Reliable drug safety reference databases are essential for pharmacovigilance, yet existing resources like SIDER are outdated and static. We introduce PVLens, an automated system that extracts labeled safety information from FDA Structured Product Labels (SPLs) and maps terms to MedDRA. In validation against 97 drug labels, PVLens achieved an F1 score of 0.882, with high recall (0.983) and moderate precision (0.799). By offering a scalable, more accurate and continuously updated alternative to SIDER, PVLens enhances real-time pharamcovigilance with improved accuracy and contemporaneous insights. Keywords: Pharmacovigilance, Natural Language Processing (NLP), Drug Safety, ADR 1 Introduction A clear understanding of known adverse effects, along with continuous surveillance for emerging safety concerns, is essential for patients, healthcare professionals, and pharmacovigilance (PV) scientists.

Ontology Alignment (OA) is fundamental for achieving semantic interoperability across diverse knowledge systems. We present OntoAligner, a comprehensive, modular, and robust Python toolkit for ontology alignment, designed to address current limitations with existing tools faced by practitioners. Existing tools are limited in scalability, modularity, and ease of integration with recent AI advances. OntoAligner provides a flexible architecture integrating existing lightweight OA techniques such as fuzzy matching but goes beyond by supporting contemporary methods with retrieval-augmented generation and large language models for OA. The framework prioritizes extensibility, enabling researchers to integrate custom alignment algorithms and datasets. This paper details the design principles, architecture, and implementation of the OntoAligner, demonstrating its utility through benchmarks on standard OA tasks. Our evaluation highlights OntoAligner's ability to handle large-scale ontologies efficiently with few lines of code while delivering high alignment quality. By making OntoAligner open-source, we aim to provide a resource that fosters innovation and collaboration within the OA community, empowering researchers and practitioners with a toolkit for reproducible OA research and real-world applications.

We investigate the use of LLM-generated data for continual pretraining of encoder models in specialized domains with limited training data, using the scientific domain of invasion biology as a case study. To this end, we leverage domain-specific ontologies by enriching them with LLM-generated data and pretraining the encoder model as an ontology-informed embedding model for concept definitions. To evaluate the effectiveness of this method, we compile a benchmark specifically designed for assessing model performance in invasion biology. After demonstrating substantial improvements over standard LLM pretraining, we investigate the feasibility of applying the proposed approach to domains without comprehensive ontologies by substituting ontological concepts with concepts automatically extracted from a small corpus of scientific abstracts and establishing relationships between concepts through distributional statistics. Our results demonstrate that this automated approach achieves comparable performance using only a small set of scientific abstracts, resulting in a fully automated pipeline for enhancing domain-specific understanding of small encoder models that is especially suited for application in low-resource settings and achieves performance comparable to masked language modeling pretraining on much larger datasets.

Processes, workflows and guidelines are core to ensure the correct functioning of industrial companies: for the successful operations of factory lines, machinery or services, often industry operators rely on their past experience and know-how. The effect is that this Procedural Knowledge (PK) remains tacit and, as such, difficult to exploit efficiently and effectively. This paper presents PKO, the Procedural Knowledge Ontology, which enables the explicit modeling of procedures and their executions, by reusing and extending existing ontologies. PKO is built on requirements collected from three heterogeneous industrial use cases and can be exploited by any AI and data-driven tools that rely on a shared and interoperable representation to support the governance of PK throughout its life cycle. We describe its structure and design methodology, and outline its relevance, quality, and impact by discussing applications leveraging PKO for PK elicitation and exploitation.

Knowledge base population KBP plays a crucial role in populating and maintaining knowledge bases up-to-date in organizations by leveraging domain corpora. Motivated by the increasingly large context windows supported by large language models, we propose to fine-tune an autoregressive language model for end-toend KPB. Our case study involves the population of a space mission knowledge graph. To fine-tune the model we generate a dataset for end-to-end KBP tapping into existing domain resources. Our case study shows that fine-tuned language models of limited size can achieve competitive and even higher accuracy than larger models in the KBP task. Smaller models specialized for KBP offer affordable deployment and lower-cost inference. Moreover, KBP specialist models do not require the ontology to be included in the prompt, allowing for more space in the context for additional input text or output serialization.

Liver diseases pose a significant global health burden, impacting many individuals and having substantial economic and social consequences. Rising liver problems are considered a fatal disease in many countries, such as Egypt and Moldova. This study aims to develop a diagnosis and treatment model for liver disease using Basic Formal Ontology (BFO), Patient Clinical Data (PCD) ontology, and detection rules derived from a decision tree algorithm. For the development of the ontology, the National Viral Hepatitis Control Program (NVHCP) guidelines were used, which made the ontology more accurate and reliable. The Apache Jena framework uses batch processing to detect events based on these rules. Based on the event detected, queries can be directly processed using SPARQL. We convert these Decision Tree (DT) and medical guidelines-based rules into Semantic Web Rule Language (SWRL) to operationalize the ontology. Using this SWRL in the ontology to predict different types of liver disease with the help of the Pellet and Drools inference engines in Protege Tools, a total of 615 records were taken from different liver diseases. After inferring the rules, the result can be generated for the patient according to the rules, and other patient-related details, along with different precautionary suggestions, can be obtained based on these results. These rules can make suggestions more accurate with the help of Explainable Artificial Intelligence (XAI) with open API-based suggestions. When the patient has prescribed a medical test, the model accommodates this result using optical character recognition (OCR), and the same process applies when the patient has prescribed a further medical suggestion according to the test report. These models combine to form a comprehensive Decision Support System (DSS) for the diagnosis of liver disease.

The rapid progress in modern medicine presents physicians with complex challenges when planning patient treatment. Techniques from the field of Predictive Business Process Monitoring, like Next-activity-prediction (NAP) can be used as a promising technique to support physicians in treatment planning, by proposing a possible next treatment step. Existing patient data, often in the form of electronic health records, can be analyzed to recommend the next suitable step in the treatment process. However, the use of patient data poses many challenges due to its knowledge-intensive character, high variability and scarcity of medical data. To overcome these challenges, this article examines the use of the knowledge encoded in taxonomies to improve and explain the prediction of the next activity in the treatment process. This study proposes the TS4NAP approach, which uses medical taxonomies (ICD-10-CM and ICD-10-PCS) in combination with graph matching to assess the similarities of medical codes to predict the next treatment step. The effectiveness of the proposed approach will be evaluated using event logs that are derived from the MIMIC-IV dataset. The results highlight the potential of using domain-specific knowledge held in taxonomies to improve the prediction of the next activity, and thus can improve treatment planning and decision-making by making the predictions more explainable.

Efficient management of end-of-life (EoL) products is critical for advancing circularity in supply chains, particularly within the construction industry where EoL strategies are hindered by heterogenous lifecycle data and data silos. Current tools like Environmental Product Declarations (EPDs) and Digital Product Passports (DPPs) are limited by their dependency on seamless data integration and interoperability which remain significant challenges. To address these, we present the Circular Construction Product Ontology (CCPO), an applied framework designed to overcome semantic and data heterogeneity challenges in EoL decision-making for construction products. CCPO standardises vocabulary and facilitates data integration across supply chain stakeholders enabling lifecycle assessments (LCA) and robust decision-making. By aggregating disparate data into a unified product provenance, CCPO enables automated EoL recommendations through customisable SWRL rules aligned with European standards and stakeholder-specific circularity SLAs, demonstrating its scalability and integration capabilities. The adopted circular product scenario depicts CCPO's application while competency question evaluations show its superior performance in generating accurate EoL suggestions highlighting its potential to greatly improve decision-making in circular supply chains and its applicability in real-world construction environments.

The current work presents an ontology developed for physics-based simulation in engineering design, called Physics-based Simulation Ontology (PSO). The purpose of the ontology is to assist in modelling the physical phenomenon of interest in a veridical manner, while capturing the necessary and reusable information for physics-based simulation solvers. The development involved extending an existing upper ontology, Basic Formal Ontology (BFO), to define lower-level terms of PSO. PSO has two parts: PSO-Physics, which consists of terms and relations used to model physical phenomena based on the perspective of classical mechanics involving partial differential equations, and PSO-Sim, which consists of terms used to represent the information artefacts that are about the physical phenomena modelled with PSO-Physics. The former terms are used to model the physical phenomenon of interest independent of solver-specific interpretations, which can be reused across different solvers, while the latter terms are used to instantiate solver-specific input data. A case study involving two simulation solvers was conducted to demonstrate this capability of PSO. Discussion around the benefits and limitations of using BFO for the current work is also provided, which should be valuable for any future work that extends an existing upper ontology to develop ontologies for engineering applications.

Object-Centric Process Mining (OCPM) enables business process analysis from multiple perspectives. For example, an educational path can be examined from the viewpoints of students, teachers, and groups. This analysis depends on Object-Centric Event Data (OCED), which captures relationships between events and object types, representing different perspectives. Unlike traditional process mining techniques, extracting OCED minimizes the need for repeated log extractions when shifting the analytical focus. However, recording these complex relationships increases the complexity of the log extraction process. To address this challenge, this paper proposes a method for extracting OCED based on PM\inst{2}, a well-established process mining framework. Our approach introduces a structured framework that guides data analysts and engineers in extracting OCED for process analysis. We validate this framework by applying it in a real-world educational setting, demonstrating its effectiveness in extracting an Object-Centric Event Log (OCEL), which serves as the standard format for recording OCED, from a learning management system and an administrative grading system.