Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
Nucleic Acids Res. 2018 Jan 4;46(D1):D794-D801. doi: 10.1093/nar/gkx1081.
The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.
DNA 元件百科全书 (ENCODE) 数据协调中心开发了 ENCODE 门户数据库和网站，作为 ENCODE 联盟生成的数据和元数据的来源。有两个原则推动了设计。首先，实验方案、分析程序和数据本身应通过一致的基于网络的搜索和下载界面公开提供。其次，相同的界面应提供精心策划的元数据，记录数据的出处，并根据其在生物学方面的解释进行证明。自 2013 年首次发布以来，并根据联盟成员和使用门户访问 ENCODE 数据的更广泛科学界的建议，该门户已定期更新，以更好地反映这些设计原则。在这里，我们报告了这些更新，包括新实验的结果、来自其他项目的统一处理数据、新的可视化工具以及更全面的元数据来描述实验和分析。此外，该门户现在还包含了来自相关项目的元（数据），包括基因调控的基因组学、表观基因组计划、模式生物 ENCODE（modENCODE）和 modERN。该门户现在提供了超过 13000 个数据集及其附带的元数据，可在以下网址访问：https://www.encodeproject.org/。
