Arquiteturas federadas para integração de dados biomédicos

Doutoramento Ciências da ComputaçãoThe last decades have been characterized by a continuous adoption of IT solutions in the healthcare sector, which resulted in the proliferation of tremendous amounts of data over heterogeneous systems. Distinct data types are currently generated, manipulated, and stored, in the several institutions where patients are treated. The data sharing and an integrated access to this information will allow extracting relevant knowledge that can lead to better diagnostics and treatments. This thesis proposes new integration models for gathering information and extracting knowledge from multiple and heterogeneous biomedical sources. The scenario complexity led us to split the integration problem according to the data type and to the usage specificity. The first contribution is a cloud-based architecture for exchanging medical imaging services. It offers a simplified registration mechanism for providers and services, promotes remote data access, and facilitates the integration of distributed data sources. Moreover, it is compliant with international standards, ensuring the platform interoperability with current medical imaging devices. The second proposal is a sensor-based architecture for integration of electronic health records. It follows a federated integration model and aims to provide a scalable solution to search and retrieve data from multiple information systems. The last contribution is an open architecture for gathering patient-level data from disperse and heterogeneous databases. All the proposed solutions were deployed and validated in real world use cases.A adoção sucessiva das tecnologias de comunicação e de informação na área da saúde tem permitido um aumento na diversidade e na qualidade dos serviços prestados, mas, ao mesmo tempo, tem gerado uma enorme quantidade de dados, cujo valor científico está ainda por explorar. A partilha e o acesso integrado a esta informação poderá permitir a identificação de novas descobertas que possam conduzir a melhores diagnósticos e a melhores tratamentos clínicos. Esta tese propõe novos modelos de integração e de exploração de dados com vista à extração de conhecimento biomédico a partir de múltiplas fontes de dados. A primeira contribuição é uma arquitetura baseada em nuvem para partilha de serviços de imagem médica. Esta solução oferece um mecanismo de registo simplificado para fornecedores e serviços, permitindo o acesso remoto e facilitando a integração de diferentes fontes de dados. A segunda proposta é uma arquitetura baseada em sensores para integração de registos electrónicos de pacientes. Esta estratégia segue um modelo de integração federado e tem como objetivo fornecer uma solução escalável que permita a pesquisa em múltiplos sistemas de informação. Finalmente, o terceiro contributo é um sistema aberto para disponibilizar dados de pacientes num contexto europeu. Todas as soluções foram implementadas e validadas em cenários reais

DICOM-RT standart in Radiotherapy information systems - A National Study

Mestrado em Informática MédicaMaster Programme in Medical Informatic

Supporting the diagnosis of childhood brain tumours through structural reports and ontological reasoning

After Leukaemia, childhood brain tumours are the second most common form of cancer. The most accurate way to diagnosis a tumour is via a biopsy, but is not always possible. An alternative is Magnetic Resonance Spectroscopy (MRS) which analyses the chemical make-up of tissue and then used to make a diagnosis. A patient's medical records are an important part of treatment, used to communicate findings from medical images. However, these are written using unclear and ambiguous free text. A solution is to produce records using Structured Reporting. This has been incorporated into the Digital Communications in Medicine (DICOM) Standard for established imaging modalities, but not for MRS. An ontology was modelled to produce DICOM supported Structured Reports for MRS. Also, an algorithm to diagnosis different types of childhood brain cancer using MRS spectra was incorporated, allowing automated diagnostic support. A prototype Structured Reporting application was designed based on the ontology. The ontology was able to produce Structured Reports that successfully diagnosed certain childhood brain tumours based on the MRS readings. Usability testing and the diagnostic aspect of the ontology garnered positive feedback as MRS data is only currently used to diagnosis whether the tissue is cancerous or not

An architectural concept for implementing the socio-technical workflow of Digital Pathology in Chile

Virtual Microscopy opens up the possibility to remotely access high quality images at large scales for scientific research, education, and clinical application. For clinical diagnostics, Digital Pathology (DP) presents a novel opportunity to reduce variability [Bauer et al., 2013] due to the reproducible access to Whole Slide Imaging, quantitative parameters (e.g. HER2 stained membrane) [Al-Janabi et al., 2012], second opinion and Quality Assurance [Ho et al., 2013]. Despite of the mentioned advantages, the challenge remains to incorporate DP into the pathologists workflow within a heterogeneous environment of systems and infrastructures [Stathonikos et al., 2013]. Different issues must be solved in order to optimize the impact of DP in the daily clinical practice [Daniel et al., 2012] [Ho et al., 2006]. The integration needs precise planning and comprehensive evaluation for adopting this technology [Stathonikos et al., 2013]. This thesis will focus on an organizational development approach based on a Socio-Technical System (STS). The socio-technical approach covers: (i) the technical issue: tissue-scanner, NDP.view, NDP.serve, analysis software, and (ii) the social issue: pathologists, technicians. In order to improve the integration, a joint optimization (of i and ii) is necessary. The developed STS approach will optimize the integration of DP towards improved workflows in clinical environments. The improved workflows will reduce the pathologists turnaround time, improve the certainty of the diagnostics, and provide a more effective patient care within the covered institutions. An overt multi-site Participatory Observation, Questionnaires, and Business Process Modelling Notation will be used to analyse the existing pathological workflows. Based on this, the system will be modelled with the 3lgm2 Toolkit [Winter et al., 2007] under consideration of various technical subsystems that are present in the clinical environment. Afterwards, the interfaces between subsystems and its possible interoperabilities will be evaluated, taking into account the different existing standards and guidelines for image processing and management, as well as business processes in DP. In order to analyse the existing preconditions a questionnaire will be evaluated to establish a robust and valid view. In addition, the overt participatory observation will support this elevation, giving a deeper insight on the social part. This observation also covers the technical side including the whole pathological process. The socio technical model will then reveal measurable potential for optimization with incorporated DP (e.g. higher throughput for slides). The organizational development approach consists of a Socio-Technical System based on overt multi-site participatory observations, questionnaires, business process modelling and 3LGM2, will optimize the use of Digital Pathology in the daily clinical practice and raise the acceptance to incorporate integrate the new technology within the dayly workflow through the user centred process of incorporation. • Perform and evaluate a questionnaire and a participant observation of pathologists work days in private & public institutions • Create and evaluate a 3lgm2 model • Model the current pathological process (viewpoint of pathologist & technical assistant) & perform and evaluate a contextual inquiry to elevate the pathologists requirements & expectations towards the system • Test the future WF according the model parameters. This project will detect unsuspected interrelations and interdependencies within the socio- technical workflow with a pathology laboratory. The observation will reveal the action conformity as well as the environment in which the process has to be embedded. Furthermore it will establish an optimized workflow for a specific clinical environment to prepare the implementation of DP. Additionally it will be possible to quantify digitized images in order to improve decision making and lastly to improve patient care. In the future it will be possible to extend automated image analysis in order to support clinical decision support. Depending on acceptance, this can lead towards an automated clinical decision support for cases with low complexity

Use of Software Tools to Implement Quality Control of Ultrasound Images in a Large Clinical Trial

Research Question This thesis aims to answer the question as to whether software tools might be developed for automating the analysis of images used to measure ovaries in transvaginal sonography (TVS) exams. Such tools would allow the routine collection of independent and objective metrics at low cost and might be used to drive a programme of continuous Quality Improvement (QI) in TVS scanning. The tools will be assessed by processing images from thousands of TVS exams performed by the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS). Background This research is important because TVS is core to any ovarian cancer (OC) screening strategy yet independent and objective quality control (QC) metrics for this procedure are not routinely obtained due to the high cost of manual image inspection. Improving the quality of TVS in the National Health Service (NHS) would assist in the early diagnosis of the disease and result in improved outcome for some women. Therefore, the research has clear translational potential for the >1.2 million scans performed annually by the NHS. Research Findings A study performed to process images from 1,000 TVS exams has shown the tool produces accurate and reliable QC metrics. A further study revealed that over half of these exams should have been classified as unsatisfactory as an expert review of the images showed that that the sonographer had mistakenly measured a structure that was not an ovary. It also reported a correlation between such ovary visualisation and a novel metric (DCR) measured by the tools from the examination images. Conclusion The research results suggest both a need to improve the quality of TVS scanning and the viability of achieving this objective by introducing a QI programme driven by metrics gathered by software tools able to analyze the images used to measure ovaries

