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

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)

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)

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)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (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)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

Some, but not all, of the mistakes a person makes when acting in apparently necessary self-defense are reasonable: we take them not to violate the rights of the apparent aggressor. I argue that this is explained by duties grounded in agents' entitlements to a fair distribution of the risk of suffering unjust harm. I suggest that the content of these duties is filled in by a social signaling norm, and offer some moral constraints on the form such a norm can (...) take. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (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)

We are addressing this letter to the editors of Philosophical Psychology after reading an article they decided to publish in the recent vol. 33, issue 1. The article is by Nathan Cofnas and is entitled “Research on group differences in intelligence: A defense of free inquiry” (2020). The purpose of our letter is not to invite Cofnas’s contribution into a broader dialogue, but to respectfully voice our concerns about the decision to publish the manuscript, which, in our opinion, fails to (...) meet a range of academic quality standards usually expected of academic publications. (shrink)

Sometimes speakers within a linguistic community use a term that they do not conceptualize as a slur, but which other members of that community do. Sometimes these speakers are ignorant or naïve, but not always. This article explores a puzzle raised when some speakers stubbornly maintain that a contested term t is not derogatory. Because the semantic content of a term depends on the language, to say that their use of t is semantically derogatory despite their claims and intentions, we (...) must individuate languages in a way that counts them as speaking our language L, assigns t a determinately derogatory content in L, and still accommodates the other features of slurs’ linguistic profile. Given the difficulty of doing this, there is some reason to give a non-semantic analysis of the derogatory aspect of slurs. The author suggests that rather than dismissing the stubborn as semantically incompetent, we would do better to appeal to expected uptake as moral reasons for the stubborn to adjust their linguistic practices. (shrink)

This book is a survey of the most important developments in Austrian philosophy in its classical period from the 1870s to the Anschluss in 1938. Thus it is intended as a contribution to the history of philosophy. But I hope that it will be seen also as a contribution to philosophy in its own right as an attempt to philosophize in the spirit of those, above all Roderick Chisholm, Rudolf Haller, Kevin Mulligan and Peter Simons, who have done so much (...) to demonstrate the continued fertility of the ideas and methods of the Austrian philosophers in our own day. For some time now, historians of philosophy have been gradually coming to terms with the idea that post-Kantian philosophy in the German-speaking world ought properly to be divided into two distinct traditions which we might refer to as the German and Austrian traditions, respectively. The main line of the first consists in a list of personages beginning with Kant, Fichte, Hegel and Schelling and ending with Heidegger, Adorno and Bloch. The main line of the second may be picked out similarly by means of a list beginning with Bolzano, Mach and Meinong, and ending with Wittgenstein, Neurath and Popper. As should be clear, it is the Austrian tradition that has contributed most to the contemporary mainstream of philosophical thinking in the Anglo-Saxon world. For while there are of course German thinkers who have made crucial contributions to the development of exact or analytic philosophy, such thinkers were outsiders when seen from the perspective of native German philosophical culture, and in fact a number of them found their philosophical home precisely in Vienna. When, in contrast, we examine the influence of the Austrian line, we encounter a whole series of familiar and unfamiliar links to the characteristic concerns of more recent philosophy of the analytic sort. As Michael Dummett points out in his Origins of Analytic Philosophy, the newly fashionable habit of referring to analytic philosophy as "Anglo-American" is in this light a "grave historical distortion". If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy "could at least as well be called "Anglo-Austrian" (1988, p. 7). Much valuable scholarly work has been done on the thinking of Husserl and Wittgenstein, Mach and the Vienna Circle. The central axis of Austrian philosophy, however, which as I hope to show in what follows is constituted by the work of Brentano and his school, is still rather poorly understood. Work on Meinong or Twardowski by contemporary philosophers still standardly rests upon simplified and often confused renderings of a few favoured theses taken out of context. Little attention is paid to original sources, and little effort is devoted to establishing what the problems were by which the Austrian philosophers in general were exercised -- in spite of the fact that many of these same problems have once more become important as a result of the contemporary burgeoning of interest on the part of philosophers in problems in the field of cognitive science. (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 some cases, there appears to be an asymmetry in the evidential value of statistical and more individualized evidence. For example, while I may accept that Alex is guilty based on eyewitness testimony that is 80% likely to be accurate, it does not seem permissible to do so based on the fact that 80% of a group that Alex is a member of are guilty. In this paper I suggest that rather than reflecting a deep defect in statistical evidence, this (...) asymmetry might arise from a general constraint on rational inquiry. Plausibly the degree of evidential support needed to justify taking a proposition to be true depends on the stakes of error. While relying on statistical evidence plausibly raises the stakes by introducing new kinds of risk to members of the reference class, paradigmatically `individualized' evidence---evidence tracing back to A's voluntary behavior---can lower the stakes. The net result explains the apparent evidential asymmetry without positing a deep difference in the brute justificatory power of different types of evidence. (shrink)

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

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

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

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)

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)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

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

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

​I evaluate a suggestion, floated by Kimberly Ferzan (this volume), that the twitter hashtag campaign #BelieveWomen is best accommodated by non-reductionist views of testimonial justification. I argue that the issue is ultimately one about the ethical obligation to trust women, rather than a question of what grounds testimonial justification. I also suggest that the hashtag campaign does not simply assert that ‘we should trust women’, but also militates against a pernicious striking-property generic (roughly: ‘women make false sexual assault accusations’), that (...) distorts our evaluation of women’s testimony concerning sexual assault. I conclude #BelieveWomen does not demand that we believe against the evidence, or uncritically, or be more trusting than we have evidential justification to be. Rather, it aims to bring our trust closer to what is merited by the base-rate of reliable testimony from women concerning sexual assault. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The problem of moral disagreement has been presented as an objection to contextualist semantics for ‘ought’, since it is not clear that contextualism can accommodate or give a convincing gloss of such disagreement. I argue that independently of our semantics, disagreements over ‘ought’ in non-cooperative contexts are best understood as indirect metalinguistic disputes, which is easily accommodated by contextualism. If this is correct, then rather than posing a problem for contextualism, the data from moral disagreements provides some reason to adopt (...) a semantics that allows contextual variance in the meanings of ‘ought’. (shrink)

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)

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)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (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)

A popular informal argument suggests that statistics about the preponderance of criminal involvement among particular demographic groups partially justify others in making defensive mistakes against members of the group. One could worry that evidence-relative accounts of moral rights vindicate this argument. After constructing the strongest form of this objection, I offer several replies: most demographic statistics face an unmet challenge from reference class problems, even those that meet it fail to ground non-negligible conditional probabilities, even if they did, they introduce (...) new costs likely to cancel out any justificatory contribution of the statistic, but even if they didn’t, demographic facts are the wrong sort to make a moral difference to agents’ negative rights. I conclude that the popular argument should be rejected, and evidence-relative theories do not have the worrisome implication. (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)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (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)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

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)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (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)

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

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)