Description of the oft data object

library(OpenFoodTox)
library(dm, warn.conflicts = FALSE)

The main content of the R package OpenFoodTox is a data object named oft, containing 5 tables with a selection of the OpenFoodTox data published by the European Food Safety Authority (Carnesecchi et al. 2023).

Column names and relations of the data tables in the data object oft made available by the OpenFoodTox R package are shown in the graph below.

dm_draw(oft, view_type = "all")

The data object is basically a list of tibbles (a tibble is an advanced type of a dataframe). As with any list object in R, you can access the list members (i.e. the tables containing the data) using the $ operator.

head(oft$reference_points)
#> # A tibble: 6 × 15
#>   Substance      Author  Year OutputID Study TestType Species Route DurationDays
#>   <chr>          <chr>  <int>    <int> <chr> <chr>    <chr>   <chr>        <dbl>
#> 1 (-)-3,7-Dimet… EFSA …  2016     2864 Anim… subchro… Rat     oral…           84
#> 2 (-)-Hyoscyami… EFSA    2022     4117 Huma… study w… Human   Not …           NA
#> 3 (-)-Hyoscyami… EFSA …  2013     2396 Anim… not rep… Pig     Not …           NA
#> 4 (-)-Hyoscyami… EFSA …  2013     2396 Huma… study w… Human   Not …           NA
#> 5 (1R,2S,5R)-N-… EFSA …  2014     2524 Huma… subchro… Rat     oral…           90
#> 6 (1R,2S,5R)-N-… EFSA …  2012     2147 Huma… subchro… Rat     oral…           90
#> # ℹ 6 more variables: Endpoint <chr>, qualifier <chr>, value <dbl>, unit <chr>,
#> #   Effect <chr>, Toxicity <chr>

Please refer to the documentation of the dm package for a description of the advanced features available for this type of data object.

In the following descriptions of the tables contained in the oft object, the kable() function of the knitr package is used to format the data tables.

Reference points

The reference points themselves are numeric outcomes of toxicological or ecotoxicological studies, and were described as “The critical toxicological studies and reference points …” (Dorne et al. 2021).

head(oft$reference_points) |>
  knitr::kable()
Substance Author Year OutputID Study TestType Species Route DurationDays Endpoint qualifier value unit Effect Toxicity
(-)-3,7-Dimethyl-6-octen-1-ol EFSA FEEDAP 2016 2864 Animal (target species) health subchronic Rat oral: feed 84 NOEL = 50.00 mg/kg bw/day no adverse effect observed NA
(-)-Hyoscyamine and (-)-Scopolamine group EFSA 2022 4117 Human health study with volunteers Human Not reported NA NOAEL = 0.16 µg/kg bw clinical signs systemic
(-)-Hyoscyamine and (-)-Scopolamine group EFSA CONTAM 2013 2396 Animal (target species) health not reported Pig Not reported NA NOAEL = 1500.00 µg/kg not reported not reported
(-)-Hyoscyamine and (-)-Scopolamine group EFSA CONTAM 2013 2396 Human health study with volunteers Human Not reported NA NOAEL = 0.16 µg/kg bw clinical signs systemic
(1R,2S,5R)-N-(2-(Pyridine-2-yl)ethyl)-3-p-menthanecarboxamide EFSA CEF 2014 2524 Human health subchronic Rat oral: feed 90 NOAEL = 5.00 mg/kg bw/day histopathology non neoplastic endocrine
(1R,2S,5R)-N-(4-Methoxyphenyl)-5-methyl-2-(1-methylethyl)-cyclohexanecarboxamide EFSA CEF 2012 2147 Human health subchronic Rat oral: feed 90 NOAEL = 100.00 mg/kg bw/day organ weights hepatotoxicity

Apparently, this means that in a certain category of reference points, the most critical value is selected and only this is reported. Also, it seems that for pesticidal active substances, reference points for the representative formulations which are also available in EFSA outputs are not listed.

