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The rapid growth in biological sequence data is revolutionizing ourunderstanding of genotypic diversity and challenging conventional approaches toinformatics. With the increasing availability of genomic data, traditionalbioinformatic tools require substantial computational time and the creation ofever-larger indices each time a researcher seeks to gain insight from the data.To address these challenges, we pre-computed important relationships betweenbiological entities spanning the Central Dogma of Molecular Biology andcaptured this information in a relational database. The database can be queriedacross hundreds of millions of entities and returns results in a fraction ofthe time required by traditional methods. In this paper, we describe\textit{IBM Functional Genomics Platform} (formerly known as OMXWare), acomprehensive database relating genotype to phenotype for bacterial life.Continually updated, IBM Functional Genomics Platform today contains dataderived from 200,000 curated, self-consistently assembled genomes. The databasestores functional data for over 68 million genes, 52 million proteins, and 239million domains with associated biological activity annotations from GeneOntology, KEGG, MetaCyc, and Reactome. IBM Functional Genomics Platform mapsall of the many-to-many connections between each biological entity includingthe originating genome, gene, protein, and protein domain. Various microbialstudies, from infectious disease to environmental health, can benefit from therich data and connections. We describe the data selection, the pipeline tocreate and update the IBM Functional Genomics Platform, and the developer tools(Python SDK and REST APIs) which allow researchers to efficiently studymicrobial life at scale.

IBM Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale