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BioSamples 数据库：更新的样本元数据中心。

BioSamples database: an updated sample metadata hub.

机构信息

EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK.

出版信息

Nucleic Acids Res. 2019 Jan 8;47(D1):D1172-D1178. doi: 10.1093/nar/gky1061.

DOI:10.1093/nar/gky1061
PMID:30407529
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6323949/
Abstract

The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources. BioSamples has recently undergone major changes, both in terms of data content and supporting infrastructure. The data content has more than doubled from around 2 million samples in 2014 to just over 5 million samples in 2018. Fast, reciprocal data exchange was fully established between sister Biosample databases and other INSDC partners, enabling a worldwide common representation and centralization of sample metadata. The BioSamples platform has been upgraded to accommodate anticipated increases in the number of submissions via GA4GH driver projects such as the Human Cell Atlas and the EGA, as well as from mirroring of NCBI dbGaP data. The BioSamples database is now the authoritative repository for all INSDC sample metadata, an ELIXIR Deposition Database for Biomolecular Data and the EMBL-EBI sample metadata hub. To support faster turnaround for sample submission, and to increase scalability and resilience, we have upgraded the BioSamples database backend storage, APIs and user interface. Finally, the website has been redesigned to allow search and retrieval of records based on specific filters, such as 'disease' or 'organism'. These changes are targeted at answering current use cases as well as providing functionalities for future emerging and anticipated developments. Availability: The BioSamples database is freely available at http://www.ebi.ac.uk/biosamples. Content is distributed under the EMBL-EBI Terms of Use available at https://www.ebi.ac.uk/about/terms-of-use.

摘要

EMBL-EBI 的 BioSamples 数据库为样本元数据存储提供了一个中央枢纽，并与 EMBL-EBI 的其他资源建立了链接。BioSamples 最近在数据内容和支持基础设施方面都发生了重大变化。数据内容从 2014 年的约 200 万个样本增加到 2018 年的 500 多万个样本。姐妹 BioSamples 数据库和其他 INSDC 合作伙伴之间已经完全建立了快速、相互的数据交换，实现了全球范围内样本元数据的共同表示和集中化。BioSamples 平台已经升级，以适应通过 GA4GH 驱动项目（如人类细胞图谱和 EGA）以及对 NCBI dbGaP 数据的镜像而预期增加的提交数量。BioSamples 数据库现在是 INSDC 所有样本元数据的权威存储库，是 ELIXIR 生物分子数据存储库和 EMBL-EBI 样本元数据中心。为了支持更快的样本提交周转时间，并提高可扩展性和弹性，我们已经升级了 BioSamples 数据库后端存储、API 和用户界面。最后，网站进行了重新设计，允许根据特定筛选器（如“疾病”或“生物体”）搜索和检索记录。这些变化旨在满足当前的用例，并为未来新兴和预期的发展提供功能。

可用性

BioSamples 数据库可免费在 http://www.ebi.ac.uk/biosamples 上获得。内容根据可在 https://www.ebi.ac.uk/about/terms-of-use 上获得的 EMBL-EBI 使用条款进行分发。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/d9b970e0f038/gky1061fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/694f66976f75/gky1061fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/0bb5d608692f/gky1061fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/d9b970e0f038/gky1061fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/694f66976f75/gky1061fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/0bb5d608692f/gky1061fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c324/6323949/d9b970e0f038/gky1061fig3.jpg

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