Difference between revisions of "Compound intake estimator"

Revision as of 18:09, 1 April 2014

This page is a method. The page identifier is Op_en6193
Moderator:Jouni (see all)
Give your opinion to the peer rating of the content of this page. {{ #opasnet_rater: }}
Upload data Show results

Compound intake estimator calculates intakes of compounds based on food or food supplement intake, compound concentration in food, and guidance values for the compound.

Question

How to estimate intakes and compare them to guidance values?

Answer

The concern indicator is calculated for each compound separately. If the intake is smaller than the threshold of concern, the indicator is < 1 and there is no concern. The threshold of concern is acceptable daily indake (ADI), benchmark dose (BMDL10), or threshold of toxicological concern (TTC), depending on what data is available for each compound.

+ Show code - Hide code


library(OpasnetUtils)
library(ggplot2)

objects.latest("Op_en6007", code_name = "answer") # Fetch official draft objects from [[OpasnetUtils/Drafts]] (in this case, ograph)

################## USER INPUTS

N <- 10

name <- "Cinnamon essential oil"

# name is the name of product. It is used in the output graphs.

# food.amount is the amount that the consumer consumes the defined product (g /day)

food.amount <- Ovariable("food.amount", data = data.frame(Result = food.amount))

# fr.const is the fraction of a critical constituent in the food or food supplement (given as percentage)

fr.const <- Ovariable("fr.const", data = data.frame(Result = fr.const))

# extraction is a list of extraction techniques to consider. (by default, all extraction techniques)

extraction <- Ovariable("extraction", data = data.frame(Result = 1))

# addcomp is user-defined additional compounds for a supplement, if they are not in the table.
## addcompound is the name and addconc is the concentration of the additional compound.

addcompound <- ifelse(! exists('addcompound') || addcompound == ' ', NA, addcompound)
addconc <- ifelse(! exists('addconc') || addconc == ' ', 0, addconc)

addcomp <- Ovariable("addcomp", data = data.frame(Compound = addcompound, Result = addconc))

# compound.conc is the concentration of compounds in the critical constituent

compound.conc <- Ovariable(name = "compound.conc", ddata = "Op_en6193.example_data")


############## ACTUAL OUTPUT MODEL

objects.latest("Op_en6193", code_name="initiate") # Fetches the ovariables needed in the model.

# Ovariables downloaded: guidance.values, compound.intake, food.risk

food.risk <- EvalOutput(food.risk, N = N)

if(intermediates) {

	cat("Concentrations of compounds in ", name, " (mg /kg DW)\n")

	oprint(summary(compound.conc, marginals = c("Compound")))

	cat("Intakes of different compounds (mg /kg BW /d)\n")

	oprint(summary(compound.intake, marginals = c("Compound")), digits = 3)

	ograph(compound.conc, x = "Compound")

	ograph(compound.intake, x = "Compound")
}

cat("Risks relative to guidance values (ADI, TDI, BMDL10, or TTC). Values < 1 are of minimal concern and are not shown in the graph.\n")

oprint(summary(food.risk, marginals = c("Compound")))

test <- unique(food.risk@output[food.risk@output$food.riskResult >= 1 , "Compound"])

temp <- food.risk@output[food.risk@output$Compound %in% test , ]

if(nrow(temp) == 0) {
	cat("There are no compounds that exceed a guidance value.\n")
	stop("There are no compounds that exceed a guidance value.\n")
}

ggplot(temp, aes(x = Compound, y = food.riskResult, fill = Guidance)) + 
	geom_boxplot() + 
	theme_grey(base_size = 24) +
	labs(title = paste("Exposure to compounds in", name), y = "Ratio (Exposure /Guidance)") +
	theme(axis.text.x = element_text(angle = 90, hjust = 1))

Example data(%)
Obs	Extraction.technique	Compound	Result	Reference
1	Superheated water extraction, 100 °C	2-Carene	0.08; 0.1; 0.12	Jayawardena & Smith, 2010
2	Superheated water extraction, 100 °C	Z-Cinnamaldehyde	1.63; 2.1; 2.57	Jayawardena & Smith, 2010
3	Superheated water extraction, 100 °C	Cinnamaldehyde	81.14; 83.7; 86.26	Jayawardena & Smith, 2010
4	Superheated water extraction, 100 °C	Eugenol	0.45; 0.8; 1.15	Jayawardena & Smith, 2010
5	Hydrodistillation	1,8-Cineole	0.2	Chericoni et al, 2005
6	Superheated water extraction, 100 °C	Cinnamyl acetate	5.47; 7.2; 8.93	Jayawardena & Smith, 2010

Rationale

The idea of the tool is to look at consumption of a particular PFS product, and estimate whether any of the compounds in the product cause concern. The estimation follows this equation:

compound intakes = product intake (g /day) * concentration of each compound in the product (mg /g) / 60
    (60 kg is the assumed body weight of the person)

concern indicator = compound intakes (mg /kg /d) / threshold of concern (mg /kg /d)

Calculations

You need to run the code below only if you update the data tables on this page.

