Objective: Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a lack of knowledge, previous contrastive learning models trained with Unified Medical Language System (UMLS) synonyms struggle at clustering difficult terms and do not generalize well beyond UMLS terms. In this work, we leverage the world knowledge from Large Language Models (LLMs) and propose Contrastive Learning for Representing Terms via Explanations (CoRTEx) to enhance term representation and significantly improves term clustering. Materials and Methods: The model training involves generating explanations for a cleaned subset of UMLS terms using ChatGPT. We employ contrastive learning, considering term and explanation embeddings simultaneously, and progressively introduce hard negative samples. Additionally, a ChatGPT-assisted BIRCH algorithm is designed for efficient clustering of a new ontology. Results: We established a clustering test set and a hard negative test set, where our model consistently achieves the highest F1 score. With CoRTEx embeddings and the modified BIRCH algorithm, we grouped 35,580,932 terms from the Biomedical Informatics Ontology System (BIOS) into 22,104,559 clusters with O(N) queries to ChatGPT. Case studies highlight the model's efficacy in handling challenging samples, aided by information from explanations. Conclusion: By aligning terms to their explanations, CoRTEx demonstrates superior accuracy over benchmark models and robustness beyond its training set, and it is suitable for clustering terms for large-scale biomedical ontologies.

We design a user-friendly and scalable knowledge graph construction (KGC) system for extracting structured knowledge from the unstructured corpus. Different from existing KGC systems, gBuilder provides a flexible and user-defined pipeline to embrace the rapid development of IE models. More built-in template-based or heuristic operators and programmable operators are available for adapting to data from different domains. Furthermore, we also design a cloud-based self-adaptive task scheduling for gBuilder to ensure its scalability on large-scale knowledge graph construction. Experimental evaluation demonstrates the ability of gBuilder to organize multiple information extraction models for knowledge graph construction in a uniform platform, and confirms its high scalability on large-scale KGC tasks.

Building taxonomies is often a significant part of building an ontology, and many attempts have been made to automate the creation of such taxonomies from relevant data. The idea in such approaches is either that relevant definitions of the intension of concepts can be extracted as patterns in the data (e.g. in formal concept analysis) or that their extension can be built from grouping data objects based on similarity (clustering). In both cases, the process leads to an automatically constructed structure, which can either be too coarse and lacking in definition, or too fined-grained and detailed, therefore requiring to be refined into the desired taxonomy. In this paper, we explore a method that takes inspiration from both approaches in an iterative and interactive process, so that refinement and definition of the concepts in the taxonomy occur at the time of identifying those concepts in the data. We show that this method is applicable on a variety of data sources and leads to taxonomies that can be more directly integrated into ontologies.

With the recent spike in the number and availability of Large Language Models (LLMs), it has become increasingly important to provide large and realistic benchmarks for evaluating Knowledge Graph Question Answering (KGQA) systems. So far the majority of benchmarks rely on pattern-based SPARQL query generation approaches. The subsequent natural language (NL) question generation is conducted through crowdsourcing or other automated methods, such as rule-based paraphrasing or NL question templates. Although some of these datasets are of considerable size, their pitfall lies in their pattern-based generation approaches, which do not always generalize well to the vague and linguistically diverse questions asked by humans in real-world contexts. In this paper, we introduce Spider4SPARQL - a new SPARQL benchmark dataset featuring 9,693 previously existing manually generated NL questions and 4,721 unique, novel, and complex SPARQL queries of varying complexity. In addition to the NL/SPARQL pairs, we also provide their corresponding 166 knowledge graphs and ontologies, which cover 138 different domains. Our complex benchmark enables novel ways of evaluating the strengths and weaknesses of modern KGQA systems. We evaluate the system with state-of-the-art KGQA systems as well as LLMs, which achieve only up to 45\% execution accuracy, demonstrating that Spider4SPARQL is a challenging benchmark for future research.

Recent progress in generative AI, including large language models (LLMs) like ChatGPT, has opened up significant opportunities in fields ranging from natural language processing to knowledge discovery and data mining. However, there is also a growing awareness that the models can be prone to problems such as making information up or `hallucinations', and faulty reasoning on seemingly simple problems. Because of the popularity of models like ChatGPT, both academic scholars and citizen scientists have documented hallucinations of several different types and severity. Despite this body of work, a formal model for describing and representing these hallucinations (with relevant meta-data) at a fine-grained level, is still lacking. In this paper, we address this gap by presenting the Hallucination Ontology or HALO, a formal, extensible ontology written in OWL that currently offers support for six different types of hallucinations known to arise in LLMs, along with support for provenance and experimental metadata. We also collect and publish a dataset containing hallucinations that we inductively gathered across multiple independent Web sources, and show that HALO can be successfully used to model this dataset and answer competency questions.

