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)

For A. J. Ayer, the occurrence of delusions confutes the notion that we perceive the world directly. He argues instead that perceptions are caused by immaterial “sense data” which somehow represent the properties of material things to us in our experiences. J. L. Austin systematically rejects Ayer’s claims, arguing that the occurrence of delusions does not preclude the possibility of direct perception, and that, indeed, our normal perception is direct. I challenge both philosophers’ ideas by examining how they deal with (...) the phenomenon of colour. (shrink)

I respond to Tim Smartt’s (2023) skepticism about epistemic blame. Smartt’s skepticism is based on the claims that (i) mere negative epistemic evaluation can better explain everything proponents of epistemic blame say we need epistemic blame to explain; and (ii) no existing account of epistemic blame provides a plausible account of the putative force that any response deserving the label “blame” ought to have. He focuses primarily on the prominent “relationship-based” account of epistemic blame to defend these claims, arguing that (...) the account is explanatorily idle, and cannot distinguish between epistemically excused and epistemically blameworthy agents. I argue that Smartt mischaracterizes the account’s role for judgments of epistemic relationship impairment, leading to mistaken claims about the account’s predictions. I also argue that the very feature of the account that Smartt mischaracterizes is key to understanding what epistemic blame does for our epistemic responsibility practices that mere negative epistemic evaluation cannot. (shrink)

In De Anima 2.4, Aristotle claims that nutritive soul encompasses two distinct biological functions: nutrition and reproduction. We challenge a pervasive interpretation which posits ‘nutrients’ as the correlative object of the nutritive capacity. Instead, the shared object of nutrition and reproduction is that which is nourished and reproduced: the ensouled body, qua ensouled. Both functions aim at preserving this object, and thus at preserving the form, life, and being of the individual organism. In each case, we show how Aristotle’s detailed (...) biological analysis supports this ontological argument. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

We regularly make graded normative judgements in the epistemic domain. Recent work in the literature examines degrees of justification, degrees of rationality, and degrees of assertability. This paper addresses a different dimension of the gradeability of epistemic normativity, one that has been given little attention. How should we understand degrees of epistemic criticizability? In virtue of what sorts of factors can one epistemic failing be worse than another? The paper develops a dual-factor view of degrees of epistemic criticizability. According to (...) the view, degrees of epistemic criticizability are (i) an inverse function of degrees of doxastic justification and (ii) a function of degrees of agent culpability. The paper develops an account of each factor, and explains how they should be weighted. The paper also addresses the importance of modelling degrees of epistemic criticizability in a broader context. I focus on the role that such a model can play in the ethics of epistemic criticism. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

Why comply with epistemic norms? In this paper, I argue that complying with epistemic norms, engaging in epistemically responsible conduct, and being epistemically trustworthy are constitutive elements of maintaining good epistemic relations with oneself and others. Good epistemic relations are in turn both instrumentally and finally valuable: they enable the kind of coordination and knowledge acquisition underpinning much of what we tend to associate with a flourishing human life; and just as good interpersonal relations with others can be good for (...) their own sake, standing in good epistemic relations is good for its own sake. On my account, we have reason to comply with epistemic norms because it is a way of respecting the final value of something that also tends to be an instrumentally valuable thing: good epistemic relations. Situating the account within the recent social turn in debates about epistemic instrumentalism, I argue that the dual‐value aspect of good epistemic relations can explain important anti‐instrumentalist intuitions, in a well‐motivated way, within a broadly instrumentalist framework. (shrink)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

