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)

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, (...) creating a powerful information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter (...) may nonetheless support the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

Current debates surrounding the virtues and shortcomings of randomization are symptomatic of a lack of appreciation of the fact that causation can be inferred by two distinct inference methods, each requiring its own, specific experimental design. There is a non-statistical type of inference associated with controlled experiments in basic biomedical research; and a statistical variety associated with randomized controlled trials in clinical research. I argue that the main difference between the two hinges on the satisfaction of the (...) comparability requirement, which is in turn dictated by the nature of the objects of study, namely homogeneous or heterogeneous populations of biological systems. Among other things, this entails that the objection according to which randomized experiments fail to provide better evidence for causation because randomization cannot guarantee comparability is mistaken. (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)

Having scandalous unethical research practices in the mid and late 20th century, study protocols of biomedical research reviewed by the Ethics Committee (EC) has become the accepted international standard. The Declaration of Helsinki uniformly requires that all biomedical research involving human participants, including research on identifiable human material or data, should be approved by the EC. Today, concerns over the quality of the EC functions worldwide. There are research globally in this regard but (...) no data are available from Bangladesh. Hence, we conducted a questionnaire based pilot study on knowledge and attitude of EC members on bioethics and structure & function of EC in Bangladesh. (shrink)

The European project European and Latin American Systems of Ethics Regulation of Biomedical Research Project (EULABOR) has carried out the first comparative analysis of ethics regulation systems for biomedical research in seven countries in Europe and Latin America, evaluating their roles in the protection of human subjects. We developed a conceptual and methodological framework defining ‘ethics regulation system for biomedical research’ as a set of actors, institutions, codes and laws involved in overseeing the ethics (...) of biomedical research on humans. This framework allowed us to develop comprehensive national reports by conducting semi-structured interviews to key informants. These reports were summarised and analysed in a comparative analysis. The study showed that the regulatory framework for clinical research in these countries differ in scope. It showed that despite the different political contexts, actors involved and motivations for creating the regulation, in most of the studied countries it was the government who took the lead in setting up the system. The study also showed that Europe and Latin America are similar regarding national bodies and research ethics committees, but the Brazilian system has strong and noteworthy specificities. (shrink)

In this paper, we discuss the processes of racialisation on the example of biomedical research. We argue that applying the concept of racialisation in biomedical research can be much more precise, informative and suitable than currently used categories, such as race and ethnicity. For this purpose, we construct a model of the different processes affecting and co-shaping the racialisation of an individual, and consider these in relation to biomedical research, particularly to studies on hypertension. (...) We finish with a discussion on the potential application of our proposition to institutional guidelines on the use of racial categories in biomedical research. (shrink)

In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual “messiness” (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct some of (...) the biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics. (shrink)

The current prevailing view is that participation in biomedical research is above and beyond the call of duty. While some commentators have offered reasons against this, we propose a novel public goods argument for an obligation to participate in biomedical research. Biomedical knowledge is a public good, available to any individual even if that individual does not contribute to it. Participation in research is a critical way to support an important public good. Consequently, all (...) have a duty to participate. The current social norm is that individuals participate only if they have a good reason to do so. The public goods argument implies that individuals should participate unless they have a good reason not to. Such a shift would be of great aid to the progress of biomedical research, eventually making society significantly healthier and longer lived. (shrink)

Business models for biomedical research prescribe decentralization due to market selection pressures. I argue that decentralized biomedical research does not match four normative philosophical models of the role of values in science. Non-epistemic values affect the internal stages of for-profit biomedical science. Publication planning, effected by Contract Research Organizations, inhibits mechanisms for transformative criticism. The structure of contracted research precludes attribution of responsibility for foreseeable harm resulting from methodological choices. The effectiveness of business (...) strategies leads to overrepresentation of profit values versus the values of the general public. These disconnects in respect to the proper role of values in science results from structural issues ultimately linked to the distinct goals of business versus applied science, and so it seems likely that disconnects will also be found in other dimensions of attempts to combine business and science. The volume and integration in the publishing community of decentralized biomedical research imply that the entire community of biomedical research science cannot match the normative criteria of community-focused models of values in science. Several proposals for changing research funding structure might successfully relieve market pressures that drive decentralization. (shrink)

