bluuebunny/crossref_metadata_2025_split huggingface dataset:
RAGs: A Novel Approach to Computerized Genetic Risk Assessment and Decision Support from Pedigrees
Authors: Coulson A. S. , Glasspool D. W. , Emery J. , Fox J. 
Published: March 2018

Summary

Objectives:
To assist general practitioners in evaluating patients’ genetic risk of cancer on the basis of family history data.

Methods:
A new computer application, RAGs (Risk Assessment in Genetics), has been developed to help doctors create graphical family trees and assess the genetic risk of breast and colorectal cancer. RAGs possesses two features that distinguish it from similar software: (i) a user-centred design, which takes into account the requirements of the doctor-patient encounter; (ii) effective and accessible risk reporting by employing qualitative evidence for or against increased risk, which is more easily understood than numerical probabilities. The system allows any rule-based genetic risk guideline to be implemented, and may be readily modified to cater for the varying degrees of information required by different specialists.

Results:
RAGs permits fast, accurate data entry, and results in more appropriate management decisions than those made via other techniques. In addition, RAGs enables both the clinician and the patient to understand how it arrives at its conclusions, since the use of qualitative evidence allows the program to provide explanations for its reasoning.

Conclusions:
The RAGs system promises to help practitioners be more effective gatekeepers to genetic services. It may empower doctors both to make an informed choice when deciding to refer patients who are at increased genetic risk of breast or colorectal cancer, and to reassure those who are at low risk.
What is Bioinformatics? A Proposed Definition and Overview of the Field
Authors: Luscombe N. M. , Greenbaum D. , Gerstein M. 
Published: March 2018

Summary

Background:
The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science.

Objectives:
Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems.

Methods:
Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying “informatics” techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale.

Results and Conclusions:
Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (eg expression data). Additional information includes the text of scientific papers and “relationship data” from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.
Domain Ontologies in Software Engineering: Use of Protégé with the EON Architecture
Authors: Musen M. A. 
Published: March 2018

AbstractDomain ontologies are formal descriptions of the classes of concepts and the relationships among those concepts that describe an application area. The Protege software-engineering methodology provides a clear division between domain ontologies and domain-independent problemsolvers that, when mapped to domain ontologies, can solve application tasks. The Protege approach allows domain ontologies to inform the total software-engineering process, and for ontologies to be shared among a variety of problem-solving components. We illustrate the approach by describing the development of EON, a set of middleware components that automate various aspects of protocol-directed therapy. Our work illustrates the organizing effect that domain ontologies can have on the software-development process. Ontologies, like all formal representations, have limitations in their ability to capture the semantics of application areas. Nevertheless, the capability of ontologies to encode clinical distinctions not usually captured by controlled medical terminologies provides significant advantages for developers and maintainers of clinical software applications.
Modeling Concepts in Medicine for Medical Language Understanding
Authors: Miller R. A. , Baud R. H. , Scherrer J.-R. , Rassinoux A.-M. 
Published: March 2018

AbstractOver the past two decades, the construction of models for medical concept representation and for understanding of the deep meaning of medical narrative texts have been challenging areas of medical informatics research. This review highlights how these two inter-related domains have evolved, emphasizing aspects of medical modeling as a tool for medical language understanding. A representation schema, which balances partially but accurately with complete but complex representations of domainspecific knowledge, must be developed to facilitate language understanding. Representative examples are drawn from two major independent efforts undertaken by the authors: the elaboration and the subsequent adjustment of the RECIT multilingual analyzer to include a robust medical concept model, and the recasting of a frame-based interlingua system, originally developed to map equivalent concepts between controlled clinical vocabularies, to invoke a similar concept model.
Alternative Ways for Knowledge Collection, Indexing and Robust Language Retrieval
Authors: Lovis C. , Rassinoux A.-M. , Scherrer J.-R. , Baud R. H. 
Published: March 2018

AbstractDefinitions are provided of the key entities in knowledge representation for Natural Language Processing (NLP). Starting from the words, which are the natural components of any sentence, both the role of expressions and the decomposition of words into their parts are emphasized. This leads to the notion of concepts, which are either primitive or composite depending on the model where they are created. The problem of finding the most adequate degree of granularity for a concept is studied. From this reflection on basic Natural Language Processing components, four categories of linguistic knowledge are recognized, that are considered to be the building blocks of a Medical Linguistic Knowledge Base (MLKB). Following on the tracks of a recent experience in building a natural language-based patient encoding browser, a robust method for conceptual indexing and query of medical texts is presented with particular attention to the scheme of knowledge representation.
Conceptual Graph Grammar – A Simple Formalism for Sublanguage
Authors: Johnson S. B. 
Published: March 2018

