MASTER THESIS a Gnu Health Monitoring Module
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MASTER THESIS Thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Engineering at the Univer- sity of Applied Sciences Technikum Wien - Degree Program Biomedical Engineering Sciences A Gnu Health Monitoring Module By: Barbora Veselá, BSc Student Number: 51867978 Supervisors: FH-Prof. Dipl-Ing. Dr. Stefan Sauermann Dipl-Ing. Dr. Johannes Kropf Vienna, May 20, 2019 Abstract This thesis focuses on the development of a GNU Health Module for electrocardiogram monitor- ing and the development of an application providing a fundamental electrocardiogram analysis. The theoretical part contains a brief introduction to hospital information systems including elec- tronic patient record and healthcare data standards information, followed by a description of the GNU Health application and the implementation of the electrocardiogram analysis, written in the Python programming language. The practical part deals with the development of the GNU Health Monitoring module and the external application for signal analysis. The results, disscussion and the conclusion follow. Keywords: Hospital Information System, Gnu Health, Tryton, Monitoring Module, Python ECG Analysis Kurzfassung Diese Arbeit befasst sich mit der Entwicklung eines GNU-Gesundheitsmoduls zur Elek- trokardiogrammberwachung und der Entwicklung einer Anwendung, die eine grundlegende Elektrokardiogrammanalyse bereitstellt. Der theoretische Teil enth eine kurze Einfhrung in Krankenhausinformationssysteme, einschlieich Informationen zu Patientenakten und Gesund- heitsdatenstandards, gefolgt von einer Beschreibung der GNU Health-Anwendung und der Implementierung der Elektrokardiogramm-Analyse, die in der Programmiersprache Python geschrieben ist. Der praktische Teil befasst sich mit der Entwicklung des GNU Health Monitor- ing Moduls und der externen Anwendung zur Signalanalyse, gefolgt von Ergebnissen, Diskus- sion und Schlussfolgerung. Keywords: Krankenhausinformationssystem, GNU Health, Tryton, Überwachungsmodul, Python-EKG-Analyse Abstrakt Tato práce se zameˇrujeˇ na tvorbu GNU Health modulu pro monitorování elektrokardiogramu a vývoj aplikace poskytující základní elektrokardiogramovou analýzu. Teoretická cástˇ obsahuje strucnýˇ úvod do nemocnicníchˇ informacníchˇ systém˚uvcetnˇ eˇ elektronických záznam˚uo pacien- tech a standardech zdravotnických dat, následuje popis aplikace GNU Health a implementace elektrokardiogramové analýzy napsané v programovacím jazyce Python. Praktická cástˇ se zabývá vývojem GNU Health modulu pro monitorování a externí aplikace pro analýzu signál˚u. Následují výsledky, diskuze a záver.ˇ Keywords: Nemocnicníˇ informacníˇ systém, GNU Health, Tryton, Modul pro monitorování, Python EKG Analýza Acknowledgements I would like to thank FH-Prof. Dipl-Ing. Dr. Stefan Sauermann and Dipl-Ing. Dr. Johannes Kropf for leading my diploma work and expert advice they gave me. I also thank Austrian Institute of Technology for an opportunity to write my diploma thesis with them and their entire team for their willingness to help solve problems. Contents 1 List of Abbreviations1 2 Introduction: Hospital Information Systems (HIS)3 2.1 Security.........................................3 2.2 Database........................................4 2.3 Electronic Patient Record (EPR)...........................6 2.3.1 National Healthcare Records.........................7 2.4 Healthcare Data Standards..............................8 3 Introduction: Gnu Health 12 3.1 GNU Health Modular Design............................. 12 3.2 The Technical Information............................... 17 3.2.1 GNU Health Technical Structure....................... 17 3.2.2 Module Technical Structure.......................... 19 3.3 Contribution to GNU Health.............................. 23 4 Introduction: ECG Analysis 24 4.1 Electrocardiogram (ECG)............................... 24 4.1.1 Formation.................................... 24 4.1.2 Leads...................................... 25 4.1.3 ECG Types................................... 27 4.2 Filtration......................................... 27 4.2.1 Drift....................................... 28 4.2.2 Powerline Interference............................. 28 4.2.3 Myopotentials.................................. 29 4.3 Processing....................................... 30 4.3.1 Heart Rate................................... 30 4.3.2 Heart Rate Variability (HRV).......................... 30 4.4 Evaluation........................................ 32 4.4.1 Sensitivity (S).................................. 32 4.4.2 Predictivity (P)................................. 32 5 Goals of the Diploma Thesis 33 6 Materials and Methods: Gnu Health Monitoring Module 34 6.1 Materials........................................ 35 6.2 Methods......................................... 35 6.2.1 Module..................................... 35 6.2.2 Implementation ECG Analysis of the GNU Health Module......... 37 6.2.3 ECG Analysis.................................. 38 7 Results 44 8 Disscussion 46 9 Conclusion 47 Bibliography 48 List of Figures 54 List of Code 57 1 List of Abbreviations HIS ... Hospital Information System GDP R ... General Data Protection Regulation NIST ... National Institute of Standards and Technology LIMS ... Laboratory Information System HMIS ... Hospital Management Information System EP D ... Electronic Patient Dossier IZIP ... Electronic Health Book DSI ... Digital Service Infrastructure CEF ... Connecting Europe Facility id ... Identification Number ICU ... Intensive Care Unit LAB ... Laboratory AMB ... Ambulance PC ... Personal Computer NB ... Notebook RT G ... Radiology P ACS ... Picture Archiving and Communications system DICOM ... Digital Imaging and Communications in Medicine NCP DP ... National Council for Prescription Drug Programs AST MInternational ... American Society for Testing and Materials HL7 ... Health Level Seven ICD9 ... International Classification of Diseases, Ninght Revision WHO ... World Health Organization ICF ... International Classification of Functioning, Disability and Health AP ACHEII ... Acute Physiology and Chronic Health Evaluation II GCS ... Glasgow Coma Scale EP R ... Electronic Patient Record XML ... Extensible Markup Language JSON ... JavaScript Object Notation 1 ECG ... Electrocardiogram CT ... Computerized Tomography MRI ... Magnetic Resonance Imaging TFT ... Short-time Fourier Transform DW T ... Discrete Wavelet Transform T KEO ... Teager-Kaiser Energy Operator SD1 ... Standard Deviation of the Poincaré Plot Perpendicular to the Line-of-identity SD2 ... Standard Deviation of the Poincaré Plot Perpendicular along the Line-of-identity HRV ... Heart Rate Variability S ... Sensitivity P ... Predictivity 2 2 Introduction: Hospital Information Systems (HIS) A hospital information system (HIS) is a set of technical and programmatic resources, that pro- vide a paperless computing environment for the needs of the hospital, its departments and other health services. The users with varying degrees of authority are allowed to collect simul- taneously, process, store, analyse and display the required information related to the individual patient. [1], [2] A HIS consists of several information subsystems with many interrelationships, that provide a communication link between departments. The importance of interdisciplinary cooperation increases. [1] Each subsystem could be designed differently and has a specific function focused on its needs. There could be included modules for finance associated with economic parameters such as costs, reports and purchase, administration dealing with scheduling, admission and discharge patients, medical module for cardiology, pediatrics, genetics, surgery, intensive care unit, urology, gynecology and other departments, laboratory for providing test requests, results, pharmacy and stock management for storing and manipulating medicaments and others. [1] One of the reasons for using a HIS was the need to bring order to a hospital, medical and patient data associated with trying to obtain more comprehensive patient data and new knowl- edge, that are relatively independent of the location and time of collection. A HIS increases the effectiveness of public healthcare, streamlines the process of documentation of individual activ- ities, accelerates transmission, retrieval, and display of information, improves the organisation of work and eliminates recurrent unproductive activities. It prevents potential conflicts arising from possible misunderstandings and lack of knowledge. All of this reduces healthcare costs. [1], [2] A HIS must be able to handle large data with a wide range of many different formats for multiple users with different levels of competence. It can be assumed that more computers are connected to the hospital server. Its operation is associated with high demands on the stability and quality of devices, software, technical and program support, database and security. [2], [1] 2.1 Security A large number of different healthcare professionals have access to a hospital information sys- tem. This fact also increases the risk of abuse. The data must be capped confidential and 3 secure. The security involves the technical (quality of devices and its adequate maintenance) and data management terms (data loss, misuse, fishing or differentiated data access). [3], [2], The National Institute of Standards and Technology provides standards, guidelines, tools and technologies to protect information systems against threats to the confidentiality and integrity of information