This paper describes an undergraduate course in metaphilosophy for philosophy majors and argues that there are four potential benefits to students; namely that doing metaphilosophy (1) allows students to draw their own conclusions about what philosophy is, (2) develops students’ metacognitive skills to promote learning, (3) establishes students as members of the philosophical community, and (4) disposes students to live lives that reflect their philosophical education. It describes issues of transparency of course design and the particulars of the course, including (...) course content, and provides excerpts of student work to demonstrate student learning outcomes. Finally, it will suggest that even if it is not possible to offer a stand-alone course in metaphilosophy, instructors should provide opportunities to reflect on metaphilosophical issues in their other philosophy courses. (shrink)

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

The most notable contributions to contemporary philosophy of mind have been written by philosophers of mind for philosophers of mind. Without a good understanding of the historical framework, the technical terminology, the philosophical methodology, and the nature of the philosophical problems themselves, not only do undergraduate students face a difficult challenge when taking a first course in philosophy of mind, but instructors lacking specialized knowledge in this field might be put off from teaching the course. This paper is intended to (...) provide a framework for instructors with little background in this area of philosophy to develop a course in philosophy of mind. This course, aimed at the advanced undergraduate student, provides students with the tools necessary for understanding some of the key readings in contemporary philosophy of mind and offers unique benefits to both majors and non-majors. The course described here focuses on just two of the main problems in philosophy of mind—the mind-body problem and the problem of phenomenal consciousness—and briefly touches on other issues one might address. Finally, several solutions to common challenges that arise in an advanced philosophy course are discussed. (shrink)

The novelty in Smith’s way of looking at the economy is the discovery of a social character of wealth, something new in comparison with its definition in physical terms by the Physiocrats. The possibility of carrying out such an idealization was a result of the adoption of a Newtonian, as opposed to a Cartesian, epistemology, where an intermediate and provisional character of theoretical entities is explicitly accepted, dropping Cartesian strong epistemological realism.