Abstract In light of the complexity of unfolding disasters, the diversity of rapidly evolving events, the enormous amount of generated information, and the huge pool of casualties, emergency responders (ERs) may be overwhelmed and in consequence poor decisions may be made. In fact, the possibility of transporting the wounded victims to one of several hospitals and the dynamic changes in healthcare resource availability make the decision process more complex. To tackle this problem, we propose a multicriteria decision support service, based (...) on the Analytic Hierarchy Process (AHP) method, that aims to avoid overcrowding and outpacing the capacity of a hospital to effectively provide the best care to victims by finding out the most appropriate hospital that meets the victims’ needs. The proposed approach searches for the most appropriate healthcare institution that can effectively deal with the victims’ needs by considering the availability of the needed resources in the hospital, the victim’s wait time to receive the healthcare, and the transfer time that represents the hospital proximity to the disaster site. The evaluation and validation results showed that the assignment of hospitals was done successfully considering the needs of each victim and without overwhelming any single hospital. (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Non-well-founded set theories allow set-theoretic exotica that standard ZFC will not allow, such as a set that has itself as its sole member. We can distinguish plenitudinous non-well-founded set theories, such as Boffa set theory, that allow infinitely many such sets, from restrictive theories, such as Finsler-Aczel or AFA, that allow exactly one. Plenitudinous non-well-founded set theories face a puzzle: nothing seems to explain the identity or distinctness of various of the sets they countenance. In this paper I aim to (...) sharpen this puzzle, make clear who it does and does not apply to and, ultimately, to argue in favor of a plenitudinous theory like Boffa. (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)

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)

There is a distinction between merely having the right belief, and further basing that belief on the right reasons. Any adequate epistemology needs to be able to accommodate the basing relation that marks this distinction. However, trouble arises for Bayesianism. I argue that when we combine Bayesianism with the standard approaches to the basing relation, we get the result that no agent forms their credences in the right way; indeed, no agent even gets close. This is a serious problem, for (...) it prevents us from making epistemic distinctions between agents that are doing a reasonably good job at forming their credences and those that are forming them in clearly bad ways. I argue that if this result holds, then we have a problem for Bayesianism. However, I show how the Bayesian can avoid this problem by rejecting the standard approaches to the basing relation. By drawing on recent work on the basing relation, we can develop an account of the relation that allows us to avoid the result that no agent comes close to forming their credences in the right way. The Bayesian can successfully accommodate the basing relation. (shrink)

Causal essentialists hold that a property essentially bears its causal and nomic relations. Further, as many causal essentialists have noted, the main motivations for causal essentialism also motivate holding that properties are individuated in terms of their causal and nomic relations. This amounts to a kind of identity of indiscernibles thesis; properties that are indiscernible with respect to their causal and nomic relations are identical. This can be compared with the more well-known identity of indiscernibles thesis, according to which particulars (...) that are qualitatively indiscernible are identical. Robert Adams has developed a well-known objection to this thesis by considering a series of possibilities involving nearly qualitatively indiscernible particulars that naturally leads to a possibility involving qualitatively indiscernible particulars. I argue that we can construct parallel cases involving a series of possibilities involving properties that are nearly indiscernible with respect to their causal and nomic relations that naturally lead to possibilities involving properties that are indiscernible with respect to their causal and nomic relations. The same features that make Adams’ argument forceful also carry over to my cases, giving us a powerful objection to the causal essentialist identity of indiscernibles thesis. (shrink)

There is a widely accepted distinction between being directly responsible for a wrongdoing versus being somehow indirectly or vicariously responsible for the wrongdoing of another person or collective. Often this is couched in analyses of complicity, and complicity’s role in the relationship between individual and collective wrongdoing. Complicity is important because, inter alia, it allows us to make sense of individuals who may be blameless or blameworthy to a relatively low degree for their immediate conduct, but are nevertheless blameworthy to (...) a higher degree for their implication in some larger (or another person’s) wrongdoing. In this paper, I argue that there is a distinctively epistemic kind of complicity. First, I motivate the distinction between direct and vicarious responsibility with three interlocking arguments, respectively appealing to: i) the structure of rational agency; ii) linguistic considerations; iii) the role of “principal vs. accomplice” in legal doctrine. I show how these arguments naturally extend to the epistemic domain, motivating an epistemic form of vicarious responsibility. I then examine complicity as a mechanism of vicarious epistemic responsibility. To fill this out, I engage with an epistemic analogue of the debate about the role of intention versus causal contribution in complicity. I propose a Casual Account of Epistemic Complicity, arguing that it accommodates a wide range of cases, and enables fine-grained explanations of degrees of culpability for epistemic complicity. With an adequate account of epistemic complicity on hand, we can explain what is objectionable about an important class of epistemic agent who, on an individual level, may be epistemically blameless or blameworthy to a relatively low degree, but whose relation to other individuals or collectives nevertheless makes them epistemically blameworthy to a higher degree. I explore some broader implications of this result. (shrink)

