Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added (...) or subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory. (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)

The idea of personalised medicine (PM) has gathered momentum recently, attracting funding and generating hopes as well as scepticism. As PM gives rise to differing interpretations, there have been several attempts to clarify the concept. In an influential paper published in this journal, Schleidgen and colleagues have proposed a precise and narrow definition of PM on the basis of a systematic literature review. Given that their conclusion is at odds with those of other recent attempts to understand PM, we consider (...) whether their systematic review gives them an edge over competing interpretations. We have found some methodological weaknesses and questionable assumptions in Schleidgen and colleagues’ attempt to provide a more specific definition of PM. Our perplexities concern the lack of criteria for assessing the epistemic strength of the definitions that they consider, as well as the logical principles used to extract a more precise definition, the narrowness of the pool from which they have drawn their empirical data, and finally their overlooking the fact that definitions depend on the context of use. We are also worried that their ethical assumption that only patients’ interests are legitimate is too simplistic and drives all other stakeholders’ interests—including those that are justifiable—underground, thus compromising any hope of a transparent and fair negotiation among a plurality of actors and interests. As an alternative to the shortcomings of attempting a semantic disciplining of the concept we propose a pragmatic approach. Rather than considering PM to be a scientific concept in need of precise demarcation, we look at it as an open and negotiable concept used in a variety of contexts including at the level of orienting research goals and policy objectives. We believe that since PM is still more an ideal than an achieved reality, a plurality of visions is to be expected and we need to pay attention to the people, reasons and interests behind these alternative conceptions. In other words, the logic and politics of PM cannot be disentangled and disagreements need to be tackled addressing the normative and strategic conflicts behind them. (shrink)

We present the details of a methodology for quality assurance in large medical terminologies and describe three algorithms that can help terminology developers and users to identify potential mistakes. The methodology is based in part on linguistic criteria and in part on logical and ontological principles governing sound classifications. We conclude by outlining the results of applying the methodology in the form of a taxonomy different types of errors and potential errors detected in SNOMED-CT.

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at (...) the level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn (...) from the context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts 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 termsin SCT in a way (...) that will support quality assurance of SCT, for example, by allowing consistency checks ofdefinitions and the identification and elimination of redundancies in the SCT vocabulary. Our proposed upper-levelSCT 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. Theapproach will allow integration of SCT data with data annotated using Open Biomedical Ontologies (OBO) Foundryontologies, since the use of OGMS will ensure consistency with the Basic Formal Ontology, which is the top-levelontology of the OBO Foundry. Currently, the SCTO contains 304 classes, 28 properties, 2400 axioms, and 1555annotations. It is publicly available through the bioportal athttp://bioportal.bioontology.org/ontologies/SCTO/. Conclusion: The resulting ontology can enhance the semantics of clinical decision support systems and semanticinteroperability among distributed electronic health records. In addition, the populated ontology can be used forthe automation of mobile health applications. (shrink)

Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in (...) biomedical information systems that is designed: 1) to provide new opportunities for the sharing and management of data within and between healthcare institutions, 2) to facilitate interoperability among different terminology and record systems, and thereby 3) to allow new kinds of reasoning with biomedical data. (shrink)

Recent developments in the field of forensic medicine and the judicial practice are both factors influencing considerably toward an increasing role of toxicologists in court hearings and litigation processes. The role of forensic toxicologist has been until a few decennia before a prerogative of the medico-legal specialists, but meanwhile a subspecialty of the general toxicology seems to have been created. Vis-à-vis the increasing presence of toxicologists in penal procedures of poisoning and intoxications, Albanian courts have created their own precedents and (...) bylaws, regulating the presence, the opinion taking, and the relative importance such an expert opinion will have on the final sentence. Due to a multiplicity of factors, legal terminology with regard to drugs of abuse needs to be revised and parallel to such a revision a better defining of the role of expert toxicologist as a collector and interpreter of the scientific proofs seems necessary. Overlapping competencies with judicial bodies and confusing legislative measures will do nothing else but complicate issues that should be and can be easily resolved, through simple and appropriate interventions at different levels. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (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)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...) similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (shrink)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad (...) scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas – which see terminology work as being focused on the classification of concepts in people’s minds – and (...) we argue that they serve still as the basis for a series of influential confusions. We argue further that an ontology based unambiguously, not on concepts, but on the classification of entities in reality can, by removing these confusions, make a vital contribution to ensuring the interoperability of coding systems and healthcare records in the future. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these (...) relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the (...) patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (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)

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 desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

If SNOMED CT is to serve as a biomedical reference terminology, then steps must be taken to ensure comparability of information formulated using successive versions. New releases are therefore shipped with a history mechanism. We assessed the adequacy of this mechanism for its treatment of the distinction between changes occurring on the side of entities in reality and changes in our understanding thereof. We found that these two types are only partially distinguished and that a more detailed study is (...) required to propose clear recommendations for enhancement along at least the following lines: (1) explicit representation of the provenance of a class; (2) separation of the time-period during which a component is stated valid in SNOMED CT from the period it is (or has been) valid in reality, and (3) redesign of the historical relationships table to give users better assistance for recovery in case of introduced mistakes. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

I. EXECUTIVE SUMMARY The MRCT Center Post-trial Responsibilities: Continued Access to an Investigational Medicine Framework outlines a case-based, principled, stakeholder approach to evaluate and guide ethical responsibilities to provide continued access to an investigational medicine at the conclusion of a patient’s participation in a clinical trial. The Post-trial Responsibilities (PTR) Framework includes this Guidance Document as well as the accompanying Toolkit. A 41-member international multi-stakeholder Workgroup convened by the Multi-Regional Clinical Trials Center of Brigham and Women’s Hospital and Harvard University (...) (MRCT Center) developed this Guidance and Toolkit. Project Motivation A number of international organizations have discussed the responsibilities stakeholders have to provide continued access to investigational medicines. The World Medical Association, for example, addressed post-trial access to medicines in Paragraph 34 of the Declaration of Helsinki (WMA, 2013): “In advance of a clinical trial, sponsors, researchers and host country governments should make provisions for post-trial access for all participants who still need an intervention identified as beneficial in the trial. This information must also be disclosed to participants during the informed consent process.” This paragraph and other international guidance documents converge on several consensus points: • Post-trial access (hereafter referred to as “continued access” in this Framework [for terminology clarification – see definitions]) is the responsibility of sponsors, researchers, and host country governments; • The plan for continued access should be determined before the trial begins, and before any individual gives their informed consent; • The protocol should delineate continued access plans; and • The plan should be transparent to potential participants and explained during the informed consent process. -/- However, there is no guidance on how to fulfill these responsibilities (i.e., linking specific responsibilities with specific stakeholders, conditions, and duration). To fill this gap, the MRCT Center convened a working group in September of 2014 to develop a framework to guide stakeholders with identified responsibilities. This resultant Framework sets forth applicable principles, approaches, recommendations and ethical rationales for PTR regarding continued access to investigational medicines for research participants. (shrink)

In her book, Illness as Metaphor, Susan Sontag focuses on metaphors and myths on diseases such as cancer and tuberculosis, which occur in different historical periods. Sontag argues that the metaphors produced related to illness overhaul illness and the things that define illness now have become metaphors produced related to them rather than their concrete and physical aspects. Illness becomes not just an illness, but a phenomenon defined by evil, mystery, fear, evil, madness, passions, wealth and poverty, temporal loginess or (...) speed, and a set of metaphors or myths that are spatially identified with the space. Metaphors and myths turn into means of socially stigmatizing the illness itself rather than giving a meaning to illness. The disease literally turns into a situation that needs to be hidden in order to avoid social stigma. The explanation of mass diseases through metaphors and myths has been seen since ancient times and this understanding of mass diseases continues to exist today. As a matter of fact, the Covid-19 pandemic has also ceased to be the subject of only medical science since it first emerged, and it has turned into an issue that concerns many areas from politics to economics, from sociology to psychology. The metaphors generated on the Covid-19 disease, which we have witnessed its reflections in many areas from the discourses of daily life to the discourse of politicians, from art to literature, have a similar function with the metaphors attributed to diseases like cancer and tuberculosis that Sontag discussed. Covid-19 is not only seen as a disease, but as a disease defined by a series of metaphors such as mysterious, evil, invisible enemy, insidious danger, and democratic virus. The metaphors generated on the disease cause the struggle against the disease itself to be explained with various metaphors. The metaphors derived from Covid-19 such as "invisible enemy" and "biological war" cause the struggle against it to be turned into a military terminology, and the metaphor of "Chinese virus" is a means of social stigmatization / marginalization by racializing the virus directly. This study tackles the issue of how Covid-19, which is the subject of medical science, has become the subject of unscientific myths and metaphors attributed to the disease, and that the disease is perceived through metaphors rather than itself in the context of Susan Sontag's thought. In the study, answers for the questions of what kind of effects appeared due to the stigmatizing power of metaphors derived from the Covid-19 and whether the metaphors are the outcomes of the strategy for coping with the pandemic will be sought. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology (...) within the ACGT project thus far. (shrink)

