Pharmacokinetic natural product-drug interactions (NPDIs) occur when botanical natural products are co-consumed with pharmaceutical drugs. Understanding mechanisms of NPDIs is key to preventing adverse events. We constructed a knowledge graph framework, NP-KG, as a step toward computational discovery of pharmacokinetic NPDIs. NP-KG is a heterogeneous KG with biomedical ontologies, linked data, and full texts of the scientific literature, constructed with the Phenotype Knowledge Translator framework and the semantic relation extraction systems, SemRep and Integrated Network and Dynamic Reasoning Assembler. NP-KG was evaluated with case studies of pharmacokinetic green tea- and kratom-drug interactions through path searches and meta-path discovery to determine congruent and contradictory information compared to ground truth data. The fully integrated NP-KG consisted of 745,512 nodes and 7,249,576 edges. Evaluation of NP-KG resulted in congruent (38.98% for green tea, 50% for kratom), contradictory (15.25% for green tea, 21.43% for kratom), and both congruent and contradictory (15.25% for green tea, 21.43% for kratom) information. Potential pharmacokinetic mechanisms for several purported NPDIs, including the green tea-raloxifene, green tea-nadolol, kratom-midazolam, kratom-quetiapine, and kratom-venlafaxine interactions were congruent with the published literature. NP-KG is the first KG to integrate biomedical ontologies with full texts of the scientific literature focused on natural products. We demonstrate the application of NP-KG to identify pharmacokinetic interactions involving enzymes, transporters, and pharmaceutical drugs. We envision that NP-KG will facilitate improved human-machine collaboration to guide researchers in future studies of pharmacokinetic NPDIs. The NP-KG framework is publicly available at https://doi.org/10.5281/zenodo.6814507 and https://github.com/sanyabt/np-kg.

Knowledge graphs (KG) are used in a wide range of applications. The automation of KG generation is very desired due to the data volume and variety in industries. One important approach of KG generation is to map the raw data to a given KG schema, namely a domain ontology, and construct the entities and properties according to the ontology. However, the automatic generation of such ontology is demanding and existing solutions are often not satisfactory. An important challenge is a trade-off between two principles of ontology engineering: knowledge-orientation and data-orientation. The former one prescribes that an ontology should model the general knowledge of a domain, while the latter one emphasises on reflecting the data specificities to ensure good usability. We address this challenge by our method of ontology reshaping, which automates the process of converting a given domain ontology to a smaller ontology that serves as the KG schema. The domain ontology can be designed to be knowledge-oriented and the KG schema covers the data specificities. In addition, our approach allows the option of including user preferences in the loop. We demonstrate our on-going research on ontology reshaping and present an evaluation using real industrial data, with promising results.

Industrial analytics that includes among others equipment diagnosis and anomaly detection heavily relies on integration of heterogeneous production data. Knowledge Graphs (KGs) as the data format and ontologies as the unified data schemata are a prominent solution that offers high quality data integration and a convenient and standardised way to exchange data and to layer analytical applications over it. However, poor design of ontologies of high degree of mismatch between them and industrial data naturally lead to KGs of low quality that impede the adoption and scalability of industrial analytics. Indeed, such KGs substantially increase the training time of writing queries for users, consume high volume of storage for redundant information, and are hard to maintain and update. To address this problem we propose an ontology reshaping approach to transform ontologies into KG schemata that better reflect the underlying data and thus help to construct better KGs. In this poster we present a preliminary discussion of our on-going research, evaluate our approach with a rich set of SPARQL queries on real-world industry data at Bosch and discuss our findings.

Measuring the distance between ontological elements is fundamental for ontology matching. String-based distance metrics are notorious for shallow syntactic matching. In this exploratory study, we investigate Wasserstein distance targeting continuous space that can incorporate various types of information. We use a pre-trained word embeddings system to embed ontology element labels. We examine the effectiveness of Wasserstein distance for measuring similarity between ontologies, and discovering and refining matchings between individual elements. Our experiments with the OAEI conference track and MSE benchmarks achieved competitive results compared to the leading systems.

