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- ItemORKG: Facilitating the Transfer of Research Results with the Open Research Knowledge Graph(Sofia : Pensoft, 2021) Auer, Sören; Stocker, Markus; Vogt, Lars; Fraumann, Grischa; Garatzogianni, AlexandraThis document is an edited version of the original funding proposal entitled 'ORKG: Facilitating the Transfer of Research Results with the Open Research Knowledge Graph' that was submitted to the European Research Council (ERC) Proof of Concept (PoC) Grant in September 2020 (https://erc.europa.eu/funding/proof-concept). The proposal was evaluated by five reviewers and has been placed after the evaluations on the reserve list. The main document of the original proposal did not contain an abstract.
- ItemKnowledge Graphs - Working Group Charter (NFDI section-metadata) (1.2)(Genève : CERN, 2023) Stocker, Markus; Rossenova, Lozana; Shigapov, Renat; Betancort, Noemi; Dietze, Stefan; Murphy, Bridget; Bölling, Christian; Schubotz, Moritz; Koepler, OliverKnowledge Graphs are a key technology for implementing the FAIR principles in data infrastructures by ensuring interoperability for both humans and machines. The Working Group "Knowledge Graphs" in Section "(Meta)data, Terminologies, Provenance" of the German National Research Data Infrastructure (Nationale Forschungsdateninfrastruktur (NFDI) e.V.) aims to promote the use of knowledge graphs in all NFDI consortia, to facilitate cross-domain data interlinking and federation following the FAIR principles, and to contribute to the joint development of tools and technologies that enable transformation of structured and unstructured data into semantically reusable knowledge across different domains.
- ItemCase Study: ENVRI Science Demonstrators with D4Science(Cham : Springer, 2020) Candela, Leonardo; Stocker, Markus; Häggström, Ingemar; Enell, Carl-Fredrik; Vitale, Domenico; Papale, Dario; Grenier, Baptiste; Chen, Yin; Obst, Matthias; Zhao, Zhiming; Hellström, MargaretaWhenever a community of practice starts developing an IT solution for its use case(s) it has to face the issue of carefully selecting “the platform” to use. Such a platform should match the requirements and the overall settings resulting from the specific application context (including legacy technologies and solutions to be integrated and reused, costs of adoption and operation, easiness in acquiring skills and competencies). There is no one-size-fits-all solution that is suitable for all application context, and this is particularly true for scientific communities and their cases because of the wide heterogeneity characterising them. However, there is a large consensus that solutions from scratch are inefficient and services that facilitate the development and maintenance of scientific community-specific solutions do exist. This chapter describes how a set of diverse communities of practice efficiently developed their science demonstrators (on analysing and producing user-defined atmosphere data products, greenhouse gases fluxes, particle formation, mosquito diseases) by leveraging the services offered by the D4Science infrastructure. It shows that the D4Science design decisions aiming at streamlining implementations are effective. The chapter discusses the added value injected in the science demonstrators and resulting from the reuse of D4Science services, especially regarding Open Science practices and overall quality of service.
- ItemTinyGenius: Intertwining natural language processing with microtask crowdsourcing for scholarly knowledge graph creation(New York,NY,United States : Association for Computing Machinery, 2022) Oelen, Allard; Stocker, Markus; Auer, Sören; Aizawa, AkikoAs the number of published scholarly articles grows steadily each year, new methods are needed to organize scholarly knowledge so that it can be more efficiently discovered and used. Natural Language Processing (NLP) techniques are able to autonomously process scholarly articles at scale and to create machine readable representations of the article content. However, autonomous NLP methods are by far not sufficiently accurate to create a high-quality knowledge graph. Yet quality is crucial for the graph to be useful in practice. We present TinyGenius, a methodology to validate NLP-extracted scholarly knowledge statements using microtasks performed with crowdsourcing. The scholarly context in which the crowd workers operate has multiple challenges. The explainability of the employed NLP methods is crucial to provide context in order to support the decision process of crowd workers. We employed TinyGenius to populate a paper-centric knowledge graph, using five distinct NLP methods. In the end, the resulting knowledge graph serves as a digital library for scholarly articles.
- ItemQuestion Answering on Scholarly Knowledge Graphs(Cham : Springer, 2020) Jaradeh, Mohamad Yaser; Stocker, Markus; Auer, Sören; Hall, Mark; Merčun, Tanja; Risse, Thomas; Duchateau, FabienAnswering questions on scholarly knowledge comprising text and other artifacts is a vital part of any research life cycle. Querying scholarly knowledge and retrieving suitable answers is currently hardly possible due to the following primary reason: machine inactionable, ambiguous and unstructured content in publications. We present JarvisQA, a BERT based system to answer questions on tabular views of scholarly knowledge graphs. Such tables can be found in a variety of shapes in the scholarly literature (e.g., surveys, comparisons or results). Our system can retrieve direct answers to a variety of different questions asked on tabular data in articles. Furthermore, we present a preliminary dataset of related tables and a corresponding set of natural language questions. This dataset is used as a benchmark for our system and can be reused by others. Additionally, JarvisQA is evaluated on two datasets against other baselines and shows an improvement of two to three folds in performance compared to related methods.
