Ebook: Connecting Medical Informatics and Bio-Informatics

After a successful MEDINFO in 1992, the Swiss Society for Medical Informatics hosts again a major event in medical informatics – the 19th Medical Informatics Europe Conference, under the generic name of MIE2005. The host city, Geneva, is well known for its commitment in international healthcare, being the residence of several international organisations, including WHO. Geneva is also synonym with other major medical informatics achievements: the DIOGENE hospital information system and Natural Language Processing, both strongly connected to Geneva and its University Hospital.

The motto of the conference, "Connecting Medical Informatics and Bio-Informatics" emphasizes the convergence of these disciplines, illustrated by the Swiss Institute of Bioinformatics, also founded in Geneva, and home of the SwissProt database. It also reflects the growing role of the co-operation of different disciplines in healthcare, co-operation which tends to become integration.

The major challenge of this decade is to develop and extend the use of information technology for the improvement of patient oriented health care. It has to integrate results from other areas and scientific disciplines, and interoperability will be the key problem to be solved. All these trends were already reflected in MIE2005 submissions and addressed a large palette of topics, including classical topics as standards, terminology, coding, imaging etc.

The selection process was a difficult task for the Scientific Program Committee. We kept the scientific quality as the major determinant criterion for selection. There were over 300 submitted papers to be presented orally or as poster. A score was given by 2 and more reviewers selected from a panel of more than 160 experts. The reviews were accompanied by suggestions and advice about possible improvements of the submitted paper. The type of presentation was sometimes modified from oral presentation to a short oral presentation combined with a poster or just a poster for detailed presentation and deep discussion. In a second step, when creating the scientific programme, there were a few modifications of the presentation type, mainly due to the limited time slots available for oral presentations. The result of SPC activity is reflected by the Conference programme and the Proceedings.

The printed version has limited pages and therefore limited numbers of papers of all types of presentations (oral and poster presentations) which are most qualified. It will be cited in Medline. The full content was proposed for the CD version of the proceedings; it is an EFMI publication and contains all accepted papers in the revised version and also the workshops. This way of publishing enables searching keywords, the title and the full content.

Workshops were offered to the participants like in previous MIEs, organised or supported by EFMI working groups. A clearer distinction between presentations in workshops and presentations in scientific sessions was aimed: while a pure scientific paper presents results in a classical manner, a workshop paper would rather present and comment unfulfillments or raise questions. The workshop procedure comprises a brief introduction (usually invited), followed by several short statements or presentations. The major output is expected from discussions. The results which might be achieved will be published after MIE2005 separately. All documents, (material from the workshops) available at publishing time will be included on the CD proceedings. We plan to make it also available on the EFMI web site by the moment of this material publication.

We shall also mention that the call for tutorials resulted in a set of high ranked contributions, included in the "scientific workflow" of each MIE conference. They will provide basics and deep insight into certain disciplines and topics related to medical informatics. It may help to develop a better understanding of some presentations and workshops during MIE2005. In this context tutorials are a substantial part and the material developed should be available to a broader community.

The proceedings are an integrated part of MIE2005. We would like to thank all those who have made the printed volume and the CD possible, the authors, the scientific programme committee, the reviewers, and the teams in Geneva and Munich, Robert Baud, Jérôme Billet, Henning Müller, Claudia Hildebrand, Ruslan David, Jutta Balint, Alfred Breier, Silvia Weinzierl and some more.

Rolf Engelbrecht, Antoine Geissbuhler, Christian Lovis, Gheorghe Mihalas

IMGT, the international ImMunoGeneTics information system^® (http://imgt.cines.fr) created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Université Montpellier II and CNRS, Montpellier, France, is a high quality integrated information system, secialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex of human and other vertebrates and related proteins of the immune system that belong to the IgSF and Mhc superfamilies. IMGT/LIGM-DB, the first and the largest IMGT database, manages more than 92,000 IG and TR nucleotide sequences from human and 150 other vertebrate species in May 2005. IMGT/LIGM-DB provides expertly annotated sequences and standardized knowledge based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. The strategy developed by IMGT, for the IG and TR nucleotide sequence annotation, involves two different approaches that depend on the nature of the sequences, genomic DNA (gDNA) or complementary DNA (cDNA).

