The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilitating the integration of a dataset with other types of data increases the likelihood of reuse, and the potential of answering novel research questions. Ontologies are a useful tool for semantically tagging datasets as adding relevant metadata increases the understanding of how data was produced and increases its interoperability. Ontologies provide concepts for a particular domain as well as the relationships between concepts. By tagging data with ontology terms, data becomes both human and machine interpretable, allowing for increased reuse and interoperability. However, the task of identifying ontologies relevant to a particular research domain or technology is challenging, especially within the diverse realm of fundamental plant research. In this review, we outline the ontologies most relevant to the fundamental plant sciences and how they can be used to annotate data related to plant-specific experiments within metadata frameworks, such as Investigation-Study-Assay (ISA). We also outline repositories and platforms most useful for identifying applicable ontologies or finding ontology terms.

Model-Based Anomaly Detection has been a successful approach to identify deviations from the expected behavior of Cyber-Physical Production Systems. Since manual creation of these models is a time-consuming process, it is advantageous to learn them from data and represent them in a generic formalism like timed automata. However, these models - and by extension, the detected anomalies - can be challenging to interpret due to a lack of additional information about the system. This paper aims to improve model-based anomaly detection in CPPS by combining the learned timed automaton with a formal knowledge graph about the system. Both the model and the detected anomalies are described in the knowledge graph in order to allow operators an easier interpretation of the model and the detected anomalies. The authors additionally propose an ontology of the necessary concepts. The approach was validated on a five-tank mixing CPPS and was able to formally define both automata model as well as timing anomalies in automata execution.

A scientific paper can be divided into two major constructs which are Metadata and Full-body text. Metadata provides a brief overview of the paper while the Full-body text contains key-insights that can be valuable to fellow researchers. To retrieve metadata and key-insights from scientific papers, knowledge acquisition is a central activity. It consists of gathering, analyzing and organizing knowledge embedded in scientific papers in such a way that it can be used and reused whenever needed. Given the wealth of scientific literature, manual knowledge acquisition is a cumbersome task. Thus, computer-assisted and (semi-)automatic strategies are generally adopted. Our purpose in this research was two fold: curate Open Research Knowledge Graph (ORKG) with papers related to ontology learning and define an approach using ORKG as a computer-assisted tool to organize key-insights extracted from research papers. This approach was used to document the "epidemiological surveillance systems design and implementation" research problem and to prepare the related work of this paper. It is currently used to document "food information engineering", "Tabular data to Knowledge Graph Matching" and "Question Answering" research problems and "Neuro-symbolic AI" domain.

Wikidata is one of the largest public general-purpose Knowledge Bases (KBs). Yet, due to its collaborative nature, its schema and taxonomy have become convoluted. For the YAGO 4 KB, we combined Wikidata with the ontology from Schema.org, which reduced and cleaned up the taxonomy and constraints and made it possible to run automated reasoners on the data. However, it also cut away large parts of the Wikidata taxonomy. In this paper, we present our effort to merge the entire Wikidata taxonomy into the YAGO KB as much as possible. We pay particular attention to logical constraints and a careful distinction of classes and instances. Our work creates YAGO 4.5, which adds a rich layer of informative classes to YAGO, while at the same time keeping the KB logically consistent.

In this paper, a new perspective is suggested for unsupervised Ontology Matching (OM) or Ontology Alignment (OA) by treating it as a translation task. Ontologies are represented as graphs, and the translation is performed from a node in the source ontology graph to a path in the target ontology graph. The proposed framework, Truveta Mapper (TM), leverages a multi-task sequence-to-sequence transformer model to perform alignment across multiple ontologies in a zero-shot, unified and end-to-end manner. Multi-tasking enables the model to implicitly learn the relationship between different ontologies via transfer-learning without requiring any explicit cross-ontology manually labeled data. This also enables the formulated framework to outperform existing solutions for both runtime latency and alignment quality. The model is pre-trained and fine-tuned only on publicly available text corpus and inner-ontologies data. The proposed solution outperforms state-of-the-art approaches, Edit-Similarity, LogMap, AML, BERTMap, and the recently presented new OM frameworks in Ontology Alignment Evaluation Initiative (OAEI22), offers log-linear complexity, and overall makes the OM task efficient and more straightforward without much post-processing involving mapping extension or mapping repair. We are open sourcing our solution.

