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)

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.

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)

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

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)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Elon Musk famously predicted that an artificial intelligence superior to the smartest individual human would arrive by the year 2025. In response, Gary Marcus offered Musk a $1 million bet to the effect that he would be proved wrong. In specifying the conditions of this bet (which Musk did not take) Marcus lists the following ‘tasks that ordinary people can perform’ which, he claimed, AI will not be able to perform by the end of 2025. • Reliably drive a car (...) in a novel location that they haven’t previously encountered, even in the face of unusual circumstances like hand lettered signs, without the assistance of other humans. • Learn to ride a mountain bike off-road through forest trails. • Babysit children in an unfamiliar home and keep them safe. • Tend to the physical and psychological needs of an elderly or infirm person. Each of these tasks involves the application of practical or tacit knowledge, or what is also called ‘knowing how’, which is to say knowledge of a sort that is captured not by means of sentences or propositions or explicit rules, but rather through the expertise demonstrated in human actions. The talk addresses the puzzle that nowhere in the AI literature do we find a discussion of knowing how as a feature of human intelligence. (shrink)

White progressives in the U.S. are currently experiencing two profound reckonings that typically are assumed to be unrelated. On the one hand, the Dobbs verdict overturned the assumption that the right to choose with respect to abortion is too socially entrenched, juridically settled, or politically sacred to be denied. On the other hand, climatological conditions of possibility for comfortable existence are increasingly under threat in locales in which residents have come to expect to enjoy secure lives and livelihoods. This essay (...) highlights what Indigenous communities across the U.S. already know well. Namely, threats to reproductive freedom and climate crisis are neither new nor separable. Both phenomena have common colonial roots that continue to proliferate. Each is a result of the disruption and destruction of Indigenous kinship assemblages. Indeed, in aiming to remediate their current reckonings, white progressives routinely (if unthinkingly) support forms of settler state violence that perpetuate reproductive and climate injustice in Indigenous communities. We appeal to white progressives, notably including white feminists, to embrace the proposition that their reckonings cannot be properly understood, nor successfully addressed without prioritizing Indigenous futurity. We call for centering forms of Indigenous feminist praxis that facilitate robust Indigenous coalitions of anti-colonial resistance. (shrink)

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

This short paper seeks to throw light on the sense in which the prior knowledge used by AlphaFold is to be understood in ontological terms. The paper is a comment on the 2022 ICBO presentation by Jobst Landgrebe entitled “What AlphaFold teaches us about deep learning with prior knowledge”.

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)

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.

The Food and Drug Administration (FDA) recently issued its first approval of an oral contraceptive medication for access without a clinician’s prescription. One might expect this will lead to fewer people seeking to terminate unplanned pregnancies, including in states that imposed severe restrictions on abortion care following the Supreme Court’s reversal on abortion rights in Dobbs v. Jackson Women’s Health Organization. Despite the clear potential health benefits, increased accessibility of oral contraceptives offers no real solution to ongoing threats to patients’ (...) reproductive health and moral rights created by post-Dobbs abortion restrictions. To secure their patients’ reproductive health and well-being, clinicians must work to maximize the benefits of OTC oral contraceptives without relenting in their advocacy for safe and accessible abortion care. (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)

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

Amazon Book Review Series of “Wild Wise Weird”.

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)

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)

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)

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

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

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

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

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

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)

In October 2016, the White House, the European Parliament, and the UK House of Commons each issued a report outlining their visions on how to prepare society for the widespread use of artificial intelligence. In this article, we provide a comparative assessment of these three reports in order to facilitate the design of policies favourable to the development of a ‘good AI society’. To do so, we examine how each report addresses the following three topics: the development of a ‘good (...) AI society’; the role and responsibility of the government, the private sector, and the research community in pursuing such a development; and where the recommendations to support such a development may be in need of improvement. Our analysis concludes that the reports address adequately various ethical, social, and economic topics, but come short of providing an overarching political vision and long-term strategy for the development of a ‘good AI society’. In order to contribute to fill this gap, in the conclusion we suggest a two-pronged approach. (shrink)

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

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)

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

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

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)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

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)

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)

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)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

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)

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.

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)

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)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (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.