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)

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

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

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

The term “value of life” can refer to life’s intrinsic dignity: something nonincremental and time-unaffected in contrast to the fluctuating, incremental “value” of our lives, as they are longer or shorter and more or less flourishing. Human beings are equal in their basic moral importance: the moral indignities we condemn in the treatment of e.g. those with dementia reflect the ongoing human dignity that is being violated. Indignities licensed by the person in advance remain indignities, as when people might volunteer (...) their living, unconscious bodies for surrogacy or training in amputation techniques. Respect for someone’s dignity is significantly impacted by a failure to value that person’s very existence, whatever genuine respect and good will is shown by wanting the person’s life to go well. Valuing and respecting life is not, however, vitalism: there can be good and compelling reasons for eschewing some means of prolonging life. (shrink)

This chapter considers the ways in which whiteness as a skin color and ideology becomes a dominant level that sets the background against which all things, people and relations appear. Drawing on Merleau-Ponty's phenomenology, it takes up a series of films by Bruce Nauman and Marlon Riggs to consider ways in which this level is phenomenally challenged providing insights into the embodiment of racialization.

In recent years, calls have been made to address the relative dearth of qualitative sociological investigation into the sensory dimensions of embodiment, including within physical cultures. This article contributes to a small, innovative and developing literature utilizing sociological phenomenology to examine sensuous embodiment. Drawing upon data from three research projects, here we explore some of the ‘sensuousities’ of ‘intense embodiment’ experiences as a distance-running-woman and a boxing-woman, respectively. Our analysis addresses the relatively unexplored haptic senses, particularly the ‘touch’ of heat. (...) Heat has been argued to constitute a specific sensory mode, a trans-boundary sense. Our findings suggest that ‘lived’ heat, in our own physical-cultural experiences, has highly proprioceptive elements and is experienced as both a form of touch and as a distinct perceptual mode, dependent upon context. Our analysis coheres around two key themes that emerged as salient: (1) warming up, and (2) thermoregulation, which in lived experience were encountered as strongly interwoven. (shrink)

This paper considers the analogies and disanalogies between a certain sort of argument designed to oppose scepticism about free will and a certain sort of argument designed to oppose scepticism about the external world. In the case of free will, I offer the ancient Lazy Argument and an argument of my own, which I call the Agency Argument, as examples of the relevant genre; and in the case of the external world, I consider Moore’s alleged proof of an external world. (...) I draw attention to analogies and disanalogies between the arguments offered in each case in order to suggest that although the Agency Argument shares with its Moorean relative the unfortunate property of being dialectically ineffective against some of those it is mainly hoping to convince, it will not be dialectically ineffective against all of them. It is also argued that the Agency Argument is less vulnerable than Moore’s proof to worries about its justificatory structure. (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)

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (shrink)

According to ‘regularity theories’ of causation, the obtaining of causal relations depends on no more than the obtaining of certain kinds of regularity. Regularity theorists are thus anti-realists about necessary connections in nature. Regularity theories of one form or another have constituted the dominant view in analytic Philosophy for a long time, but have recently come in for some robust criticism, notably from Galen Strawson. Strawson’s criticisms are natural criticisms to make, but have not so far provoked much response from (...) regularity theorists. The paper considers and rebuts Strawson’s objections. For example, Strawson claims that if there were no necessary connections in nature, we ought continually to find the regularity of the Universe surprising. I argue that the fact that the Universe is regular is something we take ourselves (fallibly) to know, and hence, in the light of this knowledge, its continued orderliness is not at all surprising. -/- . (shrink)

In this paper Beebee argues that the problem of induction, which she describes as a genuine sceptical problem, is the same for Humeans than for Necessitarians. Neither scientific essentialists nor Armstrong can solve the problem of induction by appealing to IBE, for both arguments take an illicit inductive step.

The paper considers whether psychiatric kinds can be natural kinds and concludes that they can. This depends, however, on a particular conception of ‘natural kind’. We briefly describe and reject two standard accounts – what we call the ‘stipulative account’ (according to which apparently a priori criteria, such as the possession of intrinsic essences, are laid down for natural kindhood) and the ‘Kripkean account’ (according to which the natural kinds are just those kinds that obey Kripkean semantics). We then rehearse (...) a more permissive account: Richard Boyd’s ‘homeostatic property cluster’ (HPC) account. We argue that psychiatric kinds can in principle count as natural kinds on the HPC account. Moreover, specific psychiatric kinds (Tourette’s, schizophrenia, etc.) can be natural kinds even if the category psychiatric disorder is not itself a natural kind. (shrink)

