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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.
- ItemOntology Design for Pharmaceutical Research Outcomes(Cham : Springer, 2020) Say, Zeynep; Fathalla, Said; Vahdati, Sahar; Lehmann, Jens; Auer, Sören; Hall, Mark; Merčun, Tanja; Risse, Thomas; Duchateau, FabienThe network of scholarly publishing involves generating and exchanging ideas, certifying research, publishing in order to disseminate findings, and preserving outputs. Despite enormous efforts in providing support for each of those steps in scholarly communication, identifying knowledge fragments is still a big challenge. This is due to the heterogeneous nature of the scholarly data and the current paradigm of distribution by publishing (mostly document-based) over journal articles, numerous repositories, and libraries. Therefore, transforming this paradigm to knowledge-based representation is expected to reform the knowledge sharing in the scholarly world. Although many movements have been initiated in recent years, non-technical scientific communities suffer from transforming document-based publishing to knowledge-based publishing. In this paper, we present a model (PharmSci) for scholarly publishing in the pharmaceutical research domain with the goal of facilitating knowledge discovery through effective ontology-based data integration. PharmSci provides machine-interpretable information to the knowledge discovery process. The principles and guidelines of the ontological engineering have been followed. Reasoning-based techniques are also presented in the design of the ontology to improve the quality of targeted tasks for data integration. The developed ontology is evaluated with a validation process and also a quality verification method.
- 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.
- ItemRepresenting Semantified Biological Assays in the Open Research Knowledge Graph(Cham : Springer, 2020) Anteghini, Marco; D'Souza, Jennifer; Martins dos Santos, Vitor A.P.; Auer, Sören; Ishita, Emi; Pang, Natalie Lee San; Zhou, LihongIn the biotechnology and biomedical domains, recent text mining efforts advocate for machine-interpretable, and preferably, semantified, documentation formats of laboratory processes. This includes wet-lab protocols, (in)organic materials synthesis reactions, genetic manipulations and procedures for faster computer-mediated analysis and predictions. Herein, we present our work on the representation of semantified bioassays in the Open Research Knowledge Graph (ORKG). In particular, we describe a semantification system work-in-progress to generate, automatically and quickly, the critical semantified bioassay data mass needed to foster a consistent user audience to adopt the ORKG for recording their bioassays and facilitate the organisation of research, according to FAIR principles.
- 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.
- ItemDomain-Independent Extraction of Scientific Concepts from Research Articles(Cham : Springer, 2020) Brack, Arthur; D'Souza, Jennifer; Hoppe, Anett; Auer, Sören; Ewerth, Ralph; Jose, Joemon M.; Yilmaz, Emine; Magalhães, João; Castells, Pablo; Ferro, Nicola; Silva, Mário J.; Martins, FlávioWe examine the novel task of domain-independent scientific concept extraction from abstracts of scholarly articles and present two contributions. First, we suggest a set of generic scientific concepts that have been identified in a systematic annotation process. This set of concepts is utilised to annotate a corpus of scientific abstracts from 10 domains of Science, Technology and Medicine at the phrasal level in a joint effort with domain experts. The resulting dataset is used in a set of benchmark experiments to (a) provide baseline performance for this task, (b) examine the transferability of concepts between domains. Second, we present a state-of-the-art deep learning baseline. Further, we propose the active learning strategy for an optimal selection of instances from among the various domains in our data. The experimental results show that (1) a substantial agreement is achievable by non-experts after consultation with domain experts, (2) the baseline system achieves a fairly high F1 score, (3) active learning enables us to nearly halve the amount of required training data.
- ItemFunMap: Efficient Execution of Functional Mappings for Knowledge Graph Creation(Cham : Springer, 2020) Jozashoori, Samaneh; Chaves-Fraga, David; Iglesias, Enrique; Vidal, Maria-Esther; Corcho, Oscar; Pan, Jeff Z.; Tamma, Valentina; d'Amato, Claudia; Janowicz, Kryztof; Fu, Bo; Polleres, Axel; Seneviratne, Oshani; Kagal, LalanaData has exponentially grown in the last years, and knowledge graphs constitute powerful formalisms to integrate a myriad of existing data sources. Transformation functions – specified with function-based mapping languages like FunUL and RML+FnO – can be applied to overcome interoperability issues across heterogeneous data sources. However, the absence of engines to efficiently execute these mapping languages hinders their global adoption. We propose FunMap, an interpreter of function-based mapping languages; it relies on a set of lossless rewriting rules to push down and materialize the execution of functions in initial steps of knowledge graph creation. Although applicable to any function-based mapping language that supports joins between mapping rules, FunMap feasibility is shown on RML+FnO. FunMap reduces data redundancy, e.g., duplicates and unused attributes, and converts RML+FnO mappings into a set of equivalent rules executable on RML-compliant engines. We evaluate FunMap performance over real-world testbeds from the biomedical domain. The results indicate that FunMap reduces the execution time of RML-compliant engines by up to a factor of 18, furnishing, thus, a scalable solution for knowledge graph creation.
- ItemA Knowledge Graph for Industry 4.0(Cham : Springer, 2020) Bader, Sebastian R.; Grangel-Gonzalez, Irlan; Nanjappa, Priyanka; Vidal, Maria-Esther; Maleshkova, Maria; Harth, Andreas; Kirrane, Sabrina; Ngonga Ngomo, Axel-Cyrille; Paulheim, Heiko; Rula, Anisa; Gentile, Anna Lisa; Haase, Peter; Cochez, MichaelOne of the most crucial tasks for today’s knowledge workers is to get and retain a thorough overview on the latest state of the art. Especially in dynamic and evolving domains, the amount of relevant sources is constantly increasing, updating and overruling previous methods and approaches. For instance, the digital transformation of manufacturing systems, called Industry 4.0, currently faces an overwhelming amount of standardization efforts and reference initiatives, resulting in a sophisticated information environment. We propose a structured dataset in the form of a semantically annotated knowledge graph for Industry 4.0 related standards, norms and reference frameworks. The graph provides a Linked Data-conform collection of annotated, classified reference guidelines supporting newcomers and experts alike in understanding how to implement Industry 4.0 systems. We illustrate the suitability of the graph for various use cases, its already existing applications, present the maintenance process and evaluate its quality.