Biologically-oriented mud volcano database: muddy_db

Mud volcanoes (MVs) are naturally occurring hydrocarbon hotbeds with continuous methane discharge, contributing to global warming. They host microbial communities adapted to hydrocarbon oxidation. Given their research value, MVs still represent a niche topic in microbiology and are neglected by hydrocarbon-oriented research. All the data regarding MVs is sporadic and decentralized. To mitigate this problem, we built a custom Natural Language Processing pipeline (muddy_mine), and collected all the available MV data from open-access articles. Based on this data, we built the muddy_db database. The muddy_db represents the first biologically oriented database rendered as a user-friendly web app. This database includes all the relevant MV data, ranging from microbial taxonomy to hydrocarbon occurrence and geology. The muddy_mine and muddy_db tools are licensed under the GPLv3. muddy_db R Shiny web app: https://muddy-db.shinyapps.io/muddy_db/ muddy_db R package: https://github.com/TracyRage/muddy_db muddy_mine Conda package: https://github. com/TracyRage/muddy_mine.

Automated summary

Mud volcanoes are natural hydrocarbon hotbeds with unique microbial communities, but current data is scattered. To address this, researchers have built the first biologically oriented database muddy_db and integrated mud volcano data using a custom Natural Language Processing pipeline muddy_mine.