We give a brief overview of the evolution of mathematics, starting from antiquity, through Renaissance, to the 19th century, and the culmination of the train of thought of history’s greatest thinkers that lead to the grand unification of geometry and algebra. The goal of this paper is not a complete formal description of any particular theoretical framework, but to show how extremisation of mathematical rigor in requiring everything be drivable directly from first principles without any arbitrary assumptions actually leads to (...) relaxing the computational difficulty along with maximal conceptual clarity. With this, we consider a revision of the foundations of elementary geometry and algebra based on the work of Grassmann and Clifford and apply it to conceptual and practical problems of past and present modern mathematics and mathematical physics. (shrink)

This paper analyses Spalding’s Betrachtung über die Bestimmung des Menschen (1748) through a translation proposal that tries to point out the human disposal to act ethically. In accord with modern German use, I argue for a translation of Bestimmung as disposition. In the first part of the article, I deal with the relevant issues for a philosophy of human experience that are present in Spalding’s text. In the second one, I bring the translation proposal into the philosophical domain showing how (...) the Bestimmung as disposition suits the human nature, in particular for what concerns the ethics, namely the way humans are arranged to act with others, and things in a non-egoistic mode. The analysis rests on two philosophical concepts: Sorge (Heidegger) and Liebe (Jaspers), that give a description of the essential relational component of human beings in which to take care, to love, and to discover our surrounding world are the key points. (shrink)

Husserl and the phenomenology of religion have a delicate relationship that combines direct references to religious themes with broader analyses subsumable under the more general phenomenology of consciousness. This paper shows the themes and problems of a Husserlian phenomenological analysis of religious consciousness through an encounter with its elements. Word, Prayer, relationship with the Sacred and Faith are some of the indelible traces of a phenomenology of religious consciousness. The belief, however, is that phenomenology can be spoken of if and (...) only if the themes are addressed through the analysis of consciousness as the method teaches. Thus, an analysis of religious lived-experiences and transcendence (subjective and absolute) is joined by such phenomenologically diriment questions as a possible dichotomy between transcendence of immanence or immanence of transcendence. (shrink)

How can sound and space be connected not only in a metaphorical sense? Over the last decades, philosophy of sound, aesthetics, and musicology have shown increasing interest in space inquiry. However, the way we interact with each other, communicate in space, and gather information about/in space is rooted in sound in a completely different way from those of musical metaphors. In this paper, I present an analysis of the role sound plays in the constitution of both space and relations of (...) intimacy within it. Starting from the wealthy tips that E. T. Hall gives to us in order to delineate a new understanding of proxemics that includes sound experience, I argue that sound, silence, and noise are essential to determine the intimate space and the way we interact with it. Moving from a classical proxemics perspective, the analysis will focus on the intimate relation between sound, space, and body, dialoguing with phenomenology, anthropology, semiotics, and philosophy of space. (shrink)

Ever since the early days of quantum mechanics it has been suggested that consciousness could be linked to the collapse of the wave function. However, no detailed account of such an interplay is usually provided. In this paper we present an objective collapse model where the collapse operator depends on integrated information, which has been argued to measure consciousness. By doing so, we construct an empirically adequate scheme in which superpositions of conscious states are dynamically suppressed. Unlike other proposals in (...) which “consciousness causes the collapse of the wave function,” our model is fully consistent with a materialistic view of the world and does not require the postulation of entities suspicious of laying outside of the quantum realm. (shrink)

I suoni e le immagini sembrano appartenere a due forme dell’esperienza profondamente distinte. Due registri sensoriali antitetici cui corrispondono due fenomeni accostabili, ma mai completamente unibili. Eppure si ricorre spesso all’espressione immagine sonora, che cosa si intende precisamente? Esiste un punto in cui i suoni e le immagini si appartengono reciprocamente? Può un’immagine risuonare e un suono essere anche un’immagine? Il testo cerca di rispondere a questi quesiti scavando e intarsiando una concettualizzazione dell’immagine sonora attraverso un dialogo con la semiotica, (...) la fenomenologia e la filosofia dell’arte. Arricchendosi di una riflessione sul rapporto con il pensiero, l’indagine sull’immagine sonora si declina in tre momenti distinti: il suono con un fondamento d’immagine in cui l’elemento fondante è dato dalla presenza dell’immagine nel suono; il suono e l’immagine che si equivalgono orizzontalmente fondendosi l’uno con l’altra; l’immagine con un fondamento sonoro, in cui si rintracciano presenze sonore nell’immagine visiva. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

