recotox
REcoTox is a semi-automated, interactive R workflow to process US EPA ECOTOX Knowledgebase entire database ASCII files
Science Score: 67.0%
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✓codemeta.json file
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Found 3 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary
Keywords
Repository
REcoTox is a semi-automated, interactive R workflow to process US EPA ECOTOX Knowledgebase entire database ASCII files
Basic Info
Statistics
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 16
- Releases: 3
Topics
Metadata Files
README.md
Background
The search and extraction of experimental ecotoxicological information is often a tedious work. A good and comprehensive data source is the US EPA ECOTOX Knowledgebase. It contains about 1 million data points for more than 12,000 chemicals and 13,000 single species. However, for a high-throughput hazard assessment, it is not possible to extract all relevant data of the online database The purpose of REcoTox is to extract the relevant information and to aggregate the data based on the user criteria out of the entire database ASCII files.
Introduction
REcoTox is a semi-automated, interactive workflow to process US EPA ECOTOX Knowledgebase entire database ASCII files to extract and process ecotoxicological data relevant (but not restricted) to the ecotoxicity groups algae, crustaceans, and fish in the aquatic domain. The latest version of the ASCII files is available on US EPA ECOTOX Knowledgebase. The focus is aquatic ecotoxicity and the unit of the retrieved data is mg/L.
Requirements
REcoTox expects an R version >4.3.0. Please install additionally the R packages Tidyverse, data_table, EnvStats, and webchem.
Installation
For use of REcoTox, install it from GitHub, please.
To install the latest stable version (0.4.0):
remotes::install_github("tsufz/recotox@0.4.0", build = TRUE, build_manual = TRUE)
To install the latest beta version (main):
remotes::install_github("tsufz/recotox@main", build = TRUE, build_manual = TRUE)
To install the latest development version (dev):
remotes::install_github("tsufz/recotox@dev", build = TRUE, build_manual = TRUE)
Workflow
The file Query_Ecotox_DB.R contains the workflow and loads all relevant packages and functions. The workflows allows to filter for endpoints, measurements, and species. The ecotoxicity data is interactivitely enriched with chemical information (e.g. the average mass). In best case with data linked to US EPA CompTox Chemicals Dashboard for example by using the output of the batch search according to Figure 1 and Figure 2.
At least, the molecular weight or average mass is required for the recalculation of the water concentrations from molar to milligrams. The main purpose of this workflow is to generate data for the hazard assessment of chemical pressures to aquatic organisms. Thus, only relevant data is aggregated and all data is calculated to mg/L.
The data output contains long pivot tables containing all filtered datasets as the basis of further data processing and aggregation for the users' purposes. But it includes also a further pivoting step to wider pivot tables containing aggregated information, e.g. the geomean and the 5-percentile of the extracted data for each chemical, endpoint, and species.
Note
This workflow will be further developed. Contributions and suggestions are welcome. Please create an issue to initialize the discussion.
Owner
- Name: Tobias Schulze
- Login: tsufz
- Kind: user
- Location: Leipzig (Germany
- Company: Helmholtz Centre for Environmental Research - UFZ
- Website: http://www.ufz.de/index.php?en=40500
- Repositories: 34
- Profile: https://github.com/tsufz
Facilitating open mass spectral information exchange and doing research at Helmholtz Centre for Environmental Research in Leipzig, Germany.
Citation (CITATION.cff)
# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
cff-version: 1.2.0
message: 'To cite package "REcoTox" in publications use:'
type: software
title: 'REcoTox: REcoTox - a workflow to process US EPA ECOTOX Knowledgebase ASCII
files'
version: 0.4.1
abstract: REcoTox is a semi-automated, interactive workflow to process US EPA ECOTOX
Knowledgebase entire database ASCII files to extract and process ecotoxicological
data relevant (but not restricted) to the ecotoxicity groups algae, crustaceans,
and fish in the aquatic domain. The latest version of the ASCII files is available
on US EPA ECOTOX Knowledgebase. The focus is aquatic ecotoxicity and the unit of
the retrieved data is mg/L.
