The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (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)

The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and we argue that (...) they serve still as the basis for a series of influential confusions. We argue further that an ontology based unambiguously, not on concepts, but on the classification of entities in reality can, by removing these confusions, make a vital contribution to ensuring the interoperability of coding systems and healthcare records in the future. (shrink)

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)

J. David Lewis and Richard L. Smith provide a history of pragmatism and Chicago sociology based on the positions of realism and nominalism. This issue is indeed the key to understanding pragmatism’s foundations in Charles Peirce’s original formulation. Lewis and Smith claim that there are two pragmatisms, a realistic one characterized by Peirce and Mead and a nominalistic one (which Lewis and Smith claim has no value) illustrated by James and Dewey. They argue that Chicago sociology, including (...) Herbert Blumer, was under the influence of the nominalistic pragmatism, and that Mead exercised little influence during his lifetime. The argument is based on an ahistorical, a priori "metatheoretical" realism-nominalism distinction that claims to be based on Peirce's discussions of realism and nominalism. Yet the authors support their understanding of realism by appealing to Mead’s discussion of “contact experience,” and claim that Peirce’s realism must be based in non-symbolic “pure resistance.” Ironically, such a view represents the main tenet of nominalism, that only individual particulars are real, and amounts to a denial of Peirce’s category of Thirdness as reducible to the “pure resistance” of Secondness. Lewis and Smith attempt to correct the subjectivist tendencies of symbolic interactionism yet would problematically replace them with an equally subjective view of what constitutes objectivity: individual reaction with an object. American Sociology and Pragmatism tends to present a monistic universe hinging on a nominalistic interpretation of realism, a single-visioned view that places more emphasis on labels than on the substance and pragmatic import of a theorist's thoughts, resulting in serious distortions pro and con. Yet it also has opened up for serious questioning the whole foundations of symbolic interactionism and Mead's place within pragmatism and Chicago sociology. Though the authors claim to be "revisionists," it seems to me that they are also "fundamentalists" in safely preserving Mead at the center of a history they claim he did not significantly influence. In my opinion the ongoing controversy will result in a broader understanding of the antecedents of contemporary symbolic interactionism, one that will call for Mead's now dominating role as the sole representative of pragmatism for many American sociologists to be reevaluated and placed within the context of the quite substantial contributions of Peirce, James, and Dewey. (shrink)

