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)

A citation index is a bibliographic database that provides citation links between documents. The first modern citation index was suggested by the researcher Eugene Garfield in 1955 and created by him in 1964, and it represents an important innovation to knowledge organization and information retrieval. This article describes citation indexes in general, considering the modern citation indexes, including Web of Science, Scopus, Google Scholar, Microsoft Academic, Crossref, Dimensions and some special citation indexes and predecessors to the modern citation index like (...) Shepard’s Citations. We present comparative studies of the major ones and survey theoretical problems related to the role of citation indexes as subject access points (SAP), recognizing the implications to knowledge organization and information retrieval. Finally, studies on citation behavior are presented and the influence of citation indexes on knowledge organization, information retrieval and the scientific information ecosystem is recognized. (shrink)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

The paper describes and discusses unethical behavior in organizations, as a result of (interacting) disputable leadership and ethical climate. This paper presents and analyzes the well-known bond trading scandal at Salomon Brother to demonstrate the development of an unethical organizational culture under the leadership of John Gutfreund. The paper argues that leaders shape and reinforce an ethical or unethical organizational climate by what they pay attention to, how they react to crises, how they behave, how they allocate rewards, and how (...) they hire and fire individuals. (shrink)

Although Archaea inhabit the human body and possess some characteristics of pathogens, there is a notable lack of pathogenic archaeal species identified to date. We hypothesize that the scarcity of disease‐causing Archaea is due, in part, to mutually‐exclusive phage and virus populations infecting Bacteria and Archaea, coupled with an association of bacterial virulence factors with phages or mobile elements. The ability of bacterial phages to infect Bacteria and then use them as a vehicle to infect eukaryotes may be difficult for (...) archaeal viruses to evolve independently. Differences in extracellular structures between Bacteria and Archaea would make adsorption of bacterial phage particles onto Archaea (i.e. horizontal transfer of virulence) exceedingly hard. If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control. (shrink)

This article is the first in a trilogy about the concept “science”. Section 1 considers the historical development of the meaning of the term science and shows its close relation to the terms “knowl­edge” and “philosophy”. Section 2 presents four historic phases in the basic conceptualizations of science science as representing absolute certain of knowl­edge based on deductive proof; science as representing absolute certain of knowl­edge based on “the scientific method”; science as representing fallible knowl­edge based on “the scientific method”; (...) science without a belief in “the scientific method” as constitutive, hence the question about the nature of science becomes dramatic. Section 3 presents four basic understandings of the scientific method: Rationalism, which gives priority to a priori thinking; empiricism, which gives priority to the collection, description, and processing of data in a neutral way; historicism, which gives priority to the interpretation of data in the light of “paradigm” and pragmatism, which emphasizes the analysis of the purposes, consequences, and the interests of knowl­edge. The second article in the trilogy focus on different fields studying science, while the final article presets further developments in the concept of science and the general conclusion. Overall, the trilogy illuminates the most important tensions in different conceptualizations of science and argues for the role of information science and knowl­edge organization in the study of science and suggests how “science” should be understood as an object of research in these fields. (shrink)

Advancements in science and technology have not only brought hope to humankind to produce disease-free offspring, but also offer possibilities to genetically enhance the next generation’s traits and capacities. Human genetic enhancement, however, raises complex ethical questions, such as to what extent should it be allowed? It has been a great challenge for humankind to develop robust ethical guidelines for human genetic enhancement that address both public concerns and needs. We believe that research about public concerns is necessary prior to (...) developing such guidelines, yet the issues have not been thoroughly investigated in many countries, including Malaysia. Since the novel often functions as a medium for the public to express their concerns, this paper explores ethical concerns about human genetic enhancement expressed in four Malay science fiction novels namely Klon, Leksikon Ledang, Transgenesis Bisikan Rimba and Transgenik Sifar. Religion has a strong influence on the worldview of the Malays therefore some concerns such as playing God are obviously religious. Association of the negative image of scientists as well as the private research companies with the research on human genetic enhancement reflects the authors’ concerns about the main motivations for conducting such research and the extent to which such research will benefit society. (shrink)