The development of medical research networks within the framework of translational research has fostered interest in the integration of clinical and biological research data in a common database. The building of one single database integrating clinical data and biological research data requires a concept which enables scientists to retrieve information and to connect known facts to new findings.

Clinical parameters are collected by a Patient Data Management System and viewed in a database which also includes genomic data. This database is designed as an Entity Attribute Value model, which implicates the development of a data warehouse concept.

For the realization of this project, various requirements have to be taken into account which has to be fulfilled sufficiently in order to align with international standards.

Data security and protection of data privacy are most important parts of the data warehouse concept. It has to be clear how patient pseudonymization has to be carried out in order to be within the scope of data security law.

To be able to evaluate the data stored in a database consisting of clinical data collected by a Patient Data Management System and genomic research data easily, a data warehouse concept based on an Entity Attribute Value datamodel has been developed.

In this paper we demonstrate applying time series models on medical research. The Hungarian mortality rates were analysed by autoregressive integrated moving average models and seasonal time series models examined the data of acute childhood lymphoid leukaemia.

The mortality data may be analysed by time series methods such as autoregressive integrated moving average (ARIMA) modelling. This method is demonstrated by two examples: analysis of the mortality rates of ischemic heart diseases and analysis of the mortality rates of cancer of digestive system. Mathematical expressions are given for the results of analysis. The relationships between time series of mortality rates were studied with ARIMA models. Calculations of confidence intervals for autoregressive parameters by tree methods: standard normal distribution as estimation and estimation of the White's theory and the continuous time case estimation. Analysing the confidence intervals of the first order autoregressive parameters we may conclude that the confidence intervals were much smaller than other estimations by applying the continuous time estimation model.

We present a new approach to analysing the occurrence of acute childhood lymphoid leukaemia. We decompose time series into components. The periodicity of acute childhood lymphoid leukaemia in Hungary was examined using seasonal decomposition time series method. The cyclic trend of the dates of diagnosis revealed that a higher percent of the peaks fell within the winter months than in the other seasons. This proves the seasonal occurrence of the childhood leukaemia in Hungary.

The aims of this study are to determine, and to better understand, elements that are common across a range of bio-health information resources; and to characterize those resources in terms of search and display functionality. Our ultimate goal is to better define the role of bio-health information in clinical practice and in biological research. This paper reports our first step, which is to compare different web-based resources that describe cystic fibrosis. The resources came from PubMed, Nucleotide, EMBL-EBI, DDBJ, OMIM, MeSH, ICD-10, and the Cystic Fibrosis Mutation Database. We found obvious differences in terms of scope and purpose. However, while there were obvious similarities between related resources in terms of content, we also found differences among these resources in terms of display form, specificity of qualifiers, file format and the potential for computer processing. While our work is in its early stages, this study has clarified the nature of bio-health information resources and has allowed us to begin to characterize these resources in terms of their suitability in clinical practice and in biological research.

The field of bioinformatics has exploded over the past decade. Hopes have run high for the impact on preventive, diagnostic, and therapeutic capabilities of genomics and proteomics. As time has progressed, so has our understanding of this field. Although the mapping of the human genome will certainly have an impact on health care, it is a complex web to unweave. Addressing simpler “Single Nucleotide Polymorphisms” (SNPs) is not new, however, the complexity and importance of polygenic disorders and the greater role of the far more complex field of proteomics has become more clear. Proteomics operates much closer to the actual cellular level of human structure and proteins are very sensitive markers of health. Because the proteome, however, is so much more complex than the genome, and changes with time and environmental factors, mapping it and using the data in direct care delivery is even harder than for the genome. For these reasons of complexity, the expected utopia of a single gene chip or protein chip capable of analyzing an individual's genetic make-up and producing a cornucopia of useful diagnostic information appears still a distant hope. When, and if, this happens, perhaps a genetic profile of each individual will be stored with their medical record; however, in the mean time, this type of information is unlikely to prove highly useful on a broad scale. To address the more complex “polygenic” diseases and those related to protein variations, other tools will be developed in the shorter term. “Top-down” analysis of populations and diseases is likely to produce earlier wins in this area. Detailed computer-generated models will map a wide array of human and environmental factors that indicate the presence of a disease or the relative impact of a particular treatment. These models may point to an underlying genomic or proteomic cause, for which genomic or proteomic testing or therapies could then be applied for confirmation and/or treatment. These types of diagnostic and therapeutic requirements are most likely to be introduced into clinical practice through traditional forms of clinical practice guidelines and clinical decision support tools. The opportunities created by bioinformatics are enormous, however, many challenges and a great deal of additional research lay ahead before this research bears fruit widely at the care delivery level.

