In the visual representation of ontologies, in particular of part-whole relationships, 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, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...) Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

Conflict over who belongs in women-only spaces is now part of mainstream political debate. Some think women-only spaces should exclude on the basis of sex, and others think they should exclude on the basis of a person’s self-determined gender identity. Many who take the latter view appear to believe that the only reason for taking the former view could be antipathy towards men who identify as women. In this paper, we’ll revisit the second-wave feminist literature on separatism, in order to (...) uncover the reasons for women-only spaces as feminists originally conceived them. Once these reasons are understood, those participating in debates over women-only spaces will be in a better position to adjudicate on whether shifting from sex to gender identity puts any significant interests at stake. (shrink)

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.

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Twentieth century philosophers introduced the distinction between “objective rightness” and “subjective rightness” to achieve two primary goals. The first goal is to reduce the paradoxical tension between our judgments of (i) what is best for an agent to do in light of the actual circumstances in which she acts and (ii) what is wisest for her to do in light of her mistaken or uncertain beliefs about her circumstances. The second goal is to provide moral guidance to an agent who (...) may be uncertain about the circumstances in which she acts, and hence is unable to use her standard moral principle directly in deciding what to do. This paper distinguishes two important senses of “moral guidance”; proposes criteria of adequacy for accounts of subjective rightness; canvasses existing definitions for “subjective rightness”; finds them all deficient; and proposes a new and more successful account. It argues that each comprehensive moral theory must include multiple principles of subjective rightness to address the epistemic situations of the full range of moral decision-makers, and shows that accounts of subjective rightness formulated in terms of what it would reasonable for the agent to believe cannot provide that guidance. -/- . (shrink)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review the (...) paper and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract (...) fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (shrink)

For centuries it has been a mainstay of European and American moral thought that keeping promises—and the allied activity of upholding contracts—is one of the most important requirements of morality. On some historically powerful views the obligation to uphold promises or contracts not only regulates private relationships, but also provides the moral foundation for our duty to support and obey legitimate governments. Some theorists believe that the concept of keeping promises has gradually moved to center stage in European moral thought. (...) They see this movement as part of an historical shift from a moral conception in which an individual’s duties are mainly externally imposed and unalterable, to a conception in which duties are largely chosen by the individual. (shrink)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (Arp, Smith, and (...) Spear 2015). BCIO uses as its top-level ontology Basic Formal Ontology (BFO). The methods outlined in Wright, et al. are a valuable contribution to the field, especially the use of formal mechanisms for literature annotation and expert stakeholder review, and the BCIO will certainly play an important role in the extension of OBO Foundry ontologies into the behavioural domain. (shrink)

A moral code consists of principles that assign moral status to individual actions – principles that evaluate acts as right or wrong, prohibited or obligatory, permissible or supererogatory. Many theorists have held that such principles must serve two distinct functions. On the one hand, they serve a theoretical function, insofar as they specify the characteristics in virtue of which acts possess their moral status. On the other hand, they serve a practical function, insofar as they provide an action-guide: a standard (...) by reference to which a person can choose which acts to perform and which not. Although the theoretical and practical functions of moral principles are closely linked, it is not at all obvious that what enables a principle to fill one of these roles automatically equips it to fill the other. In this paper I shall briefly examine some of the reasons why a moral principle might fail to fill its practical role, i.e., be incapable of guiding decisions. I shall then sketch three common responses to this kind of failure, and examine in some detail the adequacy of one of the most popular of these responses. (shrink)

Because we must often make decisions in light of imperfect information about our prospective actions, the standard principles of objective obligation must be supplemented with principles of subjective obligation (which evaluate actions in light of what the agent believes about their circumstances and consequences). The point of principles of subjective obligation is to guide agents in making decisions. But should these principles be stated in terms of what the agent actually believes or what it would be reasonable for her to (...) believe about her prospective actions? I show that there are many decisions for which “reasonable belief” principles can’t be used by the decision-maker, especially in cases in which whether (or how) the agent investigates or deliberates affects the nature of the prospective action itself. I conclude that subjective rightness depends on what the agent actually believes, not what it would be reasonable for her to believe. (shrink)

Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...) andere im Bereich der Biologie und Biomedizin von der OBO Foundry. Es soll aufgezeigt werden, wie die Verpflichtung zu speziellen Kriterien der Ontologieentwicklung die Nützlichkeit und Effektivität der Ontologien positiv beeinflusst, indem die Pflege der terminologischen Systeme und ihre Interoperabilität vereinfacht werden. -/- Ergebnisse: SNOMED CT und die OBO Foundry unterscheiden sich grundlegend in ihren Ansätzen und Zielen. Unabhängig davon kann jedoch ein allgemeiner Trend zur strengeren Formalisierung und Fokussierung auf Interoperabilität zwischen unterschiedlichen Domänen und ihren Repräsentationen beobachtet werden. (shrink)

John Searle’s The Construction of Social Reality and Hernando de Soto’s The Mystery of Capital shifted the focus of current thought on capital and economic development to the cultural and conceptual ideas that underpin market economies and that are taken for granted in developed nations. This collection of essays assembles 21 philosophers, economists, and political scientists to help readers understand these exciting new theories.

Batı’da teorik felsefe; Analitik Felsefe (AF), Kıta Felsefesi (KF) ve Felsefe Tarihi (FT) olmak üzere üçe ayrılır. Fakat üçünde de işler yolunda değildir. AF, felsefenin bir bilim olabileceği iddiasından kuşku duyduğu için gerçek dünyayla ilgilenmiyorken başından beri uygun bir teorik yöntem izlemeyen Kıta Felsefesinin uygulanışı, belirli politik ve etik yargılara hizmet edecek şekilde özelleştirilmiştir. FT çalışmalarının gidişatı ise eldeki eserin nesnel değerinden daha çok ilgili filozofun ait olduğu ulus veya kültüre göre bölgesel bir temelde gelişmiştir. Felsefede ilerleme sağlanacaksa bu ancak (...) bahsi geçen tuzaklardan kaçınılarak gerçekleşebilir. (shrink)

Translation of "Von der Armut am Geiste; ein Dialog des jungen Lukács," by Ágnes Heller. This translation originally appeared in The Philosophical Forum, Spring-Summer 1972.

in Abortion and the Status of the Fetus, Volume XIII of the series, “Philosophy of Medicine,” eds. William B. Bondeson, H. Tristram Englehardt, Stuart Spicker, and Daniel H. Winship (Dordrecht, Holland/Boston, Massachusetts: D. Reidel, 1983), pp. 229-245.

An ontology of geographic kinds is designed to yield a better understanding of the structure of the geographic world, and to support the development of geographic information systems that are conceptually sound. This paper first demonstrates that geographical objects and kinds are not just larger versions of the everyday objects and kinds previously studied in cognitive science. Geographic objects are not merely located in space, as are the manipulable objects of table-top space. Rather, they are tied intrinsically to space, and (...) this means that their spatial boundaries are in many cases the most salient features for categorization. The ontology presented here will accordingly be based on topology (the theory of boundary, contact and separation) and on mereology (the theory of extended wholes and parts). Geographic reality comprehends mesoscopic entities, many of which are best viewed as shadows cast onto the spatial plane by human reasoning and language. Because of this, geographic categories are much more likely to show cultural differences in category definitions than are the manipulable objects of table-top space. (shrink)

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – and (...) this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

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. (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)

Three-dimensionalists , sometimes referred to as endurantists, think that objects persist through time by being “wholly present” at every time they exist. But what is it for something to be wholly present at a time? It is surprisingly difficult to say. The threedimensionalist is free, of course, to take ‘is wholly present at’ as one of her theory’s primitives, but this is problematic for at least one reason: some philosophers claim not to understand her primitive. Clearly the three-dimensionalist would be (...) better off if she could state her theory in terms accessible to all. We think she can. What is needed is a definition of ‘is wholly present at’ that all can understand. in this paper, we offer one. (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

