Orta Doğu Teknik Üniversitesi- Bilgi Toplumu Teknolojileri- Mükemmeliyet merkez projesi

TÜBİTAK EEEAG Proje01.02.200

Hakemistojen käytettävyys hajautuneen potilastiedon hallinnassa

Tässä työssä käsitellään sähköisiä potilaskertomuksia (EHR) sekä tiedonhakua niistä hakemistoja hyödyntäen. Aluksi työssä esitellään keskeisimmät sähköisten potilaskertomusten standardit, kuten HL7 versiot 2 ja 3, CDA ja IHE XDS sekä BPPC. Tämän jälkeen siirrytään tarkastelemaan tarkemmin potilastiedon hakemistoja. Työssä tarkastellaan erityisesti IHE XDS –profiilia, joka kuvaa hakemistoon perustuvan sähköisten potilaskertomusten tiedonvälitystavan potilastietojärjestelmien välillä. ebXML:ään pohjautuvan IHE XDS:n keskeiset komponentit ovat arkisto (Document repository), asiakirjahakemisto (Document registry), asiakirjan tuottaja (Document source) ja asiakirjan käyttäjä (Document consumer). Työssä kuvataan näiden eri komponenttien tehtävät hakemistossa. Työssä kuvataan myös potilaskertomusten hakemista käyttäen IHE XDS-hakemista sekä OWL- ja SPARQL –kieleliä. Työssä esitellään myös muutamia kansallisia potilaskertomusjärjestelmiä, kuten suomen KanTa –järjestelmä sekä Hollannin ja Singaporen kansallisia potilaskertomusten arkistot sekä yleiseurooppalainen epSOS-hanke. Pohdintaosiossa arvioidaan potilaskertomusten hakemiseen käytettävissä olevien menetelmien tehokkuutta

Comparative study of healthcare messaging standards for interoperability in ehealth systems

Advances in the information and communication technology have created the field of "health informatics," which amalgamates healthcare, information technology and business. The use of information systems in healthcare organisations dates back to 1960s, however the use of technology for healthcare records, referred to as Electronic Medical Records (EMR), management has surged since 1990’s (Net-Health, 2017) due to advancements the internet and web technologies. Electronic Medical Records (EMR) and sometimes referred to as Personal Health Record (PHR) contains the patient’s medical history, allergy information, immunisation status, medication, radiology images and other medically related billing information that is relevant. There are a number of benefits for healthcare industry when sharing these data recorded in EMR and PHR systems between medical institutions (AbuKhousa et al., 2012). These benefits include convenience for patients and clinicians, cost-effective healthcare solutions, high quality of care, resolving the resource shortage and collecting a large volume of data for research and educational needs. My Health Record (MyHR) is a major project funded by the Australian government, which aims to have all data relating to health of the Australian population stored in digital format, allowing clinicians to have access to patient data at the point of care. Prior to 2015, MyHR was known as Personally Controlled Electronic Health Record (PCEHR). Though the Australian government took consistent initiatives there is a significant delay (Pearce and Haikerwal, 2010) in implementing eHealth projects and related services. While this delay is caused by many factors, interoperability is identified as the main problem (Benson and Grieve, 2016c) which is resisting this project delivery. To discover the current interoperability challenges in the Australian healthcare industry, this comparative study is conducted on Health Level 7 (HL7) messaging models such as HL7 V2, V3 and FHIR (Fast Healthcare Interoperability Resources). In this study, interoperability, security and privacy are main elements compared. In addition, a case study conducted in the NSW Hospitals to understand the popularity in usage of health messaging standards was utilised to understand the extent of use of messaging standards in healthcare sector. Predominantly, the project used the comparative study method on different HL7 (Health Level Seven) messages and derived the right messaging standard which is suitable to cover the interoperability, security and privacy requirements of electronic health record. The issues related to practical implementations, change over and training requirements for healthcare professionals are also discussed

