Medical management of urolithiasis in the Middle Ages: Thesaurus Pauperum of Pope John XXI.

BACKGROUND/OBJECTIVE: This paper will present a brief description of medicine in the Middle Ages, and more comprehensive analysis of the medical management of urolithiasis in Thesaurus Pauperum, the main text of Pedro Hispano. METHOD: An in-depth reading of the Italian translation of Thesaurus Pauperum, and a review of the literature of the life of Pedro Rebuli Guiliani, known as Pedro Hispano, was performed. RESULT: Pedro Hispano was born in Portugal around 1205. He studied philosophy, theology and medicine in Paris. He was named professor of medicine at the University of Siena in 1247 and was elected Pope, as John XXI, in 1276. His primary medical book was Thesaurus Pauperum ('Treasure of the Poor'), a prescription handbook for common diseases, directed not only to physicians but also to ordinary people. We focused on the description of medical management of urolithiasis in Thesaurus Pauperum. CONCLUSION: This text is interesting not so much on account of the pharmacopoeia used, but instead, because it is, probably, one of the first medical text reporting therapeutics close to the modern evidence-based medicine.

Knowledge Representation and Management: a Linked Data Perspective.

INTRODUCTION: Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. OBJECTIVE: The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies. METHODS: We selected three prominent linked data studies, namely Bio2RDF, Open PHACTS and EBI RDF platform, and selected 14 studies published after 2014 (inclusive) that cited any of the three studies. We manually analyzed these 14 papers in relation to how they use linked data techniques. RESULTS: The analyses show a tendency to use linked data techniques in Life and Health Sciences, and even if some studies do not follow all of the recommendations, many of them already represent and manage their knowledge using RDF and biomedical ontologies. CONCLUSION: These insights from RDF and biomedical ontologies are having a strong impact on how knowledge is generated from biomedical data, by making data elements increasingly connected and by providing a better description of their semantics. As health institutes become more data centric, we believe that the adoption of linked data techniques will continue to grow and be an effective solution to knowledge representation and management.

Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities.

SNOMED CT's Release Format 2 (RF2) has been announced as an improvement over its predecessor, for instance because of its more consistent and almost formal approach towards describing changes in components over different versions, as well as changes in the structure of SNOMED CT itself. We explore two sorts of changes that are only partially formalized in RF2: the relationships between associative relations and reasons for inactivations as expressed in Association Reference Sets and Attribute Value Reference Sets on the one hand, and the various patterns according to which semantic tags appearing in fully specified names change over subsequent versions with or without being related to inactivations. We propose a data conversion methodology that combines assertions about SNOMED CT components into history profiles and use elements of these profiles to build Formal Concept Analysis contexts to discover valid implications that can render implicit assumptions hidden in SNOMED CT's structure explicit.

Can prevention classification be improved by considering the function of prevention?

Universal, selective and indicated forms of prevention have been adopted as improvements on previous notions of primary and secondary prevention. However, some conceptual confusion remains concerning the placing of environmental, community-based or mass media preventive interventions within this typology. It is suggested that a new dimension of functional types of prevention, namely environmental, developmental and informational prevention should be specified alongside the forms of prevention in a taxonomy matrix. The main advantage of this new taxonomy is that a matrix combining the form and function dimensions of prevention can be used to identify and map out prevention strategies, to consider where research evidence is present and where more is needed, and to evaluate the relative effectiveness of different categories and components of prevention for specific health and social issues. Such evaluations would provide empirical evidence as to whether the different categories of prevention are related to outcomes or processes of prevention in ways that suggest the value of the taxonomy for understanding and increasing the impact of prevention science. This new prevention taxonomy has been useful for conceptualising and planning prevention activities in a case study involving the Swedish National Institute for Public Health. Future work should assess (1) the robustness of this new taxonomy and (2) the theoretical and empirical basis for profiling prevention investments across the various forms and functions of prevention.

Measuring the evolution of ontology complexity: the gene ontology case study.

Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent branches, i.e. biological processes (BP), cellular components (CC) and molecular functions (MF). For each case, we measured complexity by computing metrics related to the size, the nodes connectivity and the hierarchical structure. The number of classes and relations increased monotonously for each branch, with different growth rates. BP and CC had similar connectivity, superior to that of MF. Connectivity increased monotonously for BP, decreased for CC and remained stable for MF, with a marked increase for the three branches in November and December 2012. Hierarchy-related measures showed that CC and MF had similar proportions of leaves, average depths and average heights. BP had a lower proportion of leaves, and a higher average depth and average height. For BP and MF, the late 2012 increase of connectivity resulted in an increase of the average depth and average height and a decrease of the proportion of leaves, indicating that a major enrichment effort of the intermediate-level hierarchy occurred. The variation of the number of classes and relations in an ontology does not provide enough information about the evolution of its complexity. However, connectivity and hierarchy-related metrics revealed different patterns of values as well as of evolution for the three branches of the Gene Ontology. CC was similar to BP in terms of connectivity, and similar to MF in terms of hierarchy. Overall, BP complexity increased, CC was refined with the addition of leaves providing a finer level of annotations but decreasing slightly its complexity, and MF complexity remained stable.

History of metaphoric signs in radiology.

PURPOSE: To survey the nearly 100 year history of metaphoric sign naming in radiology describing the pace of their overall accumulation in the radiology canon, their specific rates of growth by modality and subspecialty and the characteristics of the referents to which the signs are attached. MATERIALS AND METHODS: A comprehensive list of metaphoric signs was compiled from a search of articles in several major English language radiology journals, from a roster compiled in a monograph on the subject published in 1984 and from a search of several databases to find signs published in the first half of the 20th century. RESULTS: The growth of radiological metaphorical signs naming was slow for several decades after the first one was published in 1918. It then increased rapidly until the 1980s encompassing all modalities and subspecialties. Recently the practice has shown a marked and steady decline. CONCLUSION: Metaphoric sign naming was a frequently reported contribution to the radiological literature in the second half of the 20th century corresponding with Radiology's growth as a descriptive discipline. Its decline since then may be a consequence of Radiology's evolution into a more analytic, data-driven field of inquiry.