+ Show code - Hide code


library(OpasnetUtils)

################## PRE-DEFINED INPUTS

# food.conc is a temporary object about the concentration of a compound in food.
# compound.conc is the concentration of a compound in the critical constituent (or food, if fr.const == 1) 
# fr.const is the fraction of the critical constituent in the whole food
# extraction is a criteria to select specific extraction techniques
# addcomp is an additional compound not in the product. Data about its concentration in food is given by the user.

# compound.intake is the intakes of the compounds via food or food supplement, each given as mg /kg /d.

compound.intake <- Ovariable("compound.intake", 
	dependencies = data.frame(Names = c("food.amount", "compound.conc", "fr.const", "extraction", "addcomp")), 
	formula = function(...) {
		food.conc <- compound.conc * 10 * fr.const / 100 # compound.conc from w/w% to mg/g; fr.const from % to fraction

		food.conc <- food.conc * extraction # remove extractions that are not considered.

		# addcomp  must not contain columns that are not in food.conc. It is multiplied by 1 to make 
		# the result column name "Result".
		food.conc@output <- orbind(food.conc, addcomp * 1)

		test <- colnames(food.conc@output) != "Extraction.technique"
		food.conc@marginal	<- food.conc@marginal[test]
		food.conc@output 	<- food.conc@output[test] # unit: mg /g

		out <- food.amount / 60 * food.conc # scale to 60 kg person
		return(out)
	}
)

# guidance.values is the guidance value (ADI, BMDL10, TTC or similar) for compounds. unit: mg /kg /d
# cramer is cramer classes of compounds
# cramer.values are the thresholds of toxicological concern for each Cramer class

cramer <- tidy(opbase.data("Op_en6193", subset = "cramer_classes_of_compounds"))
cramer$Result <- NULL
cramer$Guidance <- "TTC" # Threshold for toxicological concern

cramer.values <- tidy(opbase.data("Op_en6193", subset = "cramer_values"))
cramer.values <- merge(cramer, cramer.values)
cramer.values[["Cramer class"]] <- NULL
cramer.values$Result <- cramer.values$Result / 1000 # from ug /kg /d to mg /kg /d

guidance.values <- tidy(opbase.data("Op_en6193", subset = "guidance_values"))
guidance.values <- orbind(cramer.values, guidance.values)
guidance.values <- Ovariable("guidance.values", data = guidance.values)

# food.risk calculates "hazard quotients" or risks relative to guidance values. Value < 1 are of minimal concern

food.risk <- Ovariable(name = "food.risk",
	dependencies = data.frame(Name = c("compound.intake", "guidance.values")),
	formula = function(...) {

		# guidance.risk is intake compared with guidance values.

		out <- compound.intake / guidance.values 

		removepoorguidance <- function(dat, goodg) { # Remove inferior guidance values

			# Compounds that have good guidance values (goodg).
			hasgoodg <- dat[dat$Guidance == goodg , "Compound"] 

			# The row contains data about a chemical with a good guidance value
			# but the data is about an inferior guidance value.

			out <- dat[!(dat$Compound %in% hasgoodg & dat$Guidance != goodg) , ]

			return(out)
		}

		out <- removepoorguidance(out@output, "ADI")
		out <- removepoorguidance(out, "TDI")
		out <- removepoorguidance(out, "BMDL10")

		return(out)
	}
)

objects.store(compound.intake, guidance.values, food.risk)

cat("The following objects were successfully stored:
compound.intake, guidance.values, food.risk\n")

Using different data on different layers: [1].

