Biomedical subjects
Barry Smith
Publications and source records attributed to Barry Smith.
Alopecia in association with sexually transmitted disease: a review.
In a patient with a sexually transmitted disease (STD), alopecia may be an important associated finding and can provide clues to diagnosis. This review focuses on the relationship between hair loss and STDs. Specifically, we review alopecia in association with syphilis and human immunodeficiency virus (HIV) infection and the medications used to treat these infections. In addition, we review the literature regarding the putative association between alopecia areata and cytomegalovirus (CMV).
A strategy for improving and integrating biomedical ontologies.
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.
How to distinguish parthood from location in bioontologies.
The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organism reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular may often be controversial. We here propose a rule-based approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy.
An ontology-based methodology for the migration of biomedical terminologies to electronic health records.
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.
Goitre and environmental iodine deficiency in the UK--Derbyshire: a review.
Endemic goitre was prevalent in the population of Derbyshire in the UK for many centuries until it declined from the 1930s. A contemporary medical survey showed that endemicity of goitre was particularly higher in the Carboniferous limestone areas of the Derbyshire-Peak District. Unlike classical goitrous areas of the world, where the distribution of goitre has been found to be related to the iodine content in the environment, there is no such relationship reported for the Derbyshire-Peak District area. The present study reviews the presence of endemic goitre in this area with reference to iodine in different environmental media using past and present data. In comparison with the world average values, the iodine contents in the soil and sediment in the Peak District are not deficient, but compared to England, Wales and Scotland averages, these levels are low. As no information on the mobility and bioavailability of iodine of this area is available, a cautious approach is necessary before any assumption is made on the aetiology of endemic goitre. The study also discusses some hypotheses relating to the possible cause of endemic goitre in the limestone areas. Further research needs are suggested depending on the land use and geochemistry of the Peak District to determine the underlying causes of the former endemic goitre in this area.
Environmental influences on the trace element content of teeth--implications for disease and nutritional status.
The aim of this study was to compare the trace element content of children's primary teeth from Uganda and the UK. The Ugandan teeth were from children living in an area where endomyocardial fibrosis (EMF), a cardiac disease, is prevalent. The latter has been putatively linked to insufficient magnesium intake and excess cerium exposure. Primary teeth were collected from 21 Ugandan and 27 UK children. The crowns and roots of the teeth were separated and the former digested and analysed for several major and trace elements by inductively coupled plasma mass spectrometry (ICP-MS) and atomic emission spectrometry (ICP-AES). In addition, the enamel and dentine of eight UK and seven Ugandan primary teeth were isolated via density separation and analysed as above. The data were assessed using non-parametric statistical tests. The Ugandan teeth contained significantly (P < 0.05) greater concentrations of strontium, barium, cerium, lanthanum, praseodymium and significantly less zinc than the UK teeth. No significant difference in the concentrations of aluminium, calcium, copper, magnesium, lead and uranium were found. Analysis of enamel and dentine demonstrated that the former was enriched with several elements including cerium. It is concluded, that the environment, influences the trace element content of primary teeth and this may be useful for monitoring nutritional status. With respect to a geochemical cause for EMF, there is no positive evidence that EMF in Uganda is associated with reduced magnesium and increased cerium uptake in primary teeth. This does not, however, exclude cerium from playing a role in the aetiology of EMF.
The role of foundational relations in the alignment of biomedical ontologies.
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 on the basis of explicit definitions. This scheme also provides a template for modeling pathology, physiological function and genotype-phenotype correlations, and it can thus 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.
Ontology-based error detection in SNOMED-CT.
Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential areas of improvement. We demonstrate the methodology by applying the algorithms to one of the most popular terminologies, SNOMED-CT. Analysis of the results provides evidence for the thesis that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.
Biodynamic ontology: applying BFO in the biomedical domain.
We propose a modular formal ontology of the biomedical domain with two components, one for biological objects, corresponding broadly to anatomy, and one for biological processes, corresponding broadly to physiology. The result constitutes what might be described as a joint venture between two perspectives--of so-called three-dimensionalism and four-dimensionalism--which are normally regarded as incompatible. We outline an approach which allows them to be combined together, and provide examples of its application in biomedicine.
Bodily systems and the spatial-functional structure of the human body.
The human body is a system made of systems. The body is divided into bodily systems proper, such as the endocrine and circulatory systems, which are subdivided into many sub-systems at a variety of levels, whereby all systems and subsystems engage in massive causal interaction with each other and with their surrounding environments. Here we offer an explicit definition of bodily system and provide a framework for understanding their causal interactions. Medical sciences provide at best informal accounts of basic notions such as system, process, and function, and while such informality is acceptable in documentation created for human beings, it falls short of what is needed for computer representations. In our analysis we will accordingly provide the framework for a formal definition of bodily system and of associated notions.
Context-based task ontologies for clinical guidelines.
Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of effort has been invested in the development of tools which can automate the representation and execution of the recommendations contained within such guidelines, 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 models. We have created DAML+OIL-based CTOs for the tasks referred to in the WHO guideline for hypertension management, drawing comparisons also with other, related guidelines. The advantages of CTOs include: contextualization of ontologies, tailoring of ontologies to specific aspects of the phenomena of interest, division of the complex tasks involved in creating ontologies into different levels, and provision of 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.
An ontological framework for the implementation of clinical guidelines in health care organizations.
The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems.
Mistakes in medical ontologies: where do they come from and how can they be detected?
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.
Sixteen days.
When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the relation between fetus and mother (connection, parthood, dependence).
Using cross-lingual information to cope with underspecification in formal ontologies.
Description logics and other formal devices are frequently used as means for preventing or detecting mistakes in ontologies. Some of these devices are also capable of inferring the existence of inter-concept relationships that have not been explicity entered into an ontology. A prerequisite, however, is that this information can be derived from those formal definitions of concepts and relationships which are included within the ontology. In this paper, we present a novel algorithm that is able to suggest relationships among existing concepts in a formal ontology that are not derivable from such formal definitions. The algorithm exploits cross-lingual information that is implicity present in the collection of terms used in various languages to denote the concepts and relationships at tissue. By using a specific experimental design, we are able to quantify the impact of cross-lingual information in coping with underspecification in formal ontologies.
The ontology of the gene ontology.
The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO's consistency and coherence and thus its future applicability in the automated processing of biological data.
A sampling and analytical methodology for dental trace element analysis.
The role of trace elements in human health and environmental pollution has developed into an extensive field of research. This study describes a sampling and analytical strategy to determine the trace element content of primary (deciduous) teeth and to assess their use in environmental health and nutrition studies. Exfoliated and extracted primary teeth were collected from 21 Ugandan and 27 UK children. The crown and root of the teeth were separated and the former digested and analysed for several elements by inductively coupled plasma mass spectrometry. The influence of country, tooth type, age and gender were statistically investigated in addition to within-person variation. A principal components analysis (PCA) was used to treat the data in a multivariate fashion and facilitated the moderation of outliers. The results demonstrated that country of origin has an important influence on the elemental composition of teeth and that tooth type should be controlled in these types of studies. Given such a restriction, the age and gender of the donor should have no effect and do not need to be controlled. In addition, where country of domicile, age and gender were controlled, the concentrations of most elements within a single tooth type were representative of an individual and therefore may be indicative of health status.