Humean compatibilism is the combination of a Humean position on laws of nature and the thesis that free will is compatible with determinism. This article's aim is to situate Humean compatibilism in the current debate among libertarians, traditional compatibilists, and semicompatibilists about free will. We argue that a Humean about laws can hold that there is a sense in which the laws of nature are 'up to us' and hence that the leading style of argument for incompatibilism?the consequence argument?has a (...) false premiss. We also display some striking similarities between Humean compatibilism and libertarianism, an incompatibilist view. For example, standard libertarians face a problem about luck, and we show that Humean compatibilists face a very similar problem. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

Emotion processing is known to be impaired in psychopathy, but less is known about the cognitive mechanisms that drive this. Our study examined experiencing and suppression of emotion processing in psychopathy. Participants, violent offenders with varying levels of psychopathy, viewed positive and negative images under conditions of passive viewing, experiencing and suppressing. Higher scoring psychopathics were more cardiovascularly responsive when processing negative information than positive, possibly reflecting an anomalously rewarding aspect of processing normally unpleasant material. When required to experience emotional (...) response, by ‘getting into the feeling’ of the emotion conveyed by a negative image, higher factor 1 psychopathic individuals showed reduced responsiveness, suggesting that they were less able to do this. These data, together with the absence of corresponding differences in subjective self-report might be used to inform clinical strategies for normalising emotion processing in psychopathic offenders to improve treatment outcome, and reduce risk amongst this client group. (shrink)

In a recent paper (Bird 2001), Alexander Bird argues that the law that common salt dissolves in water is metaphysically necessary - and he does so without presupposing dispositionalism about properties. If his argument were sound, it would thus show that at least one law of nature is meta- physically necessary, and it would do so without illicitly presupposing a position (dispositionalism) that is already committed to a necessitarian view of laws. I shall argue that Bird's argument is unsuccesful.

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (shrink)

Singularists about causation often claim that we can have experiences as of causation. This paper argues that regularity theorists need not deny that claim; hence the possibility of causal experience is no objection to regularity theories of causation. The fact that, according to a regularity theorist, causal experience requires background theory does not provide grounds for denying that it is genuine experience. The regularity theorist need not even deny that non-inferential perceptual knowledge of causation is possible, despite the fact that (...) such knowledge would sometimes allow us to make inferences about what happens in far-off places and times. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

In this paper I defend an eudaimonistic reading of Spinoza’s ethical philosophy. Eudaimonism refers to the mainstream ethical tradition of the ancient Greeks, which considers happiness a naturalistic, stable, and exclusively intrinsic good. Within this tradition, we can also draw a distinction between weak eudaimonists and strong eudaimonists. Weak eudaimonists do not ground their ethical conceptions of happiness in complete theories of metaphysics, epistemology, or psychology. Strong eudaimonists, conversely, build their conceptions of happiness around an overall philosophical system that extends (...) far beyond ethics, while nevertheless being directed at the promotion of a happy life. I will show that Spinozistic happiness is not only naturalistic, stable, and exclusively intrinsically good, but that Spinoza is also a strong eudaimonist because his ethical account of happiness is incomprehensible without appeal to metaphysical, epistemological, and psychological doctrines. As well, I will explain how the apparent subjective and relativistic features of Spinoza’s ethics do not undermine the eudaimonistic reading, because both Spinoza and the ancient eudaimonists grant that the beliefs/feelings of the subject play a necessary (but insufficient) role in happiness as the highest good. (shrink)

In a recent paper, Michael Huemer provides a new interpretation for ‘N’, the operator that occurs in Peter van Inwagen’s Consequence Argument, and argues that, given that interpretation, the Consequence Argument is sound. I have no quarrel with Huemer’s claim that the Consequence Argument is valid. I shall argue instead that his defense of its premises—a defense that allegedly involves refuting David Lewis’s response to van Inwagen—is unsuccessful.

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

This paper presents a dilemma which it has been alleged by Kim Frost must be faced by any defender of the notion of a two-way power and offers a solution to the dilemma which is distinct from Frost’s own. The dilemma is as follows: assuming that powers are to be individuated by what they are powers to do or undergo, then either there is a unified description of the manifestation-type which individuates the power, or there is not. If there is, (...) then two-way powers are revealed really to be one-way powers, after all. If there is not, then it is difficult to explain why the two-way power does not simply dissolve into a mere combination of two one-way powers. The paper offers an account of what a two-way power is that is distinct from the one Frost takes for granted, and argues that this different conception is the key to avoiding the dilemma. It is also argued that this alternative conception has several further advantages over its rival and also that it has no less of a claim than Frost’s notion to be prefigured in Aristotle’s original discussion. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

