webchem

Chemical Information from the Web

https://github.com/ropensci/webchem

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
✓
Academic publication links
Links to: scholar.google, ncbi.nlm.nih.gov, rsc.org
✓
Committers with academic emails
2 of 17 committers (11.8%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary

Keywords

cas-number chemical-information chemspider identifier r r-package ropensci rstats webscraping

Keywords from Contributors

reproducibility open-science genome geocode air-pollution metagenomics caching taxize taxonomy bioinformatics

Last synced: 6 months ago · JSON representation

Repository

Chemical Information from the Web

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/webchem
Size: 3.91 MB

Statistics

Stars: 171
Watchers: 18
Forks: 44
Open Issues: 56
Releases: 19

Topics

cas-number chemical-information chemspider identifier r r-package ropensci rstats webscraping

Created almost 11 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
---


```{r echo=FALSE}
knitr::opts_chunk$set(
  warning = FALSE, 
  message = FALSE,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  cache = TRUE
)
```
# Webchem



[![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN](https://www.r-pkg.org/badges/version/webchem)](https://CRAN.R-project.org/package=webchem) 
[![R build status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/webchem/actions)
[![Coverage](https://codecov.io/github/ropensci/webchem/coverage.svg?branch=master)](https://app.codecov.io/gh/ropensci/webchem/branch/master) 
[![Downloads](https://cranlogs.r-pkg.org/badges/webchem)](https://cran.r-project.org/package=webchem)
[![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/webchem?color=blue)](https://cran.r-project.org/package=webchem)
[![DOI](https://img.shields.io/badge/DOI-10.18637%2Fjss.v093.i13-blue)](https://doi.org/10.18637/jss.v093.i13)



`webchem` is a R package to retrieve chemical information from  the web. 
This package interacts with a suite of web APIs to retrieve chemical information.

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore (`prefix_suffix()`).
They follow the format of `source_functionality`, with the exception of functions that retrieve database identifiers which follow the format of `get_identifier`. e.g.`cs_compinfo` uses ChemSpider to retrieve compound informations and `get_csid()` retrieves ChemSpider IDs.

## Chemical databases currently accessed by webchem

At least some of the data in the following sources is accesible through `webchem` functions.  To learn more about what is available, browse the documentation [here](https://docs.ropensci.org/webchem/reference/index.html).

- [BCPC Compendium of Pesticide Common Names](https://pesticidecompendium.bcpc.org) (formerly Alan Wood's Compendium of Pesticide Common Names)
- [ChEBI](https://www.ebi.ac.uk/chebi/)
- [Chemical Identifier Resolver (CIR)](https://cactus.nci.nih.gov/chemical/structure)
- [Chemical Translation Service (CTS)](http://cts.fiehnlab.ucdavis.edu/)
- [ChemSpider](https://www.chemspider.com/) (requires an [API token](https://developer.rsc.org/))
- [ETOX](http://webetox.uba.de/webETOX/index.do)
- [Flavornet](http://www.flavornet.org) 
- [NIST](https://webbook.nist.gov) (currently gas chromatography retention indices only)
- [OPSIN](https://www.ebi.ac.uk/opsin/)
- [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
- [U.S. EPA Substance Registry Service (SRS)](https://cdxnodengn.epa.gov/cdx-srs-rest/)
- [Wikidata](https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry)

#### API keys

Some ChemSpider functions require an API key. 
Please register at RSC (https://developer.rsc.org/) to retrieve an API key.

## Installation
#### Install from CRAN (stable version)

```{r install_cran, eval=FALSE}
install.packages("webchem")
```


#### Install from Github (development version)

```{r install_github, eval=FALSE}
install.packages("devtools")
library("devtools")
install_github("ropensci/webchem")
```

### Use Cases

See how `webchem` has been used or cited in literature [here](https://scholar.google.com/scholar?cites=14244442030948237605&as_sdt=40000005&sciodt=0,22&hl=en).

### Citation

If you use `webchem` in a publication, please cite our paper:

- Szöcs E, Stirling T, Scott ER, et al (2020) webchem: An R Package to Retrieve Chemical Information from the Web. J Stat Soft 93:. https://doi.org/10.18637/jss.v093.i13


### Acknowledgements
Without the fantastic web services `webchem` wouldn't be here. Therefore, kudos to the web service providers and developers! Please remember to acknowledge these data resources in your work using `webchem`.

### Want to contribute?

Check out our [contribution guide here](https://github.com/ropensci/webchem/blob/master/CONTRIBUTING.md).

### Meta

- Please [report any issues, bugs or feature requests](https://github.com/ropensci/webchem/issues).
- License: MIT
- Get citation information for `webchem` in R with `citation("webchem")`
- Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct/). By contributing to this project, you agree to abide by its terms.

