Pharmacovigilance and clinical decision support systems utilize structured drug safety data to guide medical practice. However, existing datasets frequently depend on terminologies such as MedDRA, which limits their semantic reasoning capabilities and their interoperability with Semantic Web ontologies and knowledge graphs. To address this gap, we developed SIDEKICK, a knowledge graph that standardizes drug indications, contraindications, and adverse reactions from FDA Structured Product Labels. We developed and used a workflow based on Large Language Model (LLM) extraction and Graph-Retrieval Augmented Generation (Graph RAG) for ontology mapping. We processed over 50,000 drug labels and mapped terms to the Human Phenotype Ontology (HPO), the MONDO Disease Ontology, and RxNorm. Our semantically integrated resource outperforms the SIDER and ONSIDES databases when applied to the task of drug repurposing by side effect similarity. We serialized the dataset as a Resource Description Framework (RDF) graph and employed the Semanticscience Integrated Ontology (SIO) as upper level ontology to further improve interoperability. Consequently, SIDEKICK enables automated safety surveillance and phenotype-based similarity analysis for drug repurposing.

Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e.,ontology embeddinghas been widely investigated. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies and formally defines ontology embedding as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies they aim at and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL and discusses the challenges and future directions.

Entity alignment associates entities in different knowledge graphs if they are semantically same, and has been successfully used in the knowledge graph construction and connection. Most of the recent solutions for entity alignment are based on knowledge graph embedding, which maps knowledge entities in a low-dimension space where entities are connected with the guidance of prior aligned entity pairs. The study in this paper focuses on two important issues that limit the accuracy of current entity alignment solutions: 1) labeled data of priorly aligned entity pairs are difficult and expensive to acquire, whereas abundant of unlabeled data are not used; and 2) knowledge graph embedding is affected by entity's degree difference, which brings challenges to align high frequent and low frequent entities. We propose a semi-supervised entity alignment method (SEA) to leverage both labeled entities and the abundant unlabeled entity information for the alignment. Furthermore, we improve the knowledge graph embedding with awareness of the degree difference by performing the adversarial training. To evaluate our proposed model, we conduct extensive experiments on real-world datasets. The experimental results show that our model consistently outperforms the state-of-the-art methods with significant improvement on alignment accuracy.