INTRODUÇÃO Para compreender como a Sociologia nasceu e se desenvolveu, é essencial analisar as transformações que ocorreram a partir do século XIV, na Europa ocidental, marcando a passagem da sociedade feudal para a sociedade capitalista, ou a passagem da sociedade medieval para a sociedade moderna. Para isso, é necessário realizar uma pequena viagem histórica, já que, para entender as ideias de um autor e de determinada época, é fundamental contextualizá-las historicamente. Em cada sociedade, em todos os tempos, os seres humanos (...) elaboraram explicações religiosas, míticas, culturais, étnicas etc. para as situações em que vivem. No século XIX, a busca por outro tipo de explicação para os fenômenos da sociedade – a explicação científica – deu origem à Sociologia. Para demonstrar como o pensamento social organizou-se historicamente e como a Sociologia estruturou o saber sobre a sociedade humana, este trabalho terá como objetivo estudar alguns autores que se sobressaíram no processo de desenvolvimento dessa ciência. PREMISSA A Sociologia surgiu como um corpo de ideias a respeito do processo de constituição, consolidação e desenvolvimento da sociedade moderna. É fruto da Revolução Industrial e, nesse sentido, é denominada “ciência da crise”, porque, com base nela, procurou-se dar respostas às questões sociais desencadeadas pelo processo revolucionário que, num primeiro momento, alterou a sociedade europeia e, depois, a maior parte do mundo. Como todas as ciências, a Sociologia não despontou de repente ou da reflexão de algum autor iluminado. Constituiu-se com base em conhecimentos sobre a natureza e a sociedade que se desenvolveram a partir do século XIV, acompanhando as mudanças que marcaram a transformação da sociedade feudal e a constituição da sociedade capitalista. Entre essas mudanças, a expansão marítima europeia e a ampliação do comércio ultramarino, a Reforma protestante e o desenvolvimento científico e tecnológico podem destacados. São o pano de fundo do movimento intelectual que alterou profundamente as formas de explicar a natureza e a sociedade. Essas mudanças estão todas vinculadas e não podem ser entendidas como eventos isolados. 1 A EXPANSÃO MARÍTIMA Com a circum-navegação da África e o descobrimento da rota para as Índias e para a América, a concepção de mundo dos europeus foi consideravelmente ampliada. A definição de um mundo territorialmente bem mais vasto, com outros povos, outras culturas e outros modos de explicar as coisas, requereu a reformulação da maneira de ver e de pensar dos europeus. Assim, ao mesmo tempo que conheciam novos povos e novas culturas, os europeus instalavam colônias na África, na Ásia e na América. Em razão disso, expandiu-se o comércio de mercadorias (sedas, especiarias e produtos tropicais, como açúcar, milho, tabaco e café) entre as metrópoles e as colônias, bem como entre os países europeus. Surgiu a possibilidade de um mercado muito mais amplo e com características mundiais. Este seria o primeiro grande movimento de globalização. A exploração de metais preciosos, principalmente na América, e o tráfico de escravos para suprir a mão de obra nas colônias deram grande impulso ao comércio, que não mais ficou restrito aos mercadores das cidades-repúblicas (Veneza, Florença ou Flandres), passando também para as mãos de grandes comerciantes e de soberanos dos Estados nacionais em formação na Europa. Toda essa expansão territorial e comercial acelerou o desenvolvimento da economia monetária, com a acumulação de capitais pela burguesia comercial, que, mais tarde, teve importância decisiva na gestação do processo de industrialização da Europa. 2 A REFORMA PROTESTANTE No século XVI, assistiu-se também ao movimento que ficaria conhecido como Reforma protestante. Os reformistas questionavam as condutas do clero, a estrutura da Igreja católica e a autoridade do Papa. Os líderes do movimento promoviam a valorização do indivíduo ao pregar a livre leitura das Escrituras Sagradas e dispensar a intermediação dos ministros da Igreja nas práticas religiosas e nos assuntos relativos à fé. A Reforma contribuiu, assim, para alimentar um movimento de resistência à autoridade e à tradição que desembocaria na Ilustração. Entre seus principais líderes figuram Martinho Lutero (1483-1546) e João Calvino (1509-1564). 3 O DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO A nova maneira de se relacionar com as coisas sagradas foi acompanhada de uma nova forma de analisar o universo e a vida em sociedade. A razão passou a ser considerada essencial para conhecer o mundo; com base nela, as pessoas se consideraram livres para julgar, avaliar, pensar e emitir opiniões sem se submeter a nenhuma autoridade transcendente ou divina. A análise do universo e da vida em sociedade com base no conhecimento racional, fundado na observação e na experimentação, difundiu-se de maneira lenta, entre os séculos XV e XVII. Os pensadores que adotaram essa forma de análise enfrentaram o dogmatismo e a autoridade da Igreja. Por meio do Concílio de Trento (1545-1563) e dos processos da Inquisição, por exemplo, os membros do clero procuraram impedir toda e qualquer manifestação que pudesse pôr em dúvida a autoridade eclesiástica, fosse no campo da fé, fosse no das explicações que se propunham para a sociedade e a natureza. Os principais representantes do pensamento racional nos séculos XV a XVII foram Nicolau Maquiavel (1469-1527), Erasmo de Roterdã (1466-1536), Nicolau Copérnico (1473- 1543), Galileu Galilei (1564 -1642), Thomas Hobbes (1588 -1679), Francis Bacon (1561- 1626), René Descartes (1596 -1650) e Baruch Spinoza (1632 -1677). Os conhecimentos desses precursores alimentaram outros pensadores, como John Locke (1632-1704), Gottfried Leibniz (1646-1716) e Isaac Newton (1643-1727), que propuseram novos princípios para a compreensão da sociedade e da natureza. Vale salientar, por fim, que os pensadores europeus dos séculos XV a XVII buscaram compreender os fenômenos da natureza e da sociedade por meio da observação e da experimentação. 4 AS TRANSFORMAÇÕES NO SÉCULO XVIII No final do século XVIII, na maioria dos países europeus, a burguesia comercial, formada basicamente por comerciantes e banqueiros, constituía uma classe poderosa, em razão, na maior parte das vezes, das ligações econômicas que mantinha com as monarquias. Além de sustentar o comércio entre os países europeus, a burguesia europeia lançava seus tentáculos a vários pontos do mundo, até onde pudesse chegar, comprando e vendendo mercadorias. O capital mercantil estendia-se também a outro ramo de atividade: gradativamente se organizava a produção manufatureira. A compra de matérias-primas e a organização da produção, por meio do trabalho domiciliar ou do trabalho em oficinas, levavam ao desenvolvimento de um novo processo produtivo em contraposição ao das corporações de ofício. Os organizadores das manufaturas passaram a se interessar cada vez mais pelo aperfeiçoamento das técnicas de produção, a fim de produzir mais com menos gente e aumentar significativamente seus lucros. Para tanto, procuraram financiar a invenção de máquinas que pudessem ser utilizadas no processo produtivo. Com a invenção das máquinas de tecer e de descaroçar algodão, e a aplicação industrial da máquina a vapor e de outros tantos inventos destinados a aumentar a produtividade do trabalho, desenvolveu-se o fenômeno que veio a ser chamado de maquinofatura. O trabalho que as pessoas faziam com as mãos ou com ferramentas passava, a partir de então, a ser realizado por máquinas, elevando muito o volume da produção de mercadorias. A utilização da máquina a vapor, que podia mover outras tantas, impulsionou a indústria construtora de máquinas e, consequentemente, a indústria voltada para a produção de ferro e, posteriormente, de aço. Nesse contexto de profundas alterações no processo produtivo, no qual a utilização do trabalho mecânico era cada vez mais frequente, o trabalho artesanal continuou a existir. A maquinofatura se completou com o trabalho assalariado, no qual eram utilizadas, numa escala crescente, a mão de obra feminina e a infantil. Longe da Europa, explorava-se ouro no Brasil, prata no México e algodão nos Estados Unidos da América e na Índia. A maioria dessas atividades era realizada com a utilização do trabalho escravo ou servil. Esses elementos, conjugados, asseguraram as bases do processo de acumulação necessária para a expansão da indústria na Europa. Essas mudanças, somadas à herança cultural e intelectual do século XVII, definiram o século XVIII como explosivo. Se no século anterior a Revolução Inglesa determinou novas formas de organização política, no século XVIII a Revolução Americana e a Francesa alteraram o quadro político ocidental e serviram de exemplo e parâmetro para as revoluções políticas posteriores. As transformações na esfera da produção, a emergência de novas formas de organização política e a exigência da representação popular conferiram características muito específicas a esse século, em que pensadores como Charles de Montesquieu (1689 -1755), Voltaire (1694 - 1778), Denis Diderot (1713 -1784), Jean le Rond d’Alembert (1717 -1783), David Hume (1711 -1776), Jean-Jacques Rousseau (1712 -1778), Adam Smith (1723 -1790) e Immanuel Kant (1724 -1804) procuraram, por caminhos às vezes divergentes, refletir sobre a realidade, na tentativa de explicá-la. (shrink)

