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- ItemTowards Customizable Chart Visualizations of Tabular Data Using Knowledge Graphs(Cham : Springer, 2020) Wiens, Vitalis; Stocker, Markus; Auer, Sören; Ishita, Emi; Pang, Natalie Lee San; Zhou, LihongScientific articles are typically published as PDF documents, thus rendering the extraction and analysis of results a cumbersome, error-prone, and often manual effort. New initiatives, such as ORKG, focus on transforming the content and results of scientific articles into structured, machine-readable representations using Semantic Web technologies. In this article, we focus on tabular data of scientific articles, which provide an organized and compressed representation of information. However, chart visualizations can additionally facilitate their comprehension. We present an approach that employs a human-in-the-loop paradigm during the data acquisition phase to define additional semantics for tabular data. The additional semantics guide the creation of chart visualizations for meaningful representations of tabular data. Our approach organizes tabular data into different information groups which are analyzed for the selection of suitable visualizations. The set of suitable visualizations serves as a user-driven selection of visual representations. Additionally, customization for visual representations provides the means for facilitating the understanding and sense-making of information.
- 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.
- ItemGenerate FAIR Literature Surveys with Scholarly Knowledge Graphs(New York City, NY : Association for Computing Machinery, 2020) Oelen, Allard; Jaradeh, Mohamad Yaser; Stocker, Markus; Auer, SörenReviewing scientific literature is a cumbersome, time consuming but crucial activity in research. Leveraging a scholarly knowledge graph, we present a methodology and a system for comparing scholarly literature, in particular research contributions describing the addressed problem, utilized materials, employed methods and yielded results. The system can be used by researchers to quickly get familiar with existing work in a specific research domain (e.g., a concrete research question or hypothesis). Additionally, it can be used to publish literature surveys following the FAIR Data Principles. The methodology to create a research contribution comparison consists of multiple tasks, specifically: (a) finding similar contributions, (b) aligning contribution descriptions, (c) visualizing and finally (d) publishing the comparison. The methodology is implemented within the Open Research Knowledge Graph (ORKG), a scholarly infrastructure that enables researchers to collaboratively describe, find and compare research contributions. We evaluate the implementation using data extracted from published review articles. The evaluation also addresses the FAIRness of comparisons published with the ORKG.
- ItemFAIR Convergence Matrix: Optimizing the Reuse of Existing FAIR-Related Resources(Cambridge, MA : MIT Press, 2020) Sustkova, Hana Pergl; Hettne, Kristina Maria; Wittenburg, Peter; Jacobsen, Annika; Kuhn, Tobias; Pergl, Robert; Slifka, Jan; McQuilton, Peter; Magagna, Barbara; Sansone, Susanna-Assunta; Stocker, Markus; Imming, Melanie; Lannom, Larry; Musen, Mark; Schultes, ErikThe FAIR principles articulate the behaviors expected from digital artifacts that are Findable, Accessible, Interoperable and Reusable by machines and by people. Although by now widely accepted, the FAIR Principles by design do not explicitly consider actual implementation choices enabling FAIR behaviors. As different communities have their own, often well-established implementation preferences and priorities for data reuse, coordinating a broadly accepted, widely used FAIR implementation approach remains a global challenge. In an effort to accelerate broad community convergence on FAIR implementation options, the GO FAIR community has launched the development of the FAIR Convergence Matrix. The Matrix is a platform that compiles for any community of practice, an inventory of their self-declared FAIR implementation choices and challenges. The Convergence Matrix is itself a FAIR resource, openly available, and encourages voluntary participation by any self-identified community of practice (not only the GO FAIR Implementation Networks). Based on patterns of use and reuse of existing resources, the Convergence Matrix supports the transparent derivation of strategies that optimally coordinate convergence on standards and technologies in the emerging Internet of FAIR Data and Services.
- 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.
- ItemCreating a Scholarly Knowledge Graph from Survey Article Tables(Cham : Springer, 2020) Oelen, Allard; Stocker, Markus; Auer, Sören; Ishita, Emi; Pang, Natalie Lee San; Zhou, LihongDue to the lack of structure, scholarly knowledge remains hardly accessible for machines. Scholarly knowledge graphs have been proposed as a solution. Creating such a knowledge graph requires manual effort and domain experts, and is therefore time-consuming and cumbersome. In this work, we present a human-in-the-loop methodology used to build a scholarly knowledge graph leveraging literature survey articles. Survey articles often contain manually curated and high-quality tabular information that summarizes findings published in the scientific literature. Consequently, survey articles are an excellent resource for generating a scholarly knowledge graph. The presented methodology consists of five steps, in which tables and references are extracted from PDF articles, tables are formatted and finally ingested into the knowledge graph. To evaluate the methodology, 92 survey articles, containing 160 survey tables, have been imported in the graph. In total, 2626 papers have been added to the knowledge graph using the presented methodology. The results demonstrate the feasibility of our approach, but also indicate that manual effort is required and thus underscore the important role of human experts.
