Abstract

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes.

中文翻译：

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从ArrayExpress到BioStudies

摘要

ArrayExpress（https://www.ebi.ac.uk/arrayexpress）是EMBL-EBI的功能基因组学数据的档案，该档案成立于2002年，最初是与出版物相关的微阵列数据的档案，后来扩展为接受测序。基础数据。在过去的十年中，越来越多的生物学实验涉及多种技术，这些技术可以测定表观遗传学以及RNA和蛋白质表达等不同的生物学模式，因此建立了BioStudies数据库（https://www.ebi.ac.uk/biostudies）处理此类多模式数据。它的中心概念是研究，通常与出版物关联。BioStudies存储描述研究的元数据，提供到相关数据库的链接，例如欧洲核苷酸档案库（ENA），并托管不存在专门数据库的数据类型。随着BioStudies现已全面运行，我们能够进一步协调EMBL-EBI的档案数据基础架构，并且ArrayExpress正在迁移到BioStudies。将来，所有功能基因组学数据都将保存在BioStudies中。对于用户而言，该过程将是无缝的，他们将继续使用在线工具Annotare提交数据，并且将能够以基本上与以前相同的方式查询和下载数据。但是，某些技术方面，尤其是程序访问将发生变化。此更新将指导用户进行这些更改。