MetaMiner: Streamlined GUI Tool for Retrieving, Normalizing and Exploring Metadata
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Summary
Over the past decade, publicly available genomic data has expanded exponentially. However, the usability of these genomes heavily depends on their associated metadata. Metadata provides context about the data that from where, when and how the data was obtained. When not consistent, it limits the re-usage of the available public data and prevents data’s integration into broader genomic analyses. Here, we introduce MetaMiner, a GUI tool designed to retrieve, normalize, and interactively visualize metadata associated with prokaryotic genomes. MetaMiner streamlines the normalization of key metadata elements such as geographical locations, isolation sources, and sequencing technologies. To assess its usability, we used metadata of Acinetobacter baumannii genomes and compared it with NCBI’s data processing tools and manually curated datasets. MetaMiner demonstrated superior performance in data transformation and showed high classification accuracy, with only minor discrepancies arising from recent geopolitical changes or ambiguous submissions. This cleaned and standardized metadata is integrated into an interactive dashboard, which allows users to explore data holistically through visualizations and custom filtering options. The dashboard has interactive plots related to submission date trend, geographical origins, sequencing methods, genome quality scores (e.g., ANI > 95, BUSCO > 95), coverage, etc. Overall, MetaMiner minimizes manual curation efforts of genomic metadata and enhances the accessibility, and re-usability of publicly available genomes.
Availability and Implementation
The executables and source code are both freely available to use at https://github.com/prekijpatel/MetaMiner for non-commercial use. Detailed documentation is available at https://github.com/prekijpatel/MetaMiner/wiki .
