Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (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)

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)

In May 2021, Alan Bechaz, Racher Du, Will Cailes and Thomas Spiteri interviewed Sandra Leonie Field for UPJA’s Conversations from the Region. A series of discussions that invites philosophers from or based in Australasia to share their student and academic experiences. The segment looks into what inspires people to study philosophy, how they pursue their philosophical interests, and gives our audiences a better idea of philosophy as an undergraduate.

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)

To create fair and accountable AI and robotics, we need precise regulation and better methods to certify, explain, and audit inscrutable systems.

Since approval of the EU General Data Protection Regulation (GDPR) in 2016, it has been widely and repeatedly claimed that the GDPR will legally mandate a ‘right to explanation’ of all decisions made by automated or artificially intelligent algorithmic systems. This right to explanation is viewed as an ideal mechanism to enhance the accountability and transparency of automated decision-making. However, there are several reasons to doubt both the legal existence and the feasibility of such a right. In contrast to the (...) right to explanation of specific automated decisions claimed elsewhere, the GDPR only mandates that data subjects receive meaningful, but properly limited, information (Articles 13-15) about the logic involved, as well as the significance and the envisaged consequences of automated decision-making systems, what we term a ‘right to be informed’. Further, the ambiguity and limited scope of the ‘right not to be subject to automated decision-making’ contained in Article 22 (from which the alleged ‘right to explanation’ stems) raises questions over the protection actually afforded to data subjects. These problems show that the GDPR lacks precise language as well as explicit and well-defined rights and safeguards against automated decision-making, and therefore runs the risk of being toothless. We propose a number of legislative and policy steps that, if taken, may improve the transparency and accountability of automated decision-making when the GDPR comes into force in 2018. (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)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

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

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)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

This book offers a detailed study of the political philosophies of Thomas Hobbes and Benedict de Spinoza, focussing on their concept of power as potentia, concrete power, rather than power as potestas, authorised power. The focus on power as potentia generates a new conception of popular power. Radical democrats–whether drawing on Hobbes's 'sleeping sovereign' or on Spinoza's 'multitude'–understand popular power as something that transcends ordinary institutional politics, as for instance popular plebsites or mass movements. However, the book argues that these (...) understandings reflect a residual scholasticism which Hobbes and Spinoza ultimately repudiate. Instead, on the book's revisionist conception, a political phenomenon should be said to express popular power when it is both popular (it eliminates oligarchy and encompasses the whole polity), and also powerful (it robustly determines political and social outcomes). Two possible institutional forms that this popular power might take are distinguished: Hobbesian repressive egalitarianism, or Spinozist civic strengthening. But despite divergent institutional proposals, the book argues that both Hobbes and Spinoza share the conviction that there is nothing spontaneously egalitarian or good about human collective existence. From this point of view, the book accuses radical democrats of pernicious romanticism; the slow, meticulous work of organizational design and maintenance is the true centre of popular power. Three minute video summary available via HPBin3. Extended discussion on The Political Theory Review podcast. First chapter open access available via Oxford Scholarship Online. Videos of book talks at National University of Singapore (Centre for Legal Theory) and Universidad de Buenos Aires (Instituto de Investigaciones Gino Germani) available via YouTube. (See links below.). (shrink)

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

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (shrink)

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

Thomas Hobbes has been hailed as the philosopher of power par excellence; however, I demonstrate that Hobbes’s conceptualization of political power is not stable across his texts. Once the distinction is made between the authorized and the effective power of the sovereign, it is no longer sufficient simply to defend a doctrine of the authorized power of the sovereign; such a doctrine must be robustly complemented by an account of how the effective power commensurate to this authority might be achieved. (...) Nor is this straightforward: for effective political power can fluctuate, sometimes severely. In this light, the prevalent juridical reading of Hobbes’s political philosophy is inadequate. (shrink)