Microarray experiments aim at analyzing expression levels of genes using DNA probes. The amount of data managed for each experiment is very large. It is thus essential to provide electronic support for the capture and the management of information describing microarray experiments. We present here the SITRANS Web information system, the aim of which is to help research workers storing, browsing, sharing and publishing data.

Biomedical Informatics (BMI) is the emerging discipline that aims to facilitate integration of Bioinformatics and Medical Informatics for the purpose of accelerating discovery and the generation of novel diagnostic and therapeutic modalities. Building on the success of the European Commission-funded BIOINFOMED Study, an INFOBIOMED Network of Excellence has been constituted with the main objective of setting a structure for a collaborative approach at a European level. Initially formed by fifteen European organizations, the main objective of the INFOBIOMED network is therefore to enable the reinforcement of European BMI at the forefront of these emergent interdisciplinary fields. The paper describes the structure of the network, the integration approaches regarding databases and four pilot applications.

The Danish Health IT strategy 2003-2007 demands implementation of Electronic Health Records (EHR) in all Hospitals based on common standards. The aim is to achieve integration and semantic interoperability between different EHR systems in order to support a better communication and coherence between the health care parties. The National Board of Health has developed a common model, which is a prerequisite for the development and implementation of interoperable EHR systems. The adoption of the common EHR model has been promoted and validated through a number of pilot projects in different Hospitals. The Danish EHR Observatory, which has been monitoring the development of EHR in Denmark since 1998, have developed a methodology for Quality labelling and certification of EHR systems. The methodology for certification of EHR systems has been used to validate EHR systems from different vendors to document to which extent the systems are based on the national requirements for EHR.

Monitoring diagnostic procedures, treatment protocols and clinical outcome are key issues in maintaining quality medical care and in evaluating clinical trials. For these purposes, a user-friendly computerized method for monitoring all available information about a patient is needed.

Objective: To develop a real-time computerized data collection system for verification, analysis and storage of clinical information on an individual patient. Methods: Data was integrated on a single time axis with normalized graphics. Laboratory data was set according to standard protocols selected by the user and diagnostic images were integrated as needed. The system automatically detects variables that fall outside established limits and violations of protocols, and generates alarm signals.

Results. The system provided an effective tool for detection of medical errors, identification of discrepancies between therapeutic and diagnostic procedures, and protocol requirements.

Conclusions: The computerized case history system allows collection of medical information from multiple sources and builds an integrated presentation of clinical data for analysis of clinical trials and for patient follow-up.

The spectrum of applied pharmaceuticals, often interactive, persistently expands. In modern therapeutics, patients receive more and more drugs, cases of simultaneous administering of more than 10 different drugs are not seldom. The majority of drugs are prescribed by personal physicians, the rest by the secondary level service specialists, doctors on duty, doctors at the release from the hospital etc. Furthermore, patients keep in stock drugs prescribed in the past. In the Slovene practice of medication prescribing, a major setback is poor information linking between the doctor and the pharmacist, as well as between doctors at different levels of service. Thus, doctors have often raised the issue of timely and accurate informing on the administered drug. This issue became even more pressing upon the implementation of the scheme of substitutable drugs in 2003, allowing the pharmacist to substitute the prescribed drug for an equivalent less expensive one.

The paper outlines a project headed by the Health Insurance Institute of Slovenia (Institute) to facilitate the recording of issued drugs on the card. The information on drugs received by a patient in the past will in this way become readily accessible to the prescribing doctor as well as to the administering pharmacist. This objective requires a range of tasks to be completed: business/operational design of the system, introduction of a uniform drug information scheme at the national level, adjusting the functions of the health insurance card system, upgrading the software environment at the health care service providers, training doctors and pharmacists in applying the new information, and ensuring data security in conformity with regulations.