Real-world knowledge can be represented as a graph consisting of entities and relationships between the entities. The need for efficient and scalable solutions arises when dealing with vast genomic data, like RNA-sequencing. Knowledge graphs offer a powerful approach for various tasks in such large-scale genomic data, such as analysis and inference. In this work, variant-level information extracted from the RNA-sequences of vaccine-na\"ive COVID-19 patients have been represented as a unified, large knowledge graph. Variant call format (VCF) files containing the variant-level information were annotated to include further information for each variant. The data records in the annotated files were then converted to Resource Description Framework (RDF) triples. Each VCF file obtained had an associated CADD scores file that contained the raw and Phred-scaled scores for each variant. An ontology was defined for the VCF and CADD scores files. Using this ontology and the extracted information, a large, scalable knowledge graph was created. Available graph storage was then leveraged to query and create datasets for further downstream tasks. We also present a case study using the knowledge graph and perform a classification task using graph machine learning. We also draw comparisons between different Graph Neural Networks (GNNs) for the case study.

Over the years, RDF streaming was explored in research and practice from many angles, resulting in a wide range of RDF stream definitions. This variety presents a major challenge in discussing and integrating streaming solutions, due to the lack of a common language. This work attempts to address this critical research gap, by systematizing RDF stream types present in the literature in a novel taxonomy. The proposed RDF Stream Taxonomy (RDF-STaX) is embodied in an OWL 2 DL ontology that follows the FAIR principles, making it readily applicable in practice. Extensive documentation and additional resources are provided, to foster the adoption of the ontology. Two realized use cases are presented, demonstrating the usefulness of the resource in discussing research works and annotating streaming datasets. Another result of this contribution is the novel nanopublications dataset, which serves as a collaborative, living state-of-the-art review of RDF streaming. The aim of RDF-STaX is to address a real need of the community for a better way to systematize and describe RDF streams. The resource is designed to help drive innovation in RDF streaming, by fostering scientific discussion, cooperation, and tool interoperability.

Using knowledge graph embedding models (KGEMs) is a popular approach for predicting links in knowledge graphs (KGs). Traditionally, the performance of KGEMs for link prediction is assessed using rank-based metrics, which evaluate their ability to give high scores to ground-truth entities. However, the literature claims that the KGEM evaluation procedure would benefit from adding supplementary dimensions to assess. That is why, in this paper, we extend our previously introduced metric Sem@K that measures the capability of models to predict valid entities w.r.t. domain and range constraints. In particular, we consider a broad range of KGs and take their respective characteristics into account to propose different versions of Sem@K. We also perform an extensive study to qualify the abilities of KGEMs as measured by our metric. Our experiments show that Sem@K provides a new perspective on KGEM quality. Its joint analysis with rank-based metrics offers different conclusions on the predictive power of models. Regarding Sem@K, some KGEMs are inherently better than others, but this semantic superiority is not indicative of their performance w.r.t. rank-based metrics. In this work, we generalize conclusions about the relative performance of KGEMs w.r.t. rank-based and semantic-oriented metrics at the level of families of models. The joint analysis of the aforementioned metrics gives more insight into the peculiarities of each model. This work paves the way for a more comprehensive evaluation of KGEM adequacy for specific downstream tasks.

Order is one of the main instruments to measure the relationship between objects in (empirical) data. However, compared to methods that use numerical properties of objects, the amount of ordinal methods developed is rather small. One reason for this is the limited availability of computational resources in the last century that would have been required for ordinal computations. Another reason -- particularly important for this line of research -- is that order-based methods are often seen as too mathematically rigorous for applying them to real-world data. In this paper, we will therefore discuss different means for measuring and 'calculating' with ordinal structures -- a specific class of directed graphs -- and show how to infer knowledge from them. Our aim is to establish Ordinal Data Science as a fundamentally new research agenda. Besides cross-fertilization with other cornerstone machine learning and knowledge representation methods, a broad range of disciplines will benefit from this endeavor, including, psychology, sociology, economics, web science, knowledge engineering, scientometrics.

Humankind's understanding of the world is fundamentally linked to our perception and cognition, with \emph{human languages} serving as one of the major carriers of \emph{world knowledge}. In this vein, \emph{Large Language Models} (LLMs) like ChatGPT epitomize the pre-training of extensive, sequence-based world knowledge into neural networks, facilitating the processing and manipulation of this knowledge in a parametric space. This article explores large models through the lens of ``knowledge''. We initially investigate the role of symbolic knowledge such as Knowledge Graphs (KGs) in enhancing LLMs, covering aspects like knowledge-augmented language model, structure-inducing pre-training, knowledgeable prompts, structured CoT, knowledge editing, semantic tools for LLM and knowledgeable AI agents. Subsequently, we examine how LLMs can amplify traditional symbolic knowledge bases, encompassing aspects like using LLM as KG builder and controller, structured knowledge pretraining, LLM-enhanced symbolic reasoning, and the amalgamation of perception with cognition. Considering the intricate nature of human knowledge, we advocate for the creation of \emph{Large Knowledge Models} (LKM), specifically engineered to manage diversified spectrum of knowledge structures. This ambitious undertaking could entail several key challenges, such as disentangling knowledge representation from language models, restructuring pre-training with structured knowledge, and building large commonsense models, among others. We finally propose a five-``A'' principle to distinguish the concept of LKM.