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 automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly (...) acquiring the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T (...) as a standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this (...) problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, (...) organized into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (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)

Precision Medicine has become a common label for data-intensive and patient-driven biomedical research. Its intended future is reflected in endeavours such as the Precision Medicine Initiative in the USA. This article addresses the question whether it is possible to discern a new ‘medical cosmology’ in Precision Medicine, a concept that was developed by Nicholas Jewson to describe comprehensive transformations involving various dimensions of biomedical knowledge and practice, such as vocabularies, the roles of patients and physicians and the (...) conceptualisation of disease. Subsequently, I will elaborate my assessment of the features of Precision Medicine with the help of Michel Foucault, by exploring how precision medicine involves a transformation along three axes: the axis of biomedical knowledge, of biomedical power and of the patient as a self. Patients are encouraged to become the managers of their own health status, while the medical domain is reframed as a data-sharing community, characterised by changing power relationships between providers and patients, producers and consumers. While the emerging Precision Medicine cosmology may surpass existing knowledge frameworks; it obscures previous traditions and reduces research-subjects to mere data. This in turn, means that the individual is both subjected to the neoliberal demand to share personal information, and at the same time has acquired the positive ‘right’ to become a member of the data-sharing community. The subject has to constantly negotiate the meaning of his or her data, which can either enable self-expression, or function as a commanding Superego. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, (...) and understood by health professionals (i.e., they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

Many studies have emphasized the importance of medical, insurance, and workplace systems treating individuals fairly in work disability prevention and return-to-work. However, ethical theories and perspectives from these different systems are rarely discussed in relation to each other, even though in practice these systems constantly interact. This paper explores ethical theories and perspectives that may apply to the WDP–RTW field, and discusses these in relation to perspectives attributed to dominant stakeholders in this field, and to potential differences in different jurisdictional (...) contexts. Literature was sought primarily in biomedical ethics, business ethics, and public administration ethics. In biomedical ethics, four ethical principles are dominant: autonomy, beneficence, nonmalevolence, and justice. Business ethics involve theories on Corporate Social Responsibility, social contracts, and organizational justice. Public administration ethics focus on constitutional theory, citizenship, social equity, virtue, and public interest. Several concepts were identified as relevant for ethical analyses in the WDP–RTW field, including justice; individual autonomy; nonmalevolence; economic and social responsibility; and social contracts. These concepts provide a vocabulary that may be used to analyze stakeholders’ actions and interactions in RTW processes. It was also noted how the power balance between stakeholders will influence which ethical perspectives will influence RTW. Jurisdictional differences that influence RTW processes with regard to stakeholder responsibilities were identified, as well as varying beliefs as to who is the client in different compensation systems. A social contractual approach may inform an analysis of cultural and legal differences. (shrink)

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties (...) of SNOMED CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies.[1] To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO).[2] With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. (shrink)

How are “interesting” research problems identified and made durable by academic researchers, particularly in situations defined by multiple evaluation principles? Building on two case studies of research groups working on rare diseases in academic biomedicine, we explore how group leaders arrange their groups to encompass research problems that latch onto distinct evaluation principles by dividing and combining work into “basic-oriented” and “clinical-oriented” spheres of inquiry. Following recent developments in the sociology of valuation comparing academics to capitalist entrepreneurs in pursuit of (...) varying kinds of worth, we argue that the metaphor of the portfolio is helpful in analyzing how group leaders manage these different research lines as “alternative investment options” from which they were variously hoping to capitalize. We argue portfolio development is a useful concept for exploring how group leaders fashion “entrepreneurial” practices to manage and exploit tensions between multiple matrices of valuation and conclude with suggestions for how this vocabulary can further extend analysis of epistemic capitalism within science and technology studies. (shrink)

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

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in (...) the form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

Biomedical ontologies define entities and relations in order to represent knowledge in the biomedical domain. In addition, many ontologies further represent supplementary knowledge by linking terms from an external controlled vocabulary to the entities defined within the ontology itself. In this paper we concentrate on the domain of medical imaging, for which controlled vocabularies are emerging, but no ontology currently exists. We analyzed computed tomography reports in order to determine to which entities terms used in such reports (...) refer and which relations are used with regard to the recently published Open Biomedical Ontologies (OBO) Relation Ontology. Our analysis revealed that the majority of entities referred to in radiological reporting practice are anatomical entities and anatomical coordinates. Based on the Open Biomedical Ontologies (OBO) Relation Ontology we provide a set of additional relations for the ontological structuring of image features such as shape, morphology, size and signal, frequently found in the reports. On the basis of these results we conclude that the construction of an imaging ontology may benefit greatly from already existing reference ontologies such as the Foundational Model of Anatomy (FMA), which represent those entities to which radiological reports most frequently refer. (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the (...) salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

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

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

Contemporary Bioethics: A Reader with Cases is the most cutting-edge bioethics anthology/casebook available. Incorporating introductions, readings, and cases that span the breadth of the discipline, this exceptional volume captures the spirit of bioethics as a rich, exciting, and continuously evolving field. Addressing all of the essential topics--including abortion, reproductive ethics, end-of-life care, research ethics, and the allocation of resources--it also moves beyond the "classic" approach of other books by extending into timely and provocative issues like terrorism, cosmetic surgery, immigration, genetic (...) manipulations, links between first- and third-world health, and--unique to this book--environmental sustainability and climate change. In addition, Contemporary Bioethics is the only book of its kind that includes both philosophical and religious perspectives.The text opens with a substantial introduction that presents key ethical principles, theories, and methods and shows students how to use these tools to frame and address ethical dilemmas in medicine. Covering the brief yet captivating history of the field, the introduction also considers the role of religion in the development of bioethics and examines differences between secular and religious modes of argumentation. Each of the seven topical chapters contains an in-depth introduction, a selection of concise readings representing a diverse range of moral perspectives, discussion questions, and a collection of full-length and provocative case studies that enable students to further explore the issues.Ideal for introductory courses in bioethics and biomedical ethics, Contemporary Bioethics is supplemented by a Instructor's Manual on CD and a Companion Website containing resources for both students and professors, including chapter summaries, additional cases with discussion questions, ideas for further reading, vocabulary flashcards, self-quizzes, and more. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data (...) and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

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

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is a comprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic health data. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but these efforts have been hampered by the size and complexity of SCT. -/- Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the terms in SCT (...) in a way that will support quality assurance of SCT, for example, by allowing consistency checks of definitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-level SCT ontology (SCTO) is based on the Ontology for General Medical Science (OGMS). -/- Results: The SCTO is implemented in OWL 2, to support automatic inference and consistency checking. The approach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundry ontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-level ontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555 annotations. It is publicly available through the bioportal. -/- Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semantic interoperability among distributed electronic health records. In addition, the populated ontology can be used for the automation of mobile health applications. (shrink)

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and (...) some of its anticipated uses. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data (...) and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led (...) to a proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (shrink)

Information Retrieval systems benefit from the use of long queries containing a large volume of search-relevant information. This situation is not common, as users of such systems tend to use very short and precise queries with few keywords. In this work we propose a modification of the Latent Dirichlet Allocation (LDA) technique using data from the document collection and its vocabulary for a better representation of short queries. Additionally, a study is carried out on how the modification of the proposed (...) LDA weighted vectors increase the performance using relevant documents as feedback. The work shown in this paper is tested using three biomedical corpora (TREC Genomics 2004, TREC Genomics 2005 and OHSUMED) and one legal corpus (FIRE 2017). Results prove that the application of the proposed representation technique, as well as the feedback adjustment, clearly outperforms the baseline methods (BM25 and non-modified LDA). (shrink)