Data about guidance values

Guidance values(mg /kg-BW /d)
Obs	Compound	Guidance	Result
1	1,8-Cineole	ADI	2.8
2	4-Terpineol	ADI	1.2
3	Benzylbenzoate	ADI	5
4	Cinnamaldehyde	ADI	0.7
5	Coumarin	TDI	0.1
6	Estragole	BMD10	3.3-6.5
7	Eugenol	ADI	2.5
8	Fenchone	ADI	10.64
9	Limonene	ADI	1
10	Linalool	ADI	0.5
11	Myrcene	ADI	2.5
12	Trans-anethole	ADI	2
13	Safrole	BMDL10	1.9-5.1
14	α-Terpineol	ADI	1.2

Cramer values(µg /kg-BW /d)
Obs	Cramer class	Threshold of toxicological concern	Description
1	1	30
2	2	1.5
3	3	1.5
4	4	0.0025	This comes from Apiole?! Is this correct?

Values 30 and 1.5 µg /kg /d come from EFSA (2012)^[1]

Cramer classes of compounds

Cramer classes of compounds(-)
Obs	Compound	Cramer class	Notes
1	1,8-Cineole	3	A new line was created for 1.8-Cineole based on "ß-Phellandrene + 1,8-Cineole: 1+3"
2	2-Carene	1
3	2-Methoxycinnamaldehyde	1
4	3-Phenylpropyl acetate	1
5	4-Methoxyphenylacetone	1
6	4-Terpineol	3
7	Allo-ocimene	1
8	Apiole	4	This is 0.0025 ug/kg/d!? Is this Cramer class at all?
9	Aromadendrene	1
10	Aromatic compound		Class could not be assigned
11	Benzaldehyde	1
12	Benzenepropanal	1
13	Benzenepropanol acetate	1
14	Benzenepropanol	1
15	Benzylbenzoate	1
16	Borneol	1
17	Cadinene	1
18	Calamenene	2
19	Camphene	1
20	Camphor	3
21	Carvacrol	1
22	Carveol isomere	1	Carveol (2-methyl-5-prop-1-en-2-ylcyclohex-2-en-1-ol) is 1. Isomere is not specified so the class was assigned to the general compound
23	Caryophyllene alcohol	3
24	Caryophyllene oxide	3
25	Caryophyllene	1
26	Chavicol	1
27	Cinnamaldehyde	1
28	Cinnamic acid	1
29	Cinnamyl acetate	1
30	Cinnamyl alcohol	1
31	Cis-anethole	2
32	Cis-limonene oxide	2
33	Cis-P-menth-2-en-1-ol	3
34	Cis-sabinene hydrate	2
35	Cis-ß-Ocimene	1
36	Cis-α-ocimene	1
37	Cis-β-ocimene	1
38	Coumarin	3
39	Cryptone	2
40	Cymene isomere	1	cymene is 1. Isomere is not specified so the class was assigned to the general compound
41	E-Anethole	1
42	e-Cadinene + Pioncarvone		Class could not be assigned
43	E-Cinnamyl acetate	1
44	E-o-Methoxycinnamaldehye	1
45	Epoxy-6.7-Humulene + Mw=220		Class could not be assigned
46	Estragole	1	Test compound, not real value
47	Eugenol acetate	3
48	Eugenol	1
49	Fenchyl acetate	1
50	Humulene epoxide II	3
51	Isoledene	1
52	Limonene	1
53	Linalool	3
54	Methoxy eugenol	3
55	Methyl cinnamaldehyde	1
56	Methyl eugenol	1
57	Monoterpenes		Class could not be assigned
58	N-Hexadecanoic acid	1
59	N-Octadecanoic acid	1
60	o-Cymene	1
61	p-Anisaldehyde	1
62	Para-Methoxy cinnamic aldehyde	1
63	p-Cymene	1
64	P-Cymene-8-ol	3
65	Phenyl cyclohexene	2
66	Phenylmethyle isovalerate	1
67	Rutin	1	Test compound, not real value
68	Sabinene	1
69	Safrole	3
70	Sesquiterpene epoxide		Class could not be assigned. Sesquierpene is class 3, but don't now if something changes with epoxide
71	Sesquiterpenol Mw=220		Class could not be assigned
72	Sesquiterpenol Mw=222		Class could not be assigned
73	Spathulenol	3
74	ß-Bisabolene	1
75	ß-Cubebene	1
76	ß-Elemene	1
77	ß-Myrcene	1
78	ß-Phellandrene	1	ß-Phellandrene + 1,8-Cineole: 1+3
79	ß-Pinene	1
80	Styrene	1
81	Terpinen-4-ol	3
82	Terpinolene isomere	1	terpinolene is 1 , isomere not known. Isomere is not specified so the class was assigned to the general compound
83	Terpinolene	1
84	Tetradecanal	1
85	Trans-2-methoxycinnamaldehyde	1
86	Trans-limonene oxide	2
87	Trans-pinene hydrate	2
88	Trans-Pinocarveol	1
89	Trans-Piperitol	1
90	Trans-P-menth-2-en-1-ol	3
91	Trans-ß-Ocimene	1
92	Z-Cinnamaldehyde	1
93	α-Cadinol	3
94	α-Calacorene	2
95	α-Copaene	1
96	α-Cubebene	1
97	α-Famesene		Class could not be assigned
98	α-Gurjunene	1
99	α-Humulene	1
100	α-Muurolene	1
101	α-Muurolol	3
102	α-P-Dimethylstyrene	1
103	α-Phellandrene	1
104	α-Pinene	1
105	α-Selinene	1
106	α-Terpinene	1
107	α-Terpineol	3
108	α-Thujene	1
109	β-Anise aldehyde	1
110	β-Phellandrene	1
111	β-Pinene	1
112	γ-Cadinene	1
113	γ-terpinene	1
114	γ-Terpinene	1
115	Δ3-Carene	1
116	δ-Cadinene	1

