Barry Smith

In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is critically important (Wright et al., 2020, p. 17). Our remaining concerns with BCIO relate directly to these two principles. First, we identify a number of issues with some of the classifications and definitions in BCIO that seem to be in tension with the just-mentioned principle . Second, we note some reservations about the reuse of certain classes in BCIO, namely from the Gazetteer (GAZ), the Ontology of Medically Related Social Entities (OMRSE), and the Information Artifact Ontology (IAO). While the latter principle of “reuse” is important, it is also important not to let the reuse of existing classes (or their corresponding definitions) compromise the logical integrity or the realist nature of one’s ontology.

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested.

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality.

La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui existent indépendamment de nos actes cognitifs (par exemple: la planète Terre, sa surface extérieure); et des objets qui existent seulement grâce à ces actes (par exemple: l'équateur, la Mer du Nord). Le champ visuel, lui aussi, peut être conçu comme un exemple d'une entité à extension spatiale qui est dépendante dans le sens proposé ci-dessus. L'étude présente suggère une extension de cette analogie en postulant les entités qui, pour les vrais jugements, seraient ce que le champ visuel est pour les actes de perception visuelle. Le champ de jugement est défini plus précisément comme une entité étendue complexe, contenant toutes les entités essentielles pour la vérité d'un (vrai) jugement donné. Il est possible de démontrer que le travail des linguistes cognitifs tel Talmy ou Langacker, si l'on l'interprète convenablement, produit une explication détaillée des structures des champs de jugement correspondant aux phrases de sortes différentes. Un genre nouveau de définition de la vérité en tant que correspondance pour les expressions de la langue naturelle peut donc être formulé sur cette base.

From the point of view of Brentano’s philosophy, contemporary philosophy of mind presupposes an over-crude theory of the internal structures of mental acts and states and of the corresponding types of parts, unity and dependence. We here describe Brentano’s own account of the part-whole structures obtaining in the mental sphere, and show how it opens up new possibilities for mereological investigation. One feature of Brentano’s view is that the objects of experience are themselves parts of mind, so that there is a sense in which for him (as e.g. for Leibniz) ontology is a proper part of rational or descriptive psychology.

We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche. An environment is in first approximation a volume of space; it is a specific habitat, location, or site that is suitable or adequate for given purposes (of foraging, resting, hunting, breeding, nesting, grooming) in the life of an organism or group of organisms. This spatial notion of environment can be drawn closer to biological and ecological science by taking account of the pertinent physical attributes realized within given spatial regions.

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking.

In our book, Why Machines Will Never Rule the World, Jobst Landgrebe and I argue that we can engineer machines that can emulate the behaviours only of simple systems, which means: only of those systems whose behaviour we can predict mathematically. The human brain is an example of a complex system, and thus its behaviour cannot be emulated by a machine. We use this argument to debunk the claims of those who believe that large language models are poised to achieve a level of intelligence that will equal or even surpass that of the human brain. The essay was published under the title "Why Machines Will Never Rule the World"

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest.

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration.

We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.

The paper seeks to show how the world of everyday human cognition might be treated as an object of ontological investigation in its own right. The paper is influenced by work on affordances and prototypicality of psychologists such as Gibson and Rosch, by work on cognitive universals of the anthropologist Robin Horton, and by work of Patrick Hayes and others on ‘naive’ or ‘qualitative physics’. It defends a thesis to the effect that there is, at the heart of common sense, a theoretical core of true propositions pertaining to mesoscopic objects, and that the latter are to be understood as relating mereologically to the objects studied by physical science.

