DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

The development and deployment of Common Data Elements for tissue banks for translational research in cancer – An emerging standard based approach for the Mesothelioma Virtual Tissue Bank

<p>Abstract</p> <p>Background</p> <p>Recent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) – compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).</p> <p>Methods</p> <p>The purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).</p> <p>Results</p> <p>Common Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.</p> <p>Conclusion</p> <p>The CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.</p

Clinical foundations and information architecture for the implementation of a federated health record service

Clinical care increasingly requires healthcare professionals to access patient record information that may be distributed across multiple sites, held in a variety of paper and electronic formats, and represented as mixtures of narrative, structured, coded and multi-media entries. A longitudinal person-centred electronic health record (EHR) is a much-anticipated solution to this problem, but its realisation is proving to be a long and complex journey. This Thesis explores the history and evolution of clinical information systems, and establishes a set of clinical and ethico-legal requirements for a generic EHR server. A federation approach (FHR) to harmonising distributed heterogeneous electronic clinical databases is advocated as the basis for meeting these requirements. A set of information models and middleware services, needed to implement a Federated Health Record server, are then described, thereby supporting access by clinical applications to a distributed set of feeder systems holding patient record information. The overall information architecture thus defined provides a generic means of combining such feeder system data to create a virtual electronic health record. Active collaboration in a wide range of clinical contexts, across the whole of Europe, has been central to the evolution of the approach taken. A federated health record server based on this architecture has been implemented by the author and colleagues and deployed in a live clinical environment in the Department of Cardiovascular Medicine at the Whittington Hospital in North London. This implementation experience has fed back into the conceptual development of the approach and has provided "proof-of-concept" verification of its completeness and practical utility. This research has benefited from collaboration with a wide range of healthcare sites, informatics organisations and industry across Europe though several EU Health Telematics projects: GEHR, Synapses, EHCR-SupA, SynEx, Medicate and 6WINIT. The information models published here have been placed in the public domain and have substantially contributed to two generations of CEN health informatics standards, including CEN TC/251 ENV 13606

The National Transport Data Framework

Report by Professor Peter Landshoff (Cambridge University) and Professor John Polak (Imperial College London) on a project for the Department for Transport. emails: [email protected] [email protected] NTDF is designed to be a resource for data owners to deposit descriptions into a central catalogue, so that people can search for data and find data and understand their characteristics. The value of this is to individuals, to commercial organizations, and to public bodies. For example, services that provide better information to travellers will help to make their journey less stressful and persuade them to make more use of public transport. Transport operators need very diverse information to help them plan developments to their services: demographic, geographical, economic etc. And policy makers need a similar range of information to help them decide how to divide their budget and afterwards to evaluate how valuable it has been.This work was supported by the Department for Transport (DfT)

Modern Information Systems

The development of modern information systems is a demanding task. New technologies and tools are designed, implemented and presented in the market on a daily bases. User needs change dramatically fast and the IT industry copes to reach the level of efficiency and adaptability for its systems in order to be competitive and up-to-date. Thus, the realization of modern information systems with great characteristics and functionalities implemented for specific areas of interest is a fact of our modern and demanding digital society and this is the main scope of this book. Therefore, this book aims to present a number of innovative and recently developed information systems. It is titled "Modern Information Systems" and includes 8 chapters. This book may assist researchers on studying the innovative functions of modern systems in various areas like health, telematics, knowledge management, etc. It can also assist young students in capturing the new research tendencies of the information systems' development

Hybrid semantic-document models

This thesis presents the concept of hybrid semantic-document models to aid information management when using standards for complex technical domains such as military data communication. These standards are traditionally text based documents for human interpretation, but prose sections can often be ambiguous and can lead to discrepancies and subsequent implementation problems. Many organisations produce semantic representations of the material to ensure common understanding and to exploit computer aided development. In developing these semantic representations, no relationship is maintained to the original prose. Maintaining relationships between the original prose and the semantic model has key benefits, including assessing conformance at a semantic level, and enabling original content authors to explicitly define their intentions, thus reducing ambiguity and facilitating computer aided functionality. Through the use of a case study method based on the military standard MIL-STD-6016C, a framework of relationships is proposed. These relationships can integrate with common document modelling techniques and provide the necessary functionality to allow semantic content to be mapped into document views. These relationships are then generalised for applicability to a wider context. Additionally, this framework is coupled with a templating approach which, for repeating sections, can improve consistency and further enhance quality. A reflective approach to model driven web rendering is presented and evaluated. This reflective approach uses self-inspection at runtime to read directly from the model, thus eliminating the need for any generative processes which result in data duplication across source used for different purpose

Designing privacy for scalable electronic healthcare linkage

A unified electronic health record (EHR) has potentially immeasurable benefits to society, and the current healthcare industry drive to create a single EHR reflects this. However, adoption is slow due to two major factors: the disparate nature of data and storage facilities of current healthcare systems and the security ramifications of accessing and using that data and concerns about potential misuse of that data. To attempt to address these issues this paper presents the VANGUARD (Virtual ANonymisation Grid for Unified Access of Remote Data) system which supports adaptive security-oriented linkage of disparate clinical data-sets to support a variety of virtual EHRs avoiding the need for a single schematic standard and natural concerns of data owners and other stakeholders on data access and usage. VANGUARD has been designed explicit with security in mind and supports clear delineation of roles for data linkage and usage

BMC Cancer

BackgroundRecent advances in genomics, proteomics, and the increasing demands for biomarker validation studies have catalyzed changes in the landscape of cancer research, fueling the development of tissue banks for translational research. A result of this transformation is the need for sufficient quantities of clinically annotated and well-characterized biospecimens to support the growing needs of the cancer research community. Clinical annotation allows samples to be better matched to the research question at hand and ensures that experimental results are better understood and can be verified. To facilitate and standardize such annotation in bio-repositories, we have combined three accepted and complementary sets of data standards: the College of American Pathologists (CAP) Cancer Checklists, the protocols recommended by the Association of Directors of Anatomic and Surgical Pathology (ADASP) for pathology data, and the North American Association of Central Cancer Registry (NAACCR) elements for epidemiology, therapy and follow-up data. Combining these approaches creates a set of International Standards Organization (ISO) \ue2\u20ac\u201c compliant Common Data Elements (CDEs) for the mesothelioma tissue banking initiative supported by the National Institute for Occupational Safety and Health (NIOSH) of the Center for Disease Control and Prevention (CDC).MethodsThe purpose of the project is to develop a core set of data elements for annotating mesothelioma specimens, following standards established by the CAP checklist, ADASP cancer protocols, and the NAACCR elements. We have associated these elements with modeling architecture to enhance both syntactic and semantic interoperability. The system has a Java-based multi-tiered architecture based on Unified Modeling Language (UML).ResultsCommon Data Elements were developed using controlled vocabulary, ontology and semantic modeling methodology. The CDEs for each case are of different types: demographic, epidemiologic data, clinical history, pathology data including block level annotation, and follow-up data including treatment, recurrence and vital status. The end result of such an effort would eventually provide an increased sample set to the researchers, and makes the system interoperable between institutions.ConclusionThe CAP, ADASP and the NAACCR elements represent widely established data elements that are utilized in many cancer centers. Herein, we have shown these representations can be combined and formalized to create a core set of annotations for banked mesothelioma specimens. Because these data elements are collected as part of the normal workflow of a medical center, data sets developed on the basis of these elements can be easily implemented and maintained.1U19OH009077-01/OH/NIOSH CDC HHS/United StatesUL1 TR000005/TR/NCATS NIH HHS/United State