Common sense is on the one hand a certain set of processes of natural cognition - of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

The paper seeks to show how the world of everyday human cognition might be treated as an object of ontological investigation in its own right. The paper is influenced by work on affordances and prototypicality of psychologists such as Gibson and Rosch, by work on cognitive universals of the anthropologist Robin Horton, and by work of Patrick Hayes and others on ‘naive’ or ‘qualitative physics’. It defends a thesis to the effect that there is, at the heart of common (...) sense, a theoretical core of true propositions pertaining to mesoscopic objects, and that the latter are to be understood as relating mereologically to the objects studied by physical science. (shrink)

Most interpretations of Aristotle’s Posterior Analytics believe that the term ‘ameson’ is used to describe the principles or foundations of a given system of justification or explanation as epistemically prior to or more fundamental than the other propositions in the system. Epistemic readings (as I shall call them) arguably constitute a majority in the secondary literature. This predominant view has been challenged by Robin Smith (1986) and Michael Ferejohn (1994; 2013), who propose interpretations that should be classified as (...) non-epistemic according to the definition above. My aim in this article is purely negative. I intend to show that these non-epistemic interpretations are liable to serious objections and are in conflict with some important features of Aristotle’s theory of demonstration. (shrink)

The primary sense of the word ‘hypothesis’ in modern colloquial English includes “proposition not yet settled” or “open question”. Its opposite is ‘fact’ in the sense of “proposition widely known to be true”. People are amazed that Plato [1, p. 1684] and Aristotle [Post. An. I.2 72a14–24, quoted below] used the Greek form of the word for indemonstrable first principles [sc. axioms] in general or for certain kinds of axioms. These two facts create the paradoxical situation that in many cases (...) it is impossible to translate the Greek form of the word using the English form: the primary sense of the word ‘hypothesis’ in modern colloquial English is diametrically opposed to one sense used by Plato and by his most accomplished student Given current colloquial English usage it is impossible to get the word hypothesis to carry the connotation of “settled truth” much less “axiomatic truth”. The ‘hypo-’ [under] in the Plato-Aristotle use of ‘hypothesis’ might carry the sense of “basis” or “foundational” as opposed to “less than usual or normal”. This paradox parallels the one pointed out by Robin Smith: it is impossible for the English word ‘syllogism’ to carry the meaning of its Greek form Aristotle intended. There are other cases as well: it is impossible for the English biological term ‘genus’ to carry the meaning of its Greek form the Greek genos refers to family as in our ‘genealogy’, not to “higher species” as in our ‘generic’. (shrink)

