The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks to gain insight from the data. To address these challenges, we pre-computed important relationships between biological entities spanning the Central Dogma of Molecular Biology and captured this information in a relational database. The database can be queried across hundreds of millions of entities and returns results in a fraction of the time required by traditional methods. In this paper, we describe Functional Genomics Platform (formerly known as OMXWare), a comprehensive database relating genotype to phenotype for bacterial life. Continually updated, the Functional Genomics Platform today contains data derived from 200,000 curated, self-consistently assembled genomes. The database stores functional data for over 68 million genes, 52 million proteins, and 239 million domains with associated biological activity annotations from Gene Ontology, KEGG, MetaCyc, and Reactome. The Functional Genomics Platform maps all of the many-to-many connections between each biological entity including the originating genome, gene, protein, and protein domain. Various microbial studies, from infectious disease to environmental health, can benefit from the rich data and connections. We describe the data selection, the pipeline to create and update the Functional Genomics Platform, and the developer tools (Python SDK and REST APIs)which allow researchers to efficiently study microbial life at scale.

中文翻译：

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功能基因组学平台，一个基于云的大规模研究微生物生命的平台


生物序列数据的快速增长正在彻底改变我们对基因型多样性的理解，并对传统的信息学方法提出挑战。随着基因组数据的可用性不断增加，传统的生物信息学工具需要大量的计算时间，并且每次研究人员试图从数据中获得洞察力时都需要创建更大的索引。为了应对这些挑战，我们预先计算了跨越分子生物学中心法则的生物实体之间的重要关系，并将这些信息捕获到关系数据库中。该数据库可以查询数亿个实体，并只需要传统方法所需时间的一小部分即可返回结果。在本文中，我们描述了功能基因组学平台（以前称为 OMXWare），这是一个将细菌生命的基因型与表型相关联的综合数据库。功能基因组学平台不断更新，如今包含来自 200,000 个精心策划、自洽组装的基因组的数据。该数据库存储了超过 6800 万个基因、5200 万个蛋白质和 2.39 亿个结构域的功能数据，以及来自 Gene Ontology、KEGG、MetaCyc 和 Reactome 的相关生物活性注释。功能基因组学平台绘制了每个生物实体之间的所有多对多连接，包括原始基因组、基因、蛋白质和蛋白质结构域。从传染病到环境健康的各种微生物研究都可以从丰富的数据和联系中受益。我们描述了数据选择、创建和更新功能基因组学平台的流程以及开发人员工具（Python SDK 和 REST API），这些工具使研究人员能够有效地大规模研究微生物生命。