README.Rmd

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# Webchem

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`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.

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