AbstractThere are a wide variety of computer applications that deal with various aspects of medical language: concept representation, controlled vocabulary, natural language processing, and information retrieval. While technical and theoretical methods appear to differ, all approaches investigate different aspects of the same phenomenon: medical sub language. This paper surveys the properties of medical sublanguage from a formal perspective, based on detailed analyses cited in the literature. A review of several computer systems based on sublanguage approaches shows some of the difficulties in addressing the interaction between the syntactic and semantic aspects of sUblanguage. A formalism called Conceptual Graph Grammar is presented that attempts to combine both syntax and semantics into a single notation by extending standard Conceptual Graph notation. Examples from the domain of pathology diagnoses are provided to illustrate the use of this formalism in medical language analysis. The strengths and weaknesses of the approach are then considered. Conceptual Graph Grammar is an attempt to synthesize the common properties of different approaches to sublanguage into a single formalism, and to begin to define a common foundation for language-related research in medical informatics.
Classification Systems in Nursing: Formalizing Nursing Knowledge and Implications for Nursing Information Systems
Authors: Epping P. J. M. M. , Abraham I. L. , Goossen W. T. F. 
Published: March 2018

AbstractThe development of nursing information systems (NIS) is often hampered by the fact that nursing lacks a unified nursing terminology and classification system. Currently there exist various initiatives in this area. We address the question as to how current initiatives in the development of nursing terminology and classification systems can contribute towards the development of NIS. First, the rationale behind the formalization of nursing knowledge is discussed. Next, using a framework for nursing information processing, the most important developments in the field of nursing on formalization, terminology and classification are critically reviewed. The initiatives discussed include nursing terminology projects in several countries, and the International Classification of Nursing Practice. Suggestions for further developments in the area are discussed. Finally, implications for NIS are presented, as well as the relationships of these components to other sections of an integrated computerized patient record.
Determinants of Homonym and Synonym Rates of Record Linkage in Disease Registration
Authors: Schmidtmann I. , Brenner H. 
Published: March 2018

AbstractReliable record linkage is an essential component of the quality of population-based disease registration. Quality assessment of disease registries should, therefore, include quantitative approaches to describe the extent of record-linkage errors. The homonym and synonym rates have been proposed for this purpose. The homonym rate quantifies the proportion of distinct patients excluded from registration due to erroneous linkage with other patients. The synonym rate quantifies the proportion of unrecognized duplicate notifications on patients already registered in the registry. This paper provides an algebraic assessment of the determinants of both rates. It is shown how the homonym and the synonym rate are determined by the discriminating power provided by the personal identifiers and the record linkage procedure on the one hand and the specific circumstances of disease registration on the other hand, such as the number of patients in the registry or the number of notifications per case. All these factors should be taken into account when reporting and interpreting results of record-linkage studies, particularly if comparisons are made between the performance of record-linkage procedures in different environments.
Formal Descriptions and Adaptive Mechanisms for Changes in Controlled Medical Vocabularies
Authors: Cimino J. J. 
Published: March 2018

Abstract:Standard controlled medical vocabularies are typically based on a coding scheme, while medical informatics applications tend to have a more formal conceptual foundation. When such applications attempt to use data coded with standard vocabularies, problems can arise when the standard vocabulary changes over time. A formal taxonomy is presented for describing the semantic changes which can occur in a vocabulary, such as simple addition, refinement, precoordination, disambiguation, redundancy, obsolescence, discovered redundancy, major name changes, minor name changes, code reuse, and changed codes. The taxonomy is described that used to effect change in one concept-based vocabulary (the Medical Entities Dictionary), and the utility of the approach is demonstrated by applying it to the changes appearing in the 1994 release of the International Classification of Diseases, Ninth Edition, with Clinical Modifications (ICD-9-CM).
Extended Telemedical Consultation using Arden Syntax Based Decision Support, Hypertext and WWW Technique
Authors: Ekdahl C. , Wigertz O. , Shahsavar N. , Gill H. , Forsum U. , Karlsson D. 
Published: March 2018