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The (...) proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this (...) paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

The paper discusses the possibility that the benefits of pharmacogenomics will not be distributed equally and will create orphan populations. I argue that since these inequalities are not substantially different from those produced by ‘traditional’ drugs and are not generated with the intention to discriminate, their production needs not be unethical. Still, the final result is going against deep-seated moral feelings and intuitions, as well as broadly accepted principles of just distribution of health outcomes and healthcare. I thus propose two (...) provisos that would prevent the most offensive outcomes and moderate the scope of the produced inequalities. The first proviso rejects pharmacogenomics innovations that worsen existing group inequalities and aggravate the disadvantage of communities with a history of discrimination. The second proviso requires that there is a strategy in place to even out as much as possible the distribution of benefits in the future and that a system of compensations is in place for pharmacogenomic orphans. Given that only one moral problem generated by pharmacogenomics has been tackled, the list of provisos might be expanded when other issues are considered. (shrink)

Perez-Rodriguez and de la Fuente (2017) assume that although human races do not exist in a biological sense (“geneticists and evolutionary biologists generally agree that the division of humans into races/subspecies has no defensible scientific basis,” they exist only as “sociocultural constructions” and because of that maintain an illusory reality, for example, through “racialized” practices in medicine. Agreeing with the main postulates formulated in the article, we believe that the authors treat this problem in a superficial manner and have failed (...) to capture the current state of the field of knowledge in science and the humanities. In our commentary, we want to highlight two main omissions, and to notice three important implications for “a postracial medicine.”. (shrink)

A proposed plan to rescue US biomedical research from its current ‘malaise’ will not be effective as it misdiagnoses the root cause of the disease.

Health data processing fields face ethical and legal problems regarding fundamental rights. As we know, patients can benefit in the Digital Era from having health or medical information available, and medical decisions can be more effective with a better understanding of clinical histories, medical and health data thanks to the development of Artificial Intelligence, Internet of Things and other Digital technologies. However, at the same time, we need to guarantee fundamental rights, including privacy ones. The complaint about ethical and legal (...) requirements – including constitutional ones – is particularly relevant in the processing of health data. This paper is focused on the problem of the consent required to the processing of health data and the exceptions established in the new European Union General Data Regulation, which cover the processing of this special data -within other aims- for scientific, historical and statistical research as legitimate purposes, which include biomedical research. The conclusion is that these open concepts are problematic both for the protection of privacy rights and for the legal security/certainty of research. On one hand there are several interpretation problems, regarding the processing of health data and the protection of information privacy. On the other hand, professionals must follow the Multilevel legal framework and to guarantee fundamental rights in the processing of health data, so there are also problems of interpretation for researchers. Therefore, we need a clearer legal framework for biomedical research. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their (...) domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (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.

The developments along the Mekong River, including in Cambodia, have boomed. There were 755 dams. Of these, 537 have been completed, and 152 have been planned or proposed. Of these, 52 were under construction, and 14 have been canceled or suspended. Of these dams, 392 were hydropower, 337 were irrigation, and 26 were other types (CGIAR, 2015). Even though some officials saw economic development as a result of the hydropower dam, the negative impacts of hydropower dams were seen by many (...) local experts and NGOs. The negative impacts include reduced fishing stocks and exacerbated socio-economic issues (Asia and the Pacific Policy Society, 2022). Experts have conducted some research on ecosystems and livelihoods, but there has been a lack of studies conducted by local communities to investigate their cross-border impacts as a result of the hydropower dam, despite the fact that local communities have been facing issues as a result of the Mekong Development. The community research protocol was developed to improve local communities' understanding of their local contexts and their confidence in negotiating with decision-makers and policymakers to address and respond to their needs and the findings of studies on local planning for sustainable community development. The paper aims to guide community leaders and staff in conducting community research on transboundary impacts on fisheries resources, ecosystems, and the livelihoods of local communities using their knowledge. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance (...) a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