For the past half-century, issues relating to the ethical conduct of human research have focused largely on the domain of medical, and more recently social–psychological research. The modern regime of applied ethics, emerging as it has from the Nuremberg trials and certain other historical antecedents, applies the key principles of: autonomy, respect for persons, beneficence, non-maleficence, and justice to human beings who enter trials of experimental drugs and devices :168–175, 2001). Institutions such as Institutional Review Boards and Ethics Committees oversee (...) most governmentally-funded medical research around the world, in more than a hundred nations that are signers of the Declaration of Helsinki. Increasingly, research outside of medicine has been recognized to pose potential risks to human subjects of experiments. Ethics committees now operate in the US, Canada, the U.K. and Australia to oversee all governmental-funded research, and in other jurisdictions, the range of research covered by such committees is expanding. Social science, anthropology, and other fields are falling under more clear directives to conduct a formal ethical review for basic research involving human participants. The legal and institutional response for protecting human subjects in the course of developing non-medical technologies, engineering, and design is currently vague, but some universities are establishing ethics committees to oversee their human subjects research even where the experiments involved are non-medical and not technically covered by the Declaration of Helsinki. In The Netherlands, as in most of Europe, Asia, Latin America, or Africa, no laws mandate an ethical review of non-medical research. Yet, nearly 2 years ago we launched a pilot ethics committee at our technical university and began soliciting our colleagues to submit their studies for review. In the past year, we have become officially recognized as a human subjects ethics committee for our university and we are beginning the process of requiring all studies using human subjects to apply for our approval. In this article, we consider some of the special problems relating to protecting human participants in a technology context, and discuss some of our experiences and insights about reviewing human subjects research at a technical university, concluding: that not less than in medical studies, human participants used in technology research benefit from ethical committees’ reviews, practical requirements for publications, grants, and avoiding legal liability are also served by such committees, and ethics committees in such contexts have many similarities to, but certain other special foci than medical ethics committees. We believe that this experience, and these observations, are helpful for those seeking to establish such committees in technology research contexts, and for framing the particular issues that may arise in such contexts for the benefit of researchers, and nascent committees seeking to establish their own procedures. (shrink)

There have been several calls from LIS researchers for practical or applied research not to ignore the epistemological assumptions underlying the systems and artifacts they design lest they showcase only the dominant theory at a given time. Others have also deplored the "epistemological promiscuity" or "eclecticism" of the field, its incessant borrowing of theories and models from elsewhere and the fact that the field has largely neglected the contributions that philosophy and epistemology could have made in its research. This problem (...) raises that of the boundaries of LIS and is all the more troublesome because boundaries between epistemological theories are fuzzy. Indeed, some epistemological theories share the same basic assumptions or are historically derived from one another. Gathering a wide array of acknowledged theorists in philosophy of science and epistemology, this panel aims to examine how research work in the LIS field can clearly articulate the epistemological assumptions underlying that research and under what constraints this can be achieved. The topic is of prime importance to Information studies as a whole and to ASIST as the scientific flag bearer of information scientists worldwide. (shrink)

Human research ethics has developed in both theory and practice mostly from experiences in medical research. Human participants, however, are used in a much broader range of research than ethics committees oversee, including both basic and applied research at technical universities. Although mandated in the United States, the United Kingdom, Canada, and Australia, non-medical research involving humans need not receive ethics review in much of Europe, Asia, Latin America, and Africa. Our survey of the top 50 technical universities in the (...) world shows that, where not specifically mandated by law, most technical universities do not employ ethics committees to review human studies. As the domains of basic and applied sciences expand, ethics committees are increasingly needed to guide and oversee all such research regardless of legal requirements. We offer as examples, from our experience as an ethics committee in a major European technical university, ways in which such a committee provides needed services and can help ensure more ethical studies involving humans outside the standard medical context. We provide some arguments for creating such committees, and in our supplemental article, we provide specific examples of cases and concerns that may confront technical, engineering, and design research, as well as outline the general framework we have used in creating our committee. (shrink)

