An ontology was considered as an explicit specification of a conceptualization that provides the ways of thinking about a domain [14]. Ontologies are the silver bullet for many applications, such as, database integration, peer to peer systems, e-commerce, etc. [13]. A geospatial ontology is an ontology that implements a set of geospatial entities in a hierarchical structure [7, 10, 27, 28]. In the age of artificial intelligence, geospatial data, from multiple platforms with many different types, not only is big, heterogeneous, connected, but also keeps changing continuously, which results in tremendous potential for dynamic relationships. Geospatial data, ontologies, and models must be robust enough to the dynamic changes. After mathematical operations, e.g., +,,, and, being introduced, natural numbers can be used not only to count but also to solve real life problems. The set of natural numbers, along with the operations, forms an algebraic system that can be studied by its properties without any internal details of the numbers and operation. These operations establish the relations among natural numbers, which make more sense than isolated natural numbers. Geospatial ontologies are not isolated but connected by their relations.

Many ontologies, i.e., Description Logic (DL) knowledge bases, have been developed to provide rich knowledge about various domains, and a lot of them are based on ALC, i.e., a prototypical and expressive DL, or its extensions. The main task that explores ALC ontologies is to compute semantic entailment. We developed FALCON, a Fuzzy ALC Ontology Neural reasoner, which uses fuzzy logic operators to generate model structures for arbitrary ALC ontologies, and uses multiple model structures to compute faithful semantic entailments. Theoretical results show that FALCON faithfully approximates semantic entailment over ALC ontologies and therefore endows neural networks with world models and the ability to reason over them. Experimental results show that FALCON enables approximate reasoning, paraconsistent reasoning (reasoning with inconsistencies), and improves machine learning in the biomedical domain by incorporating knowledge expressed in ALC.

Our research explores the use of natural language processing (NLP) methods to automatically classify entities for the purpose of knowledge graph population and integration with food system ontologies. We have created NLP models that can automatically classify organizations with respect to categories associated with environmental issues as well as Standard Industrial Classification (SIC) codes, which are used by the U.S. government to characterize business activities. As input, the NLP models are provided with text snippets retrieved by the Google search engine for each organization, which serves as a textual description of the organization that is used for learning. Our experimental results show that NLP models can achieve reasonably good performance for these two classification tasks, and they rely on a general framework that could be applied to many other classification problems as well. We believe that NLP models represent a promising approach for automatically harvesting information to populate knowledge graphs and aligning the information with existing ontologies through shared categories and concepts.

We present a method for automatically constructing a concept hierarchy for a given domain by querying a large language model. We apply this method to various domains using OpenAI's GPT 3.5. Our experiments indicate that LLMs can be of considerable help for constructing concept hierarchies.

This comprehensive study conducts an in-depth analysis of existing COVID-19 ontologies, scrutinizing their objectives, classifications, design methodologies, and domain focal points. The study is conducted through a dual-stage approach, commencing with a systematic review of relevant literature and followed by an ontological assessment utilizing a parametric methodology. Through this meticulous process, twenty-four COVID-19 Ontologies (CovOs) are selected and examined. The findings highlight the scope, intended purpose, granularity of ontology, modularity, formalism, vocabulary reuse, and extent of domain coverage. The analysis reveals varying levels of formality in ontology development, a prevalent preference for utilizing OWL as the representational language, and diverse approaches to constructing class hierarchies within the models. Noteworthy is the recurrent reuse of ontologies like OBO models (CIDO, GO, etc.) alongside CODO. The METHONTOLOGY approach emerges as a favored design methodology, often coupled with application-based or data-centric evaluation methods. Our study provides valuable insights for the scientific community and COVID-19 ontology developers, supplemented by comprehensive ontology metrics. By meticulously evaluating and documenting COVID-19 information-driven ontological models, this research offers a comparative cross-domain perspective, shedding light on knowledge representation variations. The present study significantly enhances understanding of CovOs, serving as a consolidated resource for comparative analysis and future development, while also pinpointing research gaps and domain emphases, thereby guiding the trajectory of future ontological advancements.

In a systematic literature and software review over 100 OWL reasoners/systems were analyzed to see if they would still be usable in 2023. This has never been done in this capacity. OWL reasoners still play an important role in knowledge organisation and management, but the last comprehensive surveys/studies are more than 8 years old. The result of this work is a comprehensive list of 95 standalone OWL reasoners and systems using an OWL reasoner. For each item, information on project pages, source code repositories and related documentation was gathered. The raw research data is provided in a Github repository for anyone to use.

