Metadata management for high content screening in OMERO.
Metadata management for high content screening in OMERO.
复制标题
元数据管理用于OMERO的高素质筛选。
DOI：
10.1016/j.ymeth.2015.10.006
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发表时间：
2016-03-01
期刊：
影响因子：
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通讯作者：
Swedlow JR
中科院分区：
文献类型：
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作者：
Li S;Besson S;Blackburn C;Carroll M;Ferguson RK;Flynn H;Gillen K;Leigh R;Lindner D;Linkert M;Moore WJ;Ramalingam B;Rozbicki E;Rustici G;Tarkowska A;Walczysko P;Williams E;Allan C;Burel JM;Moore J;Swedlow JR
HCS 数据管理因其规模、复杂性和异构性而具有挑战性。 OMERO 和 Bio-Formats 是用于大规模数据访问和管理的开源工具。 OMERO 和 Bio-Formats 可以处理图像、实验元数据和分析输出。集成多个基于图像的研究的存储库提供了对数据集成价值的测试。高内容筛选 (HCS) 实验带来了经典的数据管理挑战——必须集成和链接多个大型异构结构化和非结构化数据，以产生一组“最终”结果。这些不同的数据包括图像、试剂、实验方案、分析输出和表型，所有这些数据都必须被存储、链接并可供用户、科学家、合作者以及更广泛的社区（在适当情况下）访问。 OME 联盟构建了多个开源工具来管理、链接和共享这些不同类型的数据。 OME数据模型是一种元数据规范，支持HCS实验中记录的图像数据和元数据。 Bio-Formats 是一个 Java 库，可读取记录的图像数据和元数据，并支持多种 HCS 筛选系统。 OMERO 是一款企业数据管理应用程序，集成了图像数据、实验和分析元数据，并使其可用于可视化、挖掘、共享和下游分析。我们讨论 Bio-Formats 和 OMERO 如何处理这些不同的数据类型，以及如何使用它们来集成、链接和共享设施和公共数据存储库中的 HCS 实验。 OME 规范和软件是开源的，可从 https://www.openmicroscopy.org 获取。
HCS data management is challenging due to its scale, complexity and heterogeneity. OMERO and Bio-Formats are open-source tools for data access and management at scale. OMERO and Bio-Formats can handle images, experimental metadata and analytic outputs. Repositories integrating multiple image-based studies provide tests of the value of data integration. High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org.