Biologically-oriented mud volcano database: muddy_db

PeerJ

article

Alexei Remizovschi¹  Rahela Carpa¹ 

[1] Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University

关键词: Mud volcano;    PAH;    Database;    Data mining;    Hydrocarbon;   

DOI  :  10.7717/peerj.12463

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY