Standartox is a database and tool facilitating the retrieval of ecotoxicological test data. It is based on the EPA ECOTOX database as well as on data from several other chemical databases and allows users to filter and aggregate ecotoxicological test data in an easy way. It can either be accessed via http://standartox.uni-landau.de or this R-package standartox. Ecotoxicological test data is used in environmental risk assessment to calculate effect measures such as TU - Toxic Units or SSD - Species Sensitivity Distributions to asses environmental toxicity of chemicals.
The project lives in two repositories:
install.packages('standartox')
# remotes::install_github('andschar/standartox') # development version
Standartox consists of the two functions stx_catalog()
and
stx_query()
. The former allows you to retrieve a catalog of possible
parameters that can be used as an input for stx_query()
. The latter
fetches toxicity values from the database.
stx_catalog()
The function returns a list of all possible arguments that can bes use
in stx_query()
.
require(standartox)
catal = stx_catalog()
names(catal)
## [1] "casnr" "cname" "concentration_unit"
## [4] "concentration_type" "chemical_role" "chemical_class"
## [7] "taxa" "trophic_lvl" "habitat"
## [10] "region" "ecotox_grp" "duration"
## [13] "effect" "endpoint" "exposure"
## [16] "vers"
catal$endpoint # access the parameter endpoint
variable | n | n_total | perc |
---|---|---|---|
NOEX | 237616 | 609435 | 39 |
LOEX | 192718 | 609435 | 32 |
XX50 | 179101 | 609435 | 30 |
stx_query()
The function allows you to retrieve filtered and aggregated toxicity data according to the parameters below.
parameter | example |
---|---|
casnr | 50000, 94520, 94531 |
cname | 2718, 4, 3 |
concentration_unit | ug/l, mg/kg, ppb |
concentration_type | active ingredient, formulation, total |
chemical_role | pesticide, herbicide, drug |
chemical_class | amide, aromatic, organochlorine |
taxa | species, Fusarium oxysporum, Apis mellifera |
trophic_lvl | heterotroph, autotroph |
habitat | freshwater, terrestrial, marine |
region | europe, america_north, america_south |
ecotox_grp | invertebrate, plant, fish |
duration | 24, 96 |
effect | mortality, population, biochemistry |
endpoint | NOEX, LOEX, XX50 |
exposure | aquatic, environmental, diet |
vers | 20191212 |
You can type in parameters manually or subset the object returned by
stx_catalog()
:
require(standartox)
cas = c(Copper2Sulfate = '7758-98-7',
Permethrin = '52645-53-1',
Imidacloprid = '138261-41-3')
# query
l = stx_query(cas = cas,
endpoint = 'XX50',
taxa = grep('Oncorhynchus', catal$taxa$variable, value = TRUE), # fish genus
exposure = 'aquatic',
duration = c(24, 120))
## Standartox query running..
## Parameters:
## casnr: 7758-98-7, 52645-53-1, 138261-41-3
## duration: 24, 120
## endpoint: XX50
## exposure: aquatic
## taxa: Oncorhynchus clarkii, Oncorhynchus mykiss, Oncorhynchus nerka, Oncorhy...[truncated]
cas =
) Can be input in the form of 7758-98-7 or 7758987endpoint =
) Only one endpoint per query is allowed:
NOEX
summarises No observed effect
concentration/level
(i.e. NOEC, NOEL, NOAEL, etc.)LOEX
summarises Lowest observed effects concentration
(i.e. LOEC, LOEL, etc.)XX50
summarises Half maximal effective
concentration (i.e. EC50,
LC50, LD50, etc.)Standartox returns a list object with five entries.
