A Formal Theory of Substances, Qualities, and Universals

One of the tasks of ontology in information science is to support the classification of entities according to their kinds and qualities. We hold that to realize this task as far as entities such as material objects are concerned we need to distinguish four kinds of entities: substance particulars, quality particulars, substance universals, and quality universals. These form, so to speak, an ontological square. We present a formal theory of classification based on this idea, including both a semantics for the theory and a provably sound axiomatization

Modelling Principles and Methodologies: Relations in Anatomical Ontologies

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ and ‘part of ’

When one Logic is Not Enough: Integrating First-order Annotations in OWL Ontologies

In ontology development, there is a gap between domain ontologies which mostly use the web ontology language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the development of heterogeneous 'FOWL' ontologies that extend OWL with FOL annotations, and is able to reason over the combined set of axioms. Since FOL annotations are stored in OWL annotations, FOWL ontologies remain compatible with the existing OWL infrastructure. We show that for the OWL domain ontology OBI, the stronger integration with its FOL top-level ontology BFO via our approach enables us to detect several inconsistencies. Furthermore, existing OWL ontologies can benefit from FOL annotations. We illustrate this with FOWL ontologies containing mereotopological axioms that enable new meaningful inferences. Finally, we show that even for large domain ontologies such as ChEBI, automatic reasoning with FOL annotations can be used to detect previously unnoticed errors in the classification

Ontology Pre-training for Poison Prediction

Integrating human knowledge into neural networks has the potential to improve their robustness and interpretability. We have developed a novel approach to integrate knowledge from ontologies into the structure of a Transformer network which we call ontology pre-training: we train the network to predict membership in ontology classes as a way to embed the structure of the ontology into the network, and subsequently fine-tune the network for the particular prediction task. We apply this approach to a case study in predicting the potential toxicity of a small molecule based on its molecular structure, a challenging task for machine learning in life sciences chemistry. Our approach improves on the state of the art, and moreover has several additional benefits. First, we are able to show that the model learns to focus attention on more meaningful chemical groups when making predictions with ontology pre-training than without, paving a path towards greater robustness and interpretability. Second, the training time is reduced after ontology pre-training, indicating that the model is better placed to learn what matters for toxicity prediction with the ontology pre-training than without. This strategy has general applicability as a neuro-symbolic approach to embed meaningful semantics into neural networks

The Fragile Body in the Functional City: An Editorial

Changing circumstances force planning to re-define its role as a driving function shaping our cities today. One of the significant challenges to the century-old tradition of planning comes from the ageing population. The demand to age in place and its associated conditions particularly require renewed attention. This is, however, not an isolated and partisan topic, but speaks to the changing circumstances and highlights the dramatic shortcoming of a performance-oriented and segregationof-function-driven approach; one that is remnant of the early days of the planning discipline, but is still very much alive today. What has the discussion around ageing and the city brought up, and where are we headed? Two significant aspects are the body and moving away from a performance-oriented interpretation thereof, as well as a rethinking of participation not just as an information exercise, but as a co-design practice

Ontology Summit 2008 Communiqué: Towards an open ontology repository

Each annual Ontology Summit initiative makes a statement appropriate to each Summits theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies