Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Several authors have suggested that a more parsimonious and conceptually elegant treatment of everyday mereological and topological reasoning can be obtained by adopting a spatial ontology in which regions, not points, are the primitive entities. This paper challenges this suggestion for mereotopological reasoning in two-dimensional space. Our strategy is to define a mereotopological language together with a familiar, point-based interpretation. It is proposed that, to be practically useful, any alternative region-based spatial ontology must support the same sentences in our language (...) as this familiar interpretation. This proposal has the merit of transforming a vague, open-ended question about ontologies for practical mereotopological reasoning into a precise question in model theory. We show that (a version of) the familiar interpretation is countable and atomic, and therefore prime. We conclude that useful alternative ontologies of the plane are, if anything, less parsimonious than the one which they are supposed to replace. (shrink)

The problem of concept representation is relevant for many sub-fields of cognitive research, including psychology and philosophy, as well as artificial intelligence. In particular, in recent years it has received a great deal of attention within the field of knowledge representation, due to its relevance for both knowledge engineering as well as ontology-based technologies. However, the notion of a concept itself turns out to be highly disputed and problematic. In our opinion, one of the causes of this state of affairs (...) is that the notion of a concept is, to some extent, heterogeneous, and encompasses different cognitive phenomena. This results in a strain between conflicting requirements, such as compositionality, on the one hand and the need to represent prototypical information on the other. In some ways artificial intelligence research shows traces of this situation. In this paper, we propose an analysis of this current state of affairs. Since it is our opinion that a mature methodology with which to approach knowledge representation and knowledge engineering should also take advantage of the empirical results of cognitive psychology concerning human abilities, we outline some proposals for concept representation in formal ontologies, which take into account suggestions from psychological research. Our basic assumption is that knowledge representation systems whose design takes into account evidence from experimental psychology may therefore give better results in many applications. (shrink)

Psychological evidence suggests that laypeople understand the world around them in terms of intuitive ontologies which describe broad categories of objects in the world, such as ‘person’, ‘artefact’ and ‘animal’. However, because intuitive ontologies are the result of natural selection, they only need to be adaptive; this does not guarantee that the knowledge they provide is a genuine reflection of causal mechanisms in the world. As a result, science has parted ways with intuitive ontologies. Nevertheless, since the (...) brain is evolved to understand objects in the world according to these categories, we can expect that they continue to play a role in scientific understanding. Taking the case of human evolution, we explore relationships between intuitive ontological and scientific understanding. We show that intuitive ontologies not only shape intuitions on human evolution, but also guide the direction and topics of interest in its research programmes. Elucidating the relationships between intuitive ontologies and science may help us gain a clearer insight into scientific understanding. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as (...) a standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies (...) among leaders in the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an (...) important pillar in the infrastructure that is necessary for the accurate and safe delivery of all varieties of knowledge. (shrink)

The distinction between reference ontologies and application ontologies crept rather unobtrusively into the recent literature on knowledge engineering. A lot of the discourse surrounding this distinction – notably, the one framing the workshop generating this collection of papers – suggests the two types of ontologies are in some sort of opposition to one another. Thus, Borge et al. [3] characterize reference ontologies (more recently, foundational ontologies) as rich, axiomatic theories whose focus is to clarify the (...) intended meanings of terms used in specific domains. Application ontologies, by contrast, provide a minimal terminological structure to fit the needs of a specific community. Reflecting their minimal nature, Masolo et al. [7] refer to such ontologies as “lightweight” ontologies. An application ontology can be lightweight in a second respect as well, namely, that it may not necessarily take the form of fully-fledged axiomatic theory. Rather, it might only be a taxonomy of the relevant domain, a division of the domain into a salient collection of classes, perhaps ordered by the subclass relation. Importantly, though, for an application ontology to “fit the needs of a specific community” needn’t require representational accuracy. In the “worst” case (from a reference ontology perspective), to fit the needs of a community is just to represent uncritically what people in that community think about the ontology’s domain. (shrink)

