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Knowledge graphs have become the primary vehicle for data integration and are critical to the success of modern AI, but the diversity of KG modelling practices, from lightweight vocabularies to richly axiomatised ontologies, makes…
A clone on a set X is a set of finitary operations on X which contains all the projections and is closed under composition. The set of all clones forms a complete lattice Cl(X) with greatest element O, the set of all finitary operations.…
Ontologies are formal representations of concepts and complex relationships among them. They have been widely used to capture comprehensive domain knowledge in areas such as biology and medicine, where large and complex ontologies can…
The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although…
The present study is aimed at analysing the benefits of an ontological approach in Functional Structural Plant Modelling. The ontological approach has been used at two levels, to refine the conceptual modelling approach, and to define the…
Personal ontologies have been proposed as a means to support the semantic management of user information. Assuming that a personal ontology system is in use, new tools have to be developed at user interface level to exploit the enhanced…
Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time,…
Trees -- i.e., the type of data structure known under this name -- are central to many aspects of knowledge organization. We investigate some central design choices concerning the ontological modeling of such trees. In particular, we…
Your computer is continuously executing programs, but does it really understand them? Not in any meaningful sense. That burden falls upon human knowledge workers, who are increasingly asked to write and understand code. They deserve to have…
This work presents the architecture used in the ongoing OntologyNavigator project. It is a research tool to help advanced learners to find adapted IT papers to create scientific bibliographies. The purpose is the use of an IT representation…
Ontologies are built on systems that conceptually evolve over time. In addition, techniques and languages for building ontologies evolve too. This has led to numerous studies in the field of ontology versioning and ontology evolution. This…
In this paper, we introduce a novel interpreting framework that learns an interpretable model based on an ontology-based sampling technique to explain agnostic prediction models. Different from existing approaches, our algorithm considers…
The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such caGrid, support access…
This paper presents our work on development of OWL-driven systems for formal representation and reasoning about terminological knowledge and facts in petrology. The long-term aim of our project is to provide solid foundations for a…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
Ontologies play a crucial role in organizing and representing knowledge. However, even current ontologies do not encompass all relevant concepts and relationships. Here, we explore the potential of large language models (LLM) to expand an…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
With the growth of data-oriented research in humanities, a large number of research datasets have been created and published through web services. However, how to discover, integrate and reuse these distributed heterogeneous research…
Reusing ontologies in practice is still very challenging, especially when multiple ontologies are (jointly) involved. Moreover, despite recent advances, the realization of systematic ontology quality assurance remains a difficult problem.…
We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our…