An axiom of medical research ethics is that a protocol is moral only if it has a “favorable risk-benefit ratio”. This axiom is usually interpreted in the following way: a medical research protocol is moral only if it has a positive expected value -- that is, if it is likely to do more good (to both subjects and society) than harm. I argue that, thus interpreted, the axiom has two problems. First, it is unusable, because it (...) requires us to know more about the potential outcomes of research than we ever could. Second, it is false, because it conflicts with the so-called “soft paternalist” principles of liberal democracy. In place of this flawed rule I propose a new way of making risk-benefit assessments, one that does comport with the principles of liberalism. I argue that a protocol is moral only if it would be entered into by competent subjects who are informed about the protocol. The new rule this eschews all pseudo-utilitarian calculation about the protocol’s likely harms and benefits. (shrink)

What proper role should considerations of risk, particularly to research subjects, play when it comes to conducting research on human enhancement in the military context? We introduce the currently visible military enhancement techniques (1) and the standard discussion of risk for these (2), in particular what we refer to as the ‘Assumption’, which states that the demands for risk-avoidance are higher for enhancement than for therapy. We challenge the Assumption through the introduction of three categories of enhancements (3): (...) therapeutic, preventive, and pure enhancements. This demands a revision of the Assumption (4), alongside which we propose some further general principles bearing on how to balance risks and benefits in the context of military enhancement research. We identify a particular type of therapeutic enhancements as providing a more responsible path to human trials of the relevant interventions than pure enhancement applications. Finally, we discuss some possible objections to our line of thought (5). While acknowledging their potential insights, we ultimately find them to be unpersuasive, at least provided that our proposal is understood as fully non-coercive towards the candidates for such therapeutic enhancement trials. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. (...) In the naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

When agents know a protocol, this leads them to have expectations about future observations. Agents can update their knowledge by matching their actual observations with the expected ones. They eliminate states where they do not match. In this paper, we study how agents perceive protocols that are not commonly known, and propose a semantics-driven logical framework to reason about knowledge in such scenarios. In particular, we introduce the notion of epistemic expectation models and a propositional dynamic logic-style epistemic (...) logic for reasoning about knowledge via matching agentsÊ expectations to their observations. It is shown how epistemic expectation models can be obtained from epistemic protocols. Furthermore, a characterization is presented of the effective equivalence of epistemic protocols. We introduce a new logic that incorporates updates of protocols and that can model reasoning about knowledge and observations. Finally, the framework is extended to incorporate fact-changing actions, and a worked-out example is given. © 2013 Elsevier B.V. (shrink)

Recent debates in psychopathy studies have articulated concerns about false-positives in assessment and research sampling. These are pressing concerns for research progress, since scientific quality depends on sample quality, that is, if we wish to study psychopathy we must be certain that the individuals we study are, in fact, psychopaths. Thus, if conventional assessment tools yield substantial false-positives, this would explain why central research is laden with discrepancies and nonreplicable findings. This paper draws on moral psychology in (...) order to develop tentative theory-driven exclusion criteria applicable in research sampling. Implementing standardized procedures to discriminate between research participants has the potential to yield more homogenous and discrete samples, a vital prerequisite for research progress in etiology, epidemiology, and treatment strategies. (shrink)