Evaluating semantic relatedness of Web resources is still an open challenge. This paper focuses on knowledge-based methods, which represent an alternative to corpus-based approaches, and rely in general on the availability of knowledge graphs. In particular, we have selected 10 methods from the existing literature, that have been organized according to it adjacent resources, triple patterns, and triple weights-based methods. They have been implemented and evaluated by using DBpedia as reference RDF knowledge graph. Since DBpedia is continuously evolving, the experimental results provided by these methods in the literature are not comparable. For this reason, in this work, such methods have been experimented by running them all at once on the same DBpedia release and against 14 well-known golden datasets. On the basis of the correlation values with human judgment obtained according to the experimental results, weighting the RDF triples in combination with evaluating all the directed paths linking the compared resources is the best strategy in order to compute semantic relatedness in DBpedia.

This paper surveys the current state of the art in document automation (DA). The objective of DA is to reduce the manual effort during the generation of documents by automatically creating and integrating input from different sources and assembling documents conforming to defined templates. There have been reviews of commercial solutions of DA, particularly in the legal domain, but to date there has been no comprehensive review of the academic research on DA architectures and technologies. The current survey of DA reviews the academic literature and provides a clearer definition and characterization of DA and its features, identifies state-of-the-art DA architectures and technologies in academic research, and provides ideas that can lead to new research opportunities within the DA field in light of recent advances in generative AI and large language models.

This study evaluates the applicability and efficiency of ChatGPT for ontology alignment using a naive approach. ChatGPT's output is compared to the results of the Ontology Alignment Evaluation Initiative 2022 campaign using conference track ontologies. This comparison is intended to provide insights into the capabilities of a conversational large language model when used in a naive way for ontology matching, and to investigate the potential advantages and disadvantages of this approach.

Procedural knowledge describes how to accomplish tasks and mitigate problems. Such knowledge is commonly held by domain experts, e.g. operators in manufacturing who adjust parameters to achieve quality targets. To the best of our knowledge, no real-world datasets containing process data and corresponding procedural knowledge are publicly available, possibly due to corporate apprehensions regarding the loss of knowledge advances. Therefore, we provide a framework to generate synthetic datasets that can be adapted to different domains. The design choices are inspired by two real-world datasets of procedural knowledge we have access to. Apart from containing representations of procedural knowledge in Resource Description Framework (RDF)-compliant knowledge graphs, the framework simulates parametrisation processes and provides consistent process data. We compare established embedding methods on the resulting knowledge graphs, detailing which out-of-the-box methods have the potential to represent procedural knowledge. This provides a baseline which can be used to increase the comparability of future work. Furthermore, we validate the overall characteristics of a synthesised dataset by comparing the results to those achievable on a real-world dataset. The framework and evaluation code, as well as the dataset used in the evaluation, are available open source.

While classical planning languages make the closed-domain and closed-world assumption, there have been various approaches to extend those with DL reasoning, which is then interpreted under the usual open-world semantics. Current approaches for planning with DL ontologies integrate the DL directly into the planning language, and practical approaches have been developed based on first-order rewritings or rewritings into datalog. We present here a new approach in which the planning specification and ontology are kept separate, and are linked together using an interface. This allows planning experts to work in a familiar formalism, while existing ontologies can be easily integrated and extended by ontology experts. Our approach for planning with those ontology-mediated planning problems is optimized for cases with comparatively small domains, and supports the whole OWL DL fragment. The idea is to rewrite the ontology-mediated planning problem into a classical planning problem to be processed by existing planning tools. Different to other approaches, our rewriting is data-dependent. A first experimental evaluation of our approach shows the potential and limitations of this approach.