A Community-Driven Validation Service for Standard Medical Imaging Objects

Digital medical imaging laboratories contain many distinct types of equipment provided by different manufacturers. Interoperability is a critical issue and the DICOM protocol is a de facto standard in those environments. However, manufacturers' implementation of the standard may have non-conformities at several levels, which will hinder systems' integration. Moreover, medical staff may be responsible for data inconsistencies when entering data. Those situations severely affect the quality of healthcare services since they can disrupt system operations. The existence of software able to confirm data quality and compliance with the DICOM standard is important for programmers, IT staff and healthcare technicians. Although there are a few solutions that try to accomplish this goal, they are unable to deal with certain situations that require user input. Furthermore, these cases usually require the setup of a working environment, which makes the sharing of validation information more difficult. This article proposes and describes the development of a Web DICOM validation service for the community. This solution requires no configuration by the user, promotes validation results share-ability in the community and preserves patient data privacy since files are de-identified on the client side.Comment: Computer Standards & Interfaces, 201

Genomic sequencing capacity, data retention, and personal access to raw data in Europe

Whole genome/exome sequencing (WGS/WES) has become widely adopted in research and, more recently, in clinical settings. Many hope that the information obtained from the interpretation of these data will have medical benefits for patients and—in some cases—also their biological relatives. Because of the manifold possibilities to reuse genomic data, enabling sequenced individuals to access their own raw (uninterpreted) genomic data is a highly debated issue. This paper reports some of the first empirical findings on personal genome access policies and practices. We interviewed 39 respondents, working at 33 institutions in 21 countries across Europe. These sequencing institutions generate massive amounts of WGS/WES data and represent varying organisational structures and operational models. Taken together, in total, these institutions have sequenced ∼317,259 genomes and exomes to date. Most of the sequencing institutions reported that they are able to store raw genomic data in compliance with various national regulations, although there was a lack of standardisation of storage formats. Interviewees from 12 of the 33 institutions included in our study reported that they had received requests for personal access to raw genomic data from sequenced individuals. In the absence of policies on how to process such requests, these were decided on an ad hoc basis; in the end, at least 28 requests were granted, while there were no reports of requests being rejected. Given the rights, interests, and liabilities at stake, it is essential that sequencing institutions adopt clear policies and processes for raw genomic data retention and personal access

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

Security in transnational interoperable PPDR communications: threats and requirements

The relevance of cross border security operations has been identified as a priority at European level for a long time. A European network where Public Protection and Disaster Relief (PPDR) forces share communications processes and a legal framework would greatly enforce response to disaster recovery and security against crime. Nevertheless, uncertainty on costs, timescale and functionalities have slowed down the interconnection of PPDR networks across countries and limited the transnational cooperation of their PPDR forces so far. In this context, the European research project ISITEP is aimed at developing the legal, operational and technical framework to achieve a cost effective solution for PPDR interoperability across European countries. Inter alia, ISITEP project is specifying a new Inter-System-Interface (ISI) interface for the interconnection of current TETRA and TETRAPOL networks that can be deployed over Internet Protocol (IP) connectivity. This approach turns communications security as a central aspect to consider when deploying the new IP ISI protocol between PPDR national networks. Ensuring that threats to the interconnected communications systems and terminals are sufficiently and appropriately reduced by technical, procedural and environmental countermeasures is vital to realise the trusted and secure communication system needed for the pursued PPDR transnational cooperation activities. In this context, this paper describes the framework and methodology defined to carry out the development of the security requirements and provides a discussion on the undertaken security risk and vulnerability analysis.Peer ReviewedPostprint (author's final draft

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies

Towards an E-Government Enterprise Architecture Framework for Developing Economies

The growth and uptake of e-government in developing economies are still affected by the interoperability challenge, which can be perceived as an orchestration of several issues that imply the existence of gaps in methods used for e-government planning and implementation. To a great extent, various counterparts in developed economies have succeeded in addressing the method-related gaps by developing e-government enterprise architectures, as blueprints for guiding e-government initiatives in a holistic and manageable way. However, existing e-government enterprise architectures are country-specific to appropriately serve their intended purpose, while enterprise architecture frameworks or methods are generic to accommodate several enterprise contexts. The latter do not directly accommodate the unique peculiarities of e-government efforts. Thus, a detailed method is lacking that can be adapted by developing economies to develop e-government enterprise architectures that fit their contexts. To address the gap, this article presents research that adopted a Design Science approach to develop an e-Government Enterprise Architecture Framework (EGEAF), as an explicit method for guiding the design of e-government enterprise architectures in a developing economy. EGEAF was designed by extending the Architecture Development Method of The Open Group Architecture Framework (TOGAF ADM) to address requirements for developing interoperable e-government solutions in a developing economy. EGEAF was evaluated using two scenarios in the Ugandan context, and findings indicate that it is feasible; its design is understandable to enable its adoption and extension to accommodate requirements for developing interoperable e-government solutions in other developing economies