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 hydr...

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Autores principales:	Alexei Remizovschi, Rahela Carpa
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Mud volcano PAH Database Data mining Hydrocarbon Medicine R
Acceso en línea:	https://doaj.org/article/ffe7a3ff4c11482bbe70bc0ab144c05b
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id	oai:doaj.org-article:ffe7a3ff4c11482bbe70bc0ab144c05b
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spelling	oai:doaj.org-article:ffe7a3ff4c11482bbe70bc0ab144c05b2021-11-11T15:05:55ZBiologically-oriented mud volcano database: muddy_db10.7717/peerj.124632167-8359https://doaj.org/article/ffe7a3ff4c11482bbe70bc0ab144c05b2021-11-01T00:00:00Zhttps://peerj.com/articles/12463.pdfhttps://peerj.com/articles/12463/https://doaj.org/toc/2167-8359Mud 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.Alexei RemizovschiRahela CarpaPeerJ Inc.articleMud volcanoPAHDatabaseData miningHydrocarbonMedicineRENPeerJ, Vol 9, p e12463 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Mud volcano PAH Database Data mining Hydrocarbon Medicine R
spellingShingle	Mud volcano PAH Database Data mining Hydrocarbon Medicine R Alexei Remizovschi Rahela Carpa Biologically-oriented mud volcano database: muddy_db
description	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.
format	article
author	Alexei Remizovschi Rahela Carpa
author_facet	Alexei Remizovschi Rahela Carpa
author_sort	Alexei Remizovschi
title	Biologically-oriented mud volcano database: muddy_db
title_short	Biologically-oriented mud volcano database: muddy_db
title_full	Biologically-oriented mud volcano database: muddy_db
title_fullStr	Biologically-oriented mud volcano database: muddy_db
title_full_unstemmed	Biologically-oriented mud volcano database: muddy_db
title_sort	biologically-oriented mud volcano database: muddy_db
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/ffe7a3ff4c11482bbe70bc0ab144c05b
work_keys_str_mv	AT alexeiremizovschi biologicallyorientedmudvolcanodatabasemuddydb AT rahelacarpa biologicallyorientedmudvolcanodatabasemuddydb
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Biologically-oriented mud volcano database: muddy_db

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