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We have merged two established anatomical terminologies with an evolving ontology of biological structure: the Foundational Model of Anatomy. We describe the problems we have encountered and the solutions we have developed. We believe that both the problems and solutions generalize to the integration of any legacy terminology with a disciplined ontology within the same domain.
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.
Medical terminological systems (TSs) play an increasingly important role in health care by supporting recording, retrieval and analysis of patient information. As the size and complexity of TSs are growing, the need arises for means to audit them, i.e. verify and maintain (logical) consistency and (semantic) correctness of their contents. In this paper we describe two methods based on description logics (DLs) for the audit of TSs. One method uses non-primitive definitions to detect concepts with equivalent definitions. The other method is characterized by stringent assumptions that are made about concept definitions, in order to detect inconsistent definitions. We discuss the possibility of applying these methods to the Foundational Model of Anatomy (FMA) to demonstrate the potentials and pitfalls of these methods. We show that the methods are complementary, and can indeed improve the contents of medical TSs.
In previous work, we proposed an approach called the Structural Difference Method (SDM) to correlating the anatomy of Homo sapiens with selected species, using the Foundational Model of Anatomy (FMA) as a framework and graph matching as a method, for determining similarities and differences between species. In this paper, we present the design of a comparative anatomy information system that utilizes the SDM and allows users to issue queries to determine the similarities and differences between two species. Our system will serve as a pilot project for cross-species anatomical information collection, storage, and retrieval. The underlying data structure of a mapping, and the syntax and semantics of the system's query language, are presented.
OBJECTIVE: To investigate the indirect alignment of two anatomical ontologies through a reference ontology and to compare it to direct alignment between these two ontologies. The ontologies under investigation are the Adult Mouse Anatomical Dictionary (MA) and the NCI Thesaurus (NCI). The Foundational Model of Anatomy serves as reference ontology. METHODS: The direct alignment employs a combination of lexical and structural similarity. The indirect alignment simply derives mappings from direct alignments to the reference ontology. RESULTS: The indirect MA-NCI alignment yielded 703 mappings and the direct alignment 715, 654 of which are common to both. The mappings specific to one approach were analyzed. CONCLUSIONS: When a reference ontology exists, indirect alignment of multiple ontologies through a reference represents a valid, cost-effective alternative to pairwise alignment.
OBJECTIVES: To examine recent research work in the development and evaluation of controlled biomedical terminologies - especially, the representation of structured, controlled definitional knowledge about the terms themselves; such terminologies are often referred to as 'ontologies'. METHODS: A review of the published literature using PubMed, as well as full-text searches of recent Medinfo and American Medical Informatics Association (AMIA) Symposia proceedings, searching for the terms 'ontology' and 'ontologies' and for articles discussing specific, prominent ontological work. RESULTS: We summaries the ontologic aspects of twelve current terminology projects: Galen, the Unified Medical Language System (UMLS), the Medical Entities Dictionary (MED), SNOMED-CT, LOINC, the Foundational Model of Anatomy (FMA), the Gene Ontology (GO), ISO Reference Terminology Model for Nursing Diagnosis, NDF-RT, RxNorm, the NCI Thesaurus, and DOLCE+. We discuss the origins, domain, and ontologic representation of each of these and attempt to summarize the impact that each has had on terminologic work and biomedical applications. We also note the contributions of the Protégé tool to many of these efforts. CONCLUSION: Terminologic research and development have advanced significantly in the past 20 years, especially since the recent orientation toward controlled biomedical ontologies. This work has had significant impact on the development of terminologies themselves, their acceptance and dissemination as standards, and their use in supporting biomedical information systems.
User feedback from the Digital Anatomist Web-based anatomy atlases, together with over 20 years of anatomy teaching experience, were used to formulate the requirements and system design for a next-generation anatomy information system. The main characteristic of this system over current image-based approaches is that it is knowledge-based. A foundational model of anatomy is accessed by an intelligent agent that uses its knowledge about the available anatomy resources and the user types to generate customized interfaces. Current usage statistics suggest that even partial implementation of this design will be of great practical value for both clinical and educational needs.
Teams are the fundamental element of work in the contemporary clinical setting. As interdisciplinary teams become an essential component of the evidence-based framework for clinical practice, their formalization, integration, and synthesis within the practice framework will become increasingly mandatory. Outlined here is a contextual model for team action that is formalized as the organizational leadership continuously addresses the structural and process components of team dynamics in a continuous and cybernetic frame that assures all of the elements of effective teamwork. The theoretical foundations for team modeling are explicated, the elements of the systems approach to team process are outlined, and a necessary synthesis of team processes is described and established as a foundation for evidence-based clinical practice.