[![ropensci](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

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GitHub Events

Total

Issues event: 11
Watch event: 8
Delete event: 1
Issue comment event: 22
Push event: 3
Pull request review event: 2
Pull request review comment event: 2
Pull request event: 5
Fork event: 3
Create event: 1

Last Year

Issues event: 11
Watch event: 8
Delete event: 1
Issue comment event: 22
Push event: 3
Pull request review event: 2
Pull request review comment event: 2
Pull request event: 5
Fork event: 3
Create event: 1

Committers

Last synced: over 1 year ago

All Time

Total Commits: 1,343
Total Committers: 17
Avg Commits per committer: 79.0
Development Distribution Score (DDS): 0.59

Past Year

Commits: 19
Committers: 2
Avg Commits per committer: 9.5
Development Distribution Score (DDS): 0.316

Top Committers

Name	Email	Commits
edisz	e**s@g**m	550
stitam	s**s@g**m	361
Aariq	s**r@g**m	322
andreas	a**r@g**m	34
Ethan Bass	e**s@g**m	26
Johannes Ranke	j**e@u**e	14
Gordon Getzinger	g**r@d**u	7
Jan Stanstrup	s**p@g**m	6
Egon Willighagen	e**n@g**m	5
jvfe	j**v@g**m	5
Tamás Stirling	4****m	5
Dahaniel	d**l@m**o	3
BrianFFish	b**r@g**m	1
Maëlle Salmon	m**n@y**e	1
Eduard Szöcs	E****D	1
Johannes Ranke	j**e@j**e	1
rOpenSci Bot	m**t@g**m	1

Committer Domains (Top 20 + Academic)

jrwb.de: 1 muench.bio: 1 duke.edu: 1 uni-bremen.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 73
Total pull requests: 57
Average time to close issues: 6 months
Average time to close pull requests: 20 days
Total issue authors: 30
Total pull request authors: 9
Average comments per issue: 3.48
Average comments per pull request: 1.67
Merged pull requests: 51
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 4
Average time to close issues: 3 days
Average time to close pull requests: about 11 hours
Issue authors: 2
Pull request authors: 2
Average comments per issue: 1.75
Average comments per pull request: 1.5
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

Aariq (18)
stitam (16)
andschar (4)
wanglu2014 (4)
eduardszoecs (4)
Ellakai (2)
maelle (2)
QizhiSu (2)
MjelleLab (1)
cujoisa (1)
f-puig (1)
CesarIsguerra (1)
pstahlhofen (1)
schymane (1)
c1au6i0 (1)

Pull Request Authors

stitam (35)
Aariq (12)
ethanbass (3)
maelle (2)
AlexisBrgn (2)
jranke (2)
gjgetzinger (1)
BrianFFish (1)
andschar (1)

Top Labels

Issue Labels

bug (14) enhancement (9) data source (5) consistent api (5) low priority (2) help wanted (1) good first issue (1) question (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- cran 1,800 last-month
Total docker downloads: 134,988

Total dependent packages: 6
(may contain duplicates)
Total dependent repositories: 16
(may contain duplicates)
Total versions: 36
Total maintainers: 1

cran.r-project.org: webchem

Chemical Information from the Web

Homepage: https://docs.ropensci.org/webchem/
Documentation: http://cran.r-project.org/web/packages/webchem/webchem.pdf
License: MIT + file LICENSE
Latest release: 1.3.1
published 7 months ago

Versions: 20
Dependent Packages: 6
Dependent Repositories: 16
Downloads: 1,800 Last month
Docker Downloads: 134,988

Rankings

Forks count: 1.7%

Stargazers count: 2.7%

Dependent repos count: 7.1%

Dependent packages count: 7.3%

Average: 9.3%

Downloads: 14.6%

Docker downloads count: 22.2%

Maintainers (1)

stirling.tamas@gmail.com

Last synced: 6 months ago

proxy.golang.org: github.com/ropensci/webchem

Documentation: https://pkg.go.dev/github.com/ropensci/webchem#section-documentation
License: other
Latest release: v1.3.1
published 7 months ago

Versions: 16
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.0 depends
base64enc * imports
data.tree * imports
dplyr * imports
httr * imports
jsonlite * imports
methods * imports
purrr * imports
rlang * imports
rvest * imports
stringr * imports
tibble * imports
utils * imports
xml2 * imports
covr * suggests
knitr * suggests
plot.matrix * suggests
rcdk * suggests
rmarkdown * suggests
robotstxt * suggests
testthat * suggests
usethis * suggests
vcr * suggests

.github/workflows/R-CMD-check.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/check-pkgdown.yml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r v2 composite