‘What is characteristic of every mental activity’, according to Brentano, is ‘the reference to something as an object. In this respect every mental activity seems to be something relational.’ But what sort of a relation, if any, is our cognitive access to the world? This question – which we shall call Brentano’s question – throws a new light on many of the traditional problems of epistemology. The paper defends a view of perceptual acts as real relations of a subject to (...) an object. To make this view coherent, a theory of different types of relations is developed, resting on ideas on formal ontology put forward by Husserl in his Logical Investigations and on the theory of relations sketched in Smith's "Acta cum fundamentis in re". The theory is applied to the notion of a Cambridge change, which proves to have an unforeseen relevance to our understanding of perception. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

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)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (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)

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

Artificial intelligence is man's attempt to use software to emulate the intelligence of human beings. But the complexity of the human neurological system formed in the course of evolution is impossible to replicate: "Human languages and societies are complex systems, indeed complex systems of many complex systems," so much so that their mathematical modeling is impossible. Barry Smith, philosopher and professor at the University at Buffalo. shows no uncertainty about this. His latest book written with Jobst Landgrebe, a mathematician (...) and entrepreneur in the AI field, leaves no doubt – starting with the title: Why machines will never rule the world (Routledge 2023). The book was presented in Turin during an evening organized by the Fondazione CRT and the Bruno Leoni Institute, in which Smith was interviewed based on questions developed by generative Ai. We have accepted the challenge to conduct an interview parallel to the one done with GPT4. (shrink)

A number of logicians and philosophers have turned their attention in recent years to the problem of developing a logic of interrogatives. Their work has thrown a great deal of light on the formal properties of questions and question-sentences and has led also to interesting innovations in our understanding of the structures of performatives in general and, for example, in the theory of presuppositions. When, however, we examine the attempts of logicians such as Belnap or Åqvist to specify what, precisely, (...) a question is, or what it is to ask or raise a question, then what we are offered is somewhat less illuminating. Two alternative reductionist accounts seem in particular to have gained most favor: questions are identified either as special sorts of statements, or as special sorts of requests. As we hope will become clear in what follows, neither of these accounts is even nearly adequate; and matters are not improved if questions are identified, by force majeure, as combinations of statements and requests. (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)

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)

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (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)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

This is the third draft of a paper that aims to clarify the apparent contradictions in the views presented in certain standards and other specifications of health informatics systems, contradictions which come to light when the latter are evaluated from the perspective of realist philosophy. One of the origins of this document was Klein’s discussion paper of 2005-07-02 entitled “Conceptology vs Reality” and the responses from Smith, as well as the several hours of discussions during the 2005 MIE meeting (...) in Geneva. (shrink)

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (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.

I argue that the offense generation pattern of slurring terms parallels that of impoliteness behaviors, and is best explained by appeal to similar purely pragmatic mechanisms. In choosing to use a slurring term rather than its neutral counterpart, the speaker signals that she endorses the term. Such an endorsement warrants offense, and consequently slurs generate offense whenever a speaker's use demonstrates a contrastive preference for the slurring term. Since this explanation comes at low theoretical cost and imposes few constraints on (...) an account of the semantics of slurs, this suggests that we should not require semantic accounts to provide an independent explanation of the offense profile. (shrink)

In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.

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)

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)

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)

Johannes Daubert he was an acknowledged leader, and in some respects the founder, of the early phenomenological movement, and was considered – as much by its members as by Husserl himself – the most brilliant member of the group. In Daubert’s unpublished writings we find a series of reflections on Lask, and on Neo-Kantianism, which form the subject-matter of this paper. They range over topics such as the ontology of the ‘Sachverhalt’ or state of affairs, truthvalues (Wahrheitswerte) and the value (...) of truth, negative judgments and the copula, and the relation between perception and judgment. (shrink)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (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)

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

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)

Ingarden distinguishes four strata making up the structure of the literary work of art: the stratum of word sounds and sound-complexes; the stratum of meaning units; the stratum of represented objectivities (characters, actions, settings, and so forth); and the stratum of schematized aspects (perspectives under which the represented objectivities are given to the reader). It is not only works of literature which manifest this four-fold structure but also certain borderline cases such as newspaper articles, scientific works, biographies, and so forth. (...) Ingarden specifies what is characteristic of a work of literature by asserting that all declarative sentences appearing in the stratum of meaning units of such work possess what he calls a quasi-judgmental character. We discuss here Ingarden’s theory of quasi-judgments and draw out its implication that all works of literature are works of fiction through and through. (shrink)

