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.

Fill out the survey!

Do you use chemical information databases in your work? Help us help you by filling out our short survey at https://forms.gle/V7dfGGn73dkesn5L6.

The webchem survey allows us to learn which databases you use and how you interact with chemical data. This is extremely valuable information for us and guides our development efforts. The survey takes about 5 minutes to fill out.

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.

Alan Wood’s Compendium of Pesticide Common Names
ChEBI
Chemical Identifier Resolver (CIR)
Chemical Translation Service (CTS)
ChemIDplus
ChemSpider (requires an API token)
ETOX
Flavornet
NIST (currently gas chromatography retention indices only)
OPSIN
PAN Pesticide Database
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

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

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.

Related Projects

You can find some related packages in the ChemPhys CRAN Task View

If you’re more familiar with Python you should check out Matt Swains repositories: ChemSpiPy, PubChemPy and CirPy provide similar functionality as webchem.

Want to contribute?

Check out our contribution guide here.

About

Chemical Information from the Web

https://docs.ropensci.org/webchem

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