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Author: Koepler, Oliver × Subject: linked data ×

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    Ontologies4Chem: The landscape of ontologies in chemistry
    (Berlin : de Gruyter, 2022) Strömert, Philip; Hunold, Johannes; Castro, André; Neumann, Steffen; Koepler, Oliver
    For a long time, databases such as CAS, Reaxys, PubChem or ChemSpider mostly rely on unique numerical identifiers or chemical structure identifiers like InChI, SMILES or others to link data across heterogeneous data sources. The retrospective processing of information and fragmented data from text publications to maintain these databases is a cumbersome process. Ontologies are a holistic approach to semantically describe data, information and knowledge of a domain. They provide terms, relations and logic to semantically annotate and link data building knowledge graphs. The application of standard taxonomies and vocabularies from the very beginning of data generation and along research workflows in electronic lab notebooks (ELNs), software tools, and their final publication in data repositories create FAIR data straightforwardly. Thus a proper semantic description of an investigation and the why, how, where, when, and by whom data was produced in conjunction with the description and representation of research data is a natural outcome in contrast to the retrospective processing of research publications as we know it. In this work we provide an overview of ontologies in chemistry suitable to represent concepts of research and research data. These ontologies are evaluated against several criteria derived from the FAIR data principles and their possible application in the digitisation of research data management workflows.
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    Towards an Open Research Knowledge Graph
    (Zenodo, 2018) Auer, Sören; Blümel, Ina; Ewerth, Ralph; Garatzogianni, Alexandra; Heller,, Lambert; Hoppe, Anett; Kasprzik, Anna; Koepler, Oliver; Nejdl, Wolfgang; Plank, Margret; Sens, Irina; Stocker, Markus; Tullney, Marco; Vidal, Maria-Esther; van Wezenbeek, Wilma
    The document-oriented workflows in science have reached (or already exceeded) the limits of adequacy as highlighted for example by recent discussions on the increasing proliferation of scientific literature and the reproducibility crisis. Despite an improved and digital access to scientific publications in the last decades, the exchange of scholarly knowledge continues to be primarily document-based: Researchers produce essays and articles that are made available in online and offline publication media as roughly granular text documents. With current developments in areas such as knowledge representation, semantic search, human-machine interaction, natural language processing, and artificial intelligence, it is possible to completely rethink this dominant paradigm of document-centered knowledge exchange and transform it into knowledge-based information flows by representing and expressing knowledge through semantically rich, interlinked knowledge graphs. The core of the establishment of knowledge-based information flows is the distributed, decentralized, collaborative creation and evolution of information models, vocabularies, ontologies, and knowledge graphs for the establishment of a common understanding of data and information between the various stakeholders as well as the integration of these technologies into the infrastructure and processes of search and knowledge exchange in the research library of the future. By integrating these information models into existing and new research infrastructure services, the information structures that are currently still implicit and deeply hidden in documents can be made explicit and directly usable. This revolutionizes scientific work because information and research results can be seamlessly interlinked with each other and better mapped to complex information needs. As a result, scientific work becomes more effective and efficient, since results become directly comparable and easier to reuse. In order to realize the vision of knowledge-based information flows in scholarly communication, comprehensive long-term technological infrastructure development and accompanying research are required. To secure information sovereignty, it is also of paramount importance to science – and urgency to science policymakers – that scientific infrastructures establish an open counterweight to emerging commercial developments in this area. The aim of this position paper is to facilitate the discussion on requirements, design decisions and a minimum viable product for an Open Research Knowledge Graph infrastructure. TIB aims to start developing this infrastructure in an open collaboration with interested partner organizations and individuals.