cccapi

A ZeroPM R package

The goal of the cccapi package is to provide a minimal and lightweight interface to the CAS Common Chemistry API services. To get access to the API services, you need to register at https://www.cas.org/services/commonchemistry-api.

The dependencies of cccapi are kept at a bare minimum: curl for handling the API requests and jsonlite to parse data from JSON format.

Installation

You can install the development version of cccapi from GitHub with:

# install.packages("remotes")
remotes::install_github("ZeroPM-H2020/cccapi")

Examples

The following examples show the functionality of the three API functions of cccapi: get_detail(), get_export(), and get_search().

This is an example which shows you how to get the record details for a CAS Registry Number. In this case, for atrazine:

library(cccapi)
atz_det <- get_detail("1912-24-9")
str(atz_det)
#> List of 15
#>  $ uri                   : chr "substance/pt/1912249"
#>  $ rn                    : chr "1912-24-9"
#>  $ name                  : chr "Atrazine"
#>  $ image                 : chr "<svg width=\"181.11\" viewBox=\"0 0 6037 4324\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__
#>  $ inchi                 : chr "InChI=1S/C8H14ClN5/c1-4-10-7-12-6(9)13-8(14-7)11-5(2)3/h5H,4H2,1-3H3,(H2,10,11,12,13,14)"
#>  $ inchiKey              : chr "InChIKey=MXWJVTOOROXGIU-UHFFFAOYSA-N"
#>  $ smile                 : chr "N(C(C)C)C=1N=C(NCC)N=C(Cl)N1"
#>  $ canonicalSmile        : chr "ClC=1N=C(N=C(N1)NC(C)C)NCC"
#>  $ molecularFormula      : chr "C<sub>8</sub>H<sub>14</sub>ClN<sub>5</sub>"
#>  $ molecularMass         : chr "215.68"
#>  $ experimentalProperties:'data.frame':  2 obs. of  3 variables:
#>   ..$ name        : chr [1:2] "Melting Point" "Density"
#>   ..$ property    : chr [1:2] "175-177 °C" "1.23 g/cm<sup>3</sup> @ Temp: 22 °C"
#>   ..$ sourceNumber: int [1:2] 1 1
#>  $ propertyCitations     :'data.frame':  1 obs. of  3 variables:
#>   ..$ docUri      : chr ""
#>   ..$ sourceNumber: int 1
#>   ..$ source      : chr "Hazardous Substances Data Bank data were obtained from the National Library of Medicine (US)"
#>  $ synonyms              : chr [1:71] "1,3,5-Triazine-2,4-diamine, 6-chloro-<em>N</em><sup>2</sup>-ethyl-<em>N</em><sup>4</sup>-(1-methylethyl)-" "<em>s</em>-Triazine, 2-chloro-4-(ethylamino)-6-(isopropylamino)-" "1,3,5-Triazine-2,4-diamine, 6-chloro-<em>N</em>-ethyl-<em>N</em>â\200²-(1-methylethyl)-" "6-Chloro-<em>N</em><sup>2</sup>-ethyl-<em>N</em><sup>4</sup>-(1-methylethyl)-1,3,5-triazine-2,4-diamine" ...
#>  $ replacedRns           : chr [1:6] "11121-31-6" "12040-45-8" "12797-72-7" "39400-72-1" ...
#>  $ hasMolfile            : logi TRUE

Here is an example which shows you how to get the MOL file for a CAS Registry Number. In this case, again, for atrazine:

atz_exp <- get_export("1912-24-9")
str(atz_exp)
#>  chr "Atrazine\nC8H14ClN5\n1912-24-9 Copyright (C) 2021 ACS\n 14 14  0  0  0  0  0  0  0  0999 V2000\n    8.0021    0"| __truncated__

And finally, here is an example which shows you how to search for CAS Registry Numbers with a partial name. See ?get_search for details on the available search options!

atz_src <- get_search("atrazin*")
str(atz_src)
#> List of 2
#>  $ count  : int 12
#>  $ results:'data.frame': 12 obs. of  3 variables:
#>   ..$ rn   : chr [1:12] "1007-28-9" "1912-24-9" "2163-68-0" "39324-65-7" ...
#>   ..$ name : chr [1:12] "Deisopropylatrazine" "Atrazine" "Hydroxyatrazine" "1,3,5-Triazine-2,4-diamine, 6-chloro-<em>N</em>-ethyl-<em>N</em>â\200²-(1-methylethyl)-, mixt. with <em>N</em>-"| __truncated__ ...
#>   ..$ image: chr [1:12] "<svg width=\"178.77\" viewBox=\"0 0 5959 4052\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__ "<svg width=\"181.11\" viewBox=\"0 0 6037 4324\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__ "<svg width=\"178.77\" viewBox=\"0 0 5959 4324\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\""| __truncated__ "" ...

Acknowledgement

This R package was developed by the EnviData initiative at the Norwegian Geotechnical Institute (NGI) as part of the project ZeroPM: Zero pollution of Persistent, Mobile substances. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101036756.

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