The construction of complex ontologies can be facilitated by adapting existing vocabularies. There is little clarity and in fact little consensus as to what modifications of vocabularies are necessary in order to re-engineer them into ontologies. In this paper we present a method that provides clear steps to follow when re-engineering a thesaurus. The method makes use of top-level ontologies and was derived from the structural differences between thesauri and ontologies as well as from best practices in modeling, (...) some of which have been advocated in the biomedical domain. We illustrate each step of our method with examples from a re-engineering case study about agricultural fertilizers based on the AGROVOC thesaurus. Our method makes clear that re-engineering thesauri requires far more than just a syntactic conversion into a formal language or other easily automatable steps. The method can not only be used for re-engineering thesauri, but does also summarize steps for building ontologies in general, and can hence be adapted for the re-engineering of other types of vocabularies or terminologies. (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)

This book is written in homage to Nicola Guarino. It is a tribute to his many scientific contributions to the new discipline, applied ontology, he struggled to establish. Nicola Guarino is widely recognized as one of the pioneers in formal and applied ontology. Renow – and sometimes even criticized – for his deep interest for the subtlest details of theoretical analysis, all throughout his career he has held the conviction that all science has to be for the benefit of society (...) at large, hence his motto that ontologies are not just for making information systems interoperable, but also – and more importantly – for making people (users of the systems) understand each other. He was among the first to realize that, to capture the intended meaning of the terms used by an information system, applied ontology has necessarily to be an interdisciplinary enterprise. Nicola’s early career developed in the areas of data systems and expert systems in physics and biomedical engineering. The lack of methodologies in expert systems led him to turn to philosophical logic as a source of inspiration, prompting him to attend the meetings of the analytic philosophy group at the University of Padua, and to discover a whole new world. It was the end of the 1980s and in that period the term ‘ontology’ started to be used to indicate a shared vocabulary across a community. Recognizing the potentials of this idea, Nicola began studying philosophical work. Knowing that language remains one of the pivotal elements in knowledge acquisition and representation, he paired it with the study of linguistic analysis. The combination of the two fields proved to be fundamental to shape his research vision, which could be summarized as: ontological analysis is hard, yet unavoidable to address the pervasive need for explicit, meaningful and transparent information systems. In other words, ontology makes sense. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

Se presentan los resultados de una investigación cualitativa hermenéutica sobre la lingüística cognitiva y la lingüística aplicada, relacionadas con otras ciencias en un contexto específico de la comunidad científica especializada. Desde una visión integral y holística de las ciencias biomédicas y humanas, asimismo, se estudian los lenguajes técnico-científicos de la ciencia y de la tecnología para facilitar la interrelación cognitiva entre las diferentes disciplinas. Este estudio permite crear capacidades para evaluar el acervo léxico en contexto, útil para la transmisión y (...) la transformación del conocimiento en un lenguaje propio acorde a la exigencia del método científico. El objetivo consistió en indagar sobre la relación de la unidad léxica con su nexo cognitivo a una unidad terminológica de uso cotidiano en la información y en la comunicación académica de la práctica médico-legal forense. Los resultados establecen diferencia y precisan cierta comprensión de la significación de unidades léxicas ambiguas de mayor relevancia y frecuencia, utilizadas en este ámbito del conocimiento, en cuatro categorías de análisis; según las características propias de la disciplina en dialogo con otras ciencias en contexto. Se evidencia la importancia de educar durante el proceso enseñanza-aprendizaje significativo de la disciplina en contexto, desde la metalingüística del objeto de estudio dimensionado y relacionado con otros objetos de estudio, que permita el proceso cognitivo del lenguaje técnico-científico transdisciplinar, la apropiación social y la circulación del conocimiento aplicado a las prácticas médico legales integrales en relación entre la Psicofarmacología, la Psiquiatría, la Antropología y la Psicología, con las ciencias biomédicas y humanas. In this work results of a qualitive hermeneutic research about a cognitive and applied linguistic related to other sciences in an specific context of a given scientific community were presented, a technical and scientific language regarding science and technology was pointed out from an integral vision in order to facilitate cognitive relationship among different disciplines. This study also allows to create capacities in order to assess vocabulary in context, useful for the transmission and transformation of knowledge according to a scientific method. The objective was directed to know about the relationship between the lexical unit and its meaning in a given communicative context and in the academic communication of a medical - legal forensic practice. The importance of educate during the teaching learning process is also mentioned in this research and the main objective is to develop an assertive medical practice among Psychopharmacology, psychiatric, anthropology and psychology with biomedical and human sciences. (shrink)