In the second half of the last century, Albanian society adopted a totalitarian way of communist thinking, that could not have spared medical disciplines. Psychiatry was and probably remains a stigmatized field, whose problems almost never were discussed openly. Specialized writings on psychiatry were available and could shed light on the themes and questions of concern. A periodical journal entitled Psychoneurological Works circulated in its print edition, with its first issue of 1959, its tenth issue of 1984 till it (...) ceased publishing some years later. The journal was a mixture of neurological and psychiatric contributions, with the latter reflecting consistent time-related shifts in thematic, terminology, and data exposure. The panegyric and enthusiastic statements served as a good disguise for the immense ailing of patients and the ethical challenges that psychiatrists were facing, while exerting their profession in the time of severe dictatorship, when the disrespect of human being reached its apogee. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

Medicalisation is a social phenomenon in which conditions that were once under legal, religious, personal or other jurisdictions are brought into the domain of medical authority. Low sexual desire in females has been medicalised, pathologised as a disease, and intervened upon with a range of pharmaceuticals. There are two polarised positions on the medicalisation of low female sexual desire: I call these the mainstream view and the critical view. I assess the central arguments for both positions. Dividing the two (...) positions are opposing models of the aetiology of low female sexual desire. I conclude by suggesting that the balance of arguments supports a modest defence of the critical view regarding the medicalisation of low female sexual desire. (shrink)

The future of health research will be characterised by three continuing trends: rising demand for health data; increasing impracticability of obtaining specific consent for secondary research; and decreasing capacity to effectively anonymise data. In this context, governments, clinicians and the research community must demonstrate that they can be responsible stewards of health data. IRBs and RECs sit at heart of this process because in many jurisdictions they have the capacity to grant consent waivers when research is judged to be of (...) particular value. However, several different terms are used to refer to this value, indicating a lack of conceptual clarity regarding the appropriate test for access to health data for research without consent. In this paper we do three things. First we describe the current confusion and instability in terminology relating to public interest in the context of consent waivers. Second we argue for harmonisation of terminology on the grounds of clarity, transparency and consistency. Third we argue that the term ‘public interest’ best reflects the normative work required to justify consent waivers because it is the broadest of the competing terms. ‘Public interest’ contains within its scope positive and negative implications of a study, as well as welfare, justice and rights considerations. In making this argument, we explain the normative basis for consent waivers, and provide a starting place for further discussion about the precise conditions in which a given study can be said to advance the public interest. Ipsos MORI study found that: … the public would be broadly happy with administrative data linking for research projects provided Those projects have social value, broadly defined. Data are de-identified. Data are kept secure. Businesses are not able to access the data for profit. (shrink)

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same (...) broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (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 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)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in (...) the WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

Pain medication is one of the responses to the mercy argument that utilitarian ethicists use for justifying active euthanasia on the grounds of prevention of cruelty and appeal to beneficence. The researcher reinforces the significance of pain medication in meeting this challenge and considers it the most preferred response among various other responses. It is because of its realism and effectiveness. In exploring the mechanism and considerations related to pain medication, the researcher briefly touches the Catholic ethical position on the (...) issue, a position that cannot be ignored in the development of contemporary bioethics. The researcher particularly deliberates on the contemporary Islamic discourse on the issue; by furthering the debate in line with the Islamic legal maxims and general guidance from the primary sources of Islamic law and ethics. The resolution on the issue is sought by synthesizing the views and legal maxims (al-Qawaid al-Fiqhiyyah) on the issue, which in conclusion provide justification for pain medication by considerably regarding pain as necessity and pressing need. However, such resolution allows pain medication to the limit and proportion that removes the pain and prohibits overdosing the patient with medication that may directly cause the death. (shrink)