Major Research Paper Abstract -/- A Part of This World: Deleuze & The Logic Of Creation. -/- Is there a particular danger in following Deleuze’s philosophy to its end result? According to Peter Hallward and Alain Badiou, Deleuze’s philosophy has some rather severe conclusions. Deleuze has been known as a vitalist thinker of life and affirmation. Hallward & Badiou seek to challenge the accepted view of Deleuze; showing that these accepted norms in Deleuzian scholarship should be challenged; and that initially (...) Deleuze calls for the evacuation of political action in order to remain firm in the realm of pure contemplation. I intend to investigate and defend Deleuze’s philosophy and against critics like Badiou and Hallward; and that not only is Deleuze’s philosophy creative and vital but also highly revolutionary and ‘a part of this world.’ I will look at several works in Deleuze’s corpus, as well as look at Deleuzian scholars whom defend Deleuze’s position -/- Hallward sees Deleuze as a theophantic thinker of the one and like Spinoza an individual mode must align oneself with the intellectual love of god, so that creativity and expressivity may mediate through them. Thus, according to Hallward the major theme of Deleuze’s philosophy is creativity; and a subject or a creature must tap into this vital spark of creation, which, is also a form of creatural confinement. Hallward states this creative act can only occur in the realm of the virtual, by lines of flight leading 'out of this world'. The subject is then re-introduced to an extra-worldly existence of contemplation and remains further away from decisions and lived experience. Deleuze, according to Hallward, falls prey to a cosmological pantheism. -/- Badiou has similar concerns. Deleuze’s philosophy is too systematic and abstract. The entirety of Deleuzes’ work is surrounded by metaphysics of the one; and essentially its repercussions lead to an overt asceticism. Badiou notes that Deleuze wants us all to surrender thought to a renewed concept of the one. Through the surrender of the one, the multiple is lost and incorporated into the realm of simulacra. Everything in this Deleuzian world is ‘always-already’ in the infinite and inhuman totality of the one. According to Badiou, this entire process is articulated in the power of inorganic life that operates through all of us. Like Hallward, Badiou sees Deleuze demolishing the subject, who is stuck between machinery and exteriority. Subjects are forced to transcend and go beyond their limits, slowly collapsing into an infinite virtuality. Badiou believes this is a powerful metaphor for a philosophy of death. Thus the conditions of Deleuzian thought are contingent upon asceticism, making a Deleuzian world a sort of ‘crowned anarchy’. Badiou sees Deleuze’s ascetic mission intimately linked with a philosophy of death, and like Hallward we should pay careful attention to the outcome of such an aristocratic philosophy. Death according to Badiou, symbolizes Deleuzian thought, not only making it dangerous, but also actualizing it as an ineffective position. Badiou also points out that Deleuze’s conceptual sources are not only limited but also repeated time and time again through a monotonous selection of concepts. Is this a fair critique and representation of Deleuzian thought? -/- Eugene Holland states, that both Hallward and Badiou have misrepresented Deleuze. Deleuze does invoke the creation of a new earth but one which we all fully believe in. The only world Deleuze wants to get out of is the world of habits, conformity, power; and forces that block creative being. According to Holland, Hallward presents us a Deleuze that inhibits an engagement with the world. However Deleuze’s creative enterprise is insistent on forming concepts that can change and transform our world. -/- So the question arises where does the problem of misrepresentation begin? It begins with both Badiou and Hallward having an erroneous account of the actual/virtual distinction in Deleuze’s Philosophy. According to Protevi, Hallward posits a dualism between the actual and the virtual, denying the role of the intensive. Hallward initially sees the relationship between the intensive and the virtual, ignoring the fact that the intensive has its own ontological register that mediates both the virtual and the actual. However, Protevi notes if one could not accept the intensive for an ontological register and had to place it with one or the other; you would have to accept an interrelationship between the actual and the intensive. Hallward places it in the realm of the virtual, thus, leading us to his major claim that Deleuze’s philosophy leads us out of the world. Protevi states, intensive processes happen in our world they are a part of this world. Hallward completely empties all creativity from the actual, thus depending on the virtual and its slippery slope. Both Hallward and Badiou have missed the point altogether. We live in an intensive/actual world and the main point about Deleuze’s politics has to do with experimentation and social interaction and the transformation and intervention of the concept. As Daniel W. Smith states, unlike Badiou, Deleuze is not searching for an axiomatic approach to the world, one that is prone to reductionism but rather with problematic, inventive and creative methods to transform a society. (shrink)

Vigorous debate over the moral propriety of cognitive enhancement exists, but the views of the public have been largely absent from the discussion. To address this gap in our knowledge, four experiments were carried out with contrastive vignettes in order to obtain quantitative data on public attitudes towards cognitive enhancement. The data collected suggest that the public is sensitive to and capable of understanding the four cardinal concerns identified by neuroethicists, and tend to cautiously accept cognitive enhancement even as they (...) recognize its potential perils. The public is biopolitically moderate, endorses both meritocratic principles and the intrinsic value of hard work, and appears to be sensitive to the salient moral issues raised in the debate. Taken together, these data suggest that public attitudes toward enhancement are sufficiently sophisticated to merit inclusion in policy deliberations, especially if we seek to align public sentiment and policy. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

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

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)

