Müller Heimo, Malservet Nicolas, Quinlan Philip, Reihs Robert, Penicaud Matthieu, Chami Antoine, Zatloukal Kurt, Dagher George
Medical University of Graz, 8010 Graz, Austria.
Institut national de la santé et de la recherche médicale, 75654 Paris, France.
Health Technol (Berl). 2017;7(1):89-95. doi: 10.1007/s12553-016-0175-x. Epub 2017 Jan 12.
The domain of biobanking has gone through many stages and as a result there are a wide range of commercial and open source software solutions available. The utilization of these software tools requires different levels of domain and technical skills for installation, configuration and ultimate us of these biobank software tools. To compound this complexity the biobanking community are required to work together in order to share knowledge and jointly build solutions to underpin the research infrastructure. We have evaluated the available tools, described them in a catalogue (BiobankApps) and made a selection of tools available to biobanks in a reference toolbox (BIBBOX) that are use-case driven. In the BiobankApps tool catalogue, both commercial and open source software solutions related to the biobanking domain are included, classified and evaluated. The evaluation covers: 1) "user review" by an authenticated user 2) domain expert: quick analysis by BBMRI members and 3) domain expert: detailed analysis and test installation with real world data. The evaluation is paired with a survey across the more "advanced" (from a technology perspective) biobanks to investigate what tools are currently used and summarises known benefits/drawbacks of the respective packages. In the second step we recommend tools for specific use cases, and install, configure and connect these in the BIBBOX framework. This service also builds on the existing work in the United Kingdom in seeking to establish the motivations for different stakeholders to become involved and therefore assisting in prioritising the use-cases based on the level of need and support within the research community. All tools associated to a use-case are available as BIBBOX applications (technically this is achieved by docker containers), which are integrated in the BIBBOX framework with central identification and user management. In future work we plan to share the acquired knowledge with other networks, develop an Application Programmable Interface (API) for the exchange of metadata with other tool catalogues and work on an ontology for the evaluation of biobank software.
生物样本库领域经历了多个阶段，因此有各种各样的商业和开源软件解决方案可供使用。使用这些软件工具进行安装、配置以及最终使用需要不同程度的领域和技术技能。更复杂的是，生物样本库社区需要共同努力，以共享知识并共同构建解决方案来支持研究基础设施。我们评估了可用工具，在一个目录（BiobankApps）中对它们进行了描述，并在一个以用例驱动的参考工具箱（BIBBOX）中为生物样本库提供了一系列工具。在BiobankApps工具目录中，包含了与生物样本库领域相关的商业和开源软件解决方案，并进行了分类和评估。评估内容包括：1）经过认证的用户进行“用户评价”；2）领域专家：由BBMRI成员进行快速分析；3）领域专家：使用真实世界数据进行详细分析和测试安装。该评估还结合了对更多“先进”（从技术角度来看）生物样本库的调查，以了解当前使用的工具，并总结各个软件包已知的优点/缺点。在第二步中，我们针对特定用例推荐工具，并在BIBBOX框架中进行安装、配置和连接。这项服务还基于英国现有的工作，旨在确定不同利益相关者参与的动机，从而根据研究社区内的需求和支持水平协助确定用例的优先级。与一个用例相关的所有工具都作为BIBBOX应用程序提供（从技术上讲，这是通过docker容器实现的），这些应用程序在BIBBOX框架中通过中央标识和用户管理进行集成。在未来的工作中，我们计划与其他网络分享所获得的知识，开发一个应用程序编程接口（API），用于与其他工具目录交换元数据，并致力于构建一个用于评估生物样本库软件的本体。
