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https://github.com/ropensci/webchem
Chemical Information from the Web
https://github.com/ropensci/webchem
cas-number chemical-information chemspider identifier r r-package ropensci rstats webscraping
Last synced: 3 months ago
JSON representation
Chemical Information from the Web
- Host: GitHub
- URL: https://github.com/ropensci/webchem
- Owner: ropensci
- License: other
- Created: 2015-03-05T14:41:50.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-02-18T20:43:21.000Z (9 months ago)
- Last Synced: 2024-07-25T13:28:12.522Z (3 months ago)
- Topics: cas-number, chemical-information, chemspider, identifier, r, r-package, ropensci, rstats, webscraping
- Language: R
- Homepage: https://docs.ropensci.org/webchem
- Size: 3.93 MB
- Stars: 160
- Watchers: 19
- Forks: 40
- Open Issues: 55
-
Metadata Files:
- Readme: README.Rmd
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
---
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
[](https://www.repostatus.org/#active)
[](https://CRAN.R-project.org/package=webchem)
[](https://github.com/ropensci/webchem/actions)
[](https://app.codecov.io/gh/ropensci/webchem/branch/master)
[](https://cran.r-project.org/package=webchem)
[](https://cran.r-project.org/package=webchem)
[](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](http://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](http://opsin.ch.cam.ac.uk/instructions.html)
- [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.
[](https://ropensci.org)