Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s 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. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the (...) construction of a new taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (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)

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. (...) The purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop (...) and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present (...) how an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such (...) as archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

This text is an English translation of those several sections of the original paper in Russian, where collection-related issues are considered. The full citation of the original paper is as following: Pavlinov I.Ya. 2016. [Bioraznoobrazie i biokollektsii: problema sootvetstvia]. In: Pavlinov I.Ya. (comp.). Aspects of Biodiversity. Archives of Zoological Museum of Lomonosov Moscow State University, Vol. 54, Pр. 733–786. -/- Orientation of biology, as a natural science, on the study and explanation of the similarities and differences between organisms led in (...) the second half of the 20th century to the recognition of a specifi c subject area of biological explorations, viz. biodiversity (BD). One of the important general scientifi c prerequisites for this shift was understanding that (at the level of ontology) the structured diversity of the living nature is its fundamental property equivocal to subjecting of some of its manifestations to certain laws. At the level of epistemology, this led to acknowledging that the “diversifi cationary” approach to description of the living beings is as justifi able as the before dominated “unifi cationary” one. This general trend has led to a signifi cant increase in the attention to BD. From a pragmatic perspective, its leitmotif was conservation of BD as a renewable resource, while from a scientifi c perspective the leitmotif was studying it was studying BD as a specifi c natural phenomenon. These two points of view are united by recognition of the need for scientific substantiation of BD conservation strategy, which implies the need for a detailed study of BD itself. At the level of ontology, one of the key problems in the study of BD (leaving aside the question of its genesis) is determination of its structure, which is interpreted as a manifestation of the structure of the Earth’s biota itself. With this, it is acknowledged that the subject area of empirical explorations is not the BD as a whole ( “Umgebung”) but its particular manifestations (“Umwelts”). It is proposed herewith to recognized, within the latter: fragments of BD (especially taxa and ecosystems), hierarchical levels of BD (primarily within- and interorganismal ones), and aspects of BD (before all taxonomic and meronomic ones). Attention is drawn to a new interpretation of bioinformatics as a discipline that studies the information support of BD explorations. An important fraction of this support are biocollections. The scientifi c value of collections means that they make it possible both empirical inferring and testing (verification) of the knowledge about BD. This makes biocollections, in their epistemological status, equivalent to experiments, and so makes studies of BD quite scientific. It is emphasized that the natural objects (naturalia), which are permanently kept in collections, contain primary (objective) information about BD, while information retrieved somehow from them is a secondary (subjective) one. Collection, as an information resource, serves as a research sample in the studies of BD. Collection pool, as the totality of all collection materials kept in repositories according to certain standards, can be treated as a general sample, and every single collection as a local sample. The main characteristic of collection-as-sample is its representativeness; so the basic strategy of development of the collection pool is to maximize its representativeness as a means to ensure correspondence of structure of biocollection pool to that of BD itself. The most fundamental characteristic of collection, as an information resource, is its scientific signifi cance. The following three main groups of more particular characteristics are distinguished: — the “proper” characteristics of every collection are its meaningfulness, informativeness, reliability, adequacy, documenting, systematicity, volume, structure, uniqueness, stability, lability; — the “external” characteristics of collection are resolution, usability, ethic constituent; — the “service” characteristics of collection are its museofication, storage system security, inclusion in metastructure, cost. In the contemporary world, development of the biocollection pool, as a specific resource for BD research, requires considerable organizational efforts, including work on their “information support” aimed at demonstrating the necessity of existence of the biocollections. (shrink)

John Bell proposed an ontology for the GRW modification of quantum mechanics in terms of flashes occurring at space- time points. This article spells out the motivation for this ontology, inquires into the status of the wave function in it, critically examines the claim of its being Lorentz invariant, and considers whether it is a parsimonious but nevertheless physically adequate ontology.

Nihilism is the thesis that no composite objects exist. Some ontologists have advocated abandoning nihilism in favor of deep nihilism, the thesis that composites do not existO, where to existO is to be in the domain of the most fundamental quantifier. By shifting from an existential to an existentialO thesis, the deep nihilist seems to secure all the benefits of a composite-free ontology without running afoul of ordinary belief in the existence of composites. I argue that, while there are (...) well-known reasons for accepting nihilism, there appears to be no reason at all to accept deep nihilism. In particular, deep nihilism draws no support either from the usual arguments for nihilism or from considerations of parsimony. (shrink)

This is a review article on Franz Brentano’s Descriptive Psychology published in 1982. We provide a detailed exposition of Brentano’s work on this topic, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.