There are at least two passages in the jamesian corpus where he seems to establish a topology of "regional ontologies", or to set up multiple "language games". the first of these is "the principles of psychology" when he talks about "the many worlds", or "...sub-universes commonly discriminated from each other...", the second is in "pragmatism", where he notes that there "are...at least three well-characterized levels, stages, or types of thought about the world we live in..." two questions immediately come (...) to mind about these levels. first, is each of these areas of equal importance, epistemologically and ontologically speaking? second, how, if at all, are these regional areas related to each other? each of these questions has a seemingly obvious answer. to wit, the world of perception is more important than any of the other areas; and second, the regional areas are related in terms of the disjunctive and conjunctive transitions which james so strenuously upholds, resulting in an overall "concatenated" picture. i argue that both of these responses are insufficient, and that the issue is more complicated than it first appears. (edited). (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED (...) CT community, and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

Contents: POSSIBLE ONTOLOGIES. Jacek Juliusz JADACKI: Preface. Book I: Zdzis??l??aw AUGUSTYNEK: Point Eventism. An Outline of a Certain Ontology. Book II: Jacek Juliusz JADACKI: Ontological Minimum. DISCUSSIONS. Katarzyna PAPRZYCKA: Carnap and Leibniz on the Problem of Being. Piotr PRZYBYSZ: Polish Discussions about Reism.

Ontologies represent the standard way to model the knowledge about specific domains. This holds also for the legal domain where several ontologies have been put forward to model specific kinds of legal knowledge. Both for standard users and for law scholars, it is often difficult to have an overall view on the existing alternatives, their main features and their interlinking with the other ontologies. To answer this need, in this paper, we address an analysis of the state-of-the-art (...) in legal ontologies and we characterise them along with some distinctive features. This paper aims to guide generic users and law experts in selecting the legal ontology that better fits their needs and in understanding its specificity so that proper extensions to the selected model could be investigated. (shrink)

Ontologies represent the standard way to model the knowledge about specific domains. This holds also for the legal domain where several ontologies have been put forward to model specific kinds of legal knowledge. Both for standard users and for law scholars, it is often difficult to have an overall view on the existing alternatives, their main features and their interlinking with the other ontologies. To answer this need, in this paper, we address an analysis of the state-of-the-art (...) in legal ontologies and we characterise them along with some distinctive features. This paper aims to guide generic users and law experts in selecting the legal ontology that better fits their needs and in understanding its specificity so that proper extensions to the selected model could be investigated. (shrink)

Ontologies represent the standard way to model the knowledge about specific domains. This holds also for the legal domain where several ontologies have been put forward to model specific kinds of legal knowledge. Both for standard users and for law scholars, it is often difficult to have an overall view on the existing alternatives, their main features and their interlinking with the other ontologies. To answer this need, in this paper, we address an analysis of the state-of-the-art (...) in legal ontologies and we characterise them along with some distinctive features. This paper aims to guide generic users and law experts in selecting the legal ontology that better fits their needs and in understanding its specificity so that proper extensions to the selected model could be investigated. (shrink)

The paper begins with a more carefully stated version of ontologically neutral (ON) logic, originally introduced in (Hailperin, 1997). A non-infinitistic semantics which includes a definition of potential infinite validity follows. It is shown, without appeal to the actual infinite, that this notion provides a necessary and sufficient condition for provability in ON logic.

In this paper back-and-forth structures are applied to the semantics of natural language. Back-and-forth structures consist of an event structure and an interval structure communicating via a relational link; transitions in the one structure correspond to transitions in the other. Such entities enable us to view temporal constructions (such as tense, aspect, and temporal connectives) as methods of moving systematically between information sources. We illustrate this with a treatment of the English present perfect, and progressive aspect, that draws on ideas (...) developed in Moens & Steedman (1988), and discuss the role of rich ontologies in formal semantics. (shrink)

Although researchers in psychiatry have been trying for decades to elucidate the pathophysiology underlying mental disorders, relatively little progress has been made. One explanation for this failure is that diagnostic categories in psychiatry are unlikely to track underlying neurological mechanisms. Because of this, the US National Institutes of Mental Health has recently developed a novel ontology to guide research in biological psychiatry: the Research Domain Criteria. In this paper, I argue that while RDoC may lead to better neuroscientific explanations for (...) mental disorders, it is unlikely that this new knowledge will then lead to an improved diagnostic system. I therefore suggest that researchers in psychiatry should work toward the development of two new ontologies: one for research and one for clinical practice. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in (...) the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist of theoretical entities and relations with explicitly defined logical structures and precise definitions, whose purpose is to provide a shared language for representing information to be distributed and integrated across diverse scientific contexts. It is tempting to view bio-ontologies as clear and formal expressions of a scientific community’s ontological commitments about their domain of inquiry, and to view their integration as tantamount to the metaphysical unification of (...) science that some philosophers have envisaged. However, I argue that the local, practical, social and technological factors that influence their design prevent us from straightforwardly reading metaphysical conclusions from them. I discuss these complications and suggest how they can be overcome, revealing more general lessons for the development of a well-founded scientific metaphysics. (shrink)

