eduardszoecs / webchem

Chemical Information from the Web

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.

Currently implemented in webchem

Source	Function(s	API Docs	API key
Chemical Identifier Resolver (CIR)	cir_query()	link	none
ChemSpider	get_csid(), csid_compinfo(), csid_extcompinfo()	link	required (link)
PubChem	get_cid(), cid_compinfo()	link	none
Chemical Translation Service (CTS)	cts_convert(), cts_compinfo()	link	none
PAN Pesticide Database	pan()	link	none
Allan Wood's Compendium of Pesticide Common Names	allanwood()	link	none

API keys

ChemSpider functions require a security token. Please register at RSC (https://www.rsc.org/rsc-id/register) to retrieve a security token.

Installation

Install from CRAN (stable version)

install.packages("webchem")

Install from Github (development version)

install.packages("devtools")
library("devtools")
install_github("ropensci/webchem")

Quickstart

library("webchem")

Chemical Identifier Resolver (CIR)

CAS numbers and molecular weight for Triclosan. Use first to return only the first hit.

cir_query('Triclosan', 'cas')
#> [1] "3380-34-5"   "112099-35-1" "88032-08-0"
cir_query('Triclosan', 'cas', first = TRUE)
#> [1] "3380-34-5"
cir_query('Triclosan', 'mw')
#> [1] "289.5451"

Query SMILES and InChIKey from CAS (Triclosan). Inputs might by ambiguous and we can specify where to search using resolver=.

cir_query('3380-34-5', 'smiles')
#> [1] "C1=CC(=CC(=C1OC2=CC=C(C=C2Cl)Cl)O)Cl"
cir_query('3380-34-5', 'stdinchikey', resolver = 'cas_number')
#> [1] "InChIKey=XEFQLINVKFYRCS-UHFFFAOYSA-N"

Convert InChiKey (Triclosan) to ChemSpider ID and retrieve the number of rings

cir_query('XEFQLINVKFYRCS-UHFFFAOYSA-N', 'chemspider_id', first = TRUE)
#> [1] "<!DOCTYPE"
cir_query('XEFQLINVKFYRCS-UHFFFAOYSA-N', 'ring_count')
#> [1] "2"

ChemSpider

You'll need a API key:

token = '<YOUR TOKEN HERE'

Retrieve the ChemSpider ID of Triclosan

(id <- get_csid('Triclosan', token = token))
#> [1] "5363"

Use this ID to query information from ChemSpider

csid_extcompinfo(id, token = token)
#>                                                                          CSID 
#>                                                                        "5363" 
#>                                                                            MF 
#>                                                      "C_{12}H_{7}Cl_{3}O_{2}" 
#>                                                                        SMILES 
#>                                              "c1cc(c(cc1Cl)O)Oc2ccc(cc2Cl)Cl" 
#>                                                                         InChI 
#> "InChI=1/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,16H" 
#>                                                                      InChIKey 
#>                                                   "XEFQLINVKFYRCS-UHFFFAOYAS" 
#>                                                                   AverageMass 
#>                                                                    "289.5418" 
#>                                                               MolecularWeight 
#>                                                                    "289.5418" 
#>                                                              MonoisotopicMass 
#>                                                                  "287.951172" 
#>                                                                   NominalMass 
#>                                                                         "288" 
#>                                                                         ALogP 
#>                                                                        "5.53" 
#>                                                                         XLogP 
#>                                                                           "5" 
#>                                                                    CommonName 
#>                                                                   "Triclosan"

PubChem

Retrieve PubChem CID

get_cid('Triclosan')
#>  [1] "5564"     "131203"   "627458"   "15942656" "16220126" "16220128"
#>  [7] "16220129" "16220130" "18413505" "22947105" "23656593" "24848164"
#> [13] "25023954" "25023955" "25023956" "25023957" "25023958" "25023959"
#> [19] "25023960" "25023961" "25023962" "25023963" "25023964" "25023965"
#> [25] "25023966" "25023967" "25023968" "25023969" "25023970" "25023971"
#> [31] "25023972" "25023973" "45040608" "45040609" "67606151" "71752714"
cid <- get_cid('3380-34-5')