This paper presents an axiomatic formalization of a theory of top-level relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the sub-universal relation among universals and the parthood relation among individuals, as well as cross-categorial relations such as instantiation and membership. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical for (...) geographic information processing. The axiomatic theory is developed using Isabelle, a computational system for implementing logical formalisms. All proofs are computer verified and the computational representation of the theory is available online. (shrink)

Individualists about social ontology hold that social facts are “built out of” facts about individuals. In this paper, I argue that there are two distinct kinds of individualism about social ontology, two different ways individual people might be the metaphysical “builders” of the social world. The familiar kind is ontological individualism. This is the thesis that social facts supervene on, or are exhaustively grounded by, facts about individual people. What I call anchor individualism is the alternative thesis that (...) facts about individuals put in place the conditions for a social entity to exist, or the conditions for something to have a social property. Examples include conventionalist theories of the social world, such as David Hume’s theories of promises, money, and government, and collective acceptance theories, such as John Searle’s theory of institutional facts. Anchor individualism is often conflated with ontological individualism. But in fact, the two theses are in tension with one another: if one of these kinds of individualism is true, then the other is very unlikely to be. My aim in this paper is to clarify both, and argue that they should be sharply distinguished from one another. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease (...) Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is required (...) to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

Notions such as śūnyatā, catuṣkoṭi, and Indra's net, which figure prominently in Buddhist philosophy, are difficult to readily accommodate within our ordinary thinking about everyday objects. Famous Buddhist scholar Nāgārjuna considered two levels of reality: one called conventional reality, and the other ultimate reality. Within this framework, śūnyatā refers to the claim that at the ultimate level objects are devoid of essence or "intrinsic properties", but are interdependent by virtue of their relations to other objects. Catuṣkoṭi refers to the claim (...) that four truth values, including contradiction, are admissible in reasoning. Indra's net refers to the claim that every part of a whole is reflective of the whole. Here we present category theoretic constructions that are reminiscent of these Buddhist concepts. The universal mapping property definition of mathematical objects, wherein objects of a universe of discourse are defined not in terms of their content, but in terms of their relations to all objects of the universe is reminiscent of śūnyatā. The objective logic of perception, with perception modeled as [a category of] two sequential processes (sensation followed by interpretation), and with its truth value object of four truth values, is reminiscent of the Buddhist logic of catuṣkoṭi. The category of categories, wherein every category has a subcategory of sets with zero structure within which every category can be modeled, is reminiscent of Indra's net. Our thorough elaboration of the parallels between Buddhist philosophy and category theory can facilitate better understanding of Buddhist philosophy, and bring out the broader philosophical import of category theory beyond mathematics. (shrink)

The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...) But modified organisms, or hybrids, require us to think beyond the machine paradigm and its associated dichotomies between artificial and natural, organisms and artefacts. We ask: How may we conceptualise hybrids beyond limiting ontological categories? Our main claim is that the hybrids created by synthetic biology should be considered not as machines but as metabolic systems. We shall show how the philosophical account of metabolism can inform an ontology of hybrids that moves beyond what we call the “machine ontology”, considering that metabolism enables thinking beyond the dominant dichotomies and allows us to understand and design lifeforms in a bio-based economy. Thus, the aim of this paper is twofold: first, to develop the philosophical ontology of hybrids, and second, to move synthetic biology beyond the problematically limiting view of hybrids. (shrink)

Do we suddenly become justified in treating robots like humans by positing new notions like “artificial moral agency” and “artificial moral responsibility”? I answer no. Or, to be more precise, I argue that such notions may become philosophically acceptable only after crucial metaphysical issues have been addressed. My main claim, in sum, is that “artificial moral responsibility” betokens moral responsibility to the same degree that a “fake orgasm” betokens an orgasm.

Many philosophers of science are ontologically committed to a lush rainforest of special science entities ), but are often reticent about the criteria that determine which entities count as real. On the other hand, the metaphysics literature is much more forthcoming about such criteria, but often links ontological commitment to irreducibility. We argue that the irreducibility criteria are in tension with scientific realism: for example, they would exclude viruses, which are plausibly theoretically reducible and yet play a sufficiently important role (...) in scientific accounts of the world that they should be included in our ontology. In this paper, we show how the inhabitants of the rainforest can be inoculated against the eliminative threat of reduction: by demonstrating that they are emergent. According to our account, emergence involves a screening off condition as well as novelty. We go on to demonstrate that this account of emergence, which is compatible with theoretical reducibility, satisfies common intuitions concerning what should and shouldn't count as real: viruses are emergent, as are trouts and turkeys, but philosophically gerrymandered objects like trout-turkeys do not qualify. (shrink)

In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...) formulated as quasi-Newtonian, via the postulation of forces proportional to acceleration; advocates of the guidance approach defend the notion that the theory is essentially first-order and incorporates some concepts akin to those of Aristotelian physics. Here I analyze whether the desideratum of an interpretation of Bohmian mechanics that is both explanatorily adequate and not committed to configuration space realism favors one of these two approaches to the theory over the other. Contrary to some recent claims in the literature, I argue that the quasi-Newtonian approach based on the idea of a quantum potential does not come out the winner. (shrink)

This paper elaborates on relationalism about space and time as motivated by a minimalist ontology of the physical world: there are only matter points that are individuated by the distance relations among them, with these relations changing. We assess two strategies to combine this ontology with physics, using classical mechanics as example: the Humean strategy adopts the standard, non-relationalist physical theories as they stand and interprets their formal apparatus as the means of bookkeeping of the change of the (...) distance relations instead of committing us to additional elements of the ontology. The alternative theory strategy seeks to combine the relationalist ontology with a relationalist physical theory that reproduces the predictions of the standard theory in the domain where these are empirically tested. We show that, as things stand, this strategy cannot be accomplished without compromising a minimalist relationalist ontology. (shrink)

Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at (...) the same time, (ii) through its association with specific players and a specific occasion, tied to time and history. We discover other abstract patterns of this sort especially in the domains of law and commerce. This essay draws on the work in social ontology, we of Hernando de Soto and of John Searle to develop an ontology of the social world based on an analysis of the peculiar interdependence between quasi-abstract patterns and their representations in documents of different sorts. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

This paper investigates the connection between temporal attitudes (attitudes characterised by a concern (or lack thereof) about future and past events), beliefs about temporal ontology (beliefs about the existence of future and past events) and temporal preferences (preferences regarding where in time events are located). Our aim is to probe the connection between these preferences, attitudes, and beliefs, in order to better evaluate the normative status of these preferences. We investigate the hypothesis that there is a three-way association between (...) (a) being present-biased (that is, preferring that positive events are located in the present, and negative events are located in the non-present), (b) believing that past and future events do not exist and (c) tending to have present-focused rather than non-present-focused temporal attitudes. We find no such association. This suggests that insofar as temporal preferences and temporal attitudes are connected to the ways we represent time, they are not connected to the ways we represent temporal ontology; rather, they are more likely connected to the ways we represent relative movement in, or of, time. This has important consequences for, first, explaining why we exhibit these preferences and, second, for their normative evaluation. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of te rms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been (...) little effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. We describe our efforts towards developing an Emotion Ontology (EMO) to serve the affective science community. We here focus on conformity to the BFO upper ontology and disambiguation of polysemous terminology. (shrink)

Today, in any mature information society, we live neither online nor offline but on life, that is, we increasingly live in that special space that is both analogue and digital, both online and offline. Imagine someone asking whether the water is fresh or salty in the estuary where the river meets the sea. That someone has not understood the special nature of the place. Our information society is that place. And our technologies are perfectly evolved to take advantage of it, (...) like mangroves growing in brackish water. In the mangrove society, machine-readable data, new forms of agency and interactions are constantly evolving. The consequences of such a radical transformation are many, but one is particularly significant and rich in consequences: how should we design the mangrove society, when it comes to the relationship between the natural and the digital? In this text, I argue that the digital blue is a great ally of the environmental green. The two work best in tandem. And if the world will enjoy a sustainable development for the environment that is also socially preferable for humanity, it will be because the green and the blue will have created a virtuous circle of nature and technology. It can be done. There is just no time to waste. (shrink)

This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In (...) an appendix, however, Brentano puts forward an even more radical suggestion, inspired by the physics of Kelvin. According to this final view, space itself is an accident of a deeper substance: the present time. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to (...) extend or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

