Eduard Szöcs

Data in Environmental Science and Eco(toxico-)logy

webchem v0.0.3 is out!

A new version of the webchem package is available on CRAN. Don’t forget to update!

This version adds some new functionality especially useful for ecotoxicologists and fixes some minor bugs.

Thanks to Johannes Ranke for fixing a typo with Alan Wood’s database: The old function name was allanwood() - this function is now deprecated and the new one is alanwood().

If you want to contribute - please help me to improve webchem! Either by creating a pull request or by raising an issue if you find a bug or some functionality is missing or by any other contribution.

New data sources

SRC PHYSPROP

You can now query SRC physprop database, which contains names and physical properties for over 41,000 chemicals.

Currently, you can only search for CAS numbers (here for Diuron):

library(webchem)
physprop('330-54-1')
## $cas
## [1] "330-54-1"
## 
## $cname
## [1] "DIURON"
## 
## $mw
## [1] "233.1"
## 
## $prop
##                       variable             value             unit     temp
## 1             Water Solubility                42             mg/L 25 deg C
## 2        Log P (octanol-water)              2.68                      <NA>
## 3               Vapor Pressure       0.000000069            mm Hg 25 deg C
## 4         Henry's Law Constant    0.000000000504       atm-m3/mol 25 deg C
## 5 Atmospheric OH Rate Constant 0.000000000010877 cm3/molecule-sec 25 deg C
##   type                                ref
## 1  EXP USDA PESTICIDE PROPERTIES DATABASE
## 2  EXP             HANSCH,C ET AL. (1995)
## 3  EXP USDA PESTICIDE PROPERTIES DATABASE
## 4  EST                            VP/WSOL
## 5  EST       MEYLAN,WM & HOWARD,PH (1993)

ETOX

ETOX: Information System Ecotoxicology and Environmental Quality Targets is a nice database which holds information on substances (a lot of synonyms in there), tests and quality targets.

To use it we follow the common workflow: Search ID -> Find data with this ID.

  • First we need the ETOX-ID:
id <- get_etoxid('Triclosan')
id
## [1] "20179"
## attr(,"matched")
## [1] "Triclosan ( 20179 )"
## attr(,"distance")
## [1] 0.52632

With this ID we can query substance information:

etox_basic(id)
## $cas
## [1] "3380-34-5"
## 
## $ec
## [1] "222-182-2"
## 
## $gsbl
## [1] "117338"
## 
## $synonyms
##                                          name  language
## 5      5-chloro-2-(2,4-dichlorophenoxy)phenol   English
## 8   Phenol, 5-chloro-2-(2,4-dichlorophenoxy)-    German
## 9     2,4,4'-Trichlor-2'-hydroxydiphenylether    German
## 10                             Irgasan DP 300    German
## 11                                  Vikol THP    German
## 12     2,4,4-Trichlor-2'-hydroxydiphenylether    German
## 13   2,4,4'-Trichloro-2'-hydroxydiphenylether    German
## 15     Chlor-2-(2,4-dichlorphenoxy)phenol, 5- universal
## 16  Trichlor-2'-hydroxydiphenylether, 2,4,4'- universal
## 17   Trichlor-2'-hydroxydiphenylether, 2,4,4- universal
## 18 Trichloro-2'-hydroxydiphenylether, 2,4,4'- universal
## 19      5-Chlor-2-(2,4-dichlorphenoxy)-phenol universal
## 20    Chlor-2-(2,4-dichlorphenoxy)-phenol, 5- universal
## 21       5-Chlor-2-(2,4-dichlorphenoxy)phenol universal
## 22                                  triclosán   Spanish
## 23                                triklosaani   Finnish
## 24                                 triclosano   Italian
## 25                                  triklosan   Swedish

Or quality targets:

targets <- etox_targets(id)
targets[ , c('Substance', 'Country_or_Region', 'Designation', 'Value_Target_LR', 'Unit')]
##   Substance Country_or_Region      Designation Value_Target_LR Unit
## 1 Triclosan               AUS             PNEC           0.050 µg/l
## 2 Triclosan               CHE AA-QS_freshwater           0.020 µg/l
## 3 Triclosan               CHE           MAC-QS           0.020 µg/l
## 4 Triclosan               DEU           AA-EQS           0.020 µg/l
## 5 Triclosan               DEU          MAC-EQS           0.200 µg/l
## 6 Triclosan               DEU       QS_fw, eco           0.020 µg/l
## 7 Triclosan               DEU   MAC-QS_fw, eco           0.160 µg/l
## 8 Triclosan               DEU       QS_sw, eco           0.002 µg/l
## 9 Triclosan               DEU   MAC-QS_sw, eco           0.016 µg/l