Abstract:There is an obvious need for geographic distribution of expert knowledge among several health care units without increasing the cost of on-site expertise in locations where health care is provided. This paper describes the design of a knowledge-based decision-support system for extended consultation in clinical medicine. The system is based on Arden Syntax for Medical Logic Modules and hypertext using World Wide Web technology. It provides advice and explanations regarding the given advice. The explanations are presented in a hypertext format allowing the user to browse related information and to verify the relevance of the given advice. The system is intended to be used in a closed local network. With special precautions regarding issues of safety and patient security, the system can be used over wider areas such as in rural medicine. A prototype has been developed in the field of clinical microbiology and infectious diseases regarding infective endocarditis.
Extraction of Rules for Tuberculosis Diagnosis Using an Artificial Neural Network
Authors: Cloete I. , Beyers N. , Viktor H. L. 
Published: March 2018

Abstract:The treatment of tuberculosis (TB) is a major challenge throughout the world. The Western Cape Region of South Africa has the highest occurrence of TB in the world. Here, TB is increasing due to improperly managed treatment programmes and inadequate facilities. The development of rules to aid medical practitioners in the early and accurate diagnosis of tuberculosis should prove worthwhile. A method to extract such diagnostic rules from an artificial neural network is presented. These rules accurately represent the knowledge embedded in the “raw” TB data.
Philosophy Into Practice: A Health Informatics Course Proposal
Authors: Ball M. J. , Douglas J. V. 
Published: March 2018

Abstract:International health informaticians acknowledge the critical importance of education and training to the successful implementation of information technology in the health-care setting. As access to the Internet grows, so does the richness of resources the Internet can supply. With the changes in health care brought by communication, telematics will become the successor to informatics. The authors present the philosophy of telematics training and propose a short training course designed to help health professionals in developing nations take advantage of telematics, providing conceptual understanding and hands-on training.
User Attitudes to a Heritage Hospital Information System
Authors: Lakay D. , Isaacs S. 
Published: March 2018

Abstract:A heritage system is one that has exceeded its lifespan but continues to be used for various reasons, despite the problems it may be causing. Groote Schuur Hospital has a Hospital Information System that is more than 25 years old. The present study reports the result of a survey on users’ attitude and sense of involvement in this system. An attempt is made to determine whether users feel the need for change and whether a sense of involvement is related to this need.
Using Connectionist Modules for Decision Support
Authors: Hripcsak G. 
Published: March 2018

AbstractA connectionist model for decision support was constructed out of several back-propagation modules. Manifestations serve as input to the model; they may be real-valued, and the confidence in their measurement may be specified. The model produces as its output the posterior probability of disease. The model was trained on 1,000 cases taken from a simulated underlying population with three conditionally independent manifestations. The first manifestation had a linear relationship between value and posterior probability of disease, the second had a stepped relationship, and the third was normally distributed. An independent test set of 30,000 cases showed that the model was better able to estimate the posterior probability of disease (the standard deviation of residuals was 0.046, with a 95% confidence interval of 0.046-0.047) than a model constructed using logistic regression (with a standard deviation of residuals of 0.062, with a 95% confidence interval of 0.062-0.063). The model fitted the normal and stepped manifestations better than the linear one. It accommodated intermediate levels of confidence well.
Interpretation of Short ECGs with a Personal Computer: The Porto Program
Authors: Abreu-Lima C. , Marques de Sá J. P. 
Published: March 2018

AbstractA computer program for ECG analysis and interpretation developed at the University of Porto, Portugal is presented. The program runs on a microcomputer and employs the three-lead Frank VCG. The signals are sampled at 250 Hz with 8-bit precision during 5.5 s. Details on signal conditioning and wave recognition and measurement techniques are given. The diagnostic part of the program uses decision-tree logic. The decision rules are mainly derived from the Washington Code. The diagnostic accuracy of four classes (normal, left and right ventricular hypertrophies and myocardial infarction), evaluated in a sample of 1,075 pediatric and adult patients and classified by ECG-independent means was 76%. The program is currently being evaluated on the CSE database.
Signal Analysis for ECG Interpretation
Authors: van Bemmel J. H. , Zywietz Chr. , Kors J. A. 
Published: March 2018

AbstractIn ECG interpretation usually two main areas are discerned: the signal analysis and the diagnostic classification. This article reviews the major developments in the first area. ECG signal analysis itself is subdivided into the stages data acquisition, data transformation, feature selection, and data reduction. These stages are consecutively reviewed, while in the data transformation stage digital filtering, detection, wave typing, beat selection, and boundary recognition are discussed.
A Versatile Test for Clustering and a Proximity Analysis of Neurons
Authors: Grimson R.C. , Rose R.D. 
Published: March 2018