Contemporary scholarship interprets Sergej Bulgakov’s sophiology as an engagement of Orthodox theology with the modern world and as being on its way to becoming a political theology. In this paper I undertake a re-evaluation of the kind of engagement sophiology was and was intended to be, and of the kind of world it was destined for. It will be argued that sophiology was not so much a political-theological engagement with the world concentrating on the relation of religion and politics or (...) state and church, but rather an economic-theological engagement in the tradition of oikonomia theology that tried to understand the world in its relation to and as part of divine oikonomia. Furthermore, the world sophiology promotes engagement with is not only the real contemporary world, or the sociological ideal type of modernity, but primarily the world as such, this secular and human world over and against the divine and transcendent world. (shrink)

Desde la antigüedad hasta hoy, la tradición vitruviana ha dominado los modos en que se ha entendido el oficio de la arquitectura y la figura del arquitecto en Occidente. Esta tradición hace de la arquitectura una práctica necesariamente relacionada con la edificación. Sin embargo, en los tiempos en que Vitruvio escribía su De Architectura, diferentes nociones sobre el oficio permeaban tanto en escritos dramáticos y filosóficos como en el sentido común de la época. En Cicerón y Eurípides, pero sobre todo (...) en Plauto, encontramos arquitecturas cuyos objetivos se alejaban del arte y se acercaban a la política, y arquitectos con habilidades que tenían menos que ver con la técnica, y más con la prudencia. Con ayuda del pensamiento aristotélico, veremos que estas figuras no eran meros caprichos dramatúrgicos ni moralistas, sino que poseían un fundamento epistemológico y práctico, que encontraba en la arquitectura un modo de pen- sar y de actuar más allá de la proyección y construcción de edificios. (shrink)

The prevailing view among historians of science holds that Charles Darwin became a convinced transmutationist only in the early spring of 1837, after his Beagle collections had been examined by expert British naturalists. With respect to the fossil vertebrate evidence, some historians believe that Darwin was incapable of seeing or understanding the transmutationist implications of his specimens without the help of Richard Owen. There is ample evidence, however, that he clearly recognized the similarities between several of the fossil vertebrates he (...) collected and some of the extant fauna of South America before he returned to Britain. These comparisons, recorded in his correspondence, his diary and his notebooks during the voyage, were instances of a phenomenon that he later called the “law of the succession of types.” Moreover, on the Beagle, he was following a geological research agenda outlined in the second volume of Charles Lyell’s Principles of Geology, which implies that paleontological data alone could provide an insight into the laws which govern the appearance of new species. Since Darwin claims in On the Origin of Species that fossil vertebrate succession was one of the key lines of evidence that led him to question the fixity of species, it seems certain that he was seriously contemplating transmutation during the Beagle voyage. If so, historians of science need to reconsider both the role of Britain’s expert naturalists and the importance of the fossil vertebrate evidence in the development of Darwin’s ideas on transmutation. (shrink)

This article presents and discusses different kinds of data documents, including data sets, data studies, data papers and data journals. It provides descriptive and bibliometric data on different kinds of data documents and discusses the theoretical and philosophical problems by classifying documents according to the DIKW model (data documents, information documents, knowl­edge documents and wisdom documents). Data documents are, on the one hand, an established category today, even with its own data citation index (DCI). On the other hand, data documents (...) have blurred boundaries in relation to other kinds of documents and seem sometimes to be understood from the problematic philosophical assumption that a datum can be understood as “a single, fixed truth, valid for everyone, everywhere, at all times”. (shrink)

The contributions to this volume offer a rich, detailed, and in some respects innovative and remarkable account of that uniquely fecund and philosophically revolutionary epoch known as German Idealism. The epoch’s historical context, its driving ideas, its post-Kantian development, and its repercussions in post-Hegelian philosophy are all presented competently and concisely. The editor also included essays on some of the philosophical ideas underlying the parallel phenomenon of German Romanticism, for good reasons, since some of the foremost poets and literary theorists (...) of the age were philosophers in their own right, whose influence on the development of German Idealism was not insignificant. What emerges from this collection is the picture of a multifaceted philosophical movement embedded in and influenced by and in turn influencing a complex intellectual and literary environment. The reader of this volume will be in no danger of reducing German Idealism to a linear development that started with Kant and that was preordained to culminate in Hegel’s system. (shrink)