Plato’s references to Empedocles in the myth of the Statesman perform a crucial role in the overarching political argument of the dialogue. Empedocles conceives of the cosmos as structured like a democracy, where the constituent powers ‘rule in turn’, sharing the offices of rulership equally via a cyclical exchange of power. In a complex act of philosophical appropriation, Plato takes up Empedocles’ cosmic cycles of rule in order to ‘correct’ them: instead of a democracy in which rule is shared cyclically (...) amongst equal constituents, Plato’s cosmos undergoes cycles of the presence and absence of a single cosmic monarch who possesses ‘kingly epistēmē’. By means of a revision of Empedocles’ democratic cosmology, Plato’s richly woven myth is designed precisely to reject the appropriateness of democracy as a form of human political association and legitimate monarchy in its stead. (shrink)

Is there a distinctively epistemic kind of blame? It has become commonplace for epistemologists to talk about epistemic blame, and to rely on this notion for theoretical purposes. But not everyone is convinced. Some of the most compelling reasons for skepticism about epistemic blame focus on disanologies, or asymmetries, between the moral and epistemic domains. In this paper, I defend the idea that there is a distinctively epistemic kind of blame. I do so primarily by developing an account of the (...) nature of epistemic blame. My account draws on a prominent line of theorizing in moral philosophy that ties blame to our relationships with one another. I argue that with my account of epistemic blame on hand, the most compelling worries about epistemic blame can be deflated. There is a distinctively epistemic kind of blame. (shrink)

Does Aristotle offer a definition of the soul? In fact, he rejects the possibility of defining the soul univocally. Because “life” is a homonymous concept, so too is “soul”. Given the specific causal role that Aristotle envisages for form and essence, the soul requires multiple different definitions to capture how it functions as a cause in each form of life. Aristotle suggests demonstrations can be given which express these causal definitions; I reconstruct these demonstrations.

Evaluating counterfactuals in worlds with deterministic laws poses a puzzle. In a wide array of cases, it does not seem plausible that if a non-actual event were to occur that either the past would be different or that the laws would be different. But it’s also difficult to see how we can avoid this result. Some philosophers have argued that we can avoid this dilemma by allowing that a proposition can be a law even though it has violations. On this (...) view, for the relevant cases, the past and the laws would still hold, but the laws would have a violation. In this paper, I raise a problem for the claim that the laws and the past are preserved for all of the relevant counterfactual antecedents. I further argue that this problem undermines motivating the possibility of violations on the grounds that they allow us to hold that the past and the laws are typically counterfactually preserved, even if they are not always preserved. (shrink)

This paper provides a critical overview of recent work on epistemic blame. The paper identifies key features of the concept of epistemic blame and discusses two ways of motivating the importance of this concept. Four different approaches to the nature of epistemic blame are examined. Central issues surrounding the ethics and value of epistemic blame are identified and briefly explored. In addition to providing an overview of the state of the art of this growing but controversial field, the paper highlights (...) areas where future work is needed. (shrink)