BACKGROUND -/- Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces of (...) knowledge available in a formal (and thus computable) manner. -/- RESULTS -/- We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. -/- CONCLUSIONS -/- We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions. (shrink)

When reusing existing ontologies for publishing a dataset in RDF (or developing a new ontology), preference may be given to those providing extensive subcategorization for important classes (denoted as focus classes). The subcategories may consist not only of named classes but also of compound class expressions. We define the notion of focused categorization power of a given ontology, with respect to a focus class and a concept expression language, as the (estimated) weighted count of the categories that can be (...) built from the ontology’s signature, conform to the language, and are subsumed by the focus class. For the sake of tractable initial experiments we then formulate a restricted concept expression language based on existential restrictions, and heuristically map it to syntactic patterns over ontology axioms (so-called FCE patterns). The characteristics of the chosen concept expression language and associated FCE patterns are investigated using three different empirical sources derived from ontology collections: first, the concept expression pattern frequency in class definitions; second, the occurrence of FCE patterns in the Tbox of ontologies; and last, for class expressions generated from the Tbox of ontologies (through the FCE patterns); their ‘meaningfulness’ was assessed by different groups of users, yielding a ‘quality ordering’ of the concept expression patterns. The complementary analyses are then compared and summarized. To allow for further experimentation, a web-based prototype was also implemented, which covers the whole process of ontology reuse from keyword-based ontology search through the FCP computation to the selection of ontologies and their enrichment with new concepts built from compound expressions. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption (...) of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research (...) projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) (...) testing, and (4) data exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Several metaphysical debates have typically been modeled as oppositions between a relationist approach and a substantivalist approach. Such debates include the Bundle Theory and the Substratum Theory about ordinary material objects, the Bundle (Humean) Theory and the Substance (Cartesian) Theory of the Self, and Relationism and Substantivalism about time. In all three debates, the substantivalist side typically insists that in order to provide a good treatment of the subject-matter of the theory (time, Self, material objects), it is necessary to postulate (...) the existence of a certain kind of substance, while the other side, the relationist one, characteristically feels that this is an unnecessary expense and that one can get the job done in an ontologically cheaper way just with inter-related properties or events. In this paper I shall defend the view that there is much less of a disagreement between relational ontologies and substantival ontologies than it is usually thought. I believe that, when carefully examined, the two sides of the debate are not that different from each other, in all three cases of pairs of views mentioned above. As we will see, both the relational side and the substantival side work in the same way, suffer from and answer the same objections, and are structurally extremely similar. It will be an important question – one that I shall discuss in detail, and that is indeed the main point of interest for me in this paper – whether this means that the two sides of the debate are somehow 'equivalent' or not, and what 'equivalent' could mean. (shrink)

This commentary introduces fascia, our bodily connective tissue, as a contribution to thinking body as process beyond mind–body dualisms. Research in the field of Fascia Studies has shown that fascias’ core qualities are shifting and sliding in tensional responsiveness and that its both/and tissue-and-system features challenge clear-cut definitions. Acknowledging these characteristics of human physiology in novel ways, and in particular fascia as our largest sensory organ, becomes relevant to ontologies, alterities and research methodologies emphasizing experience and transdisciplinarity. Importantly, the (...) notion is never to theorize fascia as model or metaphor but as quotidian processual responsive proposition. (shrink)

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.

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

This article explores rival interpretations of Badiou’s strategy behind the claim ‘mathematics is ontology’, from his construction of an alternative history of being to that of Heidegger to his exposure of the radical contingency of the ‘decisions on being’ carried out by transformative practices in the four conditions of philosophy: art, politics, love and science. The goal of this exploration is to open up the possibility of another strategy that responds to Badiou’s initial intuition – that being is multiple – (...) by embracing the writing of multiple ontologies in the sphere of action. (shrink)