How does experimental philosophy address philosophical questions and problems? That is: What projects does experimental philosophy pursue? What is their philosophical relevance? And what empirical methods do they employ? Answers to these questions will reveal how experimental philosophy can contribute to the longstanding ambition of placing philosophy on the ‘secure path of a science’, as Kant put it. We argue that experimental philosophy has introduced a new methodological perspective – a ‘meta-philosophical naturalism’ that addresses philosophical questions about a phenomenon by (...) empirically investigating how people think about this phenomenon. This chapter asks how this novel perspective can be successfully implemented: How can the empirical investigation of how people think about something address genuinely philosophical problems? And what methods – and, specifically, what methods beyond the questionnaire – can this investigation employ? We first review core projects of experimental philosophy and raise the question of their philosophical relevance. For ambitious answers, we turn to experimental philosophy’s most direct historical precursor, mid-20th century ordinary language philosophy, and discuss empirical implementations of two of its research programmes that use experimental methods from psycholinguistics and corpus methods from the digital humanities. (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.

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

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

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)

Preparing general relativity for quantization in the Hamiltonian approach leads to the `problem of time,' rendering the world fundamentally timeless. One proposed solution is the `thermal time hypothesis,' which defines time in terms of states representing systems in thermal equilibrium. On this view, time is supposed to emerge thermodynamically even in a fundamentally timeless context. Here, I develop the worry that the thermal time hypothesis requires dynamics -- and hence time -- to get off the ground, thereby running into worries (...) of circularity. (shrink)

Historical research has recently made it clear that, prior to Austin and Searle, the phenomenologist Adolf Reinach (1884-1917) developed a full-fledged theory of speech acts under the heading of what he called "social acts". He we consider a second instance of a speech act theory avant la lettre, which is to be found in the common sense philosophy of Thomas Reid (1710-1796). Reid’s s work, in contrast to that of Reinach, lacks both a unified approach and the detailed analyses of (...) pertinent examples. But his writings leave no doubt that he is acutely aware of the very problems concerning language structure and use out of which contemporary speech act theory has evolved and that he goes a good way towards solving these problems in the spirit of the modern theory. (shrink)

Disaster response is a highly collaborative and critical process that requires the involvement of multiple emergency responders (ERs), ideally working together under a unified command, to enable a rapid and effective operational response. Following the 9/11 and 11/13 terrorist attacks and the devastation of hurricanes Katrina and Rita, it is apparent that inadequate communication and a lack of interoperability among the ERs engaged on-site can adversely affect disaster response efforts. Within this context, we present a scenario-based terrorism case study to (...) highlight the challenges of operational disaster command and response. In this article, which is based on the French emergency response doctrine, we outline a semantics-based common operational command system that is designed to guarantee an efficient information flow among ERs. Our focus is on offering to all ERs, a real-time operational picture of the situation in order to enable multilevel coordination among firefighters, police, healthcare units, public authorities, and other stakeholders. Our approach consolidates information to promote timely sharing of data among ERs. The proposed system is based on an ontology that has been developed to represent the different types of knowledge on the part of ERs, providing a shared vocabulary that covers a variety of interoperability concerns. (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)

This letter addresses the editorial decision to publish the article, “Research on group differences in intelligence: A defense of free inquiry” (Cofnas, 2020). Our letter points out several critical problems with Cofnas's article, which we believe should have either disqualified the manuscript upon submission or been addressed during the review process and resulted in substantial revisions.

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (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)

Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

This paper empirically raises and examines the question of ‘conceptual control’: To what extent are competent thinkers able to reason properly with new senses of words? This question is crucial for conceptual engineering. This prominently discussed philosophical project seeks to improve our representational devices to help us reason better. It frequently involves giving new senses to familiar words, through normative explanations. Such efforts enhance, rather than reduce, our ability to reason properly, only if competent language users are able to abide (...) by the relevant explanations, in language comprehension and verbal reasoning. This paper examines to what extent we have such ‘conceptual control’ in reasoning with new senses. The paper draws on psycholinguistic findings about polysemy processing to render this question empirically tractable and builds on recent findings from experimental philosophy to address it. The paper identifies a philosophically important gap in thinkers’ control over the key process of stereotypical enrichment and discusses how conceptual engineers can use empirical methods to work around this gap in conceptual control. The paper thus empirically demonstrates the urgency of the question of conceptual control and explains how experimental philosophy can empirically address the question, to render conceptual engineering feasible as an ameliorative enterprise. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a multicriteria decision support service, based (...) on the Analytic Hierarchy Process (AHP) method, that aims to avoid overcrowding and outpacing the capacity of a hospital to effectively provide the best care to victims by finding out the most appropriate hospital that meets the victims’ needs. The proposed approach searches for the most appropriate healthcare institution that can effectively deal with the victims’ needs by considering the availability of the needed resources in the hospital, the victim’s wait time to receive the healthcare, and the transfer time that represents the hospital proximity to the disaster site. The evaluation and validation results showed that the assignment of hospitals was done successfully considering the needs of each victim and without overwhelming any single hospital. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

The current rise of neurodevelopmental disorders poses a critical need to detect risk early in order to rapidly intervene. One of the tools pediatricians use to track development is the standard growth chart. The growth charts are somewhat limited in predicting possible neurodevelopmental issues. They rely on linear models and assumptions of normality for physical growth data – obscuring key statistical information about possible neurodevelopmental risk in growth data that actually has accelerated, non-linear rates-of-change and variability encompassing skewed distributions. Here, (...) we use new analytics to profile growth data from 36 newborn babies that were tracked longitudinally for 5 months. By switching to incremental (velocity-based) growth charts and combining these dynamic changes with underlying fluctuations in motor performance – as the transition from spontaneous random noise to a systematic signal – we demonstrate a method to detect very early stunting in the development of voluntary neuromotor control and to flag risk of neurodevelopmental derail. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Several important philosophical problems (including the problems of perception, free will, and scepticism) arise from antinomies that are developed through philosophical paradoxes. The critical strand of ordinary language philosophy (OLP), as practiced by J.L. Austin, provides an approach to such ‘antinomic problems’ that proceeds from an examination of ‘ordinary language’ (how people ordinarily talk about the phenomenon of interest) and ‘common sense’ (what they commonly think about it), and deploys findings to show that the problems at issue are artefacts of (...) fallacious reasoning. The approach is capable, and in need of, empirical development. Proceeding from a case-study on Austin’s paradigmatic treatment of the problem of perception, this paper identifies the key empirical assumptions informing the approach, assesses them in the light of empirical findings about default inferences, contextualisation failures, and belief fragmentation, and explores how these findings can be deployed to address the problem of perception. This facilitates a novel resolution of the problem of perception. Proceeding from this paradigm, the paper proposes ‘experimental critical OLP’ as a new research program in experimental philosophy that avoids apparent non-sequiturs of OLP, extends and transforms experimental philosophy’s ‘sources program’, and provides a promising new strategy for deploying empirical findings about how people ordinarily talk and think about phenomena, to address longstanding philosophical problems. (shrink)

When a technology is seen as the right solution to a recognized problem, the development of alternative technologies comes under threat. To secure much-needed resources, proponents of alternative technologies must, in these conditions, restart societal discussion on the status quo, a process at once technological and discursive known as ‘path creation’. In this article, we investigate discussion-restarting strategies employed by supporters of emerging technologies in the field of solar fuels, particularly the advocates of a technology referred to as ‘artificial photosynthesis’. (...) For illustrative purposes we explore four such strategies: revisiting weak spots, resizing the problem, redefining the game, and renegotiating labels. We conclude with a methodological reflection on the empirical study of discursive strategies in a socio-technical system. We further suggest a more systematic application of discourse-analytical and argumentation-theoretical insights that can complement current scholarship on path dependence and path creation. (shrink)

Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.