Howard’s moral fortification theory of criminal punishment lends itself to justifying correction for children in schools that is supportive. There are good reasons to include other students in the learning opportunity occasioned by doing right in response to wrong, which need not exploit the wrongdoing student as a mere means. Care ethics can facilitate restorative and problem-solving approaches to correction. However, there are overriding reasons against doing so when this stigmatises the wrongdoing student, since this inhibits their learning. Responses that (...) avoidably stigmatise students impermissibly undermine both the developmental ethos of education, and students’ recognition and respect for each other as equals. (shrink)

Is it right to convict a person of a crime on the basis of purely statistical evidence? Many who have considered this question agree that it is not, posing a direct challenge to legal probabilism – the claim that the criminal standard of proof should be understood in terms of a high probability threshold. Some defenders of legal probabilism have, however, held their ground: Schoeman (1987) argues that there are no clear epistemic or moral problems with convictions based on purely (...) statistical evidence, and speculates that our aversion to such convictions may be nothing more than an irrational bias. More recently, Hedden and Colyvan (2019, section VI) describe our reluctance to convict on the basis of purely statistical evidence as an ‘intuition’, but suggest that there may be no ‘in principle’ problem with such convictions (see also Papineau, forthcoming, section 6). In this paper, I argue that there is, in some cases, an in principle problem with a conviction based upon statistical evidence alone – namely, it commits us to a precedent which, if consistently followed through, could lead to the deliberate conviction of an innocent person. I conclude with some reflections on the idea that the criminal justice system should strive to maximise the accuracy of its verdicts – and the related idea that we should each strive to maximise the accuracy of our beliefs. (shrink)

Some bemoan the incivility of our times, while others complain that people have grown too quick to take offense. There is widespread disagreement about what counts as an insult and when it is appropriate to feel insulted. Here I propose a definition and a preliminary taxonomy of insults. Namely, I define insults as expressions of a lack of due regard. And I categorize insults by whether they are intended or unintended, acts or omissions, and whether they cause offense or not. (...) Unintended insults are of particular concern since greater understanding may help us to avoid them. And insults by omission warrant special consideration because they suggest an interesting extension of Grice’s theory of conversational implicature. (shrink)

This paper argues that public statues of persons typically express a positive evaluative attitude towards the subject. It also argues that states have duties to repudiate their own historical wrongdoing, and to condemn other people’s serious wrongdoing. Both duties are incompatible with retaining public statues of people who perpetrated serious rights violations. Hence, a person’s being a serious rights violator is a sufficient condition for a state’s having a duty to remove a public statue of that person. I argue that (...) this applies no less in the case of the ‘morally ambiguous’ wrongdoer, who both accomplishes significant goods and perpetrates serious rights violations. The duty to remove a statue is a defeasible duty: like most duties, it can be defeated by lesser-evil considerations. If removing a statue would, for example, spark a violent riot that would risk unjust harm to lots of people, the duty to remove could be outweighed by the duty not to foreseeably cause unjust harm. This would provide a lesser-evil justification for keeping the statue. But it matters that the duty to remove is outweighed, rather than negated, by these consequences. Unlike when a duty is negated, one still owes something in cases of outweighing. And it especially matters that it is outweighed by the predicted consequences of wrongful behaviour by others. (shrink)

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

Epistemic peer disagreement raises interesting questions, both in epistemology and in philosophy of science. When is it reasonable to defer to the opinion of others, and when should we hold fast to our original beliefs? What can we learn from the fact that an epistemic peer disagrees with us? A question that has received relatively little attention in these debates is the value of epistemic peer disagreement—can it help us to further epistemic goals, and, if so, how? We investigate this (...) through a recent case in paleoanthropology: the debate on the taxonomic status of Homo floresiensis remains unresolved, with some authors arguing the fossils represent a novel hominin species, and others claiming that they are Homo sapiens with congenital growth disorders. Our examination of this case in the recent history of science provides insights into the value of peer disagreement, indicating that it is especially valuable if one does not straightaway defer to a peer’s conclusions, but nevertheless remains open to a peer’s evidence and arguments. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which (...) could afford to be ignored. (shrink)

In this paper I respond to Marcello Di Bello’s criticisms of the ‘normic account’ of the criminal standard of proof. In so doing, I further elaborate on what the normic account predicts about certain significant legal categories of evidence, including DNA and fingerprint evidence and eyewitness identifications.

In this paper, I explore the question what a continuant is, in the context of a very interesting suggestion recently made by Rowland Stout, as part of his attempt to develop a coherent ontology of processes. Stout claims that a continuant is best thought of as something that primarily has its properties at times, rather than atemporally—and that on this construal, processes should count as continuants. While accepting that Stout is onto something here, I reject his suggestion that we should (...) accept that processes are both occurrents and continuants; nothing, I argue, can truly occur or happen, which does not have temporal parts. I make an alternative suggestion as to how one might deal with the peculiar status of processes without jettisoning a very natural account of occurrence; and assess the consequences for the category of continuant. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...) and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)