The notion of hyle seems problematic for a phenomenological foundation of experience. For this very reason, its completed invalidity was generally postulated. At the same time, there are many reflections in Husserlian writings that help us understand it better. This paper attempts to show how hyletic experience, by existing in the lived body, triggers in parallel rhythmic, vibrating, and sonorous experiences as bodily experiences. Sounds are experienced by the body before any reflections or conscious experiences of them. In this way, (...) the aporetical instance of hyletic data founds a proposal of resolution in the fundamental corporeal experience of sound. (shrink)

Whilst arguing for sounds as repeatable objects does not seem suitable to our auditory experience, considering them as events can then help us understand some of their main features. In this sense, sounds are events happening to material objects; they have a beginning and an end; they are ephemeral entities that we cannot grasp as ordinary objects. Nevertheless, supporters of event theory usually focus on the autonomous status that sounds manifest from the things in the world. Conversely, when we hear (...) sounds, we hear what and where they are sounding even in those theories that I will call detached-sound theories; in hearing them we hear how different materials create different sounds. Within the different positions of the event theory to pure-event or acousmatic proposal, the importance and role that the material has in the creation of diverse sounds does not always seem to be recognized. In this paper, I therefore aim to show how the materiality of resonating bodies and objects is given in all forms of auditory experience, not until analyzed the differences between object and event accounts in the philosophy of sound. (shrink)

Man avoids solitude through _divertissement_ because he is afraid of what staying alone entails: thinking about himself (Pascal). Furthermore, man seeks isolation in order to gain ambition and reputation (Montaigne). However, solitude is really different from isolation and it is a fundamental emotional condition. Heidegger’s analysis of the forms of boredom adapts to and relates to the specific dynamic of solitude, showing that it is a part of human being’s structure despite his experience appearing controversial. Even if man lives in (...) modern apartments and one-room apartments, he is in a condition of co-isolation (Sloterdijk) that differs from solitude. There is a space solitude (Foucault) that involves – or can involve – human isolation, but we only experience essential solitude in sleep (Merleau-Ponty, Blanchot, Perec) where man detached himself from himself and he is really alone, from himself and the others. The forms of solitude lead the analysis towards impersonal activity. (shrink)

Metamorphosis as it is represented by some pre-historical artists seems problematic for our occidental point of view. In fact, it seems to be strongly against identity and law of non-contradiction. Becoming in general is also viewed as an error or exception by our classic point of view. This very claim can conduct to theories of non-classical logic. Deleuze and Guattari in their monumental work had tried to offer enormous contributions in order to comprehend the becoming phenomenon. Through a pre-historical representations (...) analysis, with also an intrusion in contemporary art's field, I want to confront with possible metamorphosis representations remain theoretically founded in the deleuzian proposal in dialogue with phenomenological inquiry. New principle of individuation and analysis of expression provide new looks to arisen problems with classical logic and metamorphosis representations, which will be acceptable and comprehensible as art shows. (shrink)

Starting from Jaspers’ analysis of attitudes in Psychologie der Weltanschauungen and analyzing their causes, we find an essential description of the human being. The human condition of being in the world (Heidegger, Jaspers) can be troubled (Freud, Jung). However, this is characteristic for human life (Jaspers, Schellenbaum). Among all attitudes, the enthusiastic one is the more consistent with human being’s dynamic nature (Bergson, Jaspers, Schellenbaum). The human being feels himself deeply touched (Scheler, Jaspers) and becomes stunned. The aim of the (...) paper is to show that the enthusiastic view is well exposed by the act of singing. Traditionally analysed in connection with art (Cassirer, Solger, Wackenroder), the enthusiastic view gives us a “sound image” of the human being since his childhood (Gehlen, Leydi). In everyday life and by all its difficulties (Freud, Jung, Schellenbaum, Jaspers), the human being discloses his nature in acoustic manifestations (Keil, Kafka, Wackenroder) by expressing the enthusiastic mode. (shrink)

L'articolo analizza i fondamenti delle indagini percettive nell'impostazione fenomenologica. In particolare l'ambito uditivo si struttura in modalità, ricezioni ed analisi che, attraverso la critica di vari autori (Husserl, Heidegger, Dufrenne, Ihde, Schaeffer), si mostrano articolate in due direzioni (soggetto-oggetto e oggetto-soggetto). L' analisi delle componenti costitutive porta a riconoscere come ricorrente tra autori differenti quell'impostazione del problema la quale asserisce che, se da un lato non può prescindere dall'attività percettiva, come attività propria del soggetto, dall'altro questa stessa cerca una legittimità (...) emergente dalle cose stesse. La costituzione, una volta riconosciuto il darsi dell'oggetto sonoro, risiede, tuttavia, nelle attività percettive che delineano così il differenziarsi degli ascolti. (shrink)