In artificial intelligence, recent research has demonstrated the remarkable potential of Deep Convolutional Neural Networks (DCNNs), which seem to exceed state-of-the-art performance in new domains weekly, especially on the sorts of very difficult perceptual discrimination tasks that skeptics thought would remain beyond the reach of artificial intelligence. However, it has proven difficult to explain why DCNNs perform so well. In philosophy of mind, empiricists have long suggested that complex cognition is based on information derived from sensory experience, often appealing to (...) a faculty of abstraction. Rationalists have frequently complained, however, that empiricists never adequately explained how this faculty of abstraction actually works. In this paper, I tie these two questions together, to the mutual benefit of both disciplines. I argue that the architectural features that distinguish DCNNs from earlier neural networks allow them to implement a form of hierarchical processing that I call “transformational abstraction”. Transformational abstraction iteratively converts sensory-based representations of category exemplars into new formats that are increasingly tolerant to “nuisance variation” in input. Reflecting upon the way that DCNNs leverage a combination of linear and non-linear processing to efficiently accomplish this feat allows us to understand how the brain is capable of bi-directional travel between exemplars and abstractions, addressing longstanding problems in empiricist philosophy of mind. I end by considering the prospects for future research on DCNNs, arguing that rather than simply implementing 80s connectionism with more brute-force computation, transformational abstraction counts as a qualitatively distinct form of processing ripe with philosophical and psychological significance, because it is significantly better suited to depict the generic mechanism responsible for this important kind of psychological processing in the brain. (shrink)

One challenge in developing an account of the nature of epistemic blame is to explain what differentiates epistemic blame from mere negative epistemic evaluation. The challenge is to explain the difference, without invoking practices or behaviors that seem out of place in the epistemic domain. In this paper, I examine whether the most sophisticated recent account of the nature of epistemic blame—due to Jessica Brown—is up for the challenge. I argue that the account ultimately falls short, but does so in (...) an instructive way. Drawing on the lessons learned, I put forward an alternative approach to the nature of epistemic blame. My account understands epistemic blame in terms of modifications to the intentions and expectations that comprise our “epistemic relationships” with one another. This approach has a number of attractions shared by Brown’s account, but it can also explain the significance of epistemic blame. (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)

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)

In this short paper, I critically examine Veli Mitova’s proposal that social-identity groups can have collective epistemic reasons. My primary focus is the role of privileged access in her account of how collective reasons become epistemic reasons for social-identity groups. I argue that there is a potentially worrying structural asymmetry in her account of two different types of cases. More specifically, the mechanisms at play in cases of “doxastic reasons” seem fundamentally different from those at play in cases of “epistemic-conduct (...) reasons”. The upshot is a need for further explanation of what unifies these dimensions of the account. (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)

We examine moving spotlight theories of time: theories according to which there are past and future events and an objective present moment. In Section 1, we briefly discuss the origins of the view. In Section 2, we describe the traditional moving spotlight view, which we understand as an ‘enriched’ B-theory of time, and raise some problems for that view. In the next two sections, we describe versions of the moving spotlight view that we think are better and which solve those (...) problems. In Section 3, we describe a version of the view that combines permanentism – the thesis that all things always exist – with propositional temporalism, the thesis that some propositions are sometimes true and sometimes false. In Section 4, we discuss a version of the view that is like an ‘enriched’ presentism. We conclude with some brief thoughts on issues that remain outstanding. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Managing complex disaster situations is a challenging task because of the large number of actors involved and the critical nature of the events themselves. In particular, the different terminologies and technical vocabularies that are being exchanged among Emergency Responders may lead to misunderstandings. Maintaining a shared semantics for exchanged data is a major challenge. To help to overcome these issues, we elaborate a modular suite of ontologies called POLARISCO that formalizes the complex knowledge of the ERs. Such a shared vocabulary (...) resolves inconsistent terminologies and promotes semantic interoperability among ERs. In this work, we discuss developing POLARISCO as an extension of Basic Formal Ontology and the Common Core Ontologies. We conclude by presenting a real use-case to check the efficiency and applicability of the proposed ontology. (shrink)

The connection between whole and part is intimate: not only can we share the same space, but I’m incapable of leaving my parts behind; settle the nonmereological facts and you thereby settle what is a part of what; wholes don’t seem to be an additional ontological commitment over their parts. Composition as identity promises to explain this intimacy. But it threatens to make the connection too intimate, for surely the parts could have made a different whole and the whole have (...) had different parts. In this paper I attempt to offer an account of parthood that is intimate enough but not too intimate: the parts generate the whole, but they are not themselves the whole. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (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)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...) Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries. (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)