The advocates of Integrative Bioethics have insisted that this recently emerging project aspires to become a new stage of bioethical development, surpassing both biomedically oriented bioethics and global bioethics. We claim in this paper that if the project wants to successfully replace the two existing paradigms, it at least needs to properly address and surmount the lack of common moral vocabulary problem. This problem points to a semantic incommensurability due to cross-language communication in moral terms. This paper proceeds as follows. (...) In the first part, we provide an overview of Integrative Bioethics and its conceptual building blocks: mutlidisciplinarity, interdisciplinarity, and transdisciplinarity. In the second part, we disclose the problem of semantic incommensurability. The third part gives an overview of various positions on the understanding of interdisciplinarity and integration in interdisciplinary communication, and corresponding attempts at solving the lack of common moral vocabulary problem. Here we lean mostly on Holbrook’s three theses regarding the character of interdisciplinary communication. Finally, in the fourth part, we discuss a particular bioethical case—that of euthanasia—to demonstrate the challenge semantic incommensurability poses to dialogues in Integrative Bioethics. We conclude that Integrative Bioethics does not offer a methodological toolset that would warrant optimism in its advocates’ predictions of surpassing current modes of doing bioethics. Since Integrative Bioethics leaves controversial methodological questions unresolved on almost all counts and shows no attempts at overcoming the critical stumbling points, we argue for its rejection. (shrink)

In this article, I argue that law has two often neglected functions: the expressive and the communicative functions. They are especially important for legislation on moral issues, such as biomedical ethics and anti-discrimination law. The communicative function of law is a complex one: law may create a normative framework, a vocabulary to structure normative discussions, as well as institutions and procedures that promote further discussion. The expressive function of law is at stake when it expresses which fundamental standards, which (...) values are regarded as important. The recognition of these functions is not only important for descriptive purposes; it is also fruitful for normative theory. (shrink)

I show how omissions lead to robustness and can justify distortions, and I give inferentially relevant explications of abstraction and idealization. Abstraction is explicated as the omission of all and only those claims that use a specific vocabulary; idealization is explicated as the distortion of only those claims that use a specific vocabulary. With these explications, abstraction can justify idealization. As examples of how abstraction justifies idealization and leads to robustness, I discuss Beauchamp and Childress's four principles of biomedical (...) ethics and the qualitative treatment of the Schrödinger equation. (shrink)

Although big-data research has met with multiple controversies in diverse fields, political and security implications of big data in life sciences have received less attention. This paper explores how threats and risks are anticipated and acted on in biobanking, which builds research repositories for biomedical samples and data. Focusing on the biggest harmonisation cluster of biomedical research in Europe, BBMRI-ERIC, the paper analyses different logics of risk in the anticipatory discourse on biobanking. Based on document analysis, interviews with (...) ELSI experts, and field research, three types of framing of risk are reconstructed: data security, privacy, and data misuse. The paper finds that these logics downplay the broader social and political context and reflects on the limits of the practices of anticipatory governance in biobanking. It argues that this regime of governance can make it difficult for biobanks to address possible future challenges, such as access to biomedical data by authorities, pressures for integrating biobank data with other type of personal data, or their use for profiling beyond medical purposes. To address potential controversies and societal implications related to the use of big data in health research and medicine, the paper suggests to expand the vocabulary and practices of anticipatory governance, in the biobanking community and beyond. (shrink)

Mid-level ontologies are used to integrate data across disparate domains using vocabularies more specific than top-level ontologies and more general than domain-level ontologies. There are no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those (...) single ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domainlevel terms. To gain clarity, we aim to specify conditions for membership in what we call the middle architecture, which consists solely of mid-level ontologies. (shrink)