The "second-generation indigenization" hypothesis of Huntington's phenomenological observations on totalitarianism in Cold War regime collapse subtly portrayed the realpolitik interest groups' political influences with autocracy disbandment processes. The research puts democratization as the premise and globalization as purpose for the analysis, with the cultural anthropological psychopathology & criminological elements of genocide and crime against humanity explained, underlying some of the Communist Party of China (CPC)’s organizational behaviors. With the regionalism purposes & approaches to multilateralism by People's Republic of China (...) (PRC), the end of democratization is leveraged against the procedural means with power politics of declared “decmocracy”. Between quantitative autocratic controls and realpolitik local-regional interest groups, the connotation of democratization in liberal international globalization has either been used for militant purposes or pushed the landscape of regime collapse into realpolitik local groups and autocratic controls in the process of globalization, with a case study on a local branch of Argricultural Bank of China on supply-side hijacking by the State-owned Assets Supervision and Administration Commission of the State Council (SASAC). With the industrial interests omposed on realpolitik local groups, autocratic regionalism becomes of the "best interest scenario" for the realpolitik local groups with psychopathological spread of the criminological behaviors, by the cyber organizational criminal operations correlated with PRC’s approaches to international relations and multilateralism through bilateral trade & finance in monetary and currency domains, developed into the digitization of economies with criminological schemes in telecommunication, information, and informatics systems. However, the diminishing autonomy & freedom of the territorial population in turn derogated the real economy that wielded the prisoners' dilemma between autocracy and totalitarianism in a negative sum game deterioration cycle, with the censorship practices by the illicit regimes for propaganda controls sustaining "ideology security". In the democratization process of the dictatorial regime, "second-generation indigenization" is thus mapped to the sectarian interests respondent to dictatorial propaganda generation, other than a natural phenomenon out of autonomy and freedom premises in decision theory. The article recaps the coup d'état between Xi Jinping and Bo Xilai before Xi took the autocratic power, and analyzes the human rights situation in the obstacle of democratization and by the coercion mechanism imposed on the mainland China civil society for the militant purposes, with its behaviral spread of censorship to the “internet platforms” in liberal democratic countries by financial interest incentives and avoidance from war threats, whereby military backends in the cyber systems already indicate otherwise. (shrink)

Descriptive accounts of the nature of explanation in neuroscience and the global goals of such explanation have recently proliferated in the philosophy of neuroscience and with them new understandings of the experimental practices of neuroscientists have emerged. In this paper, I consider two models of such practices; one that takes them to be reductive; another that takes them to be integrative. I investigate those areas of the neuroscience of learning and memory from which the examples used to substantiate these models (...) are culled, and argue that the multiplicity of experimental protocols used in these research areas presents specific challenges for both models. In my view, these challenges have been overlooked largely because philosophers have hitherto failed to pay sufficient attention to fundamental features of experimental practice. I demonstrate that when we do pay attention to such features, evidence for reduction and integrative unity in neuroscience is simply not borne out. I end by suggesting some new directions for the philosophy of neuroscience that pertain to taking a closer look at the nature of neuroscientific experiments. (shrink)

Despite well-established results in survey methodology, many experimental philosophers have not asked whether and in what way conclusions about folk intuitions follow from people’s responses to their surveys. Rather, they appear to have proceeded on the assumption that intuitions can be simply read off from survey responses. Survey research, however, is fraught with difficulties. I review some of the relevant literature—particularly focusing on the conversational pragmatic aspects of survey research—and consider its application to common experimental philosophy surveys. I (...) argue for two claims. First, that experimental philosophers’ survey methodology leaves the facts about folk intuitions massively underdetermined; and second, that what has been regarded as evidence for the instability of philosophical intuitions is, at least in some cases, better accounted for in terms of subjects’ reactions to subtle pragmatic cues contained in the surveys. (shrink)

This article presents a case study of the structure and logic of the author’s dissertation, with a focus on theoretical content. Designed for use in proposal writing seminars or research methods courses, the article stresses the value of identifying the originating, specifying and subsidiary research questions; clarifying the subject and object of the research; situating research within a particular research tradition, and using a competing theories approach. The article stresses the need to identify conceptual problems (...) and empirical problems and their associated conceptual and operational definitions. The primary theoretical perspective is drawn from emerging sociology of externalities rooted in ecological theory, within the institutionalist tradition. (shrink)