Sharing and viewing segments of electronic patient records service (SVSEPRS) using multidimensional database model

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.The concentration on healthcare information technology has never been determined than it is today. This awareness arises from the efforts to accomplish the extreme utilization of Electronic Health Record (EHR). Due to the greater mobility of the population, EHR will be constructed and continuously updated from the contribution of one or many EPRs that are created and stored at different healthcare locations such as acute Hospitals, community services, Mental Health and Social Services. The challenge is to provide healthcare professionals, remotely among heterogeneous interoperable systems, with a complete view of the selective relevant and vital EPRs fragments of each patient during their care. Obtaining extensive EPRs at the point of delivery, together with ability to search for and view vital, valuable, accurate and relevant EPRs fragments can be still challenging. It is needed to reduce redundancy, enhance the quality of medical decision making, decrease the time needed to navigate through very high number of EPRs, which consequently promote the workflow and ease the extra work needed by clinicians. These demands was evaluated through introducing a system model named SVSEPRS (Searching and Viewing Segments of Electronic Patient Records Service) to enable healthcare providers supply high quality and more efficient services, redundant clinical diagnostic tests. Also inappropriate medical decision making process should be avoided via allowing all patients‟ previous clinical tests and healthcare information to be shared between various healthcare organizations. Multidimensional data model, which lie at the core of On-Line Analytical Processing (OLAP) systems can handle the duplication of healthcare services. This is done by allowing quick search and access to vital and relevant fragments from scattered EPRs to view more comprehensive picture and promote advances in the diagnosis and treatment of illnesses. SVSEPRS is a web based system model that helps participant to search for and view virtual EPR segments, using an endowed and well structured Centralised Multidimensional Search Mapping (CMDSM). This defines different quantitative values (measures), and descriptive categories (dimensions) allows clinicians to slice and dice or drill down to more detailed levels or roll up to higher levels to meet clinicians required fragment

Advancing clinical gait analysis through technology and policy

Thesis (S.M. in Technology and Policy)--Massachusetts Institute of Technology, Engineering Systems Division, Technology and Policy Program; and, (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 161-165).Quantitatively analyzing human gait biomechanics will improve our ability to diagnose and treat disability and to measure the effectiveness of assistive devices. Gait analysis is one technology used to analyze walking, but technical as well as economic, social, and policy issues hinder its clinical adoption. This thesis is divided into two parts that address some of these issues. Part I focuses on the role public policies have in advancing gait analysis. Through an analysis of gait analysis technologies, case studies of MRI and CT Angiography, and a high-level analysis of data standards used in gait analysis, it concludes that policies cannot directly create the institutional structures and the data standards required to advance gait analysis as a clinical diagnostic tool. Only through indirect means, such as research funding, can policies support the development of organizations to take ownership of gait analysis technologies. Part I also concludes that policies should not fund development of gait technologies but instead should fund research units working on data standards and accurate human body models. Part II focuses on a technical issue in gait analysis, namely, how to address uncertainties in joint moment calculations that occur from using different body segment inertial parameter estimation models. This is identified as a technical issue needing attention from our broader policy analysis in Part I. Using sensitivity studies of forward dynamics computer simulations coupled with an analysis of the dynamical equations of motion, Part II shows that joint moment variations resulting from different segment inertial parameters are significant at some parts of the gait cycle, particularly heel strike and leg swing.(cont.) It provides recommendations about which segment inertial parameters one should estimate more accurately depending on which joints and phases of the gait cycle one is interested in analyzing.by Junjay Tan.S.M.S.M.in Technology and Polic