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

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

ABSTRACT Genevieve Lloyd argues that when we follow Spinoza in understanding reason as a part of nature, we gain new insights into the human condition. Specifically, we gain a new political insight: we should respond to cultural difference with a pluralist ethos. This is because there is no pure universal reason; human minds find their reason shaped differently by their various embodied social contexts. Furthermore, we can use the resources of the imagination to bring this ethos about. In my response, (...) I offer a friendly challenge to Lloyd’s characterisation of the lessons of Spinoza’s philosophy. I argue that Lloyd’s Spinoza remains excessively unpolitical, even in the moment that he is brought to bear on contemporary politics. An unpluralistic attitude may well be rationally inferior, but is it really explained by insufficient or inappropriate imagination? To the contrary, a properly Spinozist account of reason must include an account of the concrete determinants of reason’s imperfect realisation in the world. In Spinoza’s own oeuvre, this is carried out through an ever-increasing—and ever more sociological—interest in the political structures within which individual reason flourishes or withers. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Although high-performance human resource practices do not directly affect corporate social performance strengths, they do positively affect CSP strengths in companies that are highly innovative or have high levels of slack. High-performance human resource management practices also directly and negatively affect CSP concerns. Drawing on the resource-based view and using secondary data from an objective, third-party database, the authors develop and test hypotheses about how high-performance HRM affects a company’s CSP strengths and concerns. Findings suggest that HRM and innovation are (...) important capabilities because they create and enhance other capabilities. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Spanish translation of Field, S. L. (2014). 'Hobbes and the question of power'. Journal of the History of Philosophy, 52(1), 61-86. Thomas Hobbes has been hailed as the philosopher of power par excellence; however, I demonstrate that Hobbes’s conceptualization of political power is not stable across his texts. Once the distinction is made between the authorized and the effective power of the sovereign, it is no longer sufficient simply to defend a doctrine of the authorized power of the sovereign; such (...) a doctrine must be robustly complemented by an account of how the effective power commensurate to this authority might be achieved. Nor is this straightforward: for effective political power can fluctuate, sometimes severely. In this light, the prevalent juridical reading of Hobbes’s political philosophy is inadequate. (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.

It is common to assimilate Marx’s and Spinoza’s conceptions of democracy. In this chapter, I assess the relation between Marx’s early idea of “true democracy” and Spinozist democracy, both the historical influence and the theoretical affinity. Drawing on Marx’s student notebooks on Spinoza’s Theological-Political Treatise, I show there was a historical influence. However, at the theoretical level, I argue that a sharp distinction must be drawn. Philosophically, Spinoza’s commitment to understanding politics through real concrete powers does not support with Marx’s (...) anti-institutional conception of true democracy. And as a matter of social theory, the gap between civil society and the state which so troubles Marx is a development of modernity that has not entered Spinoza's premodern field of view. Marx’s true democracy was also influenced by his study of Rousseau, and theoretically, it is just as close if not closer to Rousseau as to Spinoza. (shrink)

The politics of climate change is marked by the fact that countries are dragging their heels in doing what they ought to do; namely, creating a binding global treaty, and fulfilling the duties assigned to each of them under it. Many different agents are culpable in this failure. But we can imagine a stylised version of the climate change case, in which no agents are culpable: if the bad effects of climate change were triggered only by crossing a particular threshold, (...) and it was reasonably, but mistakenly, believed by each country that insufficiently many other countries were willing to cooperate in order for that threshold to remain uncrossed, no country would be required to make a unilateral contribution. Yet even without culpability, we can diagnose a moral ill: the world has gone other than it should have. If not for the mistaken beliefs, there would have been a global climate treaty, and all the avoidance of future suffering that would come with it. In this article I argue that this moral ill has implications for the non-culpable agents, in that it generates duties to disgorge actual holdings over and above the counterpart holdings in the relevant counterfactual: those holdings the agents would have had, were the world to have gone as it should. (shrink)

According to a recent interpretive orthodoxy, Spinoza is a profoundly democratic theorist of state authority. I reject this orthodoxy. To be sure, for Spinoza, a political order succeeds in proportion as it harnesses the power of the people within it. However, Spinoza shows that political inclusion is only one possible strategy to this end; equally if not more useful is political exclusion, so long as it maintains what I call the depoliticised acquiescence of those excluded.

Negri celebrates a conception of democracy in which the concrete powers of individual humans are not alienated away, but rather are added together: this is a democracy of the multitude. But how can the multitude act without alienating anyone’s power? To answer this difficulty, Negri explicitly appeals to Spinoza. Nonetheless, in this paper, I argue that Spinoza’s philosophy does not support Negri’s project. I argue that the Spinozist multitude avoids internal hierarchy through the mediation of political institutions and not in (...) spite of them; nor do these institutions merely emanate from the multitude as it is, but rather they structure, restrain and channel its passions. In particular, the required institutions are not those of a simple direct democracy. There may be other non-Spinozist arguments on which Negri can ground his theory, but he cannot legitimately defend his conception of the democratic multitude by appeal to Spinoza. (shrink)

This paper is aimed at understanding one central aspect of Bolzano's views on deductive knowledge: what it means for a proposition and for a term to be known a priori. I argue that, for Bolzano, a priori knowledge is knowledge by virtue of meaning and that Bolzano has substantial views about meaning and what it is to know the latter. In particular, Bolzano believes that meaning is determined by implicit definition, i.e. the fundamental propositions in a deductive system. I go (...) into some detail in presenting and discussing Bolzano's views on grounding, a priori knowledge and implicit definition. I explain why other aspects of Bolzano's theory and, in particular, his peculiar understanding of analyticity and the related notion of Ableitbarkeit might, as it has invariably in the past, mislead one to believe that Bolzano lacks a significant account oï a priori knowledge. Throughout the paper, I point out to the ways in which, in this respect, Bolzano's antagonistic relationship to Kant directly shaped his own views. (shrink)

Hobbes’s science of politics rests on a dual analysis of human beings: humans as complex material bodies in a network of mechanical forces, prone to passions and irrationality; and humans as subjects of right and obligation, morally exhortable by appeal to the standards of reason. The science of politics proposes an absolutist model of politics. If this proposal is not to be idle utopianism, the enduring functioning of the model needs to be compatible with the materialist analysis of human behaviour. (...) In this paper, I argue that Hobbes's attempts to render his science of politics compatible with his materialism are only partly successful; a fuller compatibility is achieved in the political writings of Spinoza. -/- Published with reply: Luke O'Sullivan, 'Sovereigns and citizens: a response to Field', ibid., 221-224. Reprinted as: Sandra Field (2015), 'Hobbes and human irrationality', in T. Nardin (ed.) Rationality in Politics and its Limits, Abingdon: Routledge, 31-44. With reply: Luke O'Sullivan, 'Sovereigns and citizens: a response to Field', ibid., 45-48. (shrink)

The European Hobbes Society Online Colloquium featured my book, Potentia: Hobbes and Spinoza on Power and Popular Politics. This is a précis of the book.

Students often have difficulty connecting theoretical and text-based scholarship to the real world. When teaching in Asia, this disconnection is exacerbated by the European/American focus of many canonical texts, whereas students' own experiences are primarily Asian. However, in my discipline of political philosophy, this problem receives little recognition nor is it comprehensively addressed. In this paper, I propose that the problem must be taken seriously, and I share my own experiences with a novel pedagogical strategy which might offer a possible (...) path forward. Recent scholarship has championed an active learning approach, where students engage in their own research, and deliver outward-facing products that have a meaning and purpose beyond the confines of the student-professor relationship. In this spirit, I have put into practice a strategy of course design, where active learning is used to overcome students' disconnection with the course content. In particular, as a major component of course assessment, students are required to write an 'opinion piece', which is then showcased on a public website. The opinion piece must address a real-world issue which the student himself or herself selects and deems important; furthermore, it must build on the theoretical tools of the course and be written in a style which makes it accessible to a wider audience. I discuss the implementation of this strategy in two political philosophy courses, including strategies to avoid 'dumbing down' and ‘diluting’ the process of critical thinking. While no formal analysis of impact of the strategy on learning outcomes has been conducted, an anonymous pedagogical survey has yielded an overwhelmingly positive response for students' self-reported perceptions of the curricular innovations. (shrink)

This volume offers a collection of in-depth explorations of pragmatism as a framework for discussions in philosophy of science and metaphysics. Each chapter involves explicit reflection on what it means to be pragmatist, and how to use pragmatism as a guiding framework in addressing topics such as realism, unification, fundamentality, truth, laws, reduction, and more. -/- .

In this paper, I articulate two Hobbesian models of interpersonal power relations that can be used to understand gender relations in society: what I will call the dominion model and the deference model. The dominion model discerns vertical subjection to another's will, whereas by contrast the deference model places individuals in a complex and shifting webs of favor and disfavor. Hobbes himself analyses gender relations through the dominion model. Indeed, more broadly this is the most prominent model of interpersonal power (...) relations throughout his texts. It is this model which is also reflected in the very rich existing feminist literature on Hobbes. However, the deference model, emerging only late in Hobbes's oeuvre, offers a superior general rubric for understanding interpersonal power relations. In particular, in light of its ability to grasp informal and diffuse relations of power, I argue that it offers useful insights for thinking about gender relations in our post-coverture era. (shrink)