Aristotle says that ὑπαρχειν has as many senses as ‘to be true’ (PrA. , A, 36, 48b2-9) and as many ways as there are different categories. (PrA., A, 37, 49a6-9) This may mean that for every ‘is’ there is a ὑπαρχειν. Τhe reason is that Aristotle uses ὑπαρχειν in converse direction of ‘is’. The equal statement of ‘A is B’ with ὑπαρχειν is ‘B ὑπαρχει to A.’ Allen Bāck points to the difference between the use of the verb with dative (...) case and its use with a subject alone in Greek language. When it is used with the dative, it retains its basic meaning, that is, ‘be already present’ or ‘exist really.’ ‘So to say that P belongs to S is to say that P exists in S, or, if you like, that P has its being in S.’ He believes that Aristotle uses this construction to insist that primary substances alone are the fundamental being and all other things only are ‘in’ substances. Thus, when the verb is used with the dative, it expresses dependent substance relation. But when it is used with a subject alone, e.g. in ‘S ὑπάρχει,’ it expresses that the subject really exists. (OI., 17a24 and 17b2) Thus, while it is the subject which is said to be the predicate, it is the predicate which ὑπάρχει to the subject. The formula of ‘τὸ Α ὑπάρχει τῷ Β’ is equivalent to ‘τὸ Β ἐστι Α.’ He uses the word for the predication of a category on substance (e.g. Met., α, 993b24-25; Met., Z, 1029a15-16; Cat., 5, 3b24-25), the predication of secondary substance on primary substance (e.g. Met., Z, 1038b21-23; Cat., 5, 2a14-19), the predication of primary substance on nothing else but itself (e.g. Met., Z, 1040b23-24), the belonging of a verb to the subject, the belonging of axioms to a single science (Met., 1005a22-23) , the belonging of PNC to all things that are (Met., IV, 3) , in the sense of really existing (Cael. 297b22, Met., 1041b4. Cf. B503, 125-126) or merely in the sense of the predication of a predicate on a subject (e.g. OI., I, 5, 17a22-24) and especially and much more repeatedly than anywhere else in his discussion of syllogism. (e.g. PrA., A, 36, 48a40-b2; PrA., B, 22, 67b28-30; PrA., A, 24a26-28) It is also used in some related senses like mere belonging (e.g. Met., A, 989a10-14; K, 1060a9-10) or to be there. (So., B, 5, 417b23-26) Some of its derived forms are also used by Aristotle. For example, ἐνυπαρχον in the sense of the thing that is ‘in’ something; (e.g. Met., A, 991a13-16; Met., Z, 1038b29-33 and 1039a3-5) ὑπερέχον in the sense of that which contains and ὑπερεχόμενον in the sense of that which is contained in something else. (e.g. Met., Δ, 1020b26-28) In a sense, the extent of the application of ὑπαρχειν is wider than ‘is’ since it is not restricted to the nominative form in which ‘is’ is used but is applicable to other cases as well: ‘For ‘That does not belong to this’ does not always mean that ‘This is not that’ but sometimes that ‘this is not of that’ or ‘for that.’ (PsA., A, 36, 48b28-33) Allen Bāck (B503, 124) points that in the Prior Analytics Aristotle uses ‘ὑπάρχει τῷ’ and ‘κατηγορεῖσθαι κατά’ interchangeably. (e.g. at 25b37-26a4) Referring to its converse construction in respect of μετέχει (if A belongs to B, then B participates in A) as a probable reason that it may have Platonist foundations. But the question is: why does Aristotle uses this construction (B belongs to A) instead of simply saying A is B? Alexander of Aphrodisias (Apr 54.21-29) wonders why Aristotle had to adhere to such artificial language, entirely unnatural for ordinary speakers of Greek. As Jonathan Barnes points out, all the three formulas of ‘τὸ Α ὑπάρχει τῷ Β,’ ‘τὸ Α κατηγορεῖται κατὰ τοῦ Β’ and ‘τὸ Α λέγεται κατὰ τοῦ Β’ are artificial in the sense that no Greek who wanted to say that pleasure was good would normally have expressed himself by way of any of them.’ Bāck thinks Aristotle may have used it ‘to stress the primacy of primary substances as the ultimate subjects.’ He also mentions the probability that it may be to emphasize that the terms are being coupled in predication without any existence condition, a suggestion he is not himself inclined with. Robin Smith notes for Aristotle that ‘belonging to’ construction is wider than ‘predicated of’ construction because it can be used for cases that cannot easily be treated as categorical sentences. While predication is restricted to cases in which the subject term is in the nominative case, belonging can indicate, as he quotes Mignucci (480-481), ‘any possible grammatical construction for a predicative relation’ . (shrink)

This review places this translation and commentary on Book A of Prior Analytics in historical, logical, and philosophical perspective. In particular, it details the author’s positions on current controversies. The author of this translation and commentary is a prolific and respected scholar, a leading figure in a large and still rapidly growing area of scholarship: Prior Analytics studies PAS. PAS treats many aspects of Aristotle’s Prior Analytics: historical context, previous writings that influenced it, preservation and transmission of its manuscripts, editions (...) of its manuscripts, interpretations, commentaries, translations, and its influence on subsequent logic, philosophy, and mathematics. All this attention is warranted because Prior Analytics marks the origin of logic: the field that, among other things, asks of a given proposition whether it follows from a given set of propositions; and, if it follows, how we determine that it follows; and, if it does not follow, how we determine that it does not follow. This translation and commentary is not suitable for use in an undergraduate course. It has too many quirks that the teacher would want to warn against. A copy editor should have dealt with these things and with other matters such as incorrect punctuation and improper end-of-line divisions. The prose is heavily laden with glaring clichés. The one-page preface contains “longer than I care to remember”, “more than I can possibly list here”, “first and foremost”, and “last and by no means least”—a sentence later is devoted to thanking the “incredibly meticulous and helpful copy-editor”. A few pages later the translator reveals the need “to find a path between the Scylla … and the Charybdis …”. Moreover, the index is far from meeting the needs of undergraduate students. The attention to scholarly detail is not what one hoped for from Oxford University Press. At 26b10-15, this translation reads “let swan and white be chosen as white things” for what Smith correctly translates “let swan and snow be selected from among those white things”. At 41b16, “angles AB and CD” should read “angles AC and BD”. Despite this book’s flaws, it will be found useful if not indispensable for those currently engaged in Prior Analytics studies. The alternatives suggested to Robin Smith’s translation choices are often worth consideration. It is to be emphasized, however, that this book is unsuitable for those entering Prior Analytics studies. (shrink)

