Skip to contents

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.

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

Have you used webchem in your work? Please let us know by opening an issue or making a pull request to edit this section!

  • Allaway RJ, La Rosa S, Guinney J, Gosline SJC (2018) Probing the chemical–biological relationship space with the Drug Target Explorer. Journal of Cheminformatics 10:41. https://doi.org/10.1186/s13321-018-0297-4
  • Bergmann AJ, Points GL, Scott RP, et al (2018) Development of quantitative screen for 1550 chemicals with GC-MS. Anal Bioanal Chem 410:3101–3110. https://doi.org/10.1007/s00216-018-0997-7
  • Brokl M, Morales V, Bishop L, et al (2019) Comparison of Mainstream Smoke Composition from CR20 Resin Filter and Empty-Cavity Filter Cigarettes by Headspace SPME Coupled with GC×GC TOFMS and Chemometric Analysis. Beiträge zur Tabakforschung International/Contributions to Tobacco Research 28:231–249. https://doi.org/10.2478/cttr-2019-0004
  • Münch D, Galizia CG (2016) DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses. Scientific Reports 6:21841. https://doi.org/10.1038/srep21841

Citation

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

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.

Meta