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)

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)

The philosopher of chemistry Andrea Woody has recently published a wide-ranging article concerning the turn to practice in the philosophy of science. Her primary example consists of the use of different forms of representations by Lothar Meyer and Mendeleev when they presented their views on chemical periodicity. Woody believes that this distinction can cast light on various issues including why Mendeleev was able to make predictions while Meyer was not. Secondly, she claims that it can clarify the much-debated question concerning (...) the relative values of prediction and accommodation of data in the way that the periodic system was accepted. Thirdly, Woody believes that such differences in the representation of periodicity can be used to argue for the explanatory nature of the periodic table in contrast with the more traditional view that the periodic table is not explanatory. (shrink)

For a period of several years the philosopher of science Hasok Chang has promoted various inter-related views including pluralism, pragmatism, and an associated view of natural kinds. He has also argued for what he calls the persistence of everyday terms in the scientific view. Chang claims that terms like phlogiston were never truly abandoned but became transformed into different concepts that remain useful. On the other hand, Chang argues that some scientific terms such as acidity have suffered a form of (...) “rupture”, especially in the case of the modern Lewis definition of acids. Chang also complains that the degree of acidity of a Lewis acid cannot be measured using a pH meter and seems to regard this as a serious problem. The present paper examines some of these views, especially what Chang claims to be a rupture in the definition of acidity. It is suggested that there has been no such rupture but a genuine generalization, on moving from the Brønsted-Lowry theory to the Lewis theory of acidity. It will be shown how the quantification and measurement of Lewis acidity can easily be realized through the use of equilibrium theory and the use of stability constants. (shrink)

A critique of dubious contrasts between "science" and "religion" drawn on the basis of cognitive-evolutionary accounts of human psychology, e.g.,. the claim that religious concepts are “likely” and “natural” for the human mind whereas scientific thinking is “rare” and “unnatural.” Initially made by biologist Lewis Wolpert in *The Unnatural Nature of Science* (1993) and anthropologist Pascal Boyer in *Religion Explained: The Evolutionary Origins of Religious Thought* (2001), they are developed at length by philosopher R. N. McCauley in a*Why Religion is (...) Natural and Science is Not* (2011). These contrasts involve tendentiously narrow or broad definitions of the terms “science” and “religion” and the obliteration of the complex historical and intellectual relations between the ideas and practices currently identified by those terms. (shrink)

This article considers two important traditions concerning the chemical elements. The first is the meaning of the term “element” including the distinctions between element as basic substance, as simple substance and as combined simple substance. In addition to briefly tracing the historical development of these distinctions, I make comments on the recent attempts to clarify the fundamental notion of element as basic substance for which I believe the term “element” is best reserved. This discussion has focused on the writings of (...) Fritz Paneth which are here analyzed from a new perspective. The other tradition concerns the reduction of chemistry to quantum mechanics and an understanding of chemical elements through their microscopic components such as protons, neutrons and electrons. I claim that the use of electronic configurations has still not yet settled the question of the placement of several elements and discuss an alternative criterion based on maximizing triads of elements. I also point out another possible limitation to the reductive approach, namely the failure, up to now, to obtain a derivation of the Madelung rule. Mention is made of some recent similarity studies which could be used to clarify the nature of ‘elements’. Although it has been suggested that the notion of element as basic substance should be considered in terms of fundamental particles like protons and electrons, I resist this move and conclude that the quantum mechanical tradition has not had much impact on the question of what is an element which remains an essentially philosophical issue. (shrink)

A critique is given of the attempt by Hettema and Kuipers to formalize the periodic table. In particular I dispute their notions of identifying a naïve periodic table with tables having a constant periodicity of eight elements and their views on the different conceptions of the atom by chemists and physicists. The views of Hettema and Kuipers on the reduction of the periodic system to atomic physics are also considered critically.

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)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Shortages of new therapeutics to treat coronavirus disease (COVID-19) have forced clinicians, public health officials, and health systems to grapple with difficult questions about how to fairly allocate potentially life-saving treatments when there are not enough for all patients in need (1). Shortages have occurred with remdesivir, tocilizumab, monoclonal antibodies, and the oral antiviral Paxlovid (2) -/- Ensuring equitable allocation is especially important in light of the disproportionate burden experienced during the COVID-19 pandemic by disadvantaged groups, including Black, Hispanic/Latino and (...) Indigenous communities, individuals with certain disabilities, and low-income persons. However, many health systems have resorted to first-come, first-served approaches to allocation, which tend to disadvantage individuals with barriers in access to care (3). There is mounting evidence of racial, ethnic, and socioeconomic disparities in access to medications for COVID-19 (4, 5). -/- One potential method to promote equitable allocation is to use a weighted lottery, which is an allocation strategy that gives all eligible patients a chance to receive the scarce treatment while also allowing the assignment of higher or lower chances according to other ethical considerations (6). We sought to assess the feasibility of implementing a weighted lottery to allocate scarce COVID-19 medications in a large U.S. health system and to determine whether the weighted lottery promotes equitable allocation. (shrink)

What is sexual orientation? The contemporary consensus among philosophers is that it is a disposition. Unsurprisingly, recent debates about the metaphysics of sexual orientation are almost entirely intramural. Behavioral dispositionalists argue that sexual orientation is a disposition to behave sexually. Desire dispositionalists argue that it is a disposition to desire sexually. We argue that sexual orientation is not best understood in terms of dispositions to behave or dispositions to desire before arguing that dispositions tout court fail to illuminate sexual orientation. (...) We then introduce and defend the idea that sexual orientation is best understood in terms of categorical phenomenal properties of sexual arousal. (shrink)

Legal philosophers and property scholars sometimes disagree over one or more of the following: the meaning of the word 'property,' the concept of property, and the nature of property. For much of the twentieth century, the work of W.N. Hohfeld and Tony Honoré represented a consensus around property. The consensus often went under the heading of property as bundle of rights, or more accurately as a set of normative relations between persons with respect to things. But by the mid-l 990s, (...) the consensus was under attack. Key figures in the attack were James Penner, a legal philosopher, and Thomas W. Merrill and Henry E. Smith, two highly regarded professors of property law. This article aims to repel the attack and argues for property as a set of normative relations between persons with respect to things. The positive case for this view of property pays special attention to the philosophy of language and the analysis of concepts. The positive case also maintains that the right to use and the power to transfer are as central to property as the right to exclude. It is possible that the virtues of Smith's modular theory of property differ from the virtues of a well-crafted bundle theory. Indeed, it may be the case that these two theories throw light on different features of property law and are not, save at the margin, competitors with each other. The label 'new essentialism' sometimes applied to the work of Penner, Merrill, and Smith seems inapt if property does not have an essence. Of course, they might refuse the label. (shrink)

The study investigated the effect of cognitive restructuring on junior secondary school mathematics test anxiety in Oshimili south L.G.A of Delta State. Two research questions and two hypotheses tested at 0.05 level of significance guided the study. Quasi-experimental research design was adopted for this study. The population for this study was a total of 1224 students. These comprised of all the JSS 2 students from Oshimili South Local Government Area of Delta State. Research sample consisted of 120 JSS 2 students (...) with high level of mathematics test anxiety selected through purposive sampling technique. The instrument adopted for this study was Maths anxiety rating scale-R. Data collected from the study were analyzed using mean and ANCOVA. Results obtained from the study indicated that Cognitive restructuring therapy (CRT) was effective on mathematics test anxiety of junior secondary school students. The results equally showed that Cognitive restructuring therapy was more effective on the female students’ mathematics anxiety than their male counterparts. Furthermore, the results indicated a significant difference in the post-test mathematics test anxiety mean scores of students treated with CRT and those in the control group. Also, there was significant difference in the post-test mathematics test anxiety mean scores of male and female students treated with CRT. Based on the findings of this study, some recommendations were noted. The researcher recommended, among others that Schools’ Guidance Counselors should be empowered to make good use of the cognitive restructuring technique, in counseling students who find it difficult to comprehend mathematics skills. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (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)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (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)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Digitalization processes are global and performed in all spheres of economic activities. The development of the digital economy correlates with the dynamics of educational, scientific and technical, and innovative activities in the country. Higher education particularly affects the development of the digital economy because it is a system training highly qualified personnel, conducting quality research, and generating innovations. The purpose of the article is the identification of promising vectors of higher education system development under the conditions of digitalization of national (...) economy. Section 1 of the article presents the authors’ methodological approach to assessment the impact of educational, research, and innovation components on digital economy development. The implementation of the authors’ approach covers the phased use of methods of statistical, index, cluster and system analysis. The influence of higher education on the structural components of the digital economy (educational, research, innovative ones) is grounded. The result of the study was the identification of main trends in the development of higher education under the conditions of digital economy. The problems of the development of higher education are systematized in the groups: contextual, legal, organizational and economic, financial, logistical problems, and problems of internationalization. Based on the results of the analysis, the authors conclude the necessity of development of a conceptual base for increasing the digital adaptability of the higher education system to new socio-economic conditions. Section 2 of the article describes the concept of the digital adaptability strategy of the higher education system. The concept was developed on the base of structural and functional, systemic and synergetic, and institutional approaches. The proposed concept is based on the idea of deepening the long-term partnership of universities with stakeholders within the Quadruple Helix model. In the conclusion section, the authors highlight the key priorities of the digital adaptability strategy of the higher education system. (shrink)

Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Abstract: Purpose - This study aimed to analyze the relationship between the determinants of organizational justice and their relationship to conscientious behavior from the point of view of officers working in the Palestinian police in Gaza Strip. Methodology - The study relied on the descriptive and analytical approach, using the questionnaire, targeting a stratified random sample of (400) officers, who hold the rank of captain and above, from the study population of 1550 officers. The study tool was distributed among the (...) sample members in all departments and governorates. Police in Gaza Strip. (353) questionnaires were retrieved, with a recovery rate of (88.3%). Findings - The existence of a positive correlation between the determinants of organizational justice and the behavior of conscience, and the existence of organizational justice in general in a medium degree and the order of its determinants is as follows: fairness of dealings and to a large degree, followed by fairness of procedures and a medium degree, and finally distribution fairness was to a small degree, while the behavior of conscience awareness came to a large extent. Significance - The existence of statistically significant differences between the respondents' averages of responding to the searched relationship due to the variables (type of administration, age group, job title, military rank, years of service). Recommendations - Work to take into account the fairness of distribution by providing adequate and fair salaries, granting bonuses for the additional efforts exerted, and budgeting in the distribution of duties and job burdens, as well as recommending attention to the interests of employees when making decisions and involving them in formulating them, explaining their justifications, and creating an organizational climate dominated by a sense of justice. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis. Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato’s dialogues, is sfounded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then show (...) how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato’s dialogues by date, more general challenges to historicist interpretations of Plato’s dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

Abstract: This study aimed to identify the behavior of organizational citizenship in Palestinian Police Force between reality and expectations, and this study comes to study the reality of human resources and their organizational behavior in the police apparatus, which is the largest security services operating in Gaza Strip, so it is expected that this study will contribute to improving this This aspect will be reflected positively on serving the country and the citizen and achieving security and safety for them. The (...) study relied on the descriptive and analytical approach, using the questionnaire, and targeting a stratified random sample of (400) officers, who hold the rank of captain and above, from the study population of 1550 officers, and the study tool was distributed to the sample members in all departments and governorates Police in Gaza Strip. (353) questionnaires were retrieved, with a recovery rate of (88.3%), and they were analyzed using (SPSS) software. The study found that the organizational citizenship behavior was largely due to all its components. The study also showed that there are statistically significant differences between the respondents ’average response towards the organizational citizenship behavior due to the variables (type of administration, age group, job title, military rank, and years of service). The study recommended taking into account the interests of employees when making decisions and involving them in formulating them, explaining their justifications, and finally, the study recommended that organizational citizenship behavior be considered an organizational value that the police seek, and to create an organizational climate in which a sense of justice prevails, given its prominent role in stability, calm and discipline at work Thus, the elevation of the police institution and the achievement of its desired goals. (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)

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 propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) 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. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (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)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

In 2035 global egg demand will have risen 50% from 1985. Because we are not able to tell in the egg whether it will become a male or female chick, billons of one day-old male chicks will be killed. International research initiatives are underway in this area, and governments encourage the development of an alternative with the goal of eliminating the culling of day-old male chicks. The Netherlands holds an exceptional position in the European egg trade, but is also the (...) only country in the European Union where the downside of the egg sector, the practice of killing day-old male chicks, is a recurrent subject of societal debate. ‘Preventing the killing of young animals’ and ‘in ovo sex determination’ are the two alternative approaches available to solve this problem. It is clear that both approaches solve the problem of killing day-old male chicks, either by keeping them alive or by preventing them from living, but they also raise a lot of new animal welfare-related dilemmas. A thorough analysis was undertaken of these dilemmas and the results are presented in this article. The analysis resulted in an ethical framework based on the two main approaches in bioethics: a consequentialist approach and a deontological approach. This ethical framework was used to develop an online survey administered to ascertain Dutch public opinion about these alternative approaches. The results show that neither alternative will be fully accepted, or accepted by more than half of Dutch society. However, the survey does provide an insight into the motives that are important for people’s choice: food safety and a good treatment of animals. Irrespective of the approach chosen, these values should be safeguarded and communicated clearly. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