The integration of Internet Protocol and Embedded Systems can enhance the communication platform. This paper describes the emerging smart technologies based on Internet of Things (IOT) and internet protocols along with embedded systems for monitoring and controlling smart devices with the help of WiFi technology and web applications. The internet protocol (IP) address has been assigned to the things to control and operate the devices via remote network that facilitates the interoperability and end-to-end communication among various devices c,onnected (...) over a network. The HTTP POST and HTTP GET command that supports the RESTful service have been used to ensure the transmission and reception of packets between the IOT Gateway and Cloud Database. The emerging smart technologies based on the Internet of Things (IoT) facilitated features like automation, controllability, interconnectivity, reliability which in turn turn paved the way for a wide range of acceptance amongst the masses. The Internet of Things (IoT) has brought in many new emerging technologies into varoius field like our daily lives, industry, agricultural sector, and many more. The world is experiencing the explosive growth with the advent of Internet of Things (IoT) these years. The potential growth of IoT is enoromous which is evidenced by all the human beings in our day to day life. (shrink)

Delineating the framework for a fundamental model of long-range coherence in biological systems is said to rely on principles beyond parameters addressed by current physical science. Just as phenomena of quantum mechanics lay beyond tools of classical Newtonian mechanics we must now enter a 3rd regime of unified field, UF mechanics. In this paper we present a battery of nine empirical protocols for manipulating long-range coherence in complex self-organized living systems (SOLS) in a manner surmounting the Copenhagen Interpretation of quantum (...) uncertainty (space-quantization) thereby allowing empirical access to underlying coherent biophysical principles driving self-organization. Interestingly, while the UF is not indicative of a 5th fundamental force in the usual phenomenal sense of quantal transfer during field interactions; it does however provide an inherent ‘force of coherence’ in an energyless ontological sense by a process called ‘topological switching’ of higher dimensional (HD) brane dynamics. It is this putative inherent property that produces long-range coherence and leads to the possibility of its direct experimental mediation. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises (...) ENVO’s motivation, content, structure, adoption, and governance approach. (shrink)

Background Genomic research on neurodevelopmental disorders (NDDs), particularly involving minors, combines and amplifies existing research ethics issues for biomedical research. We performed a review of the literature on the ethical issues associated with genomic research involving children affected by NDDs as an aid to researchers to better anticipate and address ethical concerns. Results Qualitative thematic analysis of the included articles revealed themes in three main areas: research design and ethics review, inclusion of research (...) participants, and communication of research results. Ethical issues known to be associated with genomic research in general, such as privacy risks and informed consent/assent, seem especially pressing for NDD participants because of their potentially decreased cognitive abilities, increased vulnerability, and stigma associated with mental health problems. Additionally, there are informational risks: learning genetic information about NDD may have psychological and social impact, not only for the research participant but also for family members. However, there are potential benefits associated with research participation, too: by enrolling in research, the participants may access genetic testing and thus increase their chances of receiving a (genetic) diagnosis for their neurodevelopmental symptoms, prognostic or predictive information about disease progression or the risk of concurrent future disorders. Based on the results of our review, we developed an ethics checklist for genomic research involving children affected by NDDs. Conclusions In setting up and designing genomic research efforts in NDD, researchers should partner with communities of persons with NDDs. Particular attention should be paid to preventing disproportional burdens of research participation of children with NDDs and their siblings, parents and other family members. Researchers should carefully tailor the information and informed consent procedures to avoid therapeutic and diagnostic misconception in NDD research. To better anticipate and address ethical issues in specific NDD studies, we suggest researchers to use the ethics checklist for genomic research involving children affected by NDDs presented in this paper. (shrink)

