Remizovschi Alexei, Carpa Rahela
Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Cluj, Romania.
PeerJ. 2021 Nov 9;9:e12463. doi: 10.7717/peerj.12463. eCollection 2021.
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.
泥火山是自然形成的碳氢化合物温床，会持续排放甲烷，加剧全球变暖。它们拥有适应碳氢化合物氧化的微生物群落。鉴于其研究价值，泥火山在微生物学领域仍是一个小众话题，且被以碳氢化合物为导向的研究所忽视。所有关于泥火山的数据都是零散和分散的。为缓解这一问题，我们构建了一个定制的自然语言处理管道（muddy_mine），并从开放获取的文章中收集了所有可用的泥火山数据。基于这些数据，我们构建了muddy_db数据库。muddy_db是第一个以生物学为导向的数据库，呈现为一个用户友好的网络应用程序。该数据库包含所有相关的泥火山数据，从微生物分类到碳氢化合物的存在和地质情况。muddy_mine和muddy_db工具遵循GPLv3许可。muddy_db R Shiny网络应用程序：https://muddy-db.shinyapps.io/muddy_db/ muddy_db R包：https://github.com/TracyRage/muddy_db muddy_mine Conda包：https://github.com/TracyRage/muddy_mine