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. (shrink)

I argue that a two-dimensional model of social objects is uniquely positioned to deliver explanations for some of the puzzling metaphysical features of words. I consider how a type-token model offers explanations for the metaphysical features of words, but I give reasons to find the model wanting. In its place, I employ an alternative model from social ontology to explain the puzzling data and questions that are generated from the metaphysical features of words. In the end I chart a (...) new path that foregrounds the agent-dependence and social conditions for word kinds. (shrink)

What follows is a contribution to the theory of space and of spatial objects. It takes as its starting point the philosophical subfield of ontology, which can be defined as the science of what is: of the various types and categories of objects and relations in all realms of being. More specifically, it begins with ideas set forth by Aristotle in his Categories and Metaphysics, two works which constitute the first great contributions to ontological science. Because Aristotle’s ontological ideas (...) were developed prior to the scientific discoveries of the modern era, he approached the objects and relations of everyday reality with the same ontological seriousness with which scientists today approach the objects of physics. We shall seek to show that what Aristotle has to say about these commonsensical objects and relations can, when translated into more formal terms, be of use also to contemporary ontologists. More precisely, we shall argue that his ideas can contribute to the development of a rigorous theory of those social and institutional components of everyday reality – the settings of human behavior – which are the subject of this volume. When modern-day philosophers turn their attentions to ontology they begin not with Aristotle but rather, in almost every case, with a set-theoretic ontology of the sort which is employed in standard model-theoretic semantics. Set-theoretic ontology sees the world in atomistic terms: it postulates a lowest level of atoms or urelements, from out of which successively higher levels of set-theoretic objects are then constructed. The approach to ontology to be defended here, in contrast, starts not with atoms but with the mesoscopic objects by which we are surrounded in our normal day-to-day.. (shrink)

The beliefs of economists are not solely determined by empirical evidence in direct relation to the theories and models they hold. Economists hold 'ontological presuppositions', fundamental ideas about the nature of being which direct their thinking about economic behaviour. In this volume, leading philosophers and economists examine these hidden presuppositions, searching for a 'world view' of economics. What properties are attributed to human individuals in economic theories, and which are excluded? Does economic man exist? Do markets have an essence? Do (...) macroeconomic aggregates exist? Is the economy a mechanism, the functioning of which is governed by a limited set of distinct causes? What are the methodological implications of different ontological starting points? This collection, which establishes economic ontology as a coordinated field of study, will be of great value to economists and philosophers of social sciences. (shrink)

In Lowe’s Four-Category Ontology, instantiation is a basic formal ontological relation between particulars (objects, modes) and their kinds (kinds, attributes). Therefore, instantiation must be considered as a metaphysically necessary relation, which also rules out the metaphysical possibility of kind change. Nevertheless, according to Lowe, objects obtain their identity conditions in a more general level than specific natural kinds, which allows for kind change. There also seems to be actual examples of kind change. The advocate of Four-Category Ontology is (...) obliged to resolve the tension between these mutually incompatible claims. In this article, we argue that the only viable option for the advocate of Four-Category Ontology is to bite the bullet and stick to the necessity of each of the most specific natural kind to the object instantiating it. As a major drawback, the four-category ontologist does not have any credible means to allow for kind change or determination of the identity conditions in a more general level. (shrink)

I argue for the usefulness of the evolutionary kind of biological individual.

This thesis articulates an analytic version of the ontology of idealism, according to which universal phenomenal consciousness is all there ultimately is, everything else in nature being reducible to patterns of excitation of this consciousness. The thesis’ key challenge is to explain how the seemingly distinct conscious inner lives of different subjects—such as you and me—can arise within this fundamentally unitary phenomenal field. Along the way, a variety of other challenges are addressed, such as: how we can reconcile idealism (...) with the fact that we all inhabit a common external world; why this world unfolds independently of our personal volition or imagination; why there are such tight correlations between measured patterns of brain activity and reports of experience; etc. The core idea of this thesis can be summarized thus: we, as well as all other living organisms, are dissociated alters of universal phenomenal consciousness, analogously to how a person with Dissociative Identity Disorder (DID) manifests multiple disjoint centers of subjectivity also called ‘alters.’ We, and all other living organisms, are surrounded by the transpersonal phenomenal activity of universal consciousness, which unfolds beyond the dissociative boundary of our respective alter. The inanimate world we perceive around us is the extrinsic appearance—i.e. the phenomenal image imprinted from across our dissociative boundary—of this activity. The living organisms we share the world with are the extrinsic appearances of other alters. (shrink)

Could space consist entirely of extended regions, without any regions shaped like points, lines, or surfaces? Peter Forrest and Frank Arntzenius have independently raised a paradox of size for space like this, drawing on a construction of Cantor’s. I present a new version of this argument and explore possible lines of response.

Ontological pluralism is the view that there are different ways to exist. It is a position with deep roots in the history of philosophy, and in which there has been a recent resurgence of interest. In contemporary presentations, it is stated in terms of fundamental languages: as the view that such languages contain more than one quantifier. For example, one ranging over abstract objects, and another over concrete ones. A natural worry, however, is that the languages proposed by the pluralist (...) are mere notational variants of those proposed by the monist, in which case the debate between the two positions would not seem to be substantive. Jason Turner has given an ingenious response to this worry, in terms of a principle that he calls ‘logical realism’. This paper offers a counter-response on behalf of the ‘notationalist’. I argue that, properly applied, the principle of logical realism is no threat to the claim that the languages in question are notational variants. Indeed, there seems to be every reason to think that they are. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from (...) the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

'Ontology and Metaontology: A Contemporary Guide' is a clear and accessible survey of ontology, focussing on the most recent trends in the discipline. -/- Divided into parts, the first half characterizes metaontology: the discourse on the methodology of ontological inquiry, covering the main concepts, tools, and methods of the discipline, exploring the notions of being and existence, ontological commitment, paraphrase strategies, fictionalist strategies, and other metaontological questions. The second half considers a series of case studies, introducing and familiarizing (...) the reader with concrete examples of the latest research in the field. The basic sub-fields of ontology are covered here via an accessible and captivating exposition: events, properties, universals, abstract objects, possible worlds, material beings, mereology, fictional objects. -/- The guide's modular structure allows for a flexible approach to the subject, making it suitable for both undergraduates and postgraduates looking to better understand and apply the exciting developments and debates taking place in ontology today. (shrink)

Two major lines of argument support the notion that Hildegard of Bingen’s metaphysics is peculiarly gynocentric. Contra the standard commentary on her work, the focus is not on the notion of viriditas; rather, the first line of argument presents a specific delineation of her ontology, demonstrating that it is a graded hierarchy of beings, many of which present feminine aspects of the divine, and all of which establish the metaphysical notion of interpenetrability. The second line of argument specifically contrasts (...) her thought to that of Aquinas and Meister Eckhart, noting areas of similarity and difference. It is concluded that the visionary origins of Hildegard’s work may have to some extent precluded our understanding of it, and that her work merits consideration not only philosophically and theologically but from the standpoint of its early presentation of a gynocentric worldview. (shrink)

With the present paper I maintain that the group field theory (GFT) approach to quantum gravity can help us clarify and distinguish the problems of spacetime emergence from the questions about the nature of the quanta of space. I will show that the mechanism of phase transition suggests a form of indifference between scales (or phases) and that such an indifference allows us to black-box questions about the nature of the ontology of the fundamental levels of the theory. I (...) consider the GFT approach to quantum gravity which derives spacetime as an emergent property from abstract non-geometrical tetrahedra through a processes of phase transition. Because the physical interpretation of the tetrahedra is problematic in view of their (non)-spatiotemporal nature, I will apply the considerations about phase transitions to GFT and conclude that the fundamental ontology of the theory and the mechanism of spacetime emergence can and should be treated separately. (shrink)

According to Lowe’s Four-Category Ontology, the general nature of the entities belonging to the four fundamental categories is determined by the basic formal ontological relations (instantiation and characterization) that they bear to other entities. I argue that, in closer analysis, instead of one formal relation of characterization, this category system introduces two, one connecting particulars and another universals. With regard to the characterization relation connecting particulars, it remains an open issue whether it would need further analysis. By contrast, the (...) status of instantiation as an internal relation is comparatively clear. Nevertheless, because of holding by virtue of the essences of particulars, the holding of instantiation between universals and particulars rules out the possibility of kind change and entails that particulars are essentially rigidly dependent on universals. Finally, Lowe’s analysis of necessary exemplification gives us some reasons to suspect that some property universals need not have any instances in order to exist. (shrink)