The history of the Read Codes: the inaugural James Read Memorial Lecture 2011.

General practitioner (GP) computing has its origins in the 1970s when the benefits of clinical coding and prescribing were demonstrated. During the early 1980s Dr James Read, working with Abies Informatics Ltd, developed the eponymous Read Codes, which were broader and more comprehensive than other schemes, yet intuitive and easy to use. In 1988 a joint working party of the Royal College of General Practitioners (RCGP) and the British Medical Association (BMA) recommended that the Read Codes be adopted nationally. The Read Codes have been used by almost all GPs in the UK since the mid-1990s. Many developments in general practice, including GP fundholding (where GPs held the budgets to commission elective care for their patients), the Quality and Outcomes Framework (QOF - pay for performance for improving chronic disease management) and GP commissioning (the current NHS reform in which primary care leads commissioning of services for their patients) would have been impossible without all GPs using a common clinical coding scheme. Systematized Nomenclature For Medicine - Clinical Terms (SNOMED CT) is a merger of the Read Codes with SNOMED RT - the original SNOMED reference terminology developed by the American College of Pathologists.

Adaptation and validation of the Charlson Index for Read/OXMIS coded databases.

BACKGROUND: The Charlson comorbidity index is widely used in ICD-9 administrative data, however, there is no translation for Read/OXMIS coded data despite increasing use of the General Practice Research Database (GPRD). Our main objective was to translate the Charlson index for use with Read/OXMIS coded data such as the GPRD and test its association with mortality. We also aimed to provide a version of the comorbidity index for other researchers using similar datasets. METHODS: Two clinicians translated the Charlson index into Read/OXMIS codes. We tested the association between comorbidity score and increased mortality in 146 441 patients from the GPRD using proportional hazards models. RESULTS: This Read/OXMIS translation of the Charlson index contains 3156 codes. Our validation showed a strong positive association between Charlson score and age. Cox proportional models show a positive increasing association with mortality and Charlson score. The discrimination of the logistic regression model for mortality was good (AUC = 0.853). CONCLUSION: We have translated a commonly used comorbidity index into Read/OXMIS for use in UK primary care databases. The translated index showed a good discrimination in our study population. This is the first study to develop a co-morbidity index for use with the Read/OXMIS coding system and the GPRD. A copy of the co-morbidity index is provided for other researchers using similar databases.

A brief history of nursing informatics in the United States of America.

From the beginning of modern nursing, data from standardized patient records were seen as a potentially powerful resource for assessing and improving the quality of care. As nursing informatics began to evolve in the second half of the 20th century, the lack of standards for language and data limited the functionality and usefulness of early applications. In response, nurses developed standardized languages, but until the turn of the century, neither they nor anyone else understood the attributes required to achieve computability and semantic interoperability. Collaboration across disciplines and national boundaries has led to the development of standards that meet these requirements, opening the way for powerful information tools. Many challenges remain, however. Realizing the potential of nurses to transform and improve health care and outcomes through informatics will require fundamental changes in individuals, organizations, and systems. Nurses are developing and applying informatics methods and tools to discover knowledge and improve health from the molecular to the global level and are seeking the collective wisdom of interdisciplinary and interorganizational collaboration to effect the necessary changes. NOTE: Although this article focuses on nursing informatics in the United States, nurses around the world have made substantial contributions to the field. This article alludes to a few of those advances, but a comprehensive description is beyond the scope of the present work.

Changes in Medical Documentation over the Last Five Decades.

In medical documentation, standardized coding schemes are used to facilitate sharing, transformation and reusability of data. First, classification systems coding schemes have been introduced. While classification systems are mainly used for statistical purposes, individual care documentation moves towards the use of nomenclatures coding schemes. The paper presents an overview of the development of coding schemes. Different coding schemes serve different purposes. Multiaxial schemes are the way of choice for comprehensively documenting complex care processes. There is a movement from mono-hierarchical classification systems to concept-based, multi-purpose and multi-hierarchical terminologies.

Metodologia de revisão de vocabulário controlado em Saúde Pública / Methodology for reviewing controlled vocabulary in Public Health

Vocabulários estruturados ou controlados reúnem termos e expressões que refletem conceitos específicos de linguagem técnico-cientifica de determinado campo do conhecimento, permitindo uma padronização da descrição, classificação e recuperação da informação.

["Psychiatric patient" as "somatisizing patient--"somatisizing patient" as "psychiatric patient". On the problem of the validity historical psychiatric categories]. / "Psychiker" als "Somatiker"--"Somatiker" als "Psychiker". Zur Frage der Gültigkeit psychiatriehistorischer Kategorien.

This article critically examines the distinction between "somaticists" and "psychicists", which was, and still is, commonly made in the history of early nineteenth-century psychiatry. The analysis is based on a study of the protagonists of the different orientations (Heinroth, Jacobi, Nasse). It investigates the views held on the mind-body relation, the relevance of the "somatic" and "psychic" argumentations, the terminology of psychic disorders, their treatment, and the underlying ideologies. In contrast to the customary categorizations, differences cannot be clearly defined through characteristics of an either strictly "psychological" or strictly "somatic" argumentation, but are limited to variations in emphasis and focus. The author argues that the decisive differences can be located in the convictions held about the nature of the medical profession and about the right path to a professionalized "psychic medicine".