Repositório de registos electrónicos de saúde baseado em OpenEHR

Mestrado em Engenharia de Computadores e TelemáticaAn Electronic Health Record (EHR) aggregates all relevant medical information regarding a single patient, allowing a patient centric storage approach. This way the complete medical history of a patient is stored together in one record, making it possible to save time and work by allowing the sharing of information between health care institutions. To make this sharing possible there has to be agreed on the format in which the information is saved. There are many standards to de ne the way health information is stored, exchanged and retrieved. One of this standards is the Open Electronic Health Record (OpenEHR). The goal of this thesis is to create a repository which allows to store and manage patient records which follow the OpenEHR standard. The result of the implementation consists in three software parts, being them a Extensible Markup Language (XML) repository to store health information, a set of services allowing to manage and query the information stored and a web interface to demonstrate the implemented functionalities.Um registo electrónico de saúde agrega toda a informação médica relevante de um paciente, permitindo uma filosofia de armazenamento orientada ao mesmo. Desta forma todo o historial médico do paciente encontra-se armazenado num único registo, permitindo a optimização de custos e tempo gasto nas diferentes tarefas, através de partilha de informação entre diferentes instituições médicas. Para possibilitar esta partilha é necessário definir um formato comum em que a informação é armazenada. Para tal foram definidas diversas normas que ditam as regras de armazenamento, troca e recuperação de informação médica. Uma destas normas é o Open Electronic Health Record (OpenEHR). O objectivo desta dissertação e criar um reposit orio que permite o armazenamento de registos médicos que sigam a norma OpenEHR. A implementação dá origem a três componentes de software, sendo eles uma base de dados Extensible Markup Language (XML) para armazenamento de registos médicos, um conjunto de serviços para gestão e pesquisa da informação armazenada e uma interface web para demonstração das funcionalidades implementadas

Health systems data interoperability and implementation

Objective The objective of this study was to use machine learning and health standards to address the problem of clinical data interoperability across healthcare institutions. Addressing this problem has the potential to make clinical data comparable, searchable and exchangeable between healthcare providers. Data sources Structured and unstructured data has been used to conduct the experiments in this study. The data was collected from two disparate data sources namely MIMIC-III and NHanes. The MIMIC-III database stored data from two electronic health record systems which are CareVue and MetaVision. The data stored in these systems was not recorded with the same standards; therefore, it was not comparable because some values were conflicting, while one system would store an abbreviation of a clinical concept, the other would store the full concept name and some of the attributes contained missing information. These few issues that have been identified make this form of data a good candidate for this study. From the identified data sources, laboratory, physical examination, vital signs, and behavioural data were used for this study. Methods This research employed a CRISP-DM framework as a guideline for all the stages of data mining. Two sets of classification experiments were conducted, one for the classification of structured data, and the other for unstructured data. For the first experiment, Edit distance, TFIDF and JaroWinkler were used to calculate the similarity weights between two datasets, one coded with the LOINC terminology standard and another not coded. Similar sets of data were classified as matches while dissimilar sets were classified as non-matching. Then soundex indexing method was used to reduce the number of potential comparisons. Thereafter, three classification algorithms were trained and tested, and the performance of each was evaluated through the ROC curve. Alternatively the second experiment was aimed at extracting patient’s smoking status information from a clinical corpus. A sequence-oriented classification algorithm called CRF was used for learning related concepts from the given clinical corpus. Hence, word embedding, random indexing, and word shape features were used for understanding the meaning in the corpus. Results Having optimized all the model’s parameters through the v-fold cross validation on a sampled training set of structured data ( ), out of 24 features, only ( 8) were selected for a classification task. RapidMiner was used to train and test all the classification algorithms. On the final run of classification process, the last contenders were SVM and the decision tree classifier. SVM yielded an accuracy of 92.5% when the and parameters were set to and . These results were obtained after more relevant features were identified, having observed that the classifiers were biased on the initial data. On the other side, unstructured data was annotated via the UIMA Ruta scripting language, then trained through the CRFSuite which comes with the CLAMP toolkit. The CRF classifier obtained an F-measure of 94.8% for “nonsmoker” class, 83.0% for “currentsmoker”, and 65.7% for “pastsmoker”. It was observed that as more relevant data was added, the performance of the classifier improved. The results show that there is a need for the use of FHIR resources for exchanging clinical data between healthcare institutions. FHIR is free, it uses: profiles to extend coding standards; RESTFul API to exchange messages; and JSON, XML and turtle for representing messages. Data could be stored as JSON format on a NoSQL database such as CouchDB, which makes it available for further post extraction exploration. Conclusion This study has provided a method for learning a clinical coding standard by a computer algorithm, then applying that learned standard to unstandardized data so that unstandardized data could be easily exchangeable, comparable and searchable and ultimately achieve data interoperability. Even though this study was applied on a limited scale, in future, the study would explore the standardization of patient’s long-lived data from multiple sources using the SHARPn open-sourced tools and data scaling platformsInformation ScienceM. Sc. (Computing

Semantic coordination through programmable Tuple spaces

Two of the main features of today complex software systems like pervasive computing systems and Internet-based applications are distribution and openness. Distribution revolves around three orthogonal dimensions: (i) distribution of control|systems are characterised by several independent computational entities and devices, each representing an autonomous and proactive locus of control; (ii) spatial distribution|entities and devices are physically distributed and connected in a global (such as the Internet) or local network; and (iii) temporal distribution|interacting system components come and go over time, and are not required to be available for interaction at the same time. Openness deals with the heterogeneity and dynamism of system components: complex computational systems are open to the integration of diverse components, heterogeneous in terms of architecture and technology, and are dynamic since they allow components to be updated, added, or removed while the system is running. The engineering of open and distributed computational systems mandates for the adoption of a software infrastructure whose underlying model and technology could provide the required level of uncoupling among system components. This is the main motivation behind current research trends in the area of coordination middleware to exploit tuple-based coordination models in the engineering of complex software systems, since they intrinsically provide coordinated components with communication uncoupling and further details in the references therein. An additional daunting challenge for tuple-based models comes from knowledge-intensive application scenarios, namely, scenarios where most of the activities are based on knowledge in some form|and where knowledge becomes the prominent means by which systems get coordinated. Handling knowledge in tuple-based systems induces problems in terms of syntax - e.g., two tuples containing the same data may not match due to differences in the tuple structure - and (mostly) of semantics|e.g., two tuples representing the same information may not match based on a dierent syntax adopted. Till now, the problem has been faced by exploiting tuple-based coordination within a middleware for knowledge intensive environments: e.g., experiments with tuple-based coordination within a Semantic Web middleware (surveys analogous approaches). However, they appear to be designed to tackle the design of coordination for specic application contexts like Semantic Web and Semantic Web Services, and they result in a rather involved extension of the tuple space model. The main goal of this thesis was to conceive a more general approach to semantic coordination. In particular, it was developed the model and technology of semantic tuple centres. It is adopted the tuple centre model as main coordination abstraction to manage system interactions. A tuple centre can be seen as a programmable tuple space, i.e. an extension of a Linda tuple space, where the behaviour of the tuple space can be programmed so as to react to interaction events. By encapsulating coordination laws within coordination media, tuple centres promote coordination uncoupling among coordinated components. Then, the tuple centre model was semantically enriched: a main design choice in this work was to try not to completely redesign the existing syntactic tuple space model, but rather provide a smooth extension that { although supporting semantic reasoning { keep the simplicity of tuple and tuple matching as easier as possible. By encapsulating the semantic representation of the domain of discourse within coordination media, semantic tuple centres promote semantic uncoupling among coordinated components. The main contributions of the thesis are: (i) the design of the semantic tuple centre model; (ii) the implementation and evaluation of the model based on an existent coordination infrastructure; (iii) a view of the application scenarios in which semantic tuple centres seem to be suitable as coordination media

Uma arquitectura segura e colaborativa para registos de saúde electrónicos com suporte a mobilidade