Recent advances in natural language processing have given rise to a new kind of AI architecture: the language agent. By repeatedly calling an LLM to perform a variety of cognitive tasks, language agents are able to function autonomously to pursue goals specified in natural language and stored in a human-readable format. Because of their architecture, language agents exhibit behavior that is predictable according to the laws of folk psychology: they function as though they have desires and beliefs, and then make (...) and update plans to pursue their desires given their beliefs. We argue that the rise of language agents significantly reduces the probability of an existential catastrophe due to loss of control over an AGI. This is because the probability of such an existential catastrophe is proportional to the difficulty of aligning AGI systems, and language agents significantly reduce that difficulty. In particular, language agents help to resolve three important issues related to aligning AIs: reward misspecification, goal misgeneralization, and uninterpretability. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

How should we determine the distribution of psychological traits—such as Theory of Mind, episodic memory, and metacognition—throughout the Animal kingdom? Researchers have long worried about the distorting effects of anthropomorphic bias on this comparative project. A purported corrective against this bias was offered as a cornerstone of comparative psychology by C. Lloyd Morgan in his famous “Canon”. Also dangerous, however, is a distinct bias that loads the deck against animal mentality: our tendency to tie the competence criteria for cognitive capacities (...) to an exaggerated sense of typical human performance. I dub this error “anthropofabulation”, since it combines anthropocentrism with confabulation about our own prowess. Anthropofabulation has long distorted the debate about animal minds, but it is a bias that has been little discussed and against which the Canon provides no protection. Luckily, there is a venerable corrective against anthropofabulation: a principle offered long ago by David Hume, which I call “Hume’s Dictum”. In this paper, I argue that Hume’s Dictum deserves a privileged place next to Morgan’s Canon in the methodology of comparative psychology, illustrating my point through a discussion of the debate over Theory of Mind in nonhuman animals. (shrink)

A plausible condition on having the standing to blame someone is that the target of blame's wrongdoing must in some sense be your “business”—the wrong must in some sense harm or affect you, or others close to you. This is known as the business condition on standing to blame. Many cases of epistemic blame discussed in the literature do not obviously involve examples of someone harming or affecting another. As such, not enough has been said about how an individual's epistemic (...) failing can really count as another person's business. In this paper, I deploy a relationship-based account of epistemic blame to clarify the conditions under which the business condition can be met in the epistemic domain. The basic idea is that one person's epistemic failing can be another's business in virtue of the way it impairs their epistemic relationship. (shrink)

The paper critically examines recent work on justifications and excuses in epistemology. I start with a discussion of Gerken’s claim that the “excuse maneuver” is ad hoc. Recent work from Timothy Williamson and Clayton Littlejohn provides resources to advance the debate. Focusing in particular on a key insight in Williamson’s view, I then consider an additional worry for the so-called excuse maneuver. I call it the “excuses are not enough” objection. Dealing with this objection generates pressure in two directions: one (...) is to show that excuses are a positive enough normative standing to help certain externalists with important cases; the other is to do so in a way that does not lead back to Gerken’s objection. I show how a Williamson-inspired framework is flexible enough to deal with both sources of pressure. Perhaps surprisingly, I draw on recent virtue epistemology. (shrink)

Our prominent definitions of cognition are too vague and lack empirical grounding. They have not kept up with recent developments, and cannot bear the weight placed on them across many different debates. I here articulate and defend a more adequate theory. On this theory, behaviors under the control of cognition tend to display a cluster of characteristic properties, a cluster which tends to be absent from behaviors produced by non-cognitive processes. This cluster is reverse-engineered from the empirical tests that comparative (...) psychologists use to determine whether a behavior was generated by a cognitive or a non-cognitive process. Cognition should be understood as the natural kind of psychological process that non-accidentally exhibits the properties assessed by these tests (as well as others we have not yet discovered). Finally, I review two plausible neural accounts of cognition's underlying mechanisms?one based in localization of function to particular brain regions and another based in the more recent distributed networks approach to neuroscience?which would explain why these properties non-accidentally cluster. While this notion of cognition may be useful for a number of debates, I here focus on its application to a recent crisis over the distinction between cognition and association in comparative psychology. (shrink)

