F1000Research (Aug 2022)
Sherlock: an open-source data platform to store, analyze and integrate Big Data for computational biologists [version 2; peer review: 2 approved]
Abstract
In the era of Big Data, data collection underpins biological research more than ever before. In many cases, this can be as time-consuming as the analysis itself. It requires downloading multiple public databases with various data structures, and in general, spending days preparing the data before answering any biological questions. Here, we introduce Sherlock, an open-source, cloud-based big data platform (https://earlham-sherlock.github.io/) to solve this problem. Sherlock provides a gap-filling way for computational biologists to store, convert, query, share and generate biology data while ultimately streamlining bioinformatics data management. The Sherlock platform offers a simple interface to leverage big data technologies, such as Docker and PrestoDB. Sherlock is designed to enable users to analyze, process, query and extract information from extremely complex and large data sets. Furthermore, Sherlock can handle different structured data (interaction, localization, or genomic sequence) from several sources and convert them to a common optimized storage format, for example, the Optimized Row Columnar (ORC). This format facilitates Sherlock’s ability to quickly and efficiently execute distributed analytical queries on extremely large data files and share datasets between teams. The Sherlock platform is freely available on GitHub, and contains specific loader scripts for structured data sources of genomics, interaction and expression databases. With these loader scripts, users can easily and quickly create and work with specific file formats, such as JavaScript Object Notation (JSON) or ORC. For computational biology and large-scale bioinformatics projects, Sherlock provides an open-source platform empowering data management, analytics, integration and collaboration through modern big data technologies.
