A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer

[Abstract] Introduction. The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. Methods. This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials. To ensure interoperability across different institutions, we have developed a Semantic Interoperability Layer (SIL) to facilitate homogeneous access to clinical and genetic information, based on different well-established biomedical standards and following International Health (IHE) recommendations. Results. The SIL has shown suitability for integrating biomedical knowledge and technologies to match the latest clinical advances in healthcare and the use of genomic information. This genomic data integration in the SIL has been tested with a diagnostic classifier tool that takes advantage of harmonized multi-center clinico-genomic data for training statistical predictive models. Conclusions. The SIL has been adopted in national and international research initiatives, such as the EURECA-EU research project and the CIMED collaborative Spanish project, where the proposed solution has been applied and evaluated by clinical experts focused on clinico-genomic studies.Instituto de Salud Carlos III, PI13/02020Instituto de Salud Carlos III, PI13/0028

A modular multipurpose, parameter centered electronic health record architecture

Health Information Technology is playing a key role in healthcare. Specifically, the use of electronic health records has been found to bring about most significant improvements in healthcare quality, mainly as relates to patient management, healthcare delivery and research support. Health record systems adoption has been promoted in many countries to support efficient, high quality integrated healthcare. The objective of this work is the implementation of an Electronic Health Record system based on a relational database. The system architecture is modular and based on the concentration of specific pathology related parameters in one module, therefore the system can be easily applied to different pathologies. Several examples of its application are described. It is intended to extend the system integrating genomic data

Knowledge Guided Integration of Structured and Unstructured Data in Health Decision Process

Data in the health domain is continuously increasing. It is collected from several sources, has several formats and is characterized by its sensibility (protection of personal health data). These characteristics make the management and the expert interaction with the collected data, in order to facilitate decision-making in Health Information Systems (HIS) a challenging field. In this paper, we propose a Knowledge guided integration of structured and unstructured data for health decision process. The knowledge is represented by domain ontology, which allows the integration of structured and unstructured data, stored in NoSQL format. Our motivation is to combine the confirmed advantages of ontologies and NoSQL databases both in data integration and decision aided processes. The proposed ontology has been implemented and evaluated using quality metrics. The approach was evaluated and results show response time optimization, compared with traditional approaches, and improvement of data relevance

Interoperability between information systems of the results of clinical analysis and electronic record of the patient

The issue of interoperability between institutions in underdeveloped countries always presents good opportunities for science to contribute to substantial improvements in real-world issues. Basic support systems, such as health institutions, are among those that can benefit most from scientific advances. This paper reports an analysis made on the lack of interoperability between health institutions, specifically with regard to the interaction between physicians' offices and clinical analysis laboratory. This research was validated with a real practical use case that is presented in this paper. In order to make the information stored in different computer applications of the health information system (HIS), more specifically in the Hospital Center Dr. Ayres de Menezes, in São Tomé and Príncipe, interoperable, two distinct applications were developed, Patient Management System (PMS) and Clinical Analysis Laboratory Management System (LMS) to implement interoperability between them. In this way, take advantage of the interoperability logic implemented between these two applications and later integrate other systems. The PMS requests medical exams through your Medical Consultation panel. The second system, LMS receives the exam request and after the exams are processed and validated, the results are sent to the requesting system. To make the interoperability service effective, the SOAP protocol was used, which allowed the exchange of information synchronously between these two applications, allowing for faster transactions of patients' pathological data, and greater confidentiality of this same information. And as the work progressed, we felt the need to create a functional prototype with REST to meet the cloud model proposal.A questão da interoperabilidade entre instituições em países subdesenvolvidos sempre apresenta boas oportunidades para a ciência contribuir para melhorias substanciais em questões do mundo real. Os sistemas de apoio básico, como as instituições de saúde, estão entre os que mais podem se beneficiar dos avanços científicos. Este trabalho relata uma análise feita sobre a falta de interoperabilidade entre instituições de saúde, especificamente no que diz respeito à interação entre consultórios médicos e laboratórios de análises clínicas. Esta pesquisa foi validada com um caso de uso prático real que é apresentado neste trabalho. De forma a tornar a informação armazenada nas diferentes aplicações informáticas do sistema nacional de saúde (SIS), mais concretamente no Centro Hospitalar Dr. Ayres de Menezes, em São Tomé e Príncipe, interoperáveis, foram desenvolvidas duas aplicações distintas, Sistema de Gestão de Pacientes (SGP) e Sistema de Gestão do Laboratório de Análises Clínicas (SGL) para implementar a interoperabilidade entre eles. Desta forma, aproveitar a lógica implementada entre estas duas aplicações e posteriormente integrar outros sistemas. O SGP solicita exames médicos através do seu painel de Consulta Médica. O segundo sistema, o SGL, recebe a solicitação dos exames e após os exames serem processados e validados, os resultados são enviados ao sistema solicitante. Para tornar o serviço de interoperabilidade efetivo, foi utilizado o protocolo SOAP, que permitiu a troca de informações de forma síncrona entre essas duas aplicações. Por outro lado, sentimos a necessidade de criar um protótipo funcional com REST para atender a proposta do modelo em nuvem

A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer

The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials.This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials. To ensure interoperability across different institutions, we have developed a Semantic Interoperability Layer (SIL) to facilitate homogeneous access to clinical and genetic information, based on different well-established biomedical standards and following International Health (IHE) recommendations.The SIL has shown suitability for integrating biomedical knowledge and technologies to match the latest clinical advances in healthcare and the use of genomic information. This genomic data integration in the SIL has been tested with a diagnostic classifier tool that takes advantage of harmonized multi-center clinico-genomic data for training statistical predictive models.The SIL has been adopted in national and international research initiatives, such as the EURECA-EU research project and the CIMED collaborative Spanish project, where the proposed solution has been applied and evaluated by clinical experts focused on clinico-genomic studies