The number of reference points by study type is shown below.

sort(table(oft$reference_points$Study), decreasing = TRUE)
#> 
#>                       Human health         Ecotox (water compartment) 
#>                               4019                               3298 
#> Animal (non-target species) health          Ecotox (soil compartment) 
#>                               3093                               2638 
#>     Animal (target species) health 
#>                                578

Example code extracting and printing the reference points on the springtail species Folsomia candida:

# Collect endpoints on springtails
springtail_endpoints <- oft$reference_points |>
  dplyr::filter(Species == "Folsomia candida") |>
  select(Substance, DurationDays, Endpoint, qualifier, value, unit, Effect)
head(springtail_endpoints) |>
  knitr::kable()
Substance DurationDays Endpoint qualifier value unit Effect
1,2,4-Triazole NA NOEC = 1.80e+00 mg/kg not reported
1,3-Dichloropropene NA dose level = 3.29e+05 g/ha mortality
1,3-Dichloropropene NA EC10 = 2.50e+00 mg/kg reproduction
2,3,6-trichloro-5-cyano-4-hydroxybenzamide 28 NOEC = 1.78e+00 mg/kg mortality
2,4-D NA NOEC = 1.25e+00 mg/kg not reported
2,4-DCP 28 NOEC = 6.30e-01 mg/kg reproduction

Reference values

The reference values show the outcome of a substance specific assessment. The number of reference values available for the most frequent assessment types are shown below.

sort(table(oft$reference_values$Assessment), decreasing = TRUE)[1:10]
#> 
#>                        MSI/FC            TTC Cramer Class I 
#>                          3692                          2505 
#>                           ADI critical study not identified 
#>                           915                           864 
#>           TTC Cramer Class II                          ARfD 
#>                           691                           587 
#>                          AOEL                            UL 
#>                           509                           274 
#>          TTC Cramer Class III                          PNEC 
#>                           205                           190

Some examples of Predicted No-Effect Concentration (PNEC) data can easily be extracted.

PNEC_values <- oft$reference_values |>
  dplyr::filter(Assessment == "PNEC")
head(PNEC_values) |>
  knitr::kable()
Substance Author Year OutputID Assessment qualfier value unit Population
(2E)-Methylcrotonic acid EFSA FEEDAP 2016 2841 PNEC = 903 µg/L Aquatic compartment
(2E)-Methylcrotonic acid EFSA FEEDAP 2016 2841 PNEC = 2008 µg/kg Soil compartment
1,2-Benzisothiazol-3(2H)-one 1,1-dioxide sodium salt EFSA FEEDAP 2018 3070 PNEC = 100 µg/L Aquatic compartment
1,2-Benzisothiazol-3(2H)-one 1,1-dioxide sodium salt EFSA FEEDAP 2018 3070 PNEC = 10000 µg/kg Soil macroorganisms - earthworms
1,2-Benzisothiazol-3(2H)-one 1,1-dioxide sodium salt EFSA FEEDAP 2018 3070 PNEC = 100000 µg/kg Aquatic compartment
1,2-Dimethoxy-4-(prop-1-enyl)-benzene EFSA FEEDAP 2012 155 PNEC <= 100 µg/L Aquatic compartment

Substance names

This table only contains the substance names and serves as a reference table for the reference points and the reference values.

head(oft$substance_names) |>
  knitr::kable()
Substance
((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-N-methyl-acetamide)
(+)-13alpha-Tigloyloxylupanine
(+)-13alpha-hydroxy-lupanine
(+)-Alpha-cedrene
(+)-Lupanine
(-)-17-Oxosparteine

Substance characterisation

In this table, substance characterisation data are collected1.

head(oft$substance_characterisation, n = 4) |>
  knitr::kable()
Substance component_type Component CASNumber ECRefNo MolecularFormula smiles
((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-N-methyl-acetamide) as such ((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-N-methyl-acetamide) NA NA C11H14N2O3 OCc1ccccc1/C(=N)C(=O)NC
((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-N-methyl-acetamide) metabolite Dimoxystrobin 149961-52-4 NA C19H22N2O3 CC1=CC(=C(C=C1)C)OCC2=CC=CC=C2C(=NOC)C(=O)NC
(+)-13alpha-Tigloyloxylupanine as such (+)-13-alpha-Tigloyloxylupanine 57943-34-7 NA C20H30N2O3 CC=C(C)C(=O)OC1CCN2CC3CC(C2C1)CN4C3CCCC4=O
(+)-13alpha-hydroxy-lupanine as such (+)-13-Alpha-hydroxy-lupanine 15358-48-2 NA C15H24N2O2 C1CC2C3CC(CN2C(=O)C1)C4CC(CCN4C3)O

The exact meaning of the differenct values in the column component_type (originally named has) does not seem to be documented.

