README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
---
<!-- README.md is generated from README.Rmd. Please edit that file -->

```{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

```{r coverage, echo=FALSE}
Sys.setenv(NOT_CRAN = "true")
cov <- covr::package_coverage()
pct <- covr::percent_coverage(cov)
pct_label <- sprintf("%.1f%%", pct)
  
# Choose badge color based on coverage
col <- if (pct >= 90) {
  "brightgreen"
  } else if (pct >= 75) {
    "yellow"
  } else if (pct >= 50) {
    "orange"
  } else {
    "red"
  }
  
badge_url <- sprintf(
  "https://img.shields.io/badge/coverage-%s-%s",
  URLencode(pct_label),
  col
)
```

<!-- badges: start -->

[![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![CRAN](https://www.r-pkg.org/badges/version/webchem)](https://CRAN.R-project.org/package=webchem)
[![R-multiverse status](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fcommunity.r-multiverse.org%2Fapi%2Fpackages%2Fwebchem&query=%24.Version&label=r-multiverse)](https://community.r-multiverse.org/webchem) 
[![R build status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/webchem/actions)
```{r coverage-badge, echo=FALSE, results='asis'}
cat(sprintf("[![Coverage](%s)](#test-coverage)\n\n", badge_url))
```
[![Downloads](https://cranlogs.r-pkg.org/badges/webchem)](https://cran.r-project.org/package=webchem)
[![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/webchem?color=blue)](https://cran.r-project.org/package=webchem)
[![DOI](https://img.shields.io/badge/DOI-10.18637%2Fjss.v093.i13-blue)](https://doi.org/10.18637/jss.v093.i13)

<!-- badges: end -->

`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).


```{r databases-table, echo=FALSE, results='asis'}
databases <- tibble::tribble(
  ~Database, ~Webservice, ~Offline,
  "[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/)", "✅", "❌",
  "[ChEMBL](https://www.ebi.ac.uk/chembl/)", "✅", "✅",
  "[Chemical Identifier Resolver (CIR)](https://cactus.nci.nih.gov/chemical/structure)", "✅", "❌",
  "[Chemical Translation Service (CTS)](http://cts.fiehnlab.ucdavis.edu/)", "✅", "❌",
  "[ChemSpider](https://www.chemspider.com/) (requires an [API token](https://developer.rsc.org/))", "✅", "❌",
  "[ETOX](http://webetox.uba.de/webETOX/index.do)", "✅", "❌",
  "[EU Pesticides](https://food.ec.europa.eu/plants/pesticides/eu-pesticides-database_en)",  "❌", "✅",
  "[Flavornet](http://www.flavornet.org)", "✅", "❌",
  "[FooDB](https://foodb.ca/)", "❌", "✅",
  "[NIST](https://webbook.nist.gov) (currently gas chromatography retention indices only)", "✅", "❌",
  "[OPSIN](https://www.ebi.ac.uk/opsin/)", "✅", "❌",
  "[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)", "✅", "❌"
)

knitr::kable(databases)
```

#### Offline access

For databases that support it (marked ✅ in the Offline column), `webchem` can download the database and then query it locally. Offline queries are faster, work without an internet connection, and return the same results every time, making your analyses more reproducible.

#### 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.

[![ropensci](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)