And (similar to the EPA AQUIRE database) results of toxicity tests:

tests <- etox_tests(id)
tests[ , c('Organism', 'Effect', 'Duration', 'Time_Unit','Endpoint', 'Value', 'Unit')]
##                           Organism                 Effect Duration
## 1              Anabaena flos-aquae           not reported        4
## 2          Brachionus calyciflorus           not reported        2
## 3          Brachionus calyciflorus           not reported        2
## 4          Brachionus calyciflorus           not reported        2
## 5                Brachydanio rerio Embryo-Larval-Toxicity       10
## 6               Ceriodaphnia dubia              Lethality        7
## 7               Ceriodaphnia dubia              Mortality        2
## 8               Ceriodaphnia dubia              Mortality        7
## 9               Ceriodaphnia dubia           not reported        7
## 10              Ceriodaphnia dubia           Reproduction        7
## 11              Ceriodaphnia dubia           Reproduction        7
## 12                   Daphnia magna              Mortality       21
## 13                   Daphnia magna           Reproduction       21
## 14         Desmodesmus subspicatus     Cell Proliferation        4
## 15          Dunaliella tertiolecta     Cell Proliferation        4
## 16          Dunaliella tertiolecta     Cell Proliferation        4
## 17             Oncorhynchus mykiss Embryo-Larval-Toxicity        4
## 18             Pimephales promelas              Mortality        4
## 19 Pseudokirchneriella subcapitata       Wachstumshemmung        3
## 20         Scenedesmus subspicatus                Biomass        3
## 21         Scenedesmus subspicatus           not reported        4
## 22         Scenedesmus subspicatus           not reported        4
## 23         Scenedesmus subspicatus           not reported        4
## 24         Scenedesmus subspicatus           Reproduction        3
## 25                 Hyalella azteca              Mortality       10
##    Time_Unit Endpoint   Value Unit
## 1          d     NOEC   0.810     
## 2          d     NOEC  50.000 µg/l
## 3          d     NOEC  50.000 µg/l
## 4          d     NOEC  50.000 µg/l
## 5          d     NOEC 200.000 µg/l
## 6          d     NOEC 339.000 µg/l
## 7          d     EC50 120.000 µg/l
## 8          d     NOEC  50.000 µg/l
## 9          d     NOEC   4.000 µg/l
## 10         d     NOEC   6.000 µg/l
## 11         d     NOEC 182.000 µg/l
## 12         d     NOEC 132.000 µg/l
## 13         d     NOEC  40.000 µg/l
## 14         d    ErC50   1.610 µg/l
## 15         d     NOEC   1.600 µg/l
## 16         d    EbC50   3.550 µg/l
## 17         d     NOEC  34.100 µg/l
## 18         d     LC50 260.000 µg/l
## 19         d     NOEC   0.200 µg/l
## 20         d     NOEC   0.500 µg/l
## 21         d     NOEC   0.690 µg/l
## 22         d     NOEC   0.742 µg/l
## 23         d     NOEC   2.380 µg/l
## 24         d     NOEC   0.500 µg/l
## 25         d     NOEC   5.000 µg/l

PPDB

The PPDB : Pesticides Properties DataBase is another useful data source for ecotoxicologists.

Currently, you can query the PPDB only using a CAS number and the function will definitively some improvements in future.

out <- ppdb_query('330-54-1')

The output is enormous, so I print here only a small part, e.g. the EU member states where CAS 330-54-1 (=Diuron) is approved for use.

out[[2]]
##    status county
## AT  FALSE     AT
## BE  FALSE     BE
## BG   TRUE     BG
## CY  FALSE     CY
## CZ  FALSE     CZ
## DE  FALSE     DE
## DK  FALSE     DK
## EE  FALSE     EE
## EL  FALSE     EL
## ES   TRUE     ES
## FI  FALSE     FI
## FR  FALSE     FR
## HR  FALSE     HR
## HU  FALSE     HU
## IE  FALSE     IE
## IT  FALSE     IT
## LT  FALSE     LT
## LU  FALSE     LU
## LV  FALSE     LV
## MT  FALSE     MT
## NL  FALSE     NL
## PL  FALSE     PL
## PT  FALSE     PT
## RO  FALSE     RO
## SE  FALSE     SE
## SI  FALSE     SI
## SK  FALSE     SK
## UK  FALSE     UK
Written on September 25, 2015