Visual as well as genetic biometrics are routinely employed to identify species and individuals in biological applications. However, no attempts have been made in this domain to computationally enhance visual classification of rare classes with little image data via genetics. In this paper, we thus propose aligned visual-genetic inference spaces with the aim to implicitly encode cross-domain associations for improved performance. We demonstrate for the first time that such alignment can be achieved via deep embedding models and that the approach is directly applicable to boosting long-tailed recognition (LTR) particularly for rare species. We experimentally demonstrate the efficacy of the concept via application to microscopic imagery of 30k+ planktic foraminifer shells across 32 species when used together with independent genetic data samples. Most importantly for practitioners, we show that visual-genetic alignment can significantly benefit visual-only recognition of the rarest species. Technically, we pre-train a visual ResNet50 deep learning model using triplet loss formulations to create an initial embedding space. We re-structure this space based on genetic anchors embedded via a Sequence Graph Transform (SGT) and linked to visual data by cross-domain cosine alignment. We show that an LTR approach improves the state-of-the-art across all benchmarks and that adding our visual-genetic alignment improves per-class and particularly rare tail class benchmarks significantly further. We conclude that visual-genetic alignment can be a highly effective tool for complementing visual biological data containing rare classes. The concept proposed may serve as an important future tool for integrating genetics and imageomics towards a more complete scientific representation of taxonomic spaces and life itself. Code, weights, and data splits are published for full reproducibility.

Ontological knowledge, which comprises classes and properties and their relationships, is integral to world knowledge. It is significant to explore whether Pretrained Language Models (PLMs) know and understand such knowledge. However, existing PLM-probing studies focus mainly on factual knowledge, lacking a systematic probing of ontological knowledge. In this paper, we focus on probing whether PLMs store ontological knowledge and have a semantic understanding of the knowledge rather than rote memorization of the surface form. To probe whether PLMs know ontological knowledge, we investigate how well PLMs memorize: (1) types of entities; (2) hierarchical relationships among classes and properties, e.g., Person is a subclass of Animal and Member of Sports Team is a subproperty of Member of ; (3) domain and range constraints of properties, e.g., the subject of Member of Sports Team should be a Person and the object should be a Sports Team. To further probe whether PLMs truly understand ontological knowledge beyond memorization, we comprehensively study whether they can reliably perform logical reasoning with given knowledge according to ontological entailment rules. Our probing results show that PLMs can memorize certain ontological knowledge and utilize implicit knowledge in reasoning. However, both the memorizing and reasoning performances are less than perfect, indicating incomplete knowledge and understanding.

Knowledge graphs (KGs) have emerged as a prominent data representation and management paradigm. Being usually underpinned by a schema (e.g. an ontology), KGs capture not only factual information but also contextual knowledge. In some tasks, a few KGs established themselves as standard benchmarks. However, recent works outline that relying on a limited collection of datasets is not sufficient to assess the generalization capability of an approach. In some data-sensitive fields such as education or medicine, access to public datasets is even more limited. To remedy the aforementioned issues, we release PyGraft, a Python-based tool that generates highly customized, domain-agnostic schemas and knowledge graphs. The synthesized schemas encompass various RDFS and OWL constructs, while the synthesized KGs emulate the characteristics and scale of real-world KGs. Logical consistency of the generated resources is ultimately ensured by running a description logic (DL) reasoner. By providing a way of generating both a schema and KG in a single pipeline, PyGraft's aim is to empower the generation of a more diverse array of KGs for benchmarking novel approaches in areas such as graph-based machine learning (ML), or more generally KG processing. In graph-based ML in particular, this should foster a more holistic evaluation of model performance and generalization capability, thereby going beyond the limited collection of available benchmarks. PyGraft is available at: https://github.com/nicolas-hbt/pygraft.

Relation Extraction (RE) is the task of extracting semantic relationships between entities in a sentence and aligning them to relations defined in a vocabulary, which is generally in the form of a Knowledge Graph (KG) or an ontology. Various approaches have been proposed so far to address this task. However, applying these techniques to biomedical text often yields unsatisfactory results because it is hard to infer relations directly from sentences due to the nature of the biomedical relations. To address these issues, we present a novel technique called ReOnto, that makes use of neuro symbolic knowledge for the RE task. ReOnto employs a graph neural network to acquire the sentence representation and leverages publicly accessible ontologies as prior knowledge to identify the sentential relation between two entities. The approach involves extracting the relation path between the two entities from the ontology. We evaluate the effect of using symbolic knowledge from ontologies with graph neural networks. Experimental results on two public biomedical datasets, BioRel and ADE, show that our method outperforms all the baselines (approximately by 3\%).