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Development of methodologically acceptable outcomes models for emergency medical services (EMS) is long overdue. In this article, the Emergency Medical Services Outcomes Project proposes a conceptual framework that will provide a foundation for future EMS outcomes research. The "Episode of Care Model" and the "Out-of-Hospital Unit of Service Model" are presented. The Episode of Care Model is useful in conditions in which interventions and outcomes, especially survival and major physiologic dysfunction, are linked in a time-dependent manner. Conditions such as severe trauma, anaphylaxis, airway obstruction, respiratory arrest, and nontraumatic cardiac arrest are amenable to this methodology. The Out-of-Hospital Unit of Service Model is essentially a subunit of the Episode of Care Model. It is valuable for evaluating conditions that have minimal-to-moderate therapeutic time dependency. This model should be used when studying outcomes limited to the out-of-hospital interval. An example of this is pain management for injuries sustained in motor vehicle crashes. These models can be applied to a wide spectrum of conditions and interventions. With the scrutiny of health care expenditures ever increasing, the identification of clinical interventions that objectively improve patient outcome takes on growing importance. Therefore, the development, dissemination, and use of meaningful methodologies for EMS outcomes research is key to the future of EMS system development and maintenance.
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Explore the source record for details and available documents.
Explore the source record for details and available documents.
INTRODUCTION: Predictive models play a pivotal role in the provision of risk-adjusted, operative mortality rates. The purpose of the study was to describe the development of a dedicated prognostic index for quantifying operative risk in colorectal cancer surgery. METHODS: Data were collected from 5,034 consecutive patients undergoing major surgery in a single center from October 1976 to July 2002. Primary end point was 30-day operative mortality. A multilevel Bayesian logistic regression model was developed to adjust for case-mix and accommodate the variability of outcomes between surgeons. The model was internally validated (split-sample) and tested using measures of discrimination, calibration, and subgroup analysis. RESULTS: The patients' median age was 66 (range, 18-98) years. Operative mortality was 2.3 percent with no significant variability between surgeons or through time. Multivariate analysis identified the following independent risk factors: age (odds ratio = 1.5 per 10-year increase), American Society of Anesthesiologists grade (odds ratio for ASA II, III, IV-V vs. I = 2.6, 4.3, 6.8), TNM staging (odds ratio for Stage IV vs. I-III = 2.6), mode of surgery (odds ratio for urgent vs. nonurgent = 2.1) no-cancer resection vs. cancer resection (odds ratio = 4.5), and hematocrit level. The model offered adequate discrimination (area under receiver operator characteristic curve = 0.801) and excellent agreement between observed and model-predicted outcomes over ten major colorectal procedures (P = 0.191). CONCLUSIONS: The colorectal cancer model provided an accurate means of estimating risk for individual patients in the preoperative setting. It has important implications in everyday practice, because it may be used as an adjunct in the process of informed consent and for monitoring surgical performance through time.
The purpose of this paper is to lay the groundwork for the development of a scientific theory of complex human functioning. We first discuss the assumptions on which our thinking is based, then advance the argument that behavior, and human activity in general, may be more fully understood in light of current data on the structural organization of the central nervous system. The brain is organized as a modular, distributed, self-organizing system, which is in constant transaction with the environment. Because of its plasticity, structural and functional change occurs in the brain as a result of experience throughout life. It is our thesis that complex human behavior is organized in a similar manner - that is, human personality and behavior manifest themselves as modular systems. The insights provided by an understanding of the relationship of brain and behavior may enhance the capacity to explain both normal and pathological personality functioning.
Threshold models first appeared in the literature nearly half a century ago. Threshold segments have been added to many commonly used forms of models from linear models and generalized linear models through mixed models for the analysis of cross-sectional data. Nonlinear models with thresholds for cross-sectional data are less prevalent in the literature. Nonlinear models with thresholds for longitudinal data are new. The historical developments leading to this point are reviewed as a means of introducing terms necessary for discussing features of these newer models. Nonlinear models for longitudinal data with thresholds are presented and discussed.
In this article we examine some of the basic psychophysics relevant to amplified night vision devices. These devices produce images that are substantially different from ordinary visual scenes. Distortions in contrast and luminance and the introduction of visual interference and geometrical artifacts contribute to unusual viewing conditions. We carried out experiments to determine the effect of these parameters of the image on a highly controlled visual target detection task simulated on a computer graphics system that closely models a night vision device. Our results indicate that display luminance and geometrical artifacts degrade detection performance only slightly, whereas contrast and visual interference have a substantial degrading effect.