Background: Biomedical research nowadays is increasingly carried out in multinational and multicenter settings. Due to disparate national regulations on various ethical aspects, such as informed consent, there is the risk of ethical compromises when involving human subjects in research. Although the Declaration of Helsinki is the point of reference for ethical conduct of research on humans, national normative requirements may diverge from its provisions. The aim of this research is to examine requirements on informed consent (...) in biomedical research in Germany, Poland, and Russia to determine how each national regulatory framework relates to the provisions of the Declaration of Helsinki. Methods: For this analysis, we conducted a search of the legal databases “Gesetze im Internet” for Germany, “Internetowy System Aktow Prawnych” for Poland, and “ГAPAHT – Garant” for Russia. The search was complemented by a review of secondary literature contained in the databases Google Scholar, PubMed, Polish National Library, and eLibrary ru. We have identified 21 normative regulations containing provisions on informed consent in clinical research in all three countries. The content of these documents was systematically categorized and analyzed. Results: The normative framework in all three countries shows a strong commitment towards the core ethical principles of research envisaged in the Declaration of Helsinki. Nevertheless, provisions on informed consent vary between these three countries. The differences range from the method and language in which information should be provided, through the amount of information required to be disclosed, to the form of documenting consent or withdrawal. In the case of research on vulnerable groups, these differences are particularly visible. Conclusions: The identified differences can negatively impact the ethical conduct of international clinical studies. Attention needs to be paid that flexibilities within national regulations are not misused to undermine the protection of research subjects. Achieving global or regional legislative harmonization might prove impossible. Such lack of legal consensus reinforces the significance of the international ethical agreements. (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)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who (...) develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Publication ethics is an important aspect of both the research and publication enterprises. It is particularly important in the field of biomedical science because published data may directly affect human health. In this article, we examine publication ethics policies in biomedical journals published in Central and Eastern Europe. We were interested in possible differences between East European countries that are members of the European Union (Eastern EU) and South-East European countries (South-East Europe) that are not members of (...) the European Union.The most common ethical issues addressed by all journals in the region were redundant publication, peer review process, and copyright or licensing details. Image manipulation, editors’ conflicts of interest and registration of clinical trialswere the least common ethical policies. Three aspects were significantly morecommon in journals published outside the EU: statements on the endorsement of international editorial standards, contributorship policy, and image manipulation.On the other hand, copyright or licensing information were more prevalent in journals published in the Eastern EU. The existence of significant differences amongbiomedical journals’ ethical policies calls for further research and active measuresto harmonize policies across journals. On the other hand, copyright or licensing information were more prevalent in journals published in the Eastern EU. The existence of significant differences among biomedical journals’ ethical policies calls for further research and active measures to harmonize policies across journals. (shrink)

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

The pathbreaking scientific advances of recent years call for a new philosophical consideration of the fundamental categories of biology and its neighboring disciplines. Above all, the new information technologies used in biomedical research, and the necessity to master the continuously growing flood of data that is associated therewith, demand a profound and systematic reflection on the systematization and classification of biological data. This, however, demands robust theories of basic concepts such as kind, species, part, whole, function, process, fragment, (...) sequence, expression, boundary, locus, environment, system, and so on. Concepts which belong to the implicit stock of knowledge of every biologist. They amount to a dimension of biological reality which remains constant in the course of biological evolution and whose theoretical treatment requires contemporary analogues of the tools developed in traditional Aristotelian metaphysics. To provide the necessary theories and definitions is a task for philosophy, which is thus called upon to play an important role as intermediary between biology and informatics. (shrink)

