2019-07-29 Angefertigt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn 1. Gutachter: Prof. Dr. Sören Auer 2. Gutachter: Dr. Herbert Van de Sompel Tag der Promotion 2020-03-03 Erscheinungsjahr 2020 Abstract 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. Author: Sarven Capadisli <https://csarven.ca/#i> Identifier: https://csarven.ca/linked-research-decentralised-web Created: 2016-04-13 Modified: 2019-07-29 Published: 2019-07-29 Latest Version: https://csarven.ca/archives/linked-research-decentralised-web/ce36de40-64a7-4d57- a189-f47c364daa74 TimeMap: https://csarven.ca/linked-research-decentralised-web.timemap Derived From: Linked SDMX Data Linked Research Linked Statistical Data Analysis Semantic Similarity and Correlation of Linked Statistical Data Analysis Call for Linked Research Enabling Accessible Knowledge This ‘Paper’ is a Demo Cooling Down Web Science dokieli Linked Research: An Approach for Scholarly Communication Linked Data Notifications Sparqlines: SPARQL to Sparkline Where is Web Science? From 404 to 200 Embedding Web Annotations in HTML Decentralised Authoring, Annotations and Notifications for a Read-Write Web with dokieli Full Article, Immediate, Permanent, Discoverable, and Accessible to Anyone Free of charge LDN Test Reports and Summary Linking Specifications, Test Suites, and Implementation Reports Language: English License: Creative Commons Attribution 4.0 International Notifications Inbox: https://csarven.ca/archives/linked-research-decentralised-web/inbox/ In Reply To: Call for Linked Research Document Status: Published Declaration I declare that the work covered by this thesis is composed by myself, and that it has not been submitted for any other degree or professional qualification except as specified. Acknowledgements This thesis is the result of interconnected ideas and people coming together. I would like the following to be carved in a hyperdimensional stone: Brigitte Schuster, Emilian Capadisli, Junes Capadisli. My parents and brother. Sören Auer for his supervision, endurance and support; the force that kept my work and initiatives real – a massive understatement. Captain Amy Guy for her advice and friendship. Immensely grateful; my work would not be where it is today without her collaboration as well as justifiable distractions of epic proportions. Herbert Van de Sompel for helping me to connect the fundamental dots to better situate my work in context of research communication. A mentor. Tim Berners-Lee, the Web developer that I look up to for inspiration and model perseverance to continue fighting for the Web. I am grateful to collaborate with Tim on the challenges ahead of us. Kingsley Idehen, my practise what you preach partner in crime. I have learned a lot from Kingsley as we aimed to realise cool Web stuff. Amy van der Hiel for ethical Web checks and having me remind myself to assess the value of what I do with respect to society and adjusting my aims accordingly. Her influence will continue to shape the fabric of the projects that I am involved in. Bernadette Hyland for supporting me to hang in there for the long game. Stian Soiland-Reyes for brainstorming and experimenting on various Linked Data stuff. Ruben Verborgh for being an exemplary researcher and developer to learn from, and support to better integrate our work out there in the wild. Andrea Scharnhorst for helping me to develop a sense of academic collaboration. Axel Polleres for his guidance and supporting initiatives to evolve research communication. Dame Wendy Hall for keeping the spirit of the Web in scholarly communication alive. Ilaria Liccardi for her mentorship and care to help me move my research forward. Henry Story for providing context to undoubtedly interconnected ideas in technology and philosophy. Melvin Carvalho for bouncing ideas on the intersection of McLuhan’s media theories and the Web. Christophe Lange for helping to frame my work as research where I thought it was just development. Jodi Schneider for helping to improve my argumentation in research communication. Miel Vander Sande for pushing me in the right direction to frame the design science of my work. Albert Meroño-Peñuela for collaborating on LSD and LDN, and getting interesting results. Paul Groth is partly to blame for all this work as he (indirectly) challenged me to make it so. Alexander Garcia Castro for initially nudging me to formulate my vision for scholarly communication which later set the core of my research and development. The (anti?) Social Web: from your encouragement to your dismissal of radical and lunatic scholarly endeavours; being the widest sounding board possible. Contents 1 Introduction 1.1 Motivation 1.2 Research Goals 1.2.1 Stakeholders 1.2.2 Problem Context 1.2.3 Technical Research Goals 1.2.4 Knowledge Goals 1.3 Research Questions 1.3.1 Technical Research Problems 1.3.2 Knowledge Questions 1.4 Thesis Overview 1.4.1 Structure 1.4.2 Literature Review and Citations 1.4.3 Document Convention 2 Scholarly Communication on the Web 2.1 Mediums and Paradigms 2.1.1 On Mediums 2.1.2 On Paradigms 2.1.3 Rear-View Mirror 2.2 Web: A Social Machine 2.2.1 Architecture of the Web 2.2.1.1 Identification 2.2.1.2 Interaction 2.2.1.3 Data Formats 2.2.2 Linked Data 2.2.3 Web Science 2.3 A Brief History of Scholarship on the Web 2.3.1 Open and Free 2.3.2 Archives and Repositories 2.3.3 Open Access 2.3.4 Deconstructing the Scholarly Journal 2.3.5 Open Archiving 2.3.6 Scholarly Declarations and Practices 2.3.7 Paper User Interface 2.3.8 Semantic Publishing 2.3.9 Arguments and Citations 2.3.10 Registration of Identifiers 2.4 Social Scholarly Web 2.4.1 Social
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