In June 2002, Arthur Andersen LLP became the first accounting firm in history to be criminally convicted. The repercussions were immense. From a position as one of the leading professional services firms in the world, with 85,000 staff in 84 countries and revenues in excess of $9 billion, Andersen effectively ceased to exist within a matter of months. Although Andersen’s conviction related specifically to a charge of obstructing justice, public attention focused on the audit relationship between Andersen and its major (...) client, Enron Corporation, particularly the actions (and inactions) that had allowed Enron to post spectacular year-on-year earnings and profit growth. As well as examining events leading up to the demise of Andersen, the case provides an opportunity to consider the broader controversy over accounting and corporate governance practices and, more generally, the pressures found within organisations that can foster unethical conduct. The case was prepared from public sources. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Gökhan Murteza, “Ahlak, İktisat ve Bilim: Adam Smith Felsefesine Giriş” isimli eserinde genellikle İktisat disiplininin birçok farklı konusunu felsefi açıdan tartışmaya açmıştır. Murteza’nın bu eseri, devleti ve toplumu ilgilendiren bu araştırma alanının, A. Smith ile birlikte bir bilim dalı olarak görülmeye başlanmasının sonucunda, gerçekten ahlaki olanı içerip içermediği problemi üzerinde durmaktadır.

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

This 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)

I argue that Smith proposed a new kind of imperialism, which we would describe as a species of ‘federalism,’ and that his plan influenced Bentham and Kant in their federal projects, although they seem to have been unaware of each other’s proposals. In what follows, I outline Smith’s position. I then describe Kant’s and Bentham’s debts to Smith in turn. This will also allow for greater clarity about the nature of early liberalism.

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

I frame my argument by way of Hayek's tendency to treat Hume and Smith as central articulations of the rule of law. The rest of the paper explores their defense of clientelism. First, I introduce Hume’s ideas on the utility of patronage in his essay, “Of the Independency of Parliament.” I argue that in Hume clientelism just is a feature of parliamentary business. It seems ineliminable. I then contextualize Hume’s account by comparing it to Montesquieu’s account of this system (...) of patronage in Book XIX, chapter 27 of The Spirit of the Laws. Montesquieu primarily treats it as a species of bad corruption. However, he also sees some benefits to it. I then turn to Smith and I show that he echoes Hume’s analysis of corruption in an easily ignored passage in Wealth of Nations. I then show that for Smith one argument in favor of a kind of federal parliamentary union between Great Brittain and her American colonies lies in its ability to facilitate and make more efficient the system of patronage by the Crown. While Smith’s account of these matters is quite Humean, one can discern in Smith a distinct cost-benefit argument for the acceptance of the necessity of a system of patronage in the service of the peaceful expansion and entrenchment of the rule of law in his proposal for parliamentary union. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Abstract: This study aimed to analyze the relationship between the determinants of organizational justice and altruistic behavior from the point of view of the police officers in Gaza Strip. The study relied on the descriptive and analytical approach, using the questionnaire, and targeting a stratified random sample of (400) officers, who hold the rank of captain and above, from the study population of 1550 officers, and the study tool was distributed to the sample members in all departments and governorates Police (...) in Gaza Strip. (353) questionnaires were retrieved, with a recovery rate of (88.3%). The study found the existence of a positive correlation between the determinants of organizational justice and altruistic behavior, and the study also found the existence of organizational justice in general in a moderate degree and the order of its determinants was as follows: fairness of dealings and to a large degree, followed by fairness of procedures and a medium degree, and finally, distribution fairness was to a small degree, as for altruistic behavior. It came to a large extent. There are statistically significant differences between the respondents ’average response to the researched relationship due to the variables (Type Of Administration, Age Group, Job Title, Military Rank, and Years of Service). Taking into account the fairness of distribution by providing appropriate and fair salaries, granting bonuses for the additional efforts exerted, and budgeting in the distribution of duties and job burdens, and paying attention to the interests of employees when making decisions and involving them in formulating them, explaining their justifications, and considering altruistic behavior as a value, and the creation of an organizational climate dominated by a sense of justice, because of its prominent role in stability, calm and discipline at work, and thus the elevation of the police institution and the achievement of its desired goals. (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)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (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.

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)