JUNE 2015 UPDATE: A BIBLIOGRAPHY: JOHN CORCORAN’S PUBLICATIONS ON ARISTOTLE 1972–2015 By John Corcoran -/- This presentation includes a complete bibliography of John Corcoran’s publications relevant to his research on Aristotle’s logic. Sections I, II, III, and IV list 21 articles, 44 abstracts, 3 books, and 11 reviews. It starts with two watershed articles published in 1972: the Philosophy & Phenomenological Research article from Corcoran’s Philadelphia period that antedates his Aristotle studies and the Journal of Symbolic Logic article from his (...) Buffalo period first reporting his original results; it ends with works published in 2015. A few of the items are annotated as listed or with endnotes connecting them with other work and pointing out passages that in-retrospect are seen to be misleading and in a few places erroneous. In addition, Section V, “Discussions”, is a nearly complete secondary bibliography of works describing, interpreting, extending, improving, supporting, and criticizing Corcoran’s work: 8 items published in the 1970s, 23 in the 1980s, 42 in the 1990s, 56 in the 2000s, and 69 in the current decade. The secondary bibliography is also annotated as listed or with endnotes: some simply quoting from the cited item, but several answering criticisms and identifying errors. Section VI, “Alternatives”, lists recent works on Aristotle’s logic oblivious of Corcoran’s research and, more generally, of the Lukasiewicz-initiated tradition. As is evident from Section VII, “Acknowledgements”, Corcoran’s publications benefited from consultation with other scholars, most notably Timothy Smiley, Michael Scanlan, Roberto Torretti, and Kevin Tracy. All of Corcoran’s Greek translations were done in collaboration with two or more classicists. Corcoran never published a sentence without discussing it with his colleagues and students. -/- REQUEST: Please send errors, omissions, and suggestions. I am especially interested in citations made in non-English publications. Also, let me know of passages I should comment on. (shrink)

In May 2010, philosophers, family and friends gathered at the University of Notre Dame to celebrate the career and retirement of Alvin Plantinga, widely recognized as one of the world's leading figures in metaphysics, epistemology, and the philosophy of religion. Plantinga has earned particular respect within the community of Christian philosophers for the pivotal role that he played in the recent renewal and development of philosophy of religion and philosophical theology. Each of the essays in this volume engages with some (...) particular aspect of Plantinga's views on metaphysics, epistemology, or philosophy of religion. Contributors include Michael Bergman, Ernest Sosa, Trenton Merricks, Richard Otte, Peter VanInwagen, Thomas P. Flint, Eleonore Stump, Dean Zimmerman and Nicholas Wolterstorff. The volume also includes responses to each essay by Bas van Fraassen, Stephen Wykstra, David VanderLaan, Robin Collins, Raymond VanArragon, E. J. Coffman, Thomas Crisp, and Donald Smith. (shrink)

Of all twentieth century philosophers, it is Gilles Deleuze whose work agitates most forcefully for a worldview privileging becoming over being, difference over sameness; the world as a complex, open set of multiplicities. Nevertheless, Deleuze remains singular in enlisting mathematical resources to underpin and inform such a position, refusing the hackneyed opposition between ‘static’ mathematical logic versus ‘dynamic’ physical world. This is an international collection of work commissioned from foremost philosophers, mathematicians and philosophers of science, to address the wide range (...) of problematics and influences in this most important strand of Deleuze’s thinking. Contributors are Charles Alunni, Alain Badiou, Gilles Châtelet, Manuel DeLanda, Simon Duffy, Robin Durie, Aden Evens, Arkady Plotnitsky, Jean-Michel Salanskis, Daniel Smith and David Webb. (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.

Gender classifications often are controversial. These controversies typically focus on whether gender classifications align with facts about gender kind membership: Could someone really be nonbinary? Is Chris Mosier really a man? I think this is a bad approach. Consider the possibility of ontological oppression, which arises when social kinds operating in a context unjustly constrain the behaviors, concepts, or affect of certain groups. Gender kinds operating in dominant contexts, I argue, oppress trans and nonbinary persons in this way: they marginalize (...) trans men and women, and exclude nonbinary persons. As a result, facts about membership in dominant gender kinds should not settle gender classification practices. (shrink)

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)

