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Webchem

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.

BCPC Compendium of Pesticide Common Names (formerly Alan Wood’s Compendium of Pesticide Common Names)
ChEBI
Chemical Identifier Resolver (CIR)
Chemical Translation Service (CTS)
ChemSpider (requires an API token)
ETOX
Flavornet
NIST (currently gas chromatography retention indices only)
OPSIN
PubChem
U.S. EPA Substance Registry Service (SRS)
Wikidata

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)

install.packages("webchem")

Install from Github (development version)

install.packages("devtools")
library("devtools")
install_github("ropensci/webchem")

Use Cases

See how webchem has been used or cited in literature here.

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.