Use this CID to retrieve some chemical properties:

props <- cid_compinfo(cid)
props$InChIKey
#> [1] "XEFQLINVKFYRCS-UHFFFAOYSA-N"
props$MolecularWeight
#> [1] "289.541780"
props$IUPACName
#> [1] "5-chloro-2-(2,4-dichlorophenoxy)phenol"

Chemical Translation Service (CTS)

CTS allows to convert from nearly every possible identifier to nearly every possible identifier:

cts_convert(query = '3380-34-5', from = 'CAS', to = 'PubChem CID')
#> [1] "5564"
cts_convert(query = '3380-34-5', from = 'CAS', to = 'ChemSpider')
#> [1] "5363"
(inchk <- cts_convert(query = 'Triclosan', from = 'Chemical Name', to = 'inchikey'))
#> [1] "XEFQLINVKFYRCS-UHFFFAOYSA-N"

Moreover, we can a lot of information stored in the CTS database using InChIkey

info <- cts_compinfo(inchikey = inchk)
info[1:5]
#> $inchikey
#> [1] "XEFQLINVKFYRCS-UHFFFAOYSA-N"
#> 
#> $inchicode
#> [1] "InChI=1S/C12H7Cl3O2/c13-7-1-3-11(9(15)5-7)17-12-4-2-8(14)6-10(12)16/h1-6,16H"
#> 
#> $molweight
#> [1] 289.5418
#> 
#> $exactmass
#> [1] 287.9512
#> 
#> $formula
#> [1] "C12H7Cl3O2"

PAN Pesticide Database

pan() returns a list of 73 entries, here I extract only 4 of those:

pan_list <- pan('lambda-Cyhalothrin', first = TRUE)
pan_list[c("CAS Number", "Chemical Class", "Water Solubility (Avg, mg/L)", "Adsorption Coefficient (Koc)" )]
#> $`CAS Number`
#> [1] "91465-08-6"
#> 
#> $`Chemical Class`
#> [1] "Pyrethroid"
#> 
#> $`Water Solubility (Avg, mg/L)`
#> [1] "0.0050"
#> 
#> $`Adsorption Coefficient (Koc)`
#> [1] "157000"

Allan Wood's Compendium of Pesticide Common Names

allanwood() returns a list of 9 entries and can query common names and cas numbers:

allanwood('Fluazinam', type = 'commonname')
#> $cname
#> [1] "Fluazinam"
#> 
#> $status
#> [1] "ISO 1750 (published)"
#> 
#> $pref_iupac_name
#> [1] "3-chloro-N-[3-chloro-2,6-dinitro-4-(trifluoromethyl)phenyl]-5-(trifluoromethyl)pyridin-2-amine"
#> 
#> $iupac_name
#> [1] "3-chloro-N-(3-chloro-5-trifluoromethyl-2-pyridyl)-α,α,α-trifluoro-2,6-dinitro-p-toluidine"
#> 
#> $cas
#> [1] "79622-59-6"
#> 
#> $formula
#> [1] "C13H4Cl2F6N4O4"
#> 
#> $activity
#> [1] "fungicides (pyridine fungicides)"
#> 
#> $inchikey
#> [1] "UZCGKGPEKUCDTF-UHFFFAOYSA-N"
#> 
#> $inch
#> [1] "InChI=1S/C13H4Cl2F6N4O4/c14-6-1-4(12(16,17)18)3-22-11(6)23-9-7(24(26)27)2-5(13(19,20)21)8(15)10(9)25(28)29/h1-3H,(H,22,23)"
allanwood('79622-59-6', type = 'cas')$cname
#> [1] "fluazinam"

Acknowledgements

Without the fantastic web services webchem wouldn't be here. Therefore, kudos to the web service providers and developers!

Related Projects

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

Contributors

• Eduard Szöcs
• Daniel Münch

Meta

• Please report any issues, bugs or feature requests.
• License: MIT