ArgumentHere I analyze the anatomical thought of the French physician and naturalist Félix Vicq d'Azyr (1748–1794) in order to bring to light its importance in the development of comparative anatomy at the end of the eighteenth century. I argue that his work and career can be understood as an ambitious program for a radical reform of all biomedical sciences and a reorganization of this whole field around comparative anatomy, on the conceptual as well as the institutional level. In particular, (...) he recommended a close connection between anatomical and physiological studies, and a generalization of the comparative approach towards organs and functions in man and animals. This conception led him not only to reform the scope, the methods, the style of description, and the vocabulary in anatomy, but also to construct a new classification of living beings and to pursue a quest for laws of organization. This strategy was successful, since Vicq d'Azyr was able to promote his thought as well as his institutional position efficiently. The Revolution and his untimely death prevented him from achieving his program, but his attempt would serve as an example for younger scientists like Cuvier. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

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

In all European countries, the eighteenth century was characterised by efforts to improve the vernaculars. The Transylvanian case study shows how both codified medical language and ordinary language were constructed and enriched by a large number of medical books and brochures. The publication of medical literature in Central European vernacular languages in order to popularise new medical knowledge was a comprehensive programme, designed on the one hand by intellectual, political and religious elites who urged the improvement of the fatherland and (...) the promotion of the common good by perfecting the arts and sciences. On the other hand, the imperial administration’s initiatives affected local forms of medical knowledge and the construction of vernacular languages. In the eighteenth century, the construction of vernacular languages in the Habsburg Monarchy took on a significant political character. However, in the process of building of the scientific and medical vocabulary, the main preoccupation was precision, clarity and accessibility of the neologisms being invented to encompass the medical phenomena being described. In spite of political conflicts among the ‘nations’ living in Transylvania, physicians borrowed words from German, Hungarian and Romanian. Thus they elevated several words used in everyday language to the upper social stratum of language use, leading to the invention of new terms to describe particular medical practices or phenomena. (shrink)

In the last two decades, WORDNET has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MEDICAL WORDNET. This resource is not to be conceived merely as a lexical extension of the original WORDNET to medical terminology; indeed, there is already a considerable degree of overlap between WORDNET and the vocabulary of medicine. Instead, we propose a (...) new type of repository, consisting of three large collections of (1) medically relevant word forms, structured along the lines of the existing Princeton WORDNET; (2) medically validated propositions, referred to here as medical facts, which will constitute what we shall call MEDICAL FACTNET; and (3) propositions reflecting laypersons’ medical beliefs, which will constitute what we shall call the MEDICAL BELIEFNET. We introduce a methodology for setting up the MEDICAL WORDNET. We then turn to the discussion of research challenges that have to be met in order to build this new type of information resource. (shrink)

This study examines the ethical permissibility of biomedical moral enhancement (BME) for psychopaths, considering both coercive and voluntary approaches. To do so, I will first briefly explain what psychopaths are and some normative implications of these facts. I will then ethically examine three scenarios of BME for psychopaths: (1) coercive BME for non‐criminal psychopaths, (2) coercive BME for psychopathic offenders, and (3) voluntary BME for psychopathic offenders. I will argue that coercive BME for non‐criminal psychopaths is ethically problematic due (...) to issues of cost, invasion of privacy, and stigmatic effects of compulsory diagnosis. Similarly, I will argue that coercive BME for criminals is impermissible due to violations of the rights to bodily and mental integrity. However, I will show that voluntary BME for offenders may be ethically permissible under certain conditions, challenging the critique that the consent of vulnerable prisoners cannot be considered fully voluntary. I argue that when an offender is provided with sufficient medical and legal information, incentives such as the possibility of parole review based on BME results do not preclude the voluntariness of consent. Ultimately, I aim to advance the debate on BME for psychopaths by delineating and defending conditions for the ethical permissibility of voluntary BME. (shrink)