While physician informational needs have been examined in the literature, rarely do the findings have the specificity required to drive development of Electronic Medical Records (EMRs) features. Using Delphi methodology, a comprehensive list of desirable, ranked EMR features was developed for physician residency practices. The identified EMR features and implications for system development are explored in this paper.

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in which all clinically salient particulars – from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given – should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way.

The Agence de la Biomédecine is a state agency dealing with Public Health issues related, among others, to organ, tissue and cell transplantation in France. The Agence maintains a national information system used to coordinate and administer organ procurement and transplant activities and to perform the evaluation of organ transplantation activities. This paper describes the core uses and functional requirements of Cristal, the donor, recipient and allocation software of the information system and its evolution in the new system.

Difficulties in reconstituting patients' trajectory in the public health information systems are raised by errors in patients' identification processes. A crucial issue to achieve is avoiding doubles in distributed web databases. We explored Needleman and Wunsch (N&W) algorithm in order to optimize the properties of string matching. Five variants of the N&W algorithm were developed. The algorithms were implemented for a web Multi-Source Information System. This system was dedicated to tracking patients with End-Stage Renal Disease at both regional and national level. A simulated study database of 73,210 records was created. An insertion or suppression of each character of the original string was simulated. The rate of double entries was 2% given an acceptable distance set to 5 modifications. The search was sensitive and specific with an acceptable detection time. It detected up to 10% of modifications that is above the estimated error rate. A variant of the N&W algorithm designed as “cut-off heuristic”, proved to be efficient for the search of double entries occurring in nominative distributed databases.

We need to know how clinicians' use their paper based medical records to secure a local participation in the implementation process of Electronic Patient Record (EPR). In what way their use of paper based medical records is related to, or dependent on, other people and artifacts. The research presented in this paper was done as part of a work flow analysis of the particular sequence of doing rounds at two distinct hospital departments, a thoracic surgical and a cardiology department. It was designed to develop a method that would let the hospital clinicians obtain knowledge on the daily use of the paper based medical records during rounds and thus make use of their local knowledge to start a discussion on changes in organization and knowledge before EPR can be successfully implemented.

We are grateful to the following clinicians, Cathrine H. Foss, MD. Pauline Schrødder, MD. Morten Smerup MD and Niels Henrik Stålsen, MD and the medical director Børge H. Jensen, MD, Skejby Sygehus, Aarhus University Hospital for sharing their knowledge with us.

Deglutition disorders can occur at any age but are especially prevalent in the elderly. The resulting morbidity and mortality are being recognized as major geriatric health issues, Because of difficulties in studying swallowing in the frail elderly, a new, non-invasive, user-friendly, bedside technique has been developed. Ideally suited to such patients, this tool, an intermediary between purely instrumental and clinical methods, combines respiratory inductance plethysmography (RIP) and the computer to detect swallowing automatically, Based on an automated analysis of the airflow estimated by the RIP-derived signal, this new tool was evaluated according to its capacity to detect clinical swallowing from among the 1643 automatically detected respiratory events, This evaluation used contingency tables and Receiver Operator Characteristic (ROC) curves, Results were all significant (χ2(1,n=1643)>100, p<0.01). Considering its high accuracy in detecting swallowing (area under the ROC curve greater than 0.9), this system would be proposed to study deglutition and then deglutition disorders in the frail elderly, to set up medical supervision and to evaluate the efficiency of a swallowing disorder remedial therapeutic.

Computer-interpretable guidelines (CIGs) are more likely to affect the clinician's behavior when they deliver patient-specific and just-in-time clinical advice. CIGs must take into account the data stored in the patient's electronic medical records (EMR). For chronic diseases, the outcome of past and ongoing treatments (therapeutic history) is used in the clinical guidelines. We propose a model for the conceptualization of therapeutic history, facilitating data sharing between EMRs and CIGs and the representation of therapeutic history and recommended treatments in clinical guidelines.