We want to know what gender is. But metaphysical approaches to this question solely have focused on the binary gender kinds men and women. By overlooking those who identify outside of the binary–the group I call ‘genderqueer’–we are left without tools for understanding these new and quickly growing gender identifications. This metaphysical gap in turn creates a conceptual lacuna that contributes to systematic misunderstanding of genderqueer persons. In this paper, I argue that to better understand genderqueer identities, we must recognize (...) a new type of gender kind: critical gender kinds, or kinds whose members collectively destabilize one or more pieces of dominant gender ideology. After developing a model of critical gender kinds, I suggest that genderqueer is best modeled as a critical gender kind that destabilizes the ‘binary axis’, or the piece of dominant gender ideology that says that the only possible genders are the binary, discrete, exclusive, and exhaustive kinds men and women. (shrink)

Alex Byrne’s article, “Are Women Adult Human Females?”, asks a question that Byrne treats as nearly rhetorical. Byrne’s answer is, ‘clearly, yes’. Moreover, Byrne claims, 'woman' is a biological category that does not admit of any interpretation as (also) a social category. It is important to respond to Byrne’s argument, but mostly because it is paradigmatic of a wider phenomenon. The slogan “women are adult human females” is a political slogan championed by anti-trans activists, appearing on billboards, pamphlets, and anti-trans (...) online forums. In this paper, I respond to Byrne’s argument, revealing significant problems with its background assumptions, content, and methodology. (shrink)

There has been extensive discussion of testimonial epistemic injustice, the phenomenon whereby a speaker’s testimony is rejected due to prejudice regarding who they are. But people also have their testimony rejected or preempted due to prejudice regarding what they communicate. Here, the injustice is content focused. We describe several cases of content focused injustice, and we theoretically interrogate those cases by building up a general framework through which to understand them as a genuine form of epistemic injustice that stands in (...) intertwined relationships to other forms of epistemic injustice. (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)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

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

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)

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)

What’s important about ‘coming out’? Why do we wear business suits or Star Trek pins? Part of the answer, we think, has to do with what we call agential identity. Social metaphysics has given us tools for understanding what it is to be socially positioned as a member of a particular group and what it means to self-identify with a group. But there is little exploration of the general relationship between self-identity and social position. We take up this exploration, developing (...) an account of agential identity—the self-identities we make available to others. Agential identities are the bridge between what we take ourselves to be and what others take us to be. Understanding agential identity not only fills an important gap in the literature, but also helps us explain politically important phenomena concerning discrimination, malicious identities, passing, and code-switching. These phenomena, we argue, cannot be understood solely in terms of self-identity or social position. (shrink)

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

We live in a world saturated in both racial and gendered divisions. Our focus is on one place where attitudes about these divisions diverge: language. We suspect most everyone would be horrified at the idea of adding race-specific pronouns, honorifics, generic terms, and so on to English. And yet gender-specific terms of the same sort are widely accepted and endorsed. We think this asymmetry cannot withstand scrutiny. We provide three considerations against incorporating additional race-specific terms into English, and argue that (...) these considerations also support eliminating the analogous gender-specific terms. With respect to these parts of speech, English should be no more gender-specific than it already is race-specific. (shrink)

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

In this paper, we defend two main claims. The first is a moderate claim: we have a negative duty to not use binary gender-specific pronouns he or she to refer to genderqueer individuals. We defend this with an argument by analogy. It was gravely wrong for Mark Latham to refer to Catherine McGregor, a transgender woman, using the pronoun he; we argue that such cases of misgendering are morally analogous to referring to Angel Haze, who identifies as genderqueer, as he (...) or she. The second is a radical claim: we have a negative duty to not use any gender-specific pronouns to refer to anyone, regardless of their gender identity. We offer three arguments in favor of this claim (which appeal to concerns about inegalitarianism and risk, invasions of privacy, and reinforcing essentialist ideologies). We also show why the radical claim is compatible with the moderate claim. Before concluding, we examine common concerns about incorporating either they or a neologism such as ze as a third-person singular gender-neutral pronoun. These concerns, we argue, do not provide sufficient reason to reject either the moderate or radical claim. (shrink)

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

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

Many of us hold false beliefs about matters that are relevant to public policy such as climate change and the safety of vaccines. What can be done to rectify this situation? This question can be read in two ways. According to the descriptive reading, it concerns which methods will be effective in persuading people that their beliefs are false. According to the normative reading, it concerns which methods we are permitted to use in the service of persuading people. Some effective (...) methods—a programme of brainwashing, say—would not be permissible. In this paper I compare “methods of rational persuasion” with what you might call “marketing methods” such as how one frames the problem of climate change. My aim is to show that “marketing methods” are preferable to “methods of rational persuasion”. My argument has two parts. First, I argue that the evidence suggests that “marketing methods” are more effective in persuading people to change their minds. Second, I argue that “marketing methods” are an acceptable response to the normative question. (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)

Analytic philosophy has transgender trouble. In this paper, I explore potential explanations for this trouble, focusing on the notion of 'cisgender commonsense' and its place in philosophical methodology.