Mobile phones are reportedly the most rapidly expanding e-reading device worldwide. However, the embodied, cognitive and affective implications of smartphone-supported fiction reading for leisure (m-reading) have yet to be investigated empirically. Revisiting the theoretical work of digitization scholar Anne Mangen, we argue that the digital reading experience is not only contingent on patterns of embodied reader–device interaction (Mangen, 2008 and later) but also embedded in the immediate environment and broader situational context. We call this the situation constraint. Its application to (...) Mangen’s general framework enables us to identify four novel research areas, wherein m-reading should be investigated with regard to its unique affordances. The areas are reader–device affectivity, situated embodiment, attention training and long-term immersion. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

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)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)

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. (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)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Suppose that some contradictions are true – for example, that as I walk through the door, I’m inside and I’m not inside. Then we argue 'if I'm walking through the door, I'm inside; I'm not inside; therefore, I'm not walking through the door' is an invalid instance of modus tollens.

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

In 1890 Christian von Ehrenfels published his classic paper "Über 'Gestaltqualitäten'", the first systematic investigation of the philosophy and psychology of Gestalt. Ehrenfels thereby issued an important challenge to the psychological atomism that was still predominant in his day. His paper not only exerted a powerful influence on the philosophy of the Meinong school, it also marked the beginning of the Gestalt tradition in psychology, later associated with the work of Wertheimer, Köhler and Koffka in Berlin. Includes papers by C. (...) Von Ehrenfels, Kurt Grelling and Paul Oppenheim and contributions by K. Mulligan, P.M. Simons and Barry Smith. (shrink)

This paper examines how the concepts of utility, impartiality, and universality worked together to form the foundation of Adam Smith's jurisprudence. It argues that the theory of utility consistent with contemporary rational choice theory is insufficient to account for Smith's use of utility. Smith's jurisprudence relies on the impartial spectator's sympathetic judgment over whether third parties are injured, and not individuals' expected utility associated with individuals' expected gains from rendering judgments over innocence or guilt.

NOTE: This paper is a reworking of some aspects of an earlier paper – ‘What else justification could be’ and also an early draft of chapter 2 of Between Probability and Certainty. I'm leaving it online as it has a couple of citations and there is some material here which didn't make it into the book (and which I may yet try to develop elsewhere). My concern in this paper is with a certain, pervasive picture of epistemic justification. On this (...) picture, acquiring justification for believing something is essentially a matter of minimising one’s risk of error – so one is justified in believing something just in case it is sufficiently likely, given one’s evidence, to be true. This view is motivated by an admittedly natural thought: If we want to be fallibilists about justification then we shouldn’t demand that something be certain – that we completely eliminate error risk – before we can be justified in believing it. But if justification does not require the complete elimination of error risk, then what could it possibly require if not its minimisation? If justification does not require epistemic certainty then what could it possibly require if not epistemic likelihood? When all is said and done, I’m not sure that I can offer satisfactory answers to these questions – but I will attempt to trace out some possible answers here. The alternative picture that I’ll outline makes use of a notion of normalcy that I take to be irreducible to notions of statistical frequency or predominance. (shrink)

In this paper, we contend that the “Smith case” in Gettier’s attempt to refute the justified true belief (JTB) account of knowledge does not work. This is because the said case fails to satisfy the truth condition, and thus is not a case of JTB at all. We demonstrate this claim using the framework of Donnellan’s distinction between the referential and attributive uses of definite descriptions. Accordingly, the truth value of Smith’s proposition “The man who will get the (...) job has ten coins in his pocket” partly depends on how Smith uses the definite description “the man who will get the job” when he utters the proposition. Since, upon uttering the proposition, Smith has in mind a particular individual, namely Jones, and not just whoever will fit the attribute specified in the definite description, Smith uses the definite description referentially. And so when it turns out that it is Smith who eventually gets the job, the definite description fails to refer to Jones as intended by Smith, thereby making Smith’s proposition false. To think that Smith’s proposition is still true, in this regard, is to use the definite description attributively—that it is about whoever will fit the definite description. Apparently, when Gettier claims that Smith’s proposition is still true, to demonstrate that it is a case of JTB, he, in effect, imposes his attributive understanding of Smith’s usage of the definite description on Smith’s own epistemic situation. (shrink)