Based on medical literature review and an existing treatment model, a core structure is first defined taking into account drug and non-drug treatment components and treatment type (e.g. bitherapy). These elements together with additional concepts obtained by analyzing a sample guideline relating to diabetes, are then organized into an object-oriented model, using UML formalism.

We show how this model can be used to store the patient's therapeutic history in the EMR, together with other attributes such as treatment efficacy and tolerance. We also explain how this model can efficiently code guidelines therapeutic rules.

We evaluated this model, using additional guidelines hypercholesterolemia and asthma. We found it capable for representing guideline recommendations in several domains of chronic diseases.

As formalised electronic storage of medical data becomes more and more wide spread the possibility and need for creating human readable presentations for various purposes increases. This paper presents the mGen framework - a general framework for text generation, written in Java and in the process of being open-sourced, that has been developed within the MedView project

The work presented in this paper was supported by the Swedish Agency for Innovation Systems (VINNOVA).

Electronic Health Record (EHR) systems are being developed to improve the communication of patient data. The health care domain includes many different types of data and concepts, of which some are constantly changing, and some are more lasting. This makes the development of an EHR a complex task. In order to improve the handling of this complexity, a new two-level modelling approach in EHR system development has emerged, using a concept of archetypes as the pivot in the representation of the health care knowledge. The key issue in this approach involves dividing the problem field into two separate models: A generic information model and a domain knowledge model. By analysis of how this layering has been carried out in two different two-level EHR systems – the OpenEHR (formerly the Australian GEHR, Good Electronic Health Record) and the EHR project of Aarhus County, Denmark. We have identified critical meta model parameters influencing the ability of the modelling paradigm to meet the expectation for easy handling of the development process (flexibility) and the capability to manage changing models (dynamics). The OpenEHR has defined the division line in such a way that it makes the generic model small and the domain model large. The opposite is the case of the Aarhus EHR system, where the information model is large, and the knowledge model is small. A small information model and a large knowledge model make more of the system changeable, but it also makes it less flexible to develop. The opposite is the case for a large information model and a small knowledge model.

The Austrian parliament has adopted legislation to introduce the electronic health record under the title ELGA. The present article first discusses several activities of other countries in this context. It then deals with the current situation of healthcare telematics in Austria and the next planned steps to introduce the life-long electronic health record.

This paper describes the linkage of data from three Dutch Perinatal Registries: the Dutch National Midwife Registry, the Dutch National Obstetrics Registry and the Dutch National Pediatrics Registry, for the year of 2001. All these registries are anonymous and lack a common identifier. We used probabilistic and deterministic record linkage techniques to combine data from the mother, delivery and child involving to the same pregnancy. Records of singleton and twin pregnancies were linked separately. We have developed a probabilistic close method based on maximum likelihood methods to estimate the weights of individual linking variables and the threshold value for the overall weight. Probabilistic linkage identified 80% more links than a full deterministic linkage approach. External validation revealed an error rate of less than 1%. Our method is a flexible and powerful method to link anonymous registries in the absence of a gold standard.

Delivery of good care, ability to communicate effectively about patient care and the decision-making during the care process depends on the quality of the information available to all professions and between sectors. The main purpose of an electronic health record is to support the multidisciplinary communication, cooperation and decision-making in the patient's care process. In addition, the data in electronic health records are used, e.g. in clinical research, health system management, the planning of health services and government reporting. A nationwide electronic health record will be introduced in Finland by the end 2007. Reaching this target has been a special part of the national health project. In a subproject of the introduction of a national electronic health record, core data elements of electronic health record have been defined through a consensus-based approach. The main elements are the patient identification information, the provider's identification information, care episode, risk factors, health patterns, vital signs, health problems and diagnosis, nursing minimum data set, surgical procedures, tests and examinations, information about medication, preventive measures, medical statements, functional status, technical aids, living will, tissue donor will, discharge summary, follow-up care plan and consent information. Furthermore, existing vocabularies, nomenclatures, classifications and codes were clarified. The HL7 Finland has defined the manner in which this information is expressed in the CDA R2 structure. The core information elements will be implemented in regional development projects which are partly funded by the Ministry of Social Affairs and Health. This paper presents the defining process of the national core data elements of electronic health record systems in Finland.