In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal theorists (...) from the paradox, which is as follows. (1) Any sound theory of justice is action-guiding. (2) Any sound theory of justice is ideal. (3) Any ideal theory fails to be action-guiding. Here I shall respond to Valentini in two ways. First, I shall show that both (1) and (2) are false. The falsity of either is sufficient to release ideal theorists from the paradox. Second, I shall show that Valentini’s response to (3) can be extended, because her bad kinds of ideal theory do not necessarily fail to guide action. The cumulative effect of my arguments further strengthens Valentini’s support of ideal theory. I will deal with premises (1) and (2) in Sections I and II, and (3) in Section III. (shrink)

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother. (shrink)

Law-enforcement agencies are increasingly able to leverage crime statistics to make risk predictions for particular individuals, employing a form of inference that some condemn as violating the right to be “treated as an individual.” I suggest that the right encodes agents’ entitlement to a fair distribution of the burdens and benefits of the rule of law. Rather than precluding statistical prediction, it requires that citizens be able to anticipate which variables will be used as predictors and act intentionally to avoid (...) them. Furthermore, it condemns reliance on various indexes of distributive injustice, or unchosen properties, as evidence of law-breaking. (shrink)

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

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

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

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)

This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...) for formal ontology. We provide examples to support this thesis from the domain of biomedicine. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The Emotion Ontology is an ontology covering all aspects of emotional and affective mental functioning. It is being developed following the principles of the OBO Foundry and Ontological Realism. This means that in compiling the ontology, we emphasize the importance of the nature of the entities in reality that the ontology is describing. One of the ways in which realism-based ontologies are being successfully used within biomedical science is in the annotation of scientific research results in publicly available databases. Such (...) annotation enables several objectives, including searching, browsing and cross-database data integration. A key benefit conferred by realismbased ontology is that suitably annotated research results are able to be aggregated and compared in a fashion that is based on the underlying reality that the science is studying. This has the potential of increasing the power of statistical analysis and meta-analysis in data-driven science. This aspect has been fruitfully exploited in the investigation of the functions of genes in molecular biology. Cognitive neuroscience uses functional neuroimaging to investigate the brain correlates of areas of mental functioning such as memory, planning and emotion. The use of functional neuroimaging to study affective phenomena such as the emotions is called ‘affective neuroscience’. BrainMap is the largest curated database of coordinates and metadata for studies in cognitive neuroscience, including affective neuroscience (Laird et al., 2005). BrainMap data is already classified and indexed using a terminology for classification, called the ‘Cognitive Paradigm Ontology’ (CogPO), that has been developed to facilitate searching and browsing. However, CogPO has been developed specifically for the BrainMap database, and the data are thus far not annotated to a realism-based ontology which would allow the discovery of interrelationships between research results across different databases on the basis of what the research is about. In this contribution, we describe ongoing work that aims to annotate affective neuroscience data, starting with the BrainMap database, using the Emotion Ontology. We describe our objectives and technical approach to the annotation, and mention some of the challenges. (shrink)

In addition to protecting agents’ autonomy, consent plays a crucial social role: it enables agents to secure partners in valuable interactions that would be prohibitively morally risk otherwise. To do this, consent must be observable: agents must be able to track the facts about whether they have received a consent-based permission. I argue that this morally justifies a consent-practice on which communicating that one consents is sufficient for consent, but also generates robust constraints on what sorts of behaviors can be (...) taken as consent- communicating. (shrink)

There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for classifying what the data are about. Unfortunately, such approaches (...) do not yield sustainable results where we are dealing with widely distributed, highly heterogeneous and often changing bodies of data. We argue here that the needed integration requires the use of what we call an lntegrating Semantic Framework (ISF), which provldes a consistent set of categories and relationships that can be reused over and over again to tag successive bodies of data in ways which foster more coherent representation and reasoning. (shrink)

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

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)