From the evaluation of existing solutions to an all-inclusive package for biobanks
From the evaluation of existing solutions to an all-inclusive package for biobanks
复制标题
DOI：
10.1007/s12553-016-0175-x
复制
发表时间：
2017-03-01
影响因子：
2.5
通讯作者：
Dagher, George
中科院分区：
文献类型：
--
作者：
Mueller, Heimo;Malservet, Nicolas;Dagher, George
生物库领域经历了许多阶段，因此有广泛的商业和开源软件解决方案可用。这些软件工具的使用需要不同水平的领域和技术技能，用于安装，配置和最终使用这些生物库软件工具。为了增加这种复杂性，生物库社区需要共同努力，以分享知识并共同构建解决方案，以支持研究基础设施。我们已经评估了可用的工具，在目录（BiobankApps）中描述了它们，并在参考工具箱（BIBBOX）中选择了可用于生物库的工具，这些工具是用例驱动的。在BiobankApps工具目录中，包括与生物库领域相关的商业和开源软件解决方案，并对其进行分类和评估。评价内容包括：1）由认证用户进行“用户评审”2）领域专家：由BBMRI成员进行快速分析和3）领域专家：使用真实的世界数据进行详细分析和测试安装。该评估与对更“先进”（从技术角度）生物库的调查相结合，以调查目前使用的工具，并总结各自软件包的已知优点/缺点。在第二步中，我们推荐用于特定用例的工具，并在BIBBOX框架中安装、配置和连接这些工具。这项服务还建立在联合王国现有工作的基础上，寻求建立不同利益攸关方参与的动机，从而根据研究界的需求和支持水平帮助确定用例的优先顺序。与用例相关的所有工具都可以作为BIBBOX应用程序使用（从技术上讲，这是通过Docker容器实现的），这些应用程序集成在BIBBOX框架中，具有中央识别和用户管理功能。在未来的工作中，我们计划与其他网络共享所获得的知识，开发一个应用程序可编程接口（API）的元数据与其他工具目录的交换和工作的本体生物库软件的评估。
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.