Under what conditions would an artificially intelligent system have wellbeing? Despite its clear bearing on the ethics of human interactions with artificial systems, this question has received little direct attention. Because all major theories of wellbeing hold that an individual’s welfare level is partially determined by their mental life, we begin by considering whether artificial systems have mental states. We show that a wide range of theories of mental states, when combined with leading theories of wellbeing, predict that certain existing (...) artificial systems have wellbeing. Along the way, we argue that there are good reasons to believe that artificial systems can have wellbeing even if they are not phenomenally conscious. While we do not claim to demonstrate conclusively that AI systems have wellbeing, we argue that there is a significant probability that some AI systems have or will soon have wellbeing, and that this should lead us to reassess our relationship with the intelligent systems we create. (shrink)

Philosophers and cognitive scientists have worried that research on animal mind-reading faces a ‘logical problem’: the difficulty of experimentally determining whether animals represent mental states (e.g. seeing) or merely the observable evidence (e.g. line-of-gaze) for those mental states. The most impressive attempt to confront this problem has been mounted recently by Robert Lurz. However, Lurz' approach faces its own logical problem, revealing this challenge to be a special case of the more general problem of distal content. Moreover, participants in this (...) debate do not agree on criteria for representation. As such, future debate should either abandon the representational idiom or confront underlying semantic disagreements. (shrink)

Existing work on gaslighting ties it constitutively to facts about the intentions or prejudices of the gaslighter and/or his victim’s prior experience of epistemic injustice. I argue that the concept of gaslighting is more broadly applicable than has been appreciated: what is distinctive about gaslighting, on my account, is simply that a gaslighter confronts his victim with a certain kind of choice between rejecting his testimony and doubting her own basic epistemic competence in some domain. I thus hold that gaslighting (...) is a purely epistemic phenomenon—not requiring any particular set of intentions or prejudices on the part of the gaslighter—and also that it can occur even in the absence of any prior experience of epistemic injustice. Appreciating the dilemmatic character of gaslighting allows us to understand its connection with a characteristic sort of epistemic harm, makes it easier to apply the concept of gaslighting in practice, and raises the possibility that we might discover its structure and the associated harm in surprising places. (shrink)

‘Intersectionality’ is one of the rare pieces of academic jargon to make it out of the university and into the mainstream. The message is clear and well-known: your feminism had better be intersectional. But what exactly does this mean? This paper is partly an exercise in conceptual clarification, distinguishing at least six distinct types of claim found across the literature on intersectionality, and digging further into the most philosophically complex of these claims—namely the metaphysical and explanatory. It’s also partly a (...) reply to Sara Bernstein, who argued recently that the best interpretation of the metaphysical claim is explanatory priority. We’ll argue that duly clarified, it’s far from obvious that feminism had better be intersectional. At the very least, it had better not be only intersectional. (shrink)

In ‘The normative role of knowledge’ (2012), Declan Smithies defends a ‘JK-rule’ for belief: One has justification to believe that P iff one has justification to believe that one is in a position to know that P. Similar claims have been defended by others (Huemer, 2007, Reynolds, forthcoming). In this paper, I shall argue that the JK-rule is false. The standard and familiar way of arguing against putative rules for belief or assertion is, of course, to describe putative counterexamples. My (...) argument, though, won’t be like this – indeed I doubt that there are any intuitively compelling counterexamples to the JK-rule. Nevertheless, the claim that there are counterexamples to the JK-rule can, I think, be given something approaching a formal proof. My primary aim here is to sketch this proof. I will briefly consider some broader implications for how we ought to think about the epistemic standards governing belief and assertion. (shrink)