Doutoramento em InformáticaDurante as ultimas décadas, os registos de saúde eletrónicos (EHR) têm evoluído para se adaptar a novos requisitos. O cidadão tem-se envolvido cada vez mais na prestação dos cuidados médicos, sendo mais pró ativo e desejando potenciar a utilização do seu registo. A mobilidade do cidadão trouxe mais desafios, a existência de dados dispersos, heterogeneidade de sistemas e formatos e grande dificuldade de partilha e comunicação entre os prestadores de serviços. Para responder a estes requisitos, diversas soluções apareceram, maioritariamente baseadas em acordos entre instituições, regiões e países. Estas abordagens são usualmente assentes em cenários federativos muito complexos e fora do controlo do paciente. Abordagens mais recentes, como os registos pessoais de saúde (PHR), permitem o controlo do paciente, mas levantam duvidas da integridade clinica da informação aos profissionais clínicos. Neste cenário os dados saem de redes e sistemas controlados, aumentando o risco de segurança da informação. Assim sendo, são necessárias novas soluções que permitam uma colaboração confiável entre os diversos atores e sistemas. Esta tese apresenta uma solução que permite a colaboração aberta e segura entre todos os atores envolvidos nos cuidados de saúde. Baseia-se numa arquitetura orientada ao serviço, que lida com a informação clínica usando o conceito de envelope fechado. Foi modelada recorrendo aos princípios de funcionalidade e privilégios mínimos, com o propósito de fornecer proteção dos dados durante a transmissão, processamento e armazenamento. O controlo de acesso _e estabelecido por políticas definidas pelo paciente. Cartões de identificação eletrónicos, ou certificados similares são utilizados para a autenticação, permitindo uma inscrição automática. Todos os componentes requerem autenticação mútua e fazem uso de algoritmos de cifragem para garantir a privacidade dos dados. Apresenta-se também um modelo de ameaça para a arquitetura, por forma a analisar se as ameaças possíveis foram mitigadas ou se são necessários mais refinamentos. A solução proposta resolve o problema da mobilidade do paciente e a dispersão de dados, capacitando o cidadão a gerir e a colaborar na criação e manutenção da sua informação de saúde. A arquitetura permite uma colaboração aberta e segura, possibilitando que o paciente tenha registos mais ricos, atualizados e permitindo o surgimento de novas formas de criar e usar informação clínica ou complementar.Since their early adoption Electronic Health Records (EHR) have been evolving to cope with increasing requirements from institutions, professionals and, more recently, from patients. Citizens became more involved demanding successively more control over their records and an active role on their content. Mobility brought also new requirements, data become scattered over heterogeneous systems and formats, with increasing di culties on data sharing between distinct providers. To cope with these challenges several solutions appeared, mostly based on service level agreements between entities, regions and countries. They usually required de ning complex federated scenarios and left the patient outside the process. More recent approaches, such as personal health records (PHR), enable patient control although raises clinical integrity doubts to other actors, such as physicians. Also, information security risk increase as data travels outside controlled networks and systems. To overcome this, new solutions are needed to facilitate trustable collaboration between the diverse actors and systems. In this thesis we present a solution that enables a secure and open collaboration between all healthcare actors. It is based on a service-oriented architecture that deals with the clinical data using a closed envelope concept. The architecture was modeled with minimal functionality and privileges bearing in mind strong protection of data during transmission, processing and storing. The access control is made through patient policies and authentication uses electronic identi cation cards or similar certi cates, enabling auto-enrollment. All the components require mutual authentication and uses cyphering mechanisms to assure privacy. We also present a threat model to verify, through our solution, if possible threats were mitigated or if further re nement is needed. The proposed solution solves the problem of patient mobility and data dispersion, and empowers citizens to manage and collaborate in their personal healthcare information. It also permits open and secure collaboration, enabling the patient to have richer and up to date records that can foster new ways to generate and use clinical or complementary information