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

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

In this article, Dembroff argues that the category nonbinary should not be understood in terms of presentation or psychological states, but instead in terms of how its members are politically situated with respect to the binary expectations of Western gender ideology.

This paper presents the Obstetric and Neonatal Ontology (OntONeo). This ontology has been created to provide a consensus representation of salient electronic health record (EHR) data and to serve interoperability of the associated data and information systems. More generally, it will serve interoperability of clinical and translational data, for example deriving from genomics disciplines and from clinical trials. Interoperability of EHR data is important to ensuring continuity of care during the prenatal and postnatal periods for both mother and child. As (...) a strategy to advance such interoperability we use an approach based on ontological realism and on the ontology development principles of the Open Biomedical Ontologies Foundry, including reuse of reference ontologies wherever possible. We describe the structure and coverage domain of OntONeo and the process of creating and maintaining the ontology. (shrink)

Ordinary discourse is filled with discussions about ‘sexual orientation’. This discourse might suggest a common understanding of what sexual orientation is. But even a cursory search turns up vastly differing, conflicting, and sometimes ethically troubling characterizations of sexual orientation. The conceptual jumble surrounding sexual orientation suggests that the topic is overripe for philosophical exploration. This paper lays the groundwork for such an exploration. In it, I offer an account of sexual orientation – called ‘Bidimensional Dispositionalism’ – according to which sexual (...) orientation concerns what sex[es] and gender[s] of persons one is disposed to sexually engage, and makes no reference to one’s own sex and gender. (shrink)

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...) Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

In this peer commentary on Maura Priest's "Transgender Children and the Right to Transition: Medical Ethics When Parents Mean Well but Cause Harm", I argue against the "mismatch" model of trans identity. On this model, which is prevalent in institutional and medical contexts, to be trans is to have one's gender identity "mismatch" with one's sexed body.

Autobiography of Barry Smith; emphasizes the role of Dummett and Husserl, Austrian philosophy and economics, and the Munich-Göttingen-Kraków school of realist phenomenology.

When one takes an intersectional perspective on patterns of oppression and domination, it becomes clear that familiar forms of systemic injustice, such as misogyny and anti-Black racism, are inseparable. Some feminist theorists conclude, from this, that the systems behind these injustices cannot be individuated—for example, that there isn’t patriarchy and white supremacy, but instead only white supremacist patriarchy. This chapter offers a different perspective. Philosophers have long observed that a statue and a lump of clay can be individuated although inseparable, (...) and that statues and lumps of clay do different explanatory and predictive work for the same causal outcomes. This chapter suggests that the same is true of systems such as patriarchy and white supremacy. These systems, like the injustices they produce, are inseparable. But they can be individuated, and when they are individuated, they do different explanatory and predictive work. (shrink)

Most discussions of racial fetish center on the question of whether it is caused by negative racial stereotypes. In this paper I adopt a different strategy, one that begins with the experiences of those targeted by racial fetish rather than those who possess it; that is, I shift focus away from the origins of racial fetishes to their effects as a social phenomenon in a racially stratified world. I examine the case of preferences for Asian women, also known as ‘yellow (...) fever’, to argue against the claim that racial fetishes are unobjectionable if they are merely based on personal or aesthetic preference rather than racial stereotypes. I contend that even if this were so, yellow fever would still be morally objectionable because of the disproportionate psychological burdens it places on Asian and Asian-American women, along with the role it plays in a pernicious system of racial social meanings. (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)

Interviewet er lavet i juli 2021. Dets formål er at belyse emner, der er centrale i Celikates’ tænkning, f.eks. den voksende højrefløjspopulisme, migration, voldelige versus ikke-voldelige protester, civil ulydighed og den kritiske filosofis rolle i dag. -/- When Celikates and I sat down digitally in July 2021, the interview’s primary purpose was to examine topics central to Celikates’ thinking, such as the rise of right-wing populism, migration, violent versus non-violent protest, civil disobedience, and the role of critical philosophy today.

Contextualism is the view that knowledge ascriptions – utterances of sentences containing the word “knows” - express different propositions in different contexts of utterance. But what features of context determine the propositions expressed by knowledge ascriptions? According to a version of contextualism I call conversational contextualism, the conversational dynamics or kinematics determine the propositions expressed by knowledge ascriptions. In this paper I argue that the most sophisticated version of conversational contextualism, which is the view defended by Michael Blome-Tillmann (2009; 2014), (...) faces serious problems. My (very) tentative conclusion will be that conversational contextualism should be abandoned because of these problems. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

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