Contents

Compiled date: 2021-05-19

Last edited: 2021-14-05

License: GPL-3

1 Installation

Run the following code to install the Bioconductor version of the package.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fobitools")

2 Load packages

library(fobitools)

We will also need some additional CRAN packages that will be very useful in this vignette.

library(tidyverse)
library(kableExtra)

3 Load food items from a food frequency questionnaire (FFQ) sample data

In nutritional studies, dietary data are usually collected by using different questionnaires such as FFQs (food frequency questionnaires) or 24h-DRs (24 hours dietary recall). Commonly, the text collected in these questionnaires require a manual preprocessing step before being analyzed.

This is an example of how an FFQ could look like in a common nutritional study.

load("data/sample_ffq.rda")

sample_ffq %>%
  dplyr::slice(1L:10L) %>%
  kbl(row.names = FALSE, booktabs = TRUE) %>%
  kable_styling(latex_options = c("striped"))
ID Name
ID_001 Beef: roast, steak, mince, stew casserole, curry or bolognese
ID_002 Beefburgers
ID_003 Pork: roast, chops, stew, slice or curry
ID_004 Lamb: roast, chops, stew or curry
ID_005 Chicken, turkey or other poultry: including fried, casseroles or curry
ID_006 Bacon
ID_007 Ham
ID_008 Corned beef, Spam, luncheon meats
ID_009 Sausages
ID_0010 Savoury pies, e.g. meat pie, pork pie, pasties, steak & kidney pie, sausage rolls, scotch egg

4 Automatic dietary text anotation

The fobitools::annotate_foods() function allows the automatic annotation of free nutritional text using the FOBI ontology (Castellano-Escuder et al. 2020). This function provides users with a table of food IDs, food names, FOBI IDs and FOBI names of the FOBI terms that match the input text. The input should be structured as a two column data frame, indicating the food IDs (first column) and food names (second column). Note that food names can be provided both as words and complex strings.

This function includes a text mining algorithm composed of 5 sequential layers. In this process, singulars and plurals are analyzed, irrelevant words are removed, each string of the text input is tokenized and each word is analyzed independently, and the semantic similarity between input text and FOBI items is computed. Finally, this function also shows the percentage of the annotated input text.

annotated_text <- fobitools::annotate_foods(sample_ffq)
#> 89.57% annotated
#> 3.277 sec elapsed

annotated_text$annotated %>%
  dplyr::slice(1L:10L) %>%
  kbl(row.names = FALSE, booktabs = TRUE) %>%
  kable_styling(latex_options = c("striped"))
FOOD_ID FOOD_NAME FOBI_ID FOBI_NAME
ID_00100 Oranges, satsumas, mandarins, tangerines, clementines FOODON:03309832 orange (whole, raw)
ID_00101 Grapefruit FOODON:03301702 grapefruit (whole, raw)
ID_00102 Bananas FOODON:03311513 banana (whole, ripe)
ID_00103 Grapes FOODON:03301123 grape (whole, raw)
ID_00104 Melon FOODON:03301593 melon (raw)
ID_00105 *Peaches, plums, apricots, nectarines FOODON:03301107 nectarine (whole, raw)
ID_00106 *Strawberries, raspberries, kiwi fruit FOODON:03305656 fruit (dried)
ID_00106 *Strawberries, raspberries, kiwi fruit FOODON:03414363 kiwi
ID_00106 *Strawberries, raspberries, kiwi fruit FOODON:00001057 plant fruit food product
ID_00107 Tinned fruit FOODON:03305656 fruit (dried)

4.1 The similarity argument

Additionally, the similarity argument indicates the semantic similarity cutoff used at the last layer of the text mining pipeline. It is a numeric value between 1 (exact match) and 0 (very poor match). Users can modify this value to obtain more or less accurated annotations. Authors do not recommend values below 0.85 (default).

annotated_text_95 <- fobitools::annotate_foods(sample_ffq, similarity = 0.95)
#> 86.5% annotated
#> 2.927 sec elapsed

annotated_text_95$annotated %>%
  dplyr::slice(1L:10L) %>%
  kbl(row.names = FALSE, booktabs = TRUE) %>%
  kable_styling(latex_options = c("striped"))
FOOD_ID FOOD_NAME FOBI_ID FOBI_NAME
ID_00100 Oranges, satsumas, mandarins, tangerines, clementines FOODON:03309832 orange (whole, raw)
ID_00101 Grapefruit FOODON:03301702 grapefruit (whole, raw)
ID_00102 Bananas FOODON:03311513 banana (whole, ripe)
ID_00103 Grapes FOODON:03301123 grape (whole, raw)
ID_00104 Melon FOODON:03301593 melon (raw)
ID_00105 *Peaches, plums, apricots, nectarines FOODON:03301107 nectarine (whole, raw)
ID_00106 *Strawberries, raspberries, kiwi fruit FOODON:03305656 fruit (dried)
ID_00106 *Strawberries, raspberries, kiwi fruit FOODON:03414363 kiwi
ID_00106 *Strawberries, raspberries, kiwi fruit FOODON:00001057 plant fruit food product
ID_00107 Tinned fruit FOODON:03305656 fruit (dried)

See that by increasing the similarity value from 0.85 (default value) to 0.95 (a more accurate annotation), the percentage of annotated terms decreases from 89.57% to 86.5%. Let’s check those food items annotated with similarity = 0.85 but not with similarity = 0.95.