Ingarden distinguishes four strata making up the structure of the literary work of art: the stratum of word sounds and sound-complexes; the stratum of meaning units; the stratum of represented objectivities (characters, actions, settings, and so forth); and the stratum of schematized aspects (perspectives under which the represented objectivities are given to the reader). It is not only works of literature which manifest this four-fold structure but also certain borderline cases such as newspaper articles, scientific works, biographies, and so forth. Ingarden specifies what is characteristic of a work of literature by asserting that all declarative sentences appearing in the stratum of meaning units of such work possess what he calls a quasi-judgmental character. We discuss here Ingarden’s theory of quasi-judgments and draw out its implication that all works of literature are works of fiction through and through.

La ricerca medica è afflitta da un problema di comunicazione. Comunità distinte di ricercatori si servono di terminologie diverse e spesso incompatibili per esprimere i risultati del loro lavoro, generando in questo modo problemi di integrazione tra database ogniqualvolta si presenti la necessità di inserire i dati medici nei computer. In un primo momento i problemi di integrazione tra database venivano risolti caso per caso, in seguito si è fatta strada l’idea di realizzare un’unica tassonomia di riferimento in cui tradurre, una volta soltanto, tutti i vari sistemi di classificazione. Funzionando come una sorta di lingua franca, questa tassonomia di riferimento avrebbe automaticamente garantito ad ogni database calibrato su di essa la compatibilità con tutti gli altri. È curioso come gli informatici abbiano chiamato il sistema centrale di classificazione che stavano proponendo un’ontologia, riconoscendo così l’esistenza di più di un’affinità tra il lavoro di costruzione che un simile sistema comportava e la vecchia metafisica. Il presente articolo descrive un tentativo di sfruttare le risorse della filosofia per risolvere problemi che sorgono, in particolar modo, nel campo dell’integrazione delle terminologie mediche. Vengono delineati in particolare i contorni di un’iniziativa che è il frutto della collaborazione tra l’Istituto di Ontologia Formale e Informatica Medica e la società di software belga Language and Computing, iniziativa che prevede la messa alla prova di un’ontologia fondata su solidi principi filosofici nel contesto di potenti strumenti software per l’elaborazione di testo medico.

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the development of the community-based Coronavirus Infectious Disease Ontology in early 2020. As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications.

Is it possible to compare civilizations one with another? Is it possible, in other words, to construct some neutral and objective framework in terms of which we could establish in what respects one civilization might deserve to be ranked more highly than its competitors? Morality will surely provide one axis of such a framework (and we note in passing that believers in Islam might quite reasonably claim that their fellow-believers are characteristically more moral than are many in the West). Criteria such as material well-being will need to play a role, too, as also will happiness or pleasure (and again we note that it is not clear a priori that there is more happiness in the West than there is in other civilizations). But even happiness (pace some proponents of the utilitarian philosophy) comes in different types, and to count in the civilization stakes the happiness involved would presumably need to be of the right kind. We explore what this might mean in terms of the idea of a self-chosen life plan.

The perception of spatial bodies is at least in part a perception of bodily boundaries or surfaces. The usual mathematical conception of boundaries as abstract constructions is, however, of little use for cognitive science purposes. The essay therefore seeks a more adequate conception of the ontology of boundaries building on ideas in Aristotle and Brentano on what we may call the coincidence of boundaries. It presents a formal theory of boundaries and of the continua to which they belong, of a sort which allows a resolution of certain Zeno-style paradoxes. The theory proves to be applicable not only in the cognitive science field but also in regard to problems relating to the ontology of geographical and geopolitical boundaries.

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain.

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration.

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

The paradigm of referent tracking is based on a realist presupposition which rejects so-called negative entities (congenital absent nipple, and the like) as spurious. How, then, can a referent tracking-based Electronic Health Record deal with what are standardly called ‘negative findings’? To answer this question we carried out an analysis of some 748 sentences drawn from patient charts and containing some form of negation. Our analysis shows that to deal with these sentences we need to introduce a new ontological relationship between a particular and a universal, which holds when no instance of the universal has a specific qualified ontological relation with the particular. This relation is found to be able to accommodate nearly all occurrences of negative findings in the examined sample, in ways which involve no reference to negative entities.