README.Rmd

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output: github_document
bibliography: man/bibliography.bib 
---

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knitr::opts_chunk$set(
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# muddy_db <img src="man/figures/README-hex.png" align="right" alt="" width="120" />
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### 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](https://github.com/allenai/s2orc/)
database, [CC BY-NC 2.0, unmodified](https://creativecommons.org/licenses/by-nc/2.0/) by [@lo-wang-2020-s2orc]. We used [ScispaCy](https://github.com/allenai/scispacy)
[@neumann_2019_scispacy] models and [ETE3](https://github.com/etetoolkit/ete) [@cepas_2016]
library to check taxonomy-flavored tokens against [NCBI Taxonomy](ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/) database.  

Check muddy_db web app: [muddy_db](https://muddy-db.shinyapps.io/muddy_db/)

Check our mining pipeline: [muddy_mine](https://github.com/TracyRage/muddy_mine)

Check the published [PeerJ article](https://doi.org/10.7717/peerj.12463).

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')`

2. Run **muddy_db**

`muddy::run_app()`

### References