Two-view knowledge graphs (KGs) jointly represent two components: an ontology view for abstract and commonsense concepts, and an instance view for specific entities that are instantiated from ontological concepts. As such, these KGs contain heterogeneous structures that are hierarchical, from the ontology-view, and cyclical, from the instance-view. Despite these various structures in KGs, most recent works on embedding KGs assume that the entire KG belongs to only one of the two views but not both simultaneously. For works that seek to put both views of the KG together, the instance and ontology views are assumed to belong to the same geometric space, such as all nodes embedded in the same Euclidean space or non-Euclidean product space, an assumption no longer reasonable for two-view KGs where different portions of the graph exhibit different structures. To address this issue, we define and construct a dual-geometric space embedding model (DGS) that models two-view KGs using a complex non-Euclidean geometric space, by embedding different portions of the KG in different geometric spaces. DGS utilizes the spherical space, hyperbolic space, and their intersecting space in a unified framework for learning embeddings. Furthermore, for the spherical space, we propose novel closed spherical space operators that directly operate in the spherical space without the need for mapping to an approximate tangent space. Experiments on public datasets show that DGS significantly outperforms previous state-of-the-art baseline models on KG completion tasks, demonstrating its ability to better model heterogeneous structures in KGs.

Ontology is a popular method for knowledge representation in different domains, including the legal domain, and description logics (DL) is commonly used as its description language. To handle reasoning based on inconsistent DL-based legal ontologies, the current paper presents a structured argumentation framework particularly for reasoning in legal contexts on the basis of ASPIC+, and translates the legal ontology into formulas and rules of an argumentation theory. With a particular focus on the design of autonomous vehicles from the perspective of legal AI, we show that using this combined theory of formal argumentation and DL-based legal ontology, acceptable assertions can be obtained based on inconsistent ontologies, and the traditional reasoning tasks of DL ontologies can also be accomplished. In addition, a formal definition of explanations for the result of reasoning is presented.

In manufacturing, many use cases of Industry 4.0 require vendor-neutral and machine-readable information models to describe, implement and execute resource functions. Such models have been researched under the terms capabilities and skills. Standardization of such models is required, but currently not available. This paper presents a reference model developed jointly by members of various organizations in a working group of the Plattform Industrie 4.0. This model covers definitions of most important aspects of capabilities and skills. It can be seen as a basis for further standardization efforts.

Medical vision-and-language pre-training (Med-VLP) has received considerable attention owing to its applicability to extracting generic vision-and-language representations from medical images and texts. Most existing methods mainly contain three elements: uni-modal encoders (i.e., a vision encoder and a language encoder), a multi-modal fusion module, and pretext tasks, with few studies considering the importance of medical domain expert knowledge and explicitly exploiting such knowledge to facilitate Med-VLP. Although there exist knowledge-enhanced vision-and-language pre-training (VLP) methods in the general domain, most require off-the-shelf toolkits (e.g., object detectors and scene graph parsers), which are unavailable in the medical domain. In this paper, we propose a systematic and effective approach to enhance Med-VLP by structured medical knowledge from three perspectives. First, considering knowledge can be regarded as the intermediate medium between vision and language, we align the representations of the vision encoder and the language encoder through knowledge. Second, we inject knowledge into the multi-modal fusion model to enable the model to perform reasoning using knowledge as the supplementation of the input image and text. Third, we guide the model to put emphasis on the most critical information in images and texts by designing knowledge-induced pretext tasks. To perform a comprehensive evaluation and facilitate further research, we construct a medical vision-and-language benchmark including three tasks. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on all downstream tasks. Further analyses explore the effects of different components of our approach and various settings of pre-training.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

The paper is dedicated to the use of LodView for navigation over the multilingual Linguistic Linked Open Data cloud. First, we define the class of Pubby-like tools, that LodView belongs to, and clarify the relation of this class to the classes of URI dereferenciation tools, RDF browsers and LOD visualization tools. Second, we reveal several limitations of LodView that impede its use for the designated purpose, and propose improvements to be made for fixing these limitations. These improvements are: 1) resolution of Cyrillic URIs; 2) decoding Cyrillic URIs in Turtle representations of resources; 3) support of Cyrillic literals; 4) user-friendly URLs for RDF representations of resources; 5) support of hash URIs; 6) expanding nested resources; 7) support of RDF collections; 8) pagination of resource property values; and 9) support of $\LaTeX$ math notation. Third, we partially implement several of the proposed improvements.