References

↑ EFSA (2012). Scientific Opinion on Exploring options for providing advice about possible human health risks based on the concept of Threshold of Toxicological Concern (TTC). EFSA Journal 2012;10(7):2750

[EFSA_2012-1] EFSA (2012). Scientific Opinion on Exploring options for providing advice about possible human health risks based on the concept of Threshold of Toxicological Concern (TTC). EFSA Journal 2012;10(7):2750

[1]

@@ Line 229: / Line 229: @@
 ,8-Cineole|ADI|2.8
 -Terpineol|ADI|1.2
+Benzylbenzoate|ADI|5
+Cinnamaldehyde|ADI|0.7
+Coumarin|TDI|0.1
 Estragole|BMD10|3.3-6.5
 Eugenol|ADI|2.5
@@ Line 236: / Line 239: @@
 Myrcene|ADI|2.5
 Trans-anethole|ADI|2
-Cinnamaldehyde|ADI|0.7
 Safrole|BMDL10|1.9-5.1
 α-Terpineol|ADI|1.2
--Terpineol|ADI|1.2
-Benzylbenzoate|ADI|5
-Cinnamaldehyde|ADI|0.7
-Eugenol|ADI|2.5
-Linalool|ADI|0.5
-Coumarin|TDI|0.1
 </t2b>
@@ Line 261: / Line 257: @@
 |
 <t2b name='Cramer classes of compounds' index='Compound,Cramer class' obs='Notes' unit="-">
--Methoxyphenylacetone|1|
+,8-Cineole|3|A new line was created for 1.8-Cineole based on "ß-Phellandrene + 1,8-Cineole: 1+3"
-Allo-ocimene|1|
-Apiole|4|This is 0.0025 ug/kg/d!? Is this Cramer class at all?
-Camphene|1|
-Camphor|2|
-Cis-anethole|2|
-Cis-limonene oxide|2|
-Cis-sabinene hydrate|2|
-Cis-α-ocimene|1|
-Cis-β-ocimene|1|
-Fenchyl acetate|1|
-o-Cymene|1|
-p-Anisaldehyde|1|
-p-Cymene|1|
-Sabinene|1|
-Terpinolene|1|
-Trans-limonene oxide|2|
-Trans-pinene hydrate|2|
-α-Phellandrene|1|
-α-Pinene|1|
-β-Anise aldehyde|1|
-β-Phellandrene|1|
-β-Pinene|1|
-γ-terpinene|1|
-,8-Cineole|3|
 -Carene|1|
 -Methoxycinnamaldehyde|1|
 -Phenylpropyl acetate|1|
+-Methoxyphenylacetone|1|
 -Terpineol|3|
-α-Terpineol|3|
+Allo-ocimene|1|
+Apiole|4|This is 0.0025 ug/kg/d!? Is this Cramer class at all?
 Aromadendrene|1|
 Aromatic compound||Class could not be assigned
 Benzaldehyde|1|
 Benzenepropanal|1|
+Benzenepropanol acetate|1|
 Benzenepropanol|1|
-Benzenepropanol acetate|1|
 Benzylbenzoate|1|
 Borneol|1|
@@ Line 305: / Line 279: @@
 Carvacrol|1|
 Carveol isomere|1|Carveol (2-methyl-5-prop-1-en-2-ylcyclohex-2-en-1-ol) is 1. Isomere is not specified so the class was assigned to the general compound
-Caryophyllene|1|
 Caryophyllene alcohol|3|
 Caryophyllene oxide|3|
+Caryophyllene|1|
 Chavicol|1|
 Cinnamaldehyde|1|
@@ Line 313: / Line 287: @@
 Cinnamyl acetate|1|
 Cinnamyl alcohol|1|
+Cis-anethole|2|
+Cis-limonene oxide|2|
 Cis-P-menth-2-en-1-ol|3|