- ItemOperational Research Literature as a Use Case for the Open Research Knowledge Graph(Cham : Springer, 2020) Runnwerth, Mila; Stocker, Markus; Auer, Sören; Bigatti, Anna Maria; Carette, Jacques; Davenport, James H.; Joswig, Michael; de Wolff, TimoThe Open Research Knowledge Graph (ORKG) provides machine-actionable access to scholarly literature that habitually is written in prose. Following the FAIR principles, the ORKG makes traditional, human-coded knowledge findable, accessible, interoperable, and reusable in a structured manner in accordance with the Linked Open Data paradigm. At the moment, in ORKG papers are described manually, but in the long run the semantic depth of the literature at scale needs automation. Operational Research is a suitable test case for this vision because the mathematical field and, hence, its publication habits are highly structured: A mundane problem is formulated as a mathematical model, solved or approximated numerically, and evaluated systematically. We study the existing literature with respect to the Assembly Line Balancing Problem and derive a semantic description in accordance with the ORKG. Eventually, selected papers are ingested to test the semantic description and refine it further.
- 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.
- ItemBuilding Scholarly Knowledge Bases with Crowdsourcing and Text Mining(Aachen : RWTH, 2020) Stocker, Markus; Zhang, Chengzhi; Mayr, Philipp; Lu, Wei; Zhang, YiFor centuries, scholarly knowledge has been buried in documents. While articles are great to convey the story of scientific work to peers, they make it hard for machines to process scholarly knowledge. The recent proliferation of the scholarly literature and the increasing inability of researchers to digest, reproduce, reuse its content are constant reminders that we urgently need a transformative digitalization of the scholarly literature. Building on the Open Research Knowledge Graph (http://orkg.org) as a concrete research infrastructure, in this talk we present how using crowdsourcing and text mining humans and machines can collaboratively build scholarly knowledge bases, i.e. systems that acquire, curate and publish data, information and knowledge published in the scholarly literature in structured and semantic form. We discuss some key challenges that human and technical infrastructures face as well as the possibilities scholarly knowledge bases enable.
- ItemIntegrating data and analysis technologies within leading environmental research infrastructures: Challenges and approaches(Amsterdam [u.a.] : Elsevier, 2021) Huber, Robert; D'Onofrio, Claudio; Devaraju, Anusuriya; Klump, Jens; Loescher, Henry W.; Kindermann, Stephan; Guru, Siddeswara; Grant, Mark; Morris, Beryl; Wyborn, Lesley; Evans, Ben; Goldfarb, Doron; Genazzio, Melissa A.; Ren, Xiaoli; Magagna, Barbara; Thiemann, Hannes; Stocker, MarkusWhen researchers analyze data, it typically requires significant effort in data preparation to make the data analysis ready. This often involves cleaning, pre-processing, harmonizing, or integrating data from one or multiple sources and placing them into a computational environment in a form suitable for analysis. Research infrastructures and their data repositories host data and make them available to researchers, but rarely offer a computational environment for data analysis. Published data are often persistently identified, but such identifiers resolve onto landing pages that must be (manually) navigated to identify how data are accessed. This navigation is typically challenging or impossible for machines. This paper surveys existing approaches for improving environmental data access to facilitate more rapid data analyses in computational environments, and thus contribute to a more seamless integration of data and analysis. By analysing current state-of-the-art approaches and solutions being implemented by world‑leading environmental research infrastructures, we highlight the existing practices to interface data repositories with computational environments and the challenges moving forward. We found that while the level of standardization has improved during recent years, it still is challenging for machines to discover and access data based on persistent identifiers. This is problematic in regard to the emerging requirements for FAIR (Findable, Accessible, Interoperable, and Reusable) data, in general, and problematic for seamless integration of data and analysis, in particular. There are a number of promising approaches that would improve the state-of-the-art. A key approach presented here involves software libraries that streamline reading data and metadata into computational environments. We describe this approach in detail for two research infrastructures. We argue that the development and maintenance of specialized libraries for each RI and a range of programming languages used in data analysis does not scale well. Based on this observation, we propose a set of established standards and web practices that, if implemented by environmental research infrastructures, will enable the development of RI and programming language independent software libraries with much reduced effort required for library implementation and maintenance as well as considerably lower learning requirements on users. To catalyse such advancement, we propose a roadmap and key action points for technology harmonization among RIs that we argue will build the foundation for efficient and effective integration of data and analysis.
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