EFSA output

This table is referred to from the tables containing reference points and referenec values. It shows some bibliographic information on the documents that served as data sources for the OpenFoodTox project.

head(oft$efsa_outputs) |>
  knitr::kable()
Substance OutputID LegalBasis Panel Published Title OutputType DOI URL
((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-N-methyl-acetamide) 1060 Council Directive (EEC) No 414/1991 (Repealed by Reg. EC No 1107/2009 (amended)) EFSA 2005-08-31 Conclusion regarding the peer review of the pesticide risk assessment of the active substance dimoxystrobin Conclusion on Pesticides Peer Review doi:10.2903/j.efsa.2005.46r http://dx.doi.org/10.2903/j.efsa.2005.46r
(+)-13alpha-Tigloyloxylupanine 3321 Regulation (EC) No 178/2002 (amended) EFSA CONTAM 2019-11-05 Scientific opinion on the risks for animal and human health related to the presence of quinolizidine alkaloids in feed and food, in particular in lupins and lupin-derived products EFSA opinion doi:10.2903/j.efsa.2019.5860 http://dx.doi.org/10.2903/j.efsa.2019.5860
(+)-13alpha-hydroxy-lupanine 3321 Regulation (EC) No 178/2002 (amended) EFSA CONTAM 2019-11-05 Scientific opinion on the risks for animal and human health related to the presence of quinolizidine alkaloids in feed and food, in particular in lupins and lupin-derived products EFSA opinion doi:10.2903/j.efsa.2019.5860 http://dx.doi.org/10.2903/j.efsa.2019.5860
(+)-Alpha-cedrene 2039 Commission Regulation (EC) No 1565/2000 (Repealed by Com. Implementing Reg. (EU) No 872/2012) EFSA CEF 2010-05-19 Flavouring Group Evaluation 25, Revision 1 (FGE.25Rev1): Aliphatic and aromatic hydrocarbons from chemical group 31 EFSA opinion doi:10.2903/j.efsa.2010.1334 http://dx.doi.org/10.2903/j.efsa.2010.1334
(+)-Alpha-cedrene 2102 Commission Regulation (EC) No 1565/2000 (Repealed by Com. Implementing Reg. (EU) No 872/2012) EFSA CEF 2011-06-29 Scientific Opinion on Flavouring Group Evaluation 25, Revision 2 (FGE.25Rev2): Aliphatic and aromatic hydrocarbons from chemical group 31 EFSA opinion doi:10.2903/j.efsa.2011.2177 http://dx.doi.org/10.2903/j.efsa.2011.2177
(+)-Alpha-cedrene 2299 Commission Regulation (EC) No 1565/2000 (Repealed by Com. Implementing Reg. (EU) No 872/2012) EFSA AFC 2008-12-16 Flavouring Group Evaluation 25, (FGE.25)1: Aliphatic and aromatic hydrocarbons from chemical group 3. Scientific Opinion of the Panel on Food Additives, Flavourings, Processing Aids and Materials in Contact with Food EFSA opinion doi:10.2903/j.efsa.2008.918 http://dx.doi.org/10.2903/j.efsa.2008.918

References

Carnesecchi, Edoardo, Aleksandra Mostrag, Andrea Ciacci, Alessandra Roncaglioni, Aleksey Tarkhov, Davide Gibin, Luca Sartori, Emilio Benfenati, Chihae Yang, and Jean Lou C. M. Dorne. 2023. “OpenFoodTox: EFSA’s Chemical Hazards Database.” Zenodo. https://doi.org/10.5281/zenodo.8120114.
Dorne, J. L. C. M., J. Richardson, A. Livaniou, E. Carnesecchi, L. Ceriani, R. Baldin, S. Kovarich, et al. 2021. “EFSA’s OpenFoodTox: An Open Source Toxicological Database on Chemicals in Food and Feed and Its Future Developments.” Environment International 146: 106293. https://doi.org/https://doi.org/10.1016/j.envint.2020.106293.

  1. Only the first four entries are shown, because the @ character in the SMILES codes of the later entries confuses the documentation system. It is both misinterpreted to indicate an e-mail address, and to indicate a citation↩︎