Abstract:A test for nonrandom patterns in populations of “cells” of binary attributes is formulated for applications in settings where it is impossible or impractical to completely specify the adjacency matrix, as in circumstances involving enormous numbers of cells and/or censored data. Applications are made to problems concerning spatial distributions of specially labeled cells in nervous system research.
Diagnostic Consultations: a Speech-Act Theoretical Reconstruction for the Design of Consultation Systems
Authors: Müller-Kolck U. 
Published: March 2018

Abstract:In this paper the theory of speech acts is applied for a structural reconstruction of medical diagnostic consultations. The reconstruction provides the conceptual model for a research prototype of a consultation tool which is expected to play a mediating role between the participants in the professional diagnostic discourse. Preliminary results of the design will be outlined.
WING – Entering a New Phase of Electronic Data Processing at the Gießen University Hospital
Authors: Dudeck J. , Junghans G. , Marquardt K. , Sebald P. , Michel A. , Prokosch H. U. 
Published: March 2018

AbstractAt the Gielßen University Hospital electronic data processing systems have been in routine use since 1975. In the early years developments were focused on ADT functions (admission/discharge/transfer) and laboratory systems. In the next decade additional systems were introduced supporting various functional departments. In the mid-eighties the need to stop the ongoing trend towards more and more separated standalone systems was realized and it was decided to launch a strategic evaluation and planning process which sets the foundation for an integrated hospital information system (HIS). The evaluation of the HELP system for its portability into the German hospital environment was the first step in this process. Despite its recognized capabilities in integrating decision support and communication technologies, and its powerful HIS development tools, the large differences between American and German hospital organization, influencing all existing HELP applications, and the incompatibility of the HELP tools with modern software standards were two important factors forcing the investigation of alternative solutions. With the HELP experience in mind, a HIS concept for the Gießen University Hospital was developed. This new concept centers on the idea of a centralized relational patient database on a highly reliable database server, and clinical front-end applications which might be running on various other computer systems (mainframes, departmental UNIX satellites or PCs in a LAN) integrated into a comprehensive open HIS network. The first step towards this integrated approach was performed with the implementation of ADT and results reporting functions on care units.
Natural Language Processing and Semantical Representation of Medical Texts
Authors: Baud R. H. , Rassinoux A.-M. , Scherrer J.-R. 
Published: March 2018

Abstract:For medical records, the challenge for the present decade is Natural Language Processing (NLP) of texts, and the construction of an adequate Knowledge Representation. This article describes the components of an NLP system, which is currently being developed in the Geneva Hospital, and within the European Community’s AIM programme. They are: a Natural Language Analyser, a Conceptual Graphs Builder, a Data Base Storage component, a Query Processor, a Natural Language Generator and, in addition, a Translator, a Diagnosis Encoding System and a Literature Indexing System. Taking advantage of a closed domain of knowledge, defined around a medical specialty, a method called proximity processing has been developed. In this situation no parser of the initial text is needed, and the system is based on semantical information of near words in sentences. The benefits are: easy implementation, portability between languages, robustness towards badly-formed sentences, and a sound representation using conceptual graphs.
Graphical Access to Medical Expert Systems: IV. Experiments to Determine the Role of Spoken Input
Authors: Isaacs E. , Wulfman C. E. , Rohn J. A. , Lane C. D. , Fagan L. M. 
Published: March 2018

Abstract:The goal of our research is to design improved interfaces for medical expert systems. Previously, the use of graphical techniques was explored to improve the acceptance by clinicians of the user interface. Now that devices that accept spoken input are available, we wish to design interfaces that take advantage of this potentially more natural modality for interaction. To understand how clinicians might want to speak to a medical decision-support system, we carried out an experiment that simulated the availability of a spoken interface to the ONCOCIN medical expert system. ONCOCIN provides therapy advice for patients on complex cancer therapy protocols based on a description of the patient’s current medical status and laboratory-test values. In the experiment, we had oncologists present a clinical case while observing the ONCOCIN flowsheet display. A project member listened to the presentation and filled in values for the flowsheet, as well as introducing purposeful misunderstandings of the input. The results suggest that each individual developed a stereotypical grammar for communicating with the program. Our experience with the purposeful miscommunications suggests particular ways to tailor requests for repetition based on the part of the utterance that was not understood.