In the last few years, the idea of human being has been enlarged from the individual closeness to morphogenetic openness. Concurrently with discovers and researches into invisible worlds that live with human beings – microbes, fungi, bacteria, etc. – a debate has opened up that agrees with recent positions in the field of ontology. The human being is capable of poietic openness and is defined by relations. Anyway, an absence of a rigorous conceptualisation of the individualising process remains latent to (...) the discourse. A classic principle of individualisation is probably incomplete. This paper brings into dialogue individualisation with singularisation through the manifestation process of expression in accordance with recent theoretical enactments of hybridisation processes. (shrink)

Heidegger’s ontologische Differenz imposes methodological limits which strictly mark his philosophy for rigor and determinacy. If it is not possible to think Being from the categories of the entity, it is also true that the difference is a tank of possibilities and developments to which Heidegger himself hints at. From the accuracy of the early works to the overturning of the problem in the later works, the ontological difference is a constant of Heideggerian thought. This paper seeks to push Existenz (...) from a mode of being of Dasein to a mode of giving of Seiende. In accordance with his late writings, bringing the question of the Being­-existence bond towards the perspective of the entity – and not only the entity among entities that poses the question –, the development of the problem in Heidegger’s meditation is analysed through the questions of ontological difference – the mode of negation, the between of distinction, the specific situatedness that defines experience, the Being, as a member of ontological difference, in its connection to the Nichts, the Event as a relaxation of the connection between Sein and Seiende. The entity that is exist­ent is the convergence point of the Event where Being and existent, Being and existence, are not in contrast, but protrude (ragen) towards each other revealing the traits of a Seyende des Seyns, of the entity of Being. (shrink)

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)

Listening is not an incorporeal experience; we do not listen with our non-extended minds. We listen with all our body, and music can change completely our personal structure. It is through sound experience that we change and asset ourselves. Studies in the doctrine of affects often use sonorous metaphors and concepts such as Stimmung, resonance, consonance, that refer to sound experience. In this paper, I try first of all to show how listening is rooted in body experience. Then, I argue (...) for a new consideration of the notion of person that takes into account the fundamental sonorous basis – psycho-acoustic – of its constitution. Thanks to sounds we can reach a new conceptualization of emotional relations between persons which we attain through the person’s ordo amoris. Additionally, with the analysis of sounds we grasp some aspects of emotional experience related to the singular person (intra-personal). So, if sounds are profoundly related to corporeal experience, so strongly involving affects as to modify our personal structure and form a person’s constitution, and affects can really do that, their relationship need to be inquired where both sound experience and affection are rooted: corporeity. (shrink)

Psychological and neuroscientific inquiry pointed out the value of attention for auditory perception. Recent studies have identified that the problem is not one of finding a location for a given task, but of identifying how and what one wants to do with a given stimulus. This radicalises the problem of attention in perception. In this paper I try bring experimental research into dialogue with social role of emotions and attention in sonorous and musical field from the point of view of (...) anthropology and ethnomusicology. (shrink)

-/- In Kafka's work there are many examples of metamorphic instances. Die Verwandlung is obviously the first case that we are used to know as a real metamorphic example. However, it is not the only one, for examples Odradek, but also the way Kafka describes the encounter between characters or the characteristics of some of them (Das Schloss). The paper tries to conceptualize the metamorphosis through a distinction between two forms: (1) metamorphosis or transformation that allows us to know from (...) where what is transformed comes (start) and where it arrives (arrival); (2) becoming that shows a tension between two different conditions or that not allows us to grasp something because of his intangibility. All this will be examined using the monumental work of Deleuze and Guattari and a phenomenology of metamorphosis developed by Conci. (shrink)

