European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK.
State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences Beijing, 102206 Beijing, China.
Nucleic Acids Res. 2020 Jul 2;48(W1):W380-W384. doi: 10.1093/nar/gkaa326.
The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.
《组学发现索引》是一个开源平台，可用于访问、发现和传播组学数据集。OmicsDI 整合了蛋白质组学、基因组学、代谢组学、模型和转录组学数据集。利用高效的索引系统，OmicsDI 整合了不同的生物实体，包括基因、转录本、蛋白质、代谢物以及来自 PubMed 的相应文献。此外，它还实现了一组管道，通过跟踪每个数据集报告的引文数量、重新分析和生物实体，来评估每个数据集的影响。在这里，我们介绍了 OmicsDI 的 REST 接口（www.omicsdi.org/ws/），以实现对 OmicsDI 中任何数据集或特定提供方（数据库）的所有数据集的编程访问。客户端可以使用不同的元数据信息（例如样本详细信息（物种、组织等）、仪器（质谱仪、测序仪）、关键字和其他提供的注释）在 API 上执行查询。此外，我们还在 R 和 Python 中提供了两个不同的库，以方便开发可以与 OmicsDI REST 接口进行编程交互的工具。