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)

Pharmaceuticals or other emerging technologies could be used to enhance (or diminish) feelings of lust, attraction, and attachment in adult romantic partnerships. While such interventions could conceivably be used to promote individual (and couple) well-being, their widespread development and/or adoption might lead to “medicalization” of human love and heartache—for some, a source of serious concern. In this essay, we argue that the “medicalization of love” need not necessarily be problematic, on balance, but could plausibly be expected to have either good (...) or bad consequences depending upon how it unfolds. By anticipating some of the specific ways in which these technologies could yield unwanted outcomes, bioethicists and others can help direct the course of love’s “medicalization”—should it happen to occur—more toward the “good” side than the “bad.”. (shrink)

I introduce a distinction between health need and medical need, and raise several questions about their interaction. Health needs are needs that relate directly to our health condition. Medical needs are needs which bear some relation to medical institutions or processes. I suggest that the question of whether medical insurance or public care should cover medical needs, health needs, or only needs which fit both categories is a political question that cannot be resolved definitionally. I (...) also argue against an overly strict definition of medical need on the grounds that this presupposes, wrongly, that medical intervention should always be a last resort. (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)

Assumptions about obesity—e.g., its connection to ill health, its causes, etc.—are still prevalent today, and they make up what I call the medical model of fatness. In this paper, I argue that the medical model was established on the basis of insufficient evidence and has nevertheless continued to be relied upon to justify methodological choices that further entrench the assumptions of the medical model. These choices are illegitimate in so far as they conflict with both the epistemic (...) and social aims of obesity research. I conclude the paper with a partial solution to these epistemic and social shortcomings. (shrink)

This study attempts an exposition of different perceptions of obligation to medical treatment that have emerged from the Islamic theological understanding and how they contribute to diversity of options and flexibility in clinical practice. Particularly, an attempt is made to formulate an Islamic perspective on ordinary and extraordinary means of medical treatment. This distinction is of practical significance in clinical practice, and its right understanding is also important to public funded healthcare authorities, guardians of the patients, health and (...) life insurance institutions, and employers who provide health care coverage to their employees. Not only these parties, but also lawyers and justice administration functionaries such as public prosecutors and judges are in need of understanding this distinction to deal with relevant litigations. The distinction could be made regarding terminally ill patients and non-terminally ill patients separately. The essential factors that matter in making the distinction between ordinary and extraordinary means of treatment are: (1) patient capacity (2) expert advice, and (3) nature of medication. Regarding terminally ill patients, medical treatment can become extraordinary because of (1) patient capacity and (2) nature of medication. In both these case the deciding condition applies: the expert advice taken from a group of physicians. In regards to non- terminally ill patients, extraordinary medical treatment includes three cases: (1) treatment that is known to be useless and futile, (2) treatment that endangers the life or cause more harm than what it removes, and (3) useful treatment, but the patient is unable to bear the cost. (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)

Rationale and objectives: Medical humanities are becoming increasingly recognized as positively impacting medical education and medical practice. However, the extent of medical humanities teaching in medical schools is largely unknown. We reviewed medical school curricula in Canada, the UK and the US. We also explored the relationship between medical school ranking and the inclusion of medical humanities in the curricula. -/- Methods: We searched the curriculum websites of all accredited medical schools (...) in Canada, the UK and the US to check which medical humanities topics were taught, and whether they were mandatory or optional. We then noted rankings both by Times Higher Education and U.S. News and World Report and calculated the average rank. We formally explored whether there was an association between average medical school ranking and medical humanities offerings using Spearman's correlation and inverse variance weighting meta-analysis. -/- Results: We identified 18 accredited medical school programmes in Canada, 41 in the UK, and 154 in the US. Of these, nine (56%) in Canada, 34 (73%) in the UK and 124 (80%) in the US offered at least one medical humanity that was not ethics. The most common medical humanities were medical humanities (unspecified), history, and literature (Canada); sociology and social medicine, medical humanities (unspecified), and art (UK); and medical humanities (unspecified), literature and history (US). Higher ranked medical schools appeared less likely to offer medical humanities. -/- Conclusions: The extent and content of medical humanities offerings at accredited medical schools in Canada, the UK and the US varies, and there appears to be an inverse relationship between medical school quality and medical humanities offerings. Our analysis was limited by the data provided on the Universities' websites. Given the potential for medical humanities to improve medical education and medical practice, opportunities to reduce this variation should be exploited. (shrink)