The existence of singularities alerts that one of the highest priorities of a centennial perspective on general relativity should be a careful re-thinking of the validity domain of Einstein’s field equations. We address the problem of constructing distinguishable extensions of the smooth spacetime manifold model, which can incorporate singularities, while retaining the form of the field equations. The sheaf-theoretic formulation of this problem is tantamount to extending the algebra sheaf of smooth functions to a distribution-like algebra sheaf in which the (...) former may be embedded, satisfying the pertinent cohomological conditions required for the coordinatization of all of the tensorial physical quantities, such that the form of the field equations is preserved. We present in detail the construction of these distribution-like algebra sheaves in terms of residue classes of sequences of smooth functions modulo the information of singular loci encoded in suitable ideals. Finally, we consider the application of these distribution-like solution sheaves in geometrodynamics by modeling topologically-circular boundaries of singular loci in three-dimensional space in terms of topological links. It turns out that the Borromean link represents higher order wormhole solutions. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The relationship between knowledge and vision seems really consolidated. It started in ancient Greece and we can found its basis in Plato. The history of logos as reason and as western foundation of culture gives us enormous examples in terms of metaphors and approaches in the knowledge-vision relationship. «I see it» is like «I know it». However if we look at the basis of logos we find the deep meaning of gathering, composition, bond and bind (lèghein), so as to we (...) could choose «to gather» as the best translation of logos (Hoffmann). My aim is to show how this key feature is represented by sounds. To think is to link information, memories and so on and the principal property of sound is union and merger. We can argue for a «sonorous thought» but in reality this property is simply the founding element of thought and reason. In fact if we analyse the limits of our knowledge (Kant, Plessner) we discover the incorrectness of knowledge-vision relationship – like the knowledge-discourse relationship. We should investigate this guideline as the recent research for Covid-19 vaccine has shown. (shrink)

Metamorphosis seems problematic for our occidental point of view. Becoming in general is viewed as an error or exception by our classic standpoint. In fact, it is strongly against identity and law of non-contradiction: A is fundamentally something different from B and for A it is impossible to be at the same time B. We need to think A as what-becomes-B in order to make metamorphosis possible. Anyway, how can A become B? As a matter of fact, this very claim (...) has been historically the most common critic opposed to becoming. Deleuze and Guattari in their monumental work had tried to offer an enormous contribution to a few related problems. Redefining the subject as an event described by movement and affect can exceed the metamorphosis’ aporia. This new principle of individuation provides a new look upon arisen questions primarily because affects and movements are constant coordinates that define how metamorphosis is experienced. The paper tries to show how the betweenness in action in the encounter with people, human beings, things, animals, plants and minerals defines the logic field of metamorphosis. This is shown in dialogue with the ontological turn in anthropology that is particularly focused on this affective and lively dimension of encounter especially among Amazonian populations. Actually this is also what happens in our – occidental and classical but live – relation with things and objects, as long as we try to think a real conceptualisation of experience. (shrink)

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

I argue that, if doxastic involuntarism is true, then we should reconceive what are traditionally called reasons for belief. The truth of doxastic involuntarism would rule out a certain understanding of reasons for belief according to which they are reasons to form, alter, or relinquish beliefs. Thus, reconceiving reasons for belief would require reconceiving doxastic obligations. I argue that, in fact, a reconception of reasons for belief warrants abandoning the notion of doxastic obligations, understood as obligations to perform acts of (...) belief formation, alteration, or relinquishment. Instead, the only sorts of obligations we would have that concern our doxastic states would be aretaic or practical. (shrink)

The notion of “empire” in Hardt and Negri’s political theory indicates a new postmodern sovereignty, able to lead the capital accumulation in the global market era. With the concept of “empire”, Hardt and Negri want to overtake the imperialism doctrines, considered by the two authors unable to understand correctly the global world. The aim of this essay is to clarify the conceptual contraposition between “empire” and “imperialism” offering a brief description of the international debate raised by the publication of “Empire” (...) by Hardt and Negri, in order to present the different positions and describe strengths, contradictions and aporias. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

Climate change appears to be a classic aggregation problem, in which billions of individuals perform actions none of which seem to be morally wrong taken in isolation, and yet which combine to drive the global concentration of greenhouse gases (GHGs) ever higher toward environmental (and humanitarian) catastrophe. When an individual can choose between actions that will emit differing amounts of GHGs―such as to choose a vegan rather than carnivorous meal, to ride a bike to work rather than drive a car, (...) or to take a reusable bag to the supermarket rather than send another plastic bag to landfill―does she have any reason to choose the lower-emitting actions? In this chapter I'll reject the claim that individuals don't make a difference when it comes to climate change. I first discuss making a difference with every action, as a way of getting clearer about how individuals' actions impact causally on the harms resulting from climate change, making a distinction so far overlooked in the climate ethics discussion between 'macro' thresholds like ice-cap melt, and 'micro' thresholds like severe weather events. I set aside making a difference with every action as implausible, and then move on to discuss both low probability of major difference, and high probability of minor difference. I argue that both of these are plausible characterizations of individuals' causal contributions to climate change. I conclude by noting some policy implications of having (probabilistic) individual difference-making back in play. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (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)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (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)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)