The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and that applying (...) the theory to the IPAP schizophrenia algorithm results in a representation that can be used by software agents to perform monitoring and control in a referent tracking environment. (shrink)

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

In philosophical thought experiments, as in ordinary discourse, our understanding of verbal case descriptions is enriched by automatic comprehension inferences. Such inferences have us routinely infer what else is also true of the cases described. We consider how such routine inferences from polysemous words can generate zombie intuitions: intuitions that are ‘killed’ (defeated) by contextual information but kept cognitively alive by the psycholinguistic phenomenon of linguistic salience bias. Extending ‘evidentiary’ experimental philosophy, this paper examines whether the ‘zombie argument’ against materialism (...) is built on zombie intuitions. We examine the hypothesis that contextually defeated stereotypical inferences from the noun ‘zombie’ influence intuitions about ‘philosophical zombies’. We document framing effects (‘zombie’ vs ‘duplicate’) predicted by the hypothesis. Findings undermine intuitions about the conceivability of ‘philosophical zombies’ and address the philosophical ‘hard problem of consciousness’. Findings support a deflationary response: The impression that principled obstacles prevent scientific explanation of how physical processes give rise to conscious experience is generated by philosophical arguments that rely on epistemically deficient intuitions. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (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 terms 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. To address this requirement, we are developing an Emotion Ontology (EMO). (shrink)

Intuitive judgments elicited by verbal case-descriptions play key roles in philosophical problem-setting and argument. Experimental philosophy's ‘sources project’ seeks to develop psychological explanations of philosophically relevant intuitions which help us assess our warrant for accepting them. This article develops a psycholinguistic explanation of intuitions prompted by philosophical case-descriptions. For proof of concept, we target intuitions underlying a classic paradox about perception, trace them to stereotype-driven inferences automatically executed in verb comprehension, and employ a forced-choice plausibility-ranking task to elicit the relevant (...) stereotypical associations of perception- and appearance-verbs. We obtain a debunking explanation that resolves the philosophical paradox. (shrink)

Taking the formal analogies between black holes and classical thermodynamics seriously seems to first require that classical thermodynamics applies in relativistic regimes. Yet, by scrutinizing how classical temperature is extended into special relativity, I argue that the concept falls apart. I examine four consilient procedures for establishing the classical temperature: the Carnot process, the thermometer, kinetic theory, and black-body radiation. I argue that their relativistic counterparts demonstrate no such consilience in defining the relativistic temperature. As such, classical temperature doesn’t appear (...) to survive a relativistic extension. I suggest two interpretations for this situation: eliminativism akin to simultaneity, or pluralism akin to rotation. (shrink)

Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana głównie za pomocą prostych przykładów z biologii, ale pojęcie niszy należy rozumieć — podobnie jak pojęcia części, granicy (...) i położenia — jako pojęcie strukturalne, znajdujące zastosowanie w obszernym zakresie różnych dziedzin. (shrink)

Future-bias is the preference, all else being equal, for positive states of affairs to be located in the future not the past, and for negative states of affairs to be located in the past not the future. Three explanations for future-bias have been posited: the temporal metaphysics explanation, the practical irrelevance explanation, and the three mechanisms explanation. Understanding what explains future-bias is important not only for better understanding the phenomenon itself, but also because many philosophers think that which explanation is (...) the correct one has implications for our evaluation of the normative status of future-bias. In this paper we focus on the connection between future-bias and the temporal value asymmetry. The latter refers to the fact that people tend to assign more value to a state of affairs when it is located in the future, as opposed to being equidistant in the past. All three candidate explanations offered for future-bias proceed by explaining the temporal value asymmetry, and then supposing that future-bias is simply a manifestation of that asymmetry. Recently, however, it has been argued that the conditions under which people display the temporal value asymmetry and future-bias are different, and that this is reason to doubt that the latter is a manifestation of the former. In this paper we empirically test one response to this argument against the manifestation thesis—the simulation response—according to which once we control for the degree to which people can simulate the object of their preference, we find that people display future-bias and the temporal value asymmetry in the same conditions. We find no evidence in favour of the simulation response. Moreover, our results support some previous research that suggests that the temporal value asymmetry is less robust than previously thought, and this in itself casts doubt on the idea that future bias is just a manifestation of this asymmetry. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)