In TracyRage/muddy_db: muddy_db

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

muddy_db

Description

muddy_db represents a biologically-oriented mud volcano database. It aggregates mud volcano specific terminology and taxonomy, which were mined from open-access articles, available in the S2ORC database, CC BY-NC 2.0, unmodified by [@lo-wang-2020-s2orc]. We used ScispaCy [@neumann_2019_scispacy] models and ETE3 [@cepas_2016] library to check taxonomy-flavored tokens against NCBI Taxonomy database.

Check muddy_db web app: muddy_db

Check our mining pipeline: muddy_mine

Check the published PeerJ article.

Cite this work Remizovschi A, Carpa R. 2021. Biologically-oriented mud volcano database: muddy_db. PeerJ 9:e12463 https://doi.org/10.7717/peerj.12463.

Data

muddy_db includes the following data:

• Bacterial and archaeal taxonomy (phylum, class, order, family, genus)
• Chemistry (inorganic ions, hydrocarbons)
• Geology (geological periods, minerals)
• Mud volcano specific data (microbial consortia, metabolic pathways etc.)
• Methods (amplified genes, analytics)

Install locally

1. Install package

remotes::install_github('TracyRage/muddy_db')

1. Run muddy_db

muddy::run_app()

References

TracyRage/muddy_db documentation built on Nov. 28, 2021, 7:28 p.m.