authors:
- family-names: Schulze
given-names: Tobias
email: tsufz1@gmail.com
orcid: https://orcid.org/0000-0002-9744-8914
repository: https://bioconductor.org/
date-released: '2023-05-02'
contact:
- family-names: Schulze
given-names: Tobias
email: tsufz1@gmail.com
orcid: https://orcid.org/0000-0002-9744-8914
references:
- type: software
title: 'R: A Language and Environment for Statistical Computing'
notes: Depends
url: https://www.R-project.org/
authors:
- name: R Core Team
location:
name: Vienna, Austria
year: '2023'
institution:
name: R Foundation for Statistical Computing
version: '>= 4.3.0'
- type: software
title: data.table
abstract: 'data.table: Extension of `data.frame`'
notes: Imports
url: https://r-datatable.com
repository: https://CRAN.R-project.org/package=data.table
authors:
- family-names: Dowle
given-names: Matt
email: mattjdowle@gmail.com
- family-names: Srinivasan
given-names: Arun
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year: '2023'
- type: software
title: dplyr
abstract: 'dplyr: A Grammar of Data Manipulation'
notes: Imports
url: https://dplyr.tidyverse.org
repository: https://CRAN.R-project.org/package=dplyr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
orcid: https://orcid.org/0000-0003-4757-117X
- family-names: François
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orcid: https://orcid.org/0000-0002-2444-4226
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- family-names: Müller
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orcid: https://orcid.org/0000-0002-1416-3412
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given-names: Davis
email: davis@posit.co
orcid: https://orcid.org/0000-0003-4777-038X
year: '2023'
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title: progress
abstract: 'progress: Terminal Progress Bars'
notes: Imports
url: https://github.com/r-lib/progress#readme
repository: https://CRAN.R-project.org/package=progress
authors:
- family-names: Csárdi
given-names: Gábor
- family-names: FitzJohn
given-names: Rich
year: '2023'
- type: software
title: purrr
abstract: 'purrr: Functional Programming Tools'
notes: Imports
url: https://purrr.tidyverse.org/
repository: https://CRAN.R-project.org/package=purrr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
orcid: https://orcid.org/0000-0003-4757-117X
- family-names: Henry
given-names: Lionel
email: lionel@rstudio.com
year: '2023'
- type: software
title: Rdpack
abstract: 'Rdpack: Update and Manipulate Rd Documentation Objects'
notes: Imports
url: https://geobosh.github.io/Rdpack/
repository: https://CRAN.R-project.org/package=Rdpack
authors:
- family-names: Boshnakov
given-names: Georgi N.
email: georgi.boshnakov@manchester.ac.uk
year: '2023'
- type: software
title: readr
abstract: 'readr: Read Rectangular Text Data'
notes: Imports
url: https://readr.tidyverse.org
repository: https://CRAN.R-project.org/package=readr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Hester
given-names: Jim
- family-names: Bryan
given-names: Jennifer
email: jenny@posit.co
orcid: https://orcid.org/0000-0002-6983-2759
year: '2023'
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abstract: 'tibble: Simple Data Frames'
notes: Imports
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repository: https://CRAN.R-project.org/package=tibble
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orcid: https://orcid.org/0000-0002-1416-3412
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
year: '2023'
- type: software
title: tidyr
abstract: 'tidyr: Tidy Messy Data'
notes: Imports
url: https://tidyr.tidyverse.org
repository: https://CRAN.R-project.org/package=tidyr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
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year: '2023'
- type: software
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abstract: 'R: A Language and Environment for Statistical Computing'
notes: Imports
authors:
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location:
name: Vienna, Austria
year: '2023'
institution:
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notes: Imports
url: https://docs.ropensci.org/webchem/
repository: https://CRAN.R-project.org/package=webchem
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notes: Suggests
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repository: https://bioconductor.org/
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notes: Suggests
url: https://github.com/r-lib/desc#readme
repository: https://CRAN.R-project.org/package=desc
authors:
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given-names: Gábor
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email: james.f.hester@gmail.com
year: '2023'
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
notes: Suggests
url: https://yihui.org/knitr/
repository: https://CRAN.R-project.org/package=knitr
authors:
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given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2023'
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abstract: 'markdown: Render Markdown with ''commonmark'''
notes: Suggests
url: https://github.com/rstudio/markdown
repository: https://CRAN.R-project.org/package=markdown
authors:
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email: xie@yihui.name
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notes: Suggests
url: https://pkgs.rstudio.com/rmarkdown/
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- family-names: Wickham
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- family-names: Cheng
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orcid: https://orcid.org/0000-0003-3925-190X
year: '2023'
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abstract: 'testthat: Unit Testing for R'
notes: Suggests
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repository: https://CRAN.R-project.org/package=testthat
authors:
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given-names: Hadley
email: hadley@posit.co
year: '2023'
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Tobias Schulze | t****e@u****e | 148 |
| Tobias Schulze | t****1@g****m | 9 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 2 years ago
All Time
- Total issues: 21
- Total pull requests: 5
- Average time to close issues: 21 days
- Average time to close pull requests: less than a minute
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.57
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 21
- Pull requests: 5
- Average time to close issues: 21 days
- Average time to close pull requests: less than a minute
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.57
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tsufz (21)
- pepijn-devries (1)
Pull Request Authors
- tsufz (4)