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)

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)

Dr Taylor's book analyses the disease concept as it developed in medical history and seeks to clarify it with the help of concepts largely derived from logical class theories. A solution is proposed to the problem of how to distinguish between the class of 'patients' and the class of 'healthy persons' which corresponds to the actual diagnostic practices of doctors. The earliest theories of disease postulated concrete entities which exist independently of the body. The notion of disease entity has (...) lost its original ontological connotations and instead its important feature has become the possession of a unitary and self-contained character. Dr Taylor describes the modern theories as essentially 'reactive' in character, that is the symptoms of a disease are the bodily reactions to the 'noxae'. After seeing the subject in its historical content, Dr Taylor goes on to discuss in detail the notion of the classification of diseases, making extensive use of modern views on the logic of classes. (shrink)

The scientific world-outlook is something quite different from natural science. The word “science” in its legitimate modern usage represents both a kind of knowledge and the method of obtaining that knowledge. By “science” we may mean an objective body of facts and relationships concerning the physical world and arrived at by the scientific method of observation and reasoning—preferably quantitative observation and mathematical reasoning: thus we may say that the law of constant proportions is a part of the science of chemistry. (...) But we may also use the word science to denote that scientific method which I have just mentioned: thus I may say that science is the key to the investigation of nature—or that some inaccurate or biased piece of work is unscientific. Science, in either of these senses, does not contain any world-outlook, for it is quite impersonal. Thus science in the first sense consists of certain statements and relationships e.g.—that sulphur is yellow, that Jupiter has eight satellites, that all solutions of acids in water conduct electricity; while the scientific method indicates the manner in which from the data of our sense-impressions we can infer statements and conclusions, such as the above, which will be found to represent the phenomena correctly. But a scientific world-outlook means something different, because it is a world -outlook, the attitude of a man or woman towards the whole of that of which he or she is conscious. (shrink)

Background Genuine uncertainty on superiority of one intervention over the other is called equipoise. Physician-investigators in randomized controlled trials need equipoise at least in studies with more than minimal risks. Ideally, this equipoise is also present in patient-participants. In pediatrics, data on equipoise are lacking. We hypothesize that 1) lack of equipoise at enrolment among parents may reduce recruitment; 2) lack of equipoise during participation may reduce retention in patients assigned to a less favoured treatment-strategy. Methods We compared preferences of (...) parents/patients at enrolment, documented by a questionnaire, with preferences developed during follow-up by an interview-study to investigate equipoise of child-participants and parents in the BeSt-for-Kids-study. This trial in new-onset Juvenile Idiopathic Arthritis-patients consists of three strategies. One strategy comprises initial treatment with a biological disease-modifying-antirheumatic-drug, currently not standard-of-care. Semi-structured interviews were conducted with 23 parents and 7 patients, median 11 months after enrolment. Results Initially most parents and children were not in equipoise. Parents/patients who refused participation, regularly declined due to specific preferences. Many participating families preferred the biological-first-strategy. They participated to have a chance for this initial treatment, and would even consider stopping trial-participation when not randomized for it. Their conviction of superiority of the biological-first strategy was based on knowledge from internet and close relations. According to four parents, the physician-investigator preferred the biological-first-strategy, but the majority stated that she had no preferred strategy. In phase 2, preferences tended to change to the treatment actually received. Conclusions Lack of equipoise during enrolment did not reduce study recruitment, mainly due to the fact that preferred treatment was only available within the study. Still, when developing a trial it is important to evaluate whether the physicians’ research question is in line with preferences of the patient-group. By exploring so-called ‘informed patient-group’-equipoise, successful recruitment may be enhanced and bias avoided. In our study, lack of equipoise during trial-participation did not reduce retention in those assigned to a less favoured option. We observed a change for preference towards treatment actually received, possibly explained by comparable outcomes in all three arms. (shrink)

Ethical guidance from the British Medical Association about treating doctor–patients is compared and contrasted with evidence from a qualitative study of general practitioners who have been patients. Semistructured interviews were conducted with 17 GPs who had experienced a significant illness. Their experiences were discussed and issues about both being and treating doctor–patients were revealed. Interpretative phenomenological analysis was used to evaluate the data. In this article data extracts are used to illustrate and discuss three key points that summarise the BMA (...) ethical guidance, in order to develop a picture of how far experiences map onto guidance. The data illustrate and extend the complexities of the issues outlined by the BMA document. In particular, differences between experienced GPs and those who have recently completed their training are identified. This analysis will be useful for medical professionals both when they themselves are unwell and when they treat doctor–patients. It will also inform recommendations for professionals who educate medical students or trainees. (shrink)

Collaboration on the First Edition of Spacetime Physics began in the mid-1960s when Edwin Taylor took a junior faculty sabbatical at Princeton University where John Wheeler was a professor. The resulting text emphasized the unity of spacetime and those quantities (such as proper time, proper distance, mass) that are invariant, the same for all observers, rather than those quantities (such as space and time separations) that are relative, different for different observers. The book has become a standard introduction to (...) relativity. The Second Edition of Spacetime Physics embodies what the authors have learned during an additional quarter century of teaching and research. They have updated the text to reflect the immense strides in physics during the same period and modernized and increased the number of exercises, for which the First Edition was famous. Enrichment boxes provide expanded coverage of intriguing topics. An enlarged final chapter on general relativity includes new material on gravity waves, black holes, and cosmology. The Second Edition of Spacetime Physics provides a new generation of readers with a deep and simple overview of the principles of relativity. (shrink)

Extending ethical leadership theory and research beyond the walls of the organization, we propose a spillover model wherein ethical leaders impact customer loyalty (i.e., repeat purchase amount) by first establishing trusting relations with employees, who in turn emulate their leaders’ ethical behavior. In Study 1, we examined how this initial trust (i.e., trust primacy) facilitates new employees’ moral imprinting in a controlled experiment. In Study 2, with a field design, we tested our model among new employees and their respective customers (...) over a 6-month timespan. Results indicate that perceptions of ethical leadership operate through trust primacy to affect customer repeat purchase, with accelerated growth over time. We conclude by considering theoretical and practical implications as they relate to ethical leadership and trust primacy, as well as marketing and salesforce management. (shrink)