+Cis-sabinene hydrate|2|
 Cis-ß-Ocimene|1|
+Cis-α-ocimene|1|
+Cis-β-ocimene|1|
 Coumarin|3|
 Cryptone|2|
@@ Line 323: / Line 302: @@
 E-o-Methoxycinnamaldehye|1|
 Epoxy-6.7-Humulene + Mw=220||Class could not be assigned
+Estragole|1|Test compound, not real value
+Eugenol acetate|3|
 Eugenol|1|
-Eugenol acetate|3|
+Fenchyl acetate|1|
 Humulene epoxide II|3|
 Isoledene|1|
@@ Line 335: / Line 316: @@
 N-Hexadecanoic acid|1|
 N-Octadecanoic acid|1|
-P-Cymene|1|
+o-Cymene|1|
+p-Anisaldehyde|1|
+Para-Methoxy cinnamic aldehyde|1|
+p-Cymene|1|
 P-Cymene-8-ol|3|
-Para-Methoxy cinnamic aldehyde|1|
 Phenyl cyclohexene|2|
 Phenylmethyle isovalerate|1|
+Rutin|1|Test compound, not real value
 Sabinene|1|
 Safrole|3|
@@ Line 346: / Line 330: @@
 Sesquiterpenol Mw=222||Class could not be assigned
 Spathulenol|3|
+ß-Bisabolene|1|
+ß-Cubebene|1|
+ß-Elemene|1|
+ß-Myrcene|1|
+ß-Phellandrene|1|ß-Phellandrene + 1,8-Cineole: 1+3
+ß-Pinene|1|
 Styrene|1|
 Terpinen-4-ol|3|
+Terpinolene isomere|1|terpinolene is 1 , isomere not known. Isomere is not specified so the class was assigned to the general compound
 Terpinolene|1|
-Terpinolene isomere|1|terpinolene is 1 , isomere not known. Isomere is not specified so the class was assigned to the general compound
 Tetradecanal|1|
 Trans-2-methoxycinnamaldehyde|1|
-Trans-P-menth-2-en-1-ol|3|
+Trans-limonene oxide|2|
+Trans-pinene hydrate|2|
 Trans-Pinocarveol|1|
 Trans-Piperitol|1|
+Trans-P-menth-2-en-1-ol|3|
 Trans-ß-Ocimene|1|
 Z-Cinnamaldehyde|1|
-ß-Bisabolene|1|
-ß-Cubebene|1|
-ß-Elemene|1|
-ß-Myrcene|1|
-ß-Phellandrene|1|ß-Phellandrene + 1,8-Cineole: 1+3
-,8-Cineole|3|A new line was created for 1.8-Cineole based on the row above.
-ß-Pinene|1|
 α-Cadinol|3|
 α-Calacorene|2|
@@ Line 371: / Line 356: @@
 α-Gurjunene|1|
 α-Humulene|1|
+α-Muurolene|1|
 α-Muurolol|3|
 α-P-Dimethylstyrene|1|
@@ Line 379: / Line 365: @@
 α-Terpineol|3|
 α-Thujene|1|
+β-Anise aldehyde|1|
+β-Phellandrene|1|
+β-Pinene|1|
 γ-Cadinene|1|
+γ-terpinene|1|
 γ-Terpinene|1|
+Δ3-Carene|1|
 δ-Cadinene|1|
-Δ3-Carene|1|
-α-Muurolene|1|
-Rutin|1|Test compound, not real value
-Estragole|1|Test compound, not real value
 </t2b>

Difference between revisions of "Compound intake estimator"

Revision as of 18:09, 1 April 2014

Contents

Question

Answer

Rationale

Calculations

Data about guidance values

See also

References

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Page Tools

Tools

In other websites