This book is intended as a philosophical introduction to geo-ontologies, in response to their increasing diffusion within the contemporary debate, where philosophy plays a fundamental, though still unexplored, role. Accordingly, the first part offers a short overview of the ontological background of geo-ontologies, which comprehends computer science, philosophy and geography. The second part is devoted to describe the ontology of geography, to define notions such as geographical entities and boundaries, and to trace some philosophical tools useful for spatial (...) representation. The third part investigates the emerging of geo-ontologies from the spatial turn and is concerned with a taxonomy for geo-ontologies grounded on some fundamental geographical distinctions. Finally, the last part presents the emergence of Digital Humanities and the consequent proliferation of geographical projects focused on the ancient world, in particular Greek and Roman. (shrink)

Pour la plupart des systèmes de représentation de la connaissance orientés concept, l’un des problèmes principaux relève de la commodité technique. A savoir, la représentation de connaissance en termes prototypiques, tout comme la possibilité d’exploiter des formes de raisonnement conceptuel basées sur la typicalité, ne sont pas autorisées. Au contraire, dans les sciences cognitives, il existe des données en faveur de concepts prototypiques, et des formes non-monotoniques de raisonnement conceptuel ont été largement étudiées. Ce fossé cognitif concernant la représentation et (...) le raisonnement constitue un problème pour les systèmes computationnels, puisque l’information prototypique joue un rôle crucial dans plusieurs tâches importantes. Dans la lignée des théories du raisonnement et de la rationalité dites du double processus, nous soutenons que la représentation conceptuelle dans les systèmes computationnels devrait dépendre de (au moins) deux composantes représentationnelles, chacune spécialisée dans le traitement de différents genres de processus de raisonnement. Dans cet article, nous présentons les avantages computationnels de cette approche en termes de double processus, et les comparons brièvement avec d’autres solutions d’orientation logique, adoptées pour traiter du même problème. (shrink)

Although many information system ontologies (ISOs) claim to be parsimonious, the notion of parsimony seems to influence the debate on ISOs only at the level of vague and uncritical assumption. To challenge this trend, the paper aims to clarify what it means for ISOs to be parsimonious. Specifically, section 2 shows that parsimony in computer science generally concerns software design and, together with elegance, is one of the two aspects of the broader notion of simplicity. Section 3 transforms the (...) main claims of parsimony in software design into claims about the content of ISOs, the combination of which is hereafter called “parsimony of content”—where “content” refers only to the content of ISOs. Sections 4-7 discuss the application of this parsimony to the design of ISOs, and outline different kinds (and combinations) of parsimony of content. Finally, section 8 considers whether parsimony of content could provide some criteria both for selecting and/or classifying the contents of ISOs and for choosing between different and equally consistent ISOs. (shrink)

Pour la plupart des systèmes de représentation de la connaissance orientés concept, l’un des problèmes principaux relève de la commodité technique. A savoir, la représentation de connaissance en termes prototypiques, tout comme la possibilité d’exploiter des formes de raisonnement conceptuel basées sur la typicalité, ne sont pas autorisées. Au contraire, dans les sciences cognitives, il existe des données en faveur de concepts prototypiques, et des formes non-monotoniques de raisonnement conceptuel ont été largement étudiées. Ce fossé cognitif concernant la représentation et (...) le raisonnement constitue un problème pour les systèmes computationnels, puisque l’information prototypique joue un rôle crucial dans plusieurs tâches importantes. Dans la lignée des théories du raisonnement et de la rationalité dites du double processus, nous soutenons que la représentation conceptuelle dans les systèmes computationnels devrait dépendre de deux composantes représentationnelles, chacune spécialisée dans le traitement de différents genres de processus de raisonnement. Dans cet article, nous présentons les avantages computationnels de cette approche en termes de double processus, et les comparons brièvement avec d’autres solutions d’orientation logique, adoptées pour traiter du même problème. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

Psychological evidence suggests that laypeople understand the world around them in terms of intuitive ontologies which describe broad categories of objects in the world, such as ‘person’, ‘artefact’ and ‘animal’. However, because intuitive ontologies are the result of natural selection, they only need to be adaptive; this does not guarantee that the knowledge they provide is a genuine reflection of causal mechanisms in the world. As a result, science has parted ways with intuitive ontologies. Nevertheless, since the (...) brain is evolved to understand objects in the world according to these categories, we can expect that they continue to play a role in scientific understanding. Taking the case of human evolution, we explore relationships between intuitive ontological and scientific understanding. We show that intuitive ontologies not only shape intuitions on human evolution, but also guide the direction and topics of interest in its research programmes. Elucidating the relationships between intuitive ontologies and science may help us gain a clearer insight into scientific understanding. (shrink)