The Human Genome Project is regarded by many as one of the major scientific achievements in recent science history, a large-scale endeavour that is changing the way in which biomedical research is done and expected, moreover, to yield considerable benefit for society. Thus, since the completion of the human genome sequencing effort, a debate has emerged over the question whether this effort merits to be awarded a Nobel Prize and if so, who should be the one to receive (...) it, as no more than three individuals can be selected. In this article, the HGP is taken as a case study to consider the ethical question to what extent it is still possible, in an era of big science, of large-scale consortia and global team work, to acknowledge and reward individual contributions to important breakthroughs in biomedical fields. Is it still viable to single out individuals for their decisive contributions in order to reward them in a fair and convincing way? Whereas the concept of the Nobel prize as such seems to reflect an archetypical view of scientists as solitary researchers who, at a certain point in their careers, make their one decisive discovery, this vision has proven to be problematic from the very outset. Already during the first decade of the Nobel era, Ivan Pavlov was denied the Prize several times before finally receiving it, on the basis of the argument that he had been active as a research manager rather than as a researcher himself. The question then is whether, in the case of the HGP, a research effort that involved the contributions of hundreds or even thousands of researchers worldwide, it is still possible to “individualise” the Prize? The “HGP Nobel Prize problem” is regarded as an exemplary issue in current research ethics, highlighting a number of quandaries and trends involved in contemporary life science research practices more broadly. (shrink)

1. Biomedical sciences are fast-growing fields with unprecedented speed of research outputs, especially in the quantities of papers. Philosophers aiming to study ongoing biomedical changes face cha...

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

The fourth amendment to the German Medicinal Products Act (Arzneimittelgesetz) states that nontherapeutic research in incompetent populations is permissible under the condition that potential research participants expressly declare their wish to participate in scientific research in an advance research directive. This article explores the implementation of advance research directives in Germany against the background of the international legal and ethical framework for biomedical research. In particular, it addresses a practical problem that arises from (...) the disclosure requirement for advance research directives. We show that, if the disclosure standard for advance research directives is set at a token level, nontherapeutic research in incompetent populations becomes practically impossible. To resolve this issue, we suggest the disclosure standard be set at a type level. (shrink)

For over a decade now, a community of researchers has contributed to the development of the Unified Foundational Ontology (UFO) - aimed at providing foundations for all major conceptual modeling constructs. This ontology has led to the development of an Ontology-Driven Conceptual Modeling language dubbed OntoUML, reflecting the ontological micro-theories comprising UFO. Over the years, UFO and OntoUML have been successfully employed in a number of academic, industrial and governmental settings to create conceptual models in a variety of different (...) domains. These experiences have pointed out to opportunities of improvement not only to the language itself but also to its underlying theory. In this paper, we take the first step in that direction by revising the theory of types in UFO in response to empirical evidence. The new version of this theory shows that many of the meta-types present in OntoUML (differentiating Kinds, Roles, Phases, Mixins, etc.) should be considered not as restricted to Substantial types but instead should be applied to model Endurant Types in general, including Relator types, Quality types and Mode types. We also contribute a formal characterization of this fragment of the theory, which is then used to advance a metamodel for OntoUML 2.0. Finally, we propose a computational support tool implementing this updated metamodel. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who (...) develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

“Participatory research” is an umbrella term for a wide variety of scientific research projects that include participation of members of the lay public beyond simply using humans as “subjects” of research. In this chapter, we begin by surveying the variety of participatory research approaches across fields. We examine the goals of participatory research projects, including social and scientific value. Next, we apply a theoretical framework to challenges that participatory research faces. We then survey three (...) typologies of participatory research projects, each of which can illuminate and guide decisions in project development. We end by looking at participatory research approaches in health contexts, applying the theoretical resources we introduced earlier in the chapter. (shrink)

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

The research resulted in a comprehensive overview of the Vietnamese public infrastructure market. Primary data confirmed most of the secondary data collected while adding more supporting details, with no perceivable contradiction among data sources. Macro-economically, Vietnam emerged as a high-potential market due to the rapid economic growth, the massive infrastructure demand driven by urbanization and industrialization, and the Government’s recent efforts. However, there were market uncertainties that required careful consideration, with regulatory inefficiency and corruption being the most prominent (...) ones. Culturally, Vietnam and Finland exhibited distinct differences. The thesis concluded that Vietnam was a market of high potentiality and medium risk. The author’s recommendations for market entry included a careful approach to mitigate risks concerning regulations, and the addition of a translator when negotiating to reduce the risk of cultural misunderstanding. (shrink)