- ItemToward Representing Research Contributions in Scholarly Knowledge Graphs Using Knowledge Graph Cells(New York City, NY : Association for Computing Machinery, 2020) Vogt, Lars; D'Souza, Jennifer; Stocker, Markus; Auer, SörenThere is currently a gap between the natural language expression of scholarly publications and their structured semantic content modeling to enable intelligent content search. With the volume of research growing exponentially every year, a search feature operating over semantically structured content is compelling. Toward this end, in this work, we propose a novel semantic data model for modeling the contribution of scientific investigations. Our model, i.e. the Research Contribution Model (RCM), includes a schema of pertinent concepts highlighting six core information units, viz. Objective, Method, Activity, Agent, Material, and Result, on which the contribution hinges. It comprises bottom-up design considerations made from three scientific domains, viz. Medicine, Computer Science, and Agriculture, which we highlight as case studies. For its implementation in a knowledge graph application we introduce the idea of building blocks called Knowledge Graph Cells (KGC), which provide the following characteristics: (1) they limit the expressibility of ontologies to what is relevant in a knowledge graph regarding specific concepts on the theme of research contributions; (2) they are expressible via ABox and TBox expressions; (3) they enforce a certain level of data consistency by ensuring that a uniform modeling scheme is followed through rules and input controls; (4) they organize the knowledge graph into named graphs; (5) they provide information for the front end for displaying the knowledge graph in a human-readable form such as HTML pages; and (6) they can be seamlessly integrated into any existing publishing process thatsupports form-based input abstracting its semantic technicalities including RDF semantification from the user. Thus RCM joins the trend of existing work toward enhanced digitalization of scholarly publication enabled by an RDF semantification as a knowledge graph fostering the evolution of the scholarly publications beyond written text.
- ItemSemantic and Knowledge Engineering Using ENVRI RM(Cham : Springer, 2020) Martin, Paul; Liao, Xiaofeng; Magagna, Barbara; Stocker, Markus; Zhao, Zhiming; Zhao, Zhiming; Hellström, MargaretaThe ENVRI Reference Model provides architects and engineers with the means to describe the architecture and operational behaviour of environmental and Earth science research infrastructures (RIs) in a standardised way using the standard terminology. This terminology and the relationships between specific classes of concept can be used as the basis for the machine-actionable specification of RIs or RI subsystems. Open Information Linking for Environmental RIs (OIL-E) is a framework for capturing architectural and design knowledge about environmental and Earth science RIs intended to help harmonise vocabulary, promote collaboration and identify common standards and technologies across different research infrastructure initiatives. At its heart is an ontology derived from the ENVRI Reference Model. Using this ontology, RI descriptions can be published as linked data, allowing discovery, querying and comparison using established Semantic Web technologies. It can also be used as an upper ontology by which to connect descriptions of RI entities (whether they be datasets, equipment, processes, etc.) that use other, more specific terminologies. The ENVRI Knowledge Base uses OIL-E to capture information about environmental and Earth science RIs in the ENVRI community for query and comparison. The Knowledge Base can be used to identify the technologies and standards used for particular activities and services and as a basis for evaluating research infrastructure subsystems and behaviours against certain criteria, such as compliance with the FAIR data principles.
- ItemTowards Operational Research Infrastructures with FAIR Data and Services(Cham : Springer, 2020) Zhao, Zhiming; Jeffery, Keith; Stocker, Markus; Atkinson, Malcolm; Petzold, Andreas; Zhao, Zhiming; Hellström, MargaretaEnvironmental research infrastructures aim to provide scientists with facilities, resources and services to enable scientists to effectively perform advanced research. When addressing societal challenges such as climate change and pollution, scientists usually need data, models and methods from different domains to tackle the complexity of the complete environmental system. Research infrastructures are thus required to enable all data, including services, products, and virtual research environments is FAIR for research communities: Findable, Accessible, Interoperable and Reusable. In this last chapter, we conclude and identify future challenges in research infrastructure operation, user support, interoperability, and future evolution.
- ItemTowards 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, WilmaThe 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.
- ItemCrowdsourcing Scholarly Discourse Annotations(New York, NY : ACM, 2021) Oelen, Allard; Stocker, Markus; Auer, SörenThe number of scholarly publications grows steadily every year and it becomes harder to find, assess and compare scholarly knowledge effectively. Scholarly knowledge graphs have the potential to address these challenges. However, creating such graphs remains a complex task. We propose a method to crowdsource structured scholarly knowledge from paper authors with a web-based user interface supported by artificial intelligence. The interface enables authors to select key sentences for annotation. It integrates multiple machine learning algorithms to assist authors during the annotation, including class recommendation and key sentence highlighting. We envision that the interface is integrated in paper submission processes for which we define three main task requirements: The task has to be . We evaluated the interface with a user study in which participants were assigned the task to annotate one of their own articles. With the resulting data, we determined whether the participants were successfully able to perform the task. Furthermore, we evaluated the interface’s usability and the participant’s attitude towards the interface with a survey. The results suggest that sentence annotation is a feasible task for researchers and that they do not object to annotate their articles during the submission process.