Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

CLEF is an MRC sponsored project in the E-Science programme that aims to establish policies and infrastructure for the next generation of integrated clinical and bioscience research. One of the major goals of the project is to provide a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies are needed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows and pseudonymisation mechanisms that are currently being developed. Intended constraints and monitoring policies that will apply to research interrogation of the repository are also outlined. Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research

Supporting UK-wide e-clinical trials and studies

As clinical trials and epidemiological studies become increasingly large, covering wider (national) geographical areas and involving ever broader populations, the need to provide an information management infrastructure that can support such endeavours is essential. A wealth of clinical data now exists at varying levels of care (primary care, secondary care, etc.). Simple, secure access to such data would greatly benefit the key processes involved in clinical trials and epidemiological studies: patient recruitment, data collection and study management. The Grid paradigm provides one model for seamless access to such data and support of these processes. The VOTES project (Virtual Organisations for Trials and Epidemiological Studies) is a collaboration between several UK institutions to implement a generic framework that effectively leverages the available health-care information across the UK to support more efficient gathering and processing of trial information. The structure of the information available in the health-care domain in the UK itself varies broadly in-line with the national boundaries of the constituent states (England, Scotland, Wales and Northern Ireland). Technologies must address these political boundaries and the impact these boundaries have in terms of for example, information governance, policies, and of course large-scale heterogeneous distribution of the data sets themselves. This paper outlines the methodology in implementing the framework between three specific data sources that serve as useful case studies: Scottish data from the Scottish Care Information (SCI) Store data repository, data on the General Practice Research Database (GPRD) diabetes trial at Imperial College London, and benign prostate hypoplasia (BPH) data from the University of Nottingham. The design, implementation and wider research issues are discussed along with the technological challenges encountered in the project in the application of Grid technologies

Security and confidentiality approach for the Clinical E-Science Framework (CLEF)

Objectives: CLEF is an MRC sponsored project in the E-Science programme that aims to establish methodologies and a technical infrastructure for the next generation of integrated clinical and bioscience research. Methods: The heart of the CLEF approach to this challenge is to design and develop a pseudonymised repository of histories of cancer patients that can be accessed by researchers. Robust mechanisms and policies have been developed to ensure that patient privacy and confidentiality are preserved while delivering a repository of such medically rich information for the purposes of scientific research. Results: This paper summarises the overall approach adopted by CLEF to meet data protection requirements, including the data flows, pseudonymisation measures and additional monitoring policies that are currently being developed. Conclusion: Once evaluated, it is hoped that the CLEF approach can serve as a model for other distributed electronic health record repositories to be accessed for research

Tool support for security-oriented virtual research collaborations

Collaboration is at the heart of e-Science and e-Research more generally. Successful collaborations must address both the needs of the end user researchers and the providers that make resources available. Usability and security are two fundamental requirements that are demanded by many collaborations and both concerns must be considered from both the researcher and resource provider perspective. In this paper we outline tools and methods developed at the National e-Science Centre (NeSC) that provide users with seamless, secure access to distributed resources through security-oriented research environments, whilst also allowing resource providers to define and enforce their own local access and usage policies through intuitive user interfaces. We describe these tools and illustrate their application in the ESRC-funded Data Management through e-Social Science (DAMES) and the JISC-funded SeeGEO projects

Application of Semantics to Solve Problems in Life Sciences

Fecha de lectura de Tesis: 10 de diciembre de 2018La cantidad de información que se genera en la Web se ha incrementado en los últimos años. La mayor parte de esta información se encuentra accesible en texto, siendo el ser humano el principal usuario de la Web. Sin embargo, a pesar de todos los avances producidos en el área del procesamiento del lenguaje natural, los ordenadores tienen problemas para procesar esta información textual. En este cotexto, existen dominios de aplicación en los que se están publicando grandes cantidades de información disponible como datos estructurados como en el área de las Ciencias de la Vida. El análisis de estos datos es de vital importancia no sólo para el avance de la ciencia, sino para producir avances en el ámbito de la salud. Sin embargo, estos datos están localizados en diferentes repositorios y almacenados en diferentes formatos que hacen difícil su integración. En este contexto, el paradigma de los Datos Vinculados como una tecnología que incluye la aplicación de algunos estándares propuestos por la comunidad W3C tales como HTTP URIs, los estándares RDF y OWL. Haciendo uso de esta tecnología, se ha desarrollado esta tesis doctoral basada en cubrir los siguientes objetivos principales: 1) promover el uso de los datos vinculados por parte de la comunidad de usuarios del ámbito de las Ciencias de la Vida 2) facilitar el diseño de consultas SPARQL mediante el descubrimiento del modelo subyacente en los repositorios RDF 3) crear un entorno colaborativo que facilite el consumo de Datos Vinculados por usuarios finales, 4) desarrollar un algoritmo que, de forma automática, permita descubrir el modelo semántico en OWL de un repositorio RDF, 5) desarrollar una representación en OWL de ICD-10-CM llamada Dione que ofrezca una metodología automática para la clasificación de enfermedades de pacientes y su posterior validación haciendo uso de un razonador OWL

Incorporation of two terminology projects into a system for information retrieval using NLP for term expansion

In this paper, we will discuss two medical terminology projects at the University College of Ghent, Faculty of translation studies, and the benefits of combining them to provide Dutch professionals and laymen with better access to information in biomedical databases. Our first project, the MeSH Termbase Project (MTB) is aimed at health care professionals, medical translators and also patients in need of language support. The main aim of our second project, the Multilingual Glossary of Technical and Popular Medical Terms, is the simplification of the terminology used in patient information leaflets