l$filtred
and l$filtered_all
contain the filtered Standartox
data set (the former only is a shorter and more concise version of
the latter):cas | cname | concentration | concentration_unit | effect | endpoint |
---|---|---|---|---|---|
7758-98-7 | cupric sulfate | 1100.0 | ug/l | mortality | XX50 |
7758-98-7 | cupric sulfate | 18.9 | ug/l | mortality | XX50 |
7758-98-7 | cupric sulfate | 46.4 | ug/l | mortality | XX50 |
l$aggregated
contains the several aggregates of the Standartox
data:
cname
, cas
- chemical identifiersmin
- Minimumtax_min
- Most sensitive taxongmn
- Geometric meanamn
- Arithmetic meansd
- Standard Deviation of the arithmetic meanmax
- Maximumtax_max
- Most insensitive taxonn
- Number of distinct taxa used for the aggregationtax_all
- Concatenated string of all taxa used for the
aggregationcname | cas | min | tax_min | gmn | max |
---|---|---|---|---|---|
cupric sulfate | 7758-98-7 | 6.813740e+01 | Oncorhynchus clarkii | 1.330055e+02 | 263.6153 |
imidacloprid | 138261-41-3 | 2.291000e+05 | Oncorhynchus mykiss | 2.291000e+05 | 229100.0000 |
permethrin | 52645-53-1 | 1.896481e+00 | Oncorhynchus gilae | 4.505877e+00 | 17.0000 |
l$meta
contains meta information on the request:variable | value |
---|---|
accessed | 2021-05-10 10:17:29 |
standartox_version | 20210315 |
Let’s say, we want to retrieve the 20 most tested chemicals on the genus Oncorhynchus. We allow for test durations between 48 and 120 hours and want the tests restricted to active ingredients only. Since we are only interested in the half maximal effective concentration, we choose XX50 as our endpoint. As an aggregation method we choose the geometric mean.
require(standartox)
l2 = stx_query(concentration_type = 'active ingredient',
endpoint = 'XX50',
taxa = grep('Oncorhynchus', catal$taxa$variable, value = TRUE), # fish genus
duration = c(48, 120))
## Standartox query running..
## Parameters:
## concentration_type: active ingredient
## duration: 48, 120
## endpoint: XX50
## taxa: Oncorhynchus clarkii, Oncorhynchus mykiss, Oncorhynchus nerka, Oncorhy...[truncated]
We subset the retrieved data to the 20 most tested chemicals and plot the result.
require(data.table)
dat = merge(l2$filtered, l2$aggregated, by = c('cas', 'cname'))
cas20 = l2$aggregated[ order(-n), cas ][1:20]
dat = dat[ cas %in% cas20 ]
require(ggplot2)
ggplot(dat, aes(y = reorder(cname, -gmn))) +
geom_point(aes(x = concentration, col = 'All values'),
pch = 1, alpha = 0.3) +
geom_point(aes(x = gmn, col = 'Standartox value\n(Geometric mean)'),
size = 3) +
scale_x_log10(breaks = c(0.01, 0.1, 1, 10, 100, 1000, 10000),
labels = c(0.01, 0.1, 1, 10, 100, 1000, 10000)) +
scale_color_viridis_d(name = '') +
labs(title = 'Oncorhynchus EC50 values',
subtitle = '20 most tested chemicals',
x = 'Concentration (ppb)') +
theme_minimal() +
theme(axis.title.y = element_blank())
We ask you to use the API service thoughtfully, which means to run the
stx_query()
only once and to re-run it only when parameters change or
you want to query new versions. Here is an example of how to easily
store the queried data locally from within R.
run = FALSE # set to TRUE for the first run
if (run) {
l2 = stx_query(concentration_type = 'active ingredient',
endpoint = 'XX50',
taxa = grep('Oncorhynchus', catal$taxa$variable, value = TRUE), # fish genus
duration = c(48, 120))
saveRDS(l2, file.path('path/to/directory', 'data.rds'))
} else {
l2 = readRDS(file.path('path/to/directory', 'data.rds'))
}
# put rest of the script here
# ...
The article on Standartox is published here.
Check out our contribution guide here.
citation(package = 'standartox')