The phenomenon of medical overtesting in general, and specifically in the emergency room, is well-known and regarded as harmful to both the patient and the healthcare system. Although the implications of this problem raise myriad ethical concerns, this paper explores the extent to which overtesting might mitigate race-based health inequalities. Given that medical malpractice and error greatly increase when the patients belong to a racial minority, it is no surprise that the mortality rate similarly increases in proportion to (...) white patients. For these populations, an environment that emphasizes medical overtesting may well be the desirable medical environment until care evens out among races and ethnicities; additionally, efforts to lower overtesting in conjunction with a high rate of racist medical mythology may cause harm by lower testing when it is actually warranted. Furthermore, medical overtesting may help to assuage racial distrust. This paper ultimately concludes that an environment of medical overtesting may be less pernicious than the alternative. (shrink)

Many hold that distributing healthcare according to medical need is a requirement of equality. Most egalitarians believe, however, that people ought to be equal on the whole, by some overall measure of well-being or life-prospects; it would be a massive coincidence if distributing healthcare according to medical need turned out to be an effective way of promoting equality overall. I argue that distributing healthcare according to medical need is important for reducing individuals' uncertainty surrounding their future (...) class='Hi'>medical needs. In other words, distributing healthcare according to medical need is a natural feature of healthcare insurance; it is about indemnity, not equality. (shrink)

This paper argues that epistemic errors rooted in group- or identity- based biases, especially those pertaining to disability, are undertheorized in the literature on medical error. After sketching dominant taxonomies of medical error, we turn to the field of social epistemology to understand the role that epistemic schemas play in contributing to medical errors that disproportionately affect patients from marginalized social groups. We examine the effects of this unequal distribution through a detailed case study of ableism. There (...) are four primary mechanisms through which the epistemic schema of ableism distorts communication between nondisabled physicians and disabled patients: testimonial injustice, epistemic overconfidence, epistemic erasure, and epistemic derailing. Measures against epistemic injustices in general and against schema-based medical errors in particular are ultimately issues of justice that must be better addressed at all levels of health care practice. (shrink)

Would compulsory treatment or vaccination for Covid-19 be justified? In England, there would be significant legal barriers to it. However, we offer a conditional ethical argument in favour of allowing compulsory treatment and vaccination, drawing on an ethical comparison with external constraints—such as quarantine, isolation and ‘lockdown’—that have already been authorised to control the pandemic. We argue that, if the permissive English approach to external constraints for Covid-19 has been justified, then there is a case for a similarly permissive approach (...) to compulsory medical interventions. (shrink)

: The Islamic jurists utilized the discipline of maqāṣid al-sharīʿah,in its capacity as the philosophy of Islamic law, in their legal and ethicalinterpretations, with added interest in addressing the issues of modern times.Aphoristically subsuming the major themes of the Sharīʿah, maqāṣid play apivotal role in the domain of decision-making and deduction of rulings onunprecedented ethical discourses. Ethics represent the infrastructure of Islamiclaw and the whole science of Islamic jurisprudence operates in the lightof maqāṣid to realize the ethics in people’s lives. (...) Scrutinizing the key themesof maqāṣid-based ijtihād and scope of ethics in maqāṣid, this article delvesinto the discourse on the application of maqāṣid to medical ethics. As a casestudy, this research analyses the extent of medical confidentiality in the light ofmaqāṣid and arrives at the conclusion that limited confidentiality goes more inline with the maxims of maqāṣid. (shrink)