Uma rede telemática para a prestação regional de cuidados de saúde

Doutoramento em Engenharia InformáticaAs tecnologias de informação e comunicação na área da saúde não são só um instrumento para a boa gestão de informação, mas antes um fator estratégico para uma prestação de cuidados mais eficiente e segura. As tecnologias de informação são um pilar para que os sistemas de saúde evoluam em direção a um modelo centrado no cidadão, no qual um conjunto abrangente de informação do doente deve estar automaticamente disponível para as equipas que lhe prestam cuidados, independentemente de onde foi gerada (local geográfico ou sistema). Este tipo de utilização segura e agregada da informação clínica é posta em causa pela fragmentação generalizada das implementações de sistemas de informação em saúde. Várias aproximações têm sido propostas para colmatar as limitações decorrentes das chamadas “ilhas de informação” na saúde, desde a centralização total (um sistema único), à utilização de redes descentralizadas de troca de mensagens clínicas. Neste trabalho, propomos a utilização de uma camada de unificação baseada em serviços, através da federação de fontes de informação heterogéneas. Este agregador de informação clínica fornece a base necessária para desenvolver aplicações com uma lógica regional, que demostrámos com a implementação de um sistema de registo de saúde eletrónico virtual. Ao contrário dos métodos baseados em mensagens clínicas ponto-a-ponto, populares na integração de sistemas em saúde, desenvolvemos um middleware segundo os padrões de arquitetura J2EE, no qual a informação federada é expressa como um modelo de objetos, acessível através de interfaces de programação. A arquitetura proposta foi instanciada na Rede Telemática de Saúde, uma plataforma instalada na região de Aveiro que liga oito instituições parceiras (dois hospitais e seis centros de saúde), cobrindo ~350.000 cidadãos, utilizada por ~350 profissionais registados e que permite acesso a mais de 19.000.000 de episódios. Para além da plataforma colaborativa regional para a saúde (RTSys), introduzimos uma segunda linha de investigação, procurando fazer a ponte entre as redes para a prestação de cuidados e as redes para a computação científica. Neste segundo cenário, propomos a utilização dos modelos de computação Grid para viabilizar a utilização e integração massiva de informação biomédica. A arquitetura proposta (não implementada) permite o acesso a infraestruturas de e-Ciência existentes para criar repositórios de informação clínica para aplicações em saúde.Modern health information technology is not just a supporting instrument to good information management but a strategic requirement to provide more efficient and safer health care. Health information technology is a cornerstone to build the future patient-centric health care systems in which a comprehensive set of patient data will be available to the relevant care teams, in spite of where (system or service point) it was generated. Such secure and efficient use of clinical data is challenged by the existing fragmentation of health information systems implementation. Several approaches have been proposed to address the limitations of the so called “information silos” in healthcare, ranging from full centralization (a single system) to full-decentralized clinical message exchange networks. In this work we advocate the use of a service-based unification layer, by federating distributed heterogeneous information sources. This clinical information hub provides the basis to build regional-level applications, which we have demonstrated by implementing a virtual Electronic Health Record system. Unlike the message-driven, point-to-point approaches popular in health care systems integration, we developed a middleware layer, using J2EE architectural patterns, in which the common information is represented as an object model, accessible through programming interfaces. The proposed architecture was instantiated in the Rede Telemática da Saúde network, a platform deployed in the region of Aveiro connecting eight partner institutions (two hospitals and six primary care units), covering ~ 350,000 citizens, indexing information on more than 19,000,000 episodes of care and used by ~350 registered professionals. In addition to the regional health information collaborative platform (RTSys), we introduce a second line of research towards bridging the care networks and the science networks. In the later scenario, we propose the use of Grid computing to enable the massive use and integration of biomedical information. The proposed architecture (not implemented) enables to access existing e-Science infrastructures to create clinical information repositories for health applications

The open health information mediator : an architecture for enabling interoperability in low to middle income countries.

M. Sc. University of KwaZulu-Natal, Durban 2015.Interoperability and system integration are central problems that limit the effective use of health information systems to improve efficiency and effectiveness of health service delivery. There is currently no proven technology that provides a general solution in low and middle income countries where the challenges are especially acute. Engineering health information systems in low resource environments have several challenges that include poor infrastructure, skills shortages, fragmented and piecemeal applications deployed and managed by multiple organisations as well as low levels of resourcing. An important element of modern solutions to these problems is a health information exchange that enable disparate systems to share health information. It is a challenging task to develop systems as complex as health information exchanges that will have wide applicability in low and middle income countries. This work takes a case study approach and uses the development of a health information exchange in Rwanda as the case study. This research reports on the design, implementation and analysis of an architecture, the Health Information Mediator, that is a central component of a health information exchange. While such architectures have been used successfully in high income countries their efficacy has not been demonstrated in low and middle income countries. The Rwandan case study was used to understand and identify the challenges and requirements for health information exchange in low and middle income countries. These requirements were used to derive a set of key concerns for the architecture that were then used to drive its design. Novel features of the architecture include: the ability to mediate messages at both the service provider and service consumer interfaces; support for multiple internal representations of messages to facilitate the adoption of new and evolving standards; and the provision of a general method for mediating health information exchange transactions agnostic of the type of transactions. The architecture is shown to satisfy the key concerns and was validated by implementing and deploying a reference application, the OpenHIM, within the Rwandan health information exchange. The architecture is also analysed using the Architecture Trade-off Analysis Method. It has also been successfully implemented in other low and middle income countries with relatively minor configuration changes which demonstrates the architectures generalizability