annotated_text$annotated %>%
  filter(!FOOD_ID %in% annotated_text_95$annotated$FOOD_ID) %>%
  kbl(row.names = FALSE, booktabs = TRUE) %>%
  kable_styling(latex_options = c("striped"))
FOOD_ID FOOD_NAME FOBI_ID FOBI_NAME
ID_00124 Beansprouts…130 FOODON:00002753 bean (whole)
ID_00127 Watercress FOODON:00002340 water food product
ID_00140 Beansprouts…171 FOODON:00002753 bean (whole)
ID_00143 Brocoli FOODON:03301713 broccoli floret (whole, raw)
ID_002 Beefburgers FOODON:00002737 beef hamburger (dish)

4.1.1 Network visualization of the annotated terms

Then, with the fobitools::fobi_graph() function we can visualize the annotated food terms with their corresponding FOBI relationships.

terms <- annotated_text$annotated %>%
  pull(FOBI_ID)

fobitools::fobi_graph(terms = terms,
                      get = NULL,
                      layout = "lgl",
                      labels = TRUE,
                      legend = TRUE,
                      labelsize = 6,
                      legendSize = 20)

4.2 How do I know which compounds are associated with my study food items?

Most likely we may be interested in knowing the food-related compounds in our study. Well, if so, once the foods are annotated we can obtain the metabolites associated with the annotated foods as follows:

inverse_rel <- fobitools::fobi %>%
  filter(id_BiomarkerOf %in% annotated_text$annotated$FOBI_ID) %>%
  dplyr::select(id_code, name, id_BiomarkerOf, FOBI) %>%
  dplyr::rename(METABOLITE_ID = 1, METABOLITE_NAME = 2, FOBI_ID = 3, METABOLITE_FOBI_ID = 4)

annotated_foods_and_metabolites <- left_join(annotated_text$annotated, inverse_rel, by = "FOBI_ID")

annotated_foods_and_metabolites %>%
  filter(!is.na(METABOLITE_ID)) %>%
  dplyr::slice(1L:10L) %>%
  kbl(row.names = FALSE, booktabs = TRUE) %>%
  kable_styling(latex_options = c("striped"))
FOOD_ID FOOD_NAME FOBI_ID FOBI_NAME METABOLITE_ID METABOLITE_NAME METABOLITE_FOBI_ID
ID_00101 Grapefruit FOODON:03301702 grapefruit (whole, raw) CHEBI:17377 bergaptol FOBI:030523
ID_00101 Grapefruit FOODON:03301702 grapefruit (whole, raw) FOBI:030524 bergaptol glucuronide FOBI:030524
ID_00101 Grapefruit FOODON:03301702 grapefruit (whole, raw) FOBI:030525 bergaptol sulfate FOBI:030525
ID_00102 Bananas FOODON:03311513 banana (whole, ripe) FOBI:050082 salsolinol FOBI:050082
ID_00102 Bananas FOODON:03311513 banana (whole, ripe) FOBI:050083 salsolinol 7-sulfate FOBI:050083
ID_00102 Bananas FOODON:03311513 banana (whole, ripe) FOBI:050084 salsolinol 6-sulfate FOBI:050084
ID_00103 Grapes FOODON:03301123 grape (whole, raw) CHEBI:15671 L-tartaric acid FOBI:030630
ID_00103 Grapes FOODON:03301123 grape (whole, raw) CHEBI:27881 resveratrol FOBI:030590
ID_00103 Grapes FOODON:03301123 grape (whole, raw) CHEBI:36002 cis-resveratrol FOBI:030591
ID_00103 Grapes FOODON:03301123 grape (whole, raw) CHEBI:4582 dihydroresveratrol FOBI:030600

5 Limitations

The FOBI ontology is currently in its first release version, so it does not yet include information on many metabolites, foods and food relationships. All future efforts will be directed at expanding this ontology, leading to a significant increase in the number of metabolites, foods (from FoodOn ontology (Dooley et al. 2018)) and metabolite-food relationships. The fobitools package provides the methodology for easy use of the FOBI ontology regardless of the amount of information it contains. Therefore, future FOBI improvements will also have a direct impact on the fobitools package, increasing its utility and allowing to perform, among others, more accurate, complete and robust dietary text annotations.

6 Session Information

sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] kableExtra_1.3.4 forcats_0.5.1    stringr_1.4.0    dplyr_1.0.6     
#>  [5] purrr_0.3.4      readr_1.4.0      tidyr_1.1.3      tibble_3.1.2    
#>  [9] ggplot2_3.3.3    tidyverse_1.3.1  fobitools_1.0.0  BiocStyle_2.20.0
#> 
#> loaded via a namespace (and not attached):
#>   [1] fgsea_1.18.0           colorspace_2.0-1       ellipsis_0.3.2        
#>   [4] class_7.3-19           qdapRegex_0.7.2        evd_2.3-3             
#>   [7] fs_1.5.0               rstudioapi_0.13        proxy_0.4-25          
#>  [10] farver_2.1.0           graphlayouts_0.7.1     ggrepel_0.9.1         
#>  [13] bit64_4.0.5            prodlim_2019.11.13     fansi_0.4.2           
#>  [16] lubridate_1.7.10       textclean_0.9.3        xml2_1.3.2            
#>  [19] splines_4.1.0          cachem_1.0.5           knitr_1.33            
#>  [22] polyclip_1.10-0        jsonlite_1.7.2         RecordLinkage_0.4-12.1
#>  [25] broom_0.7.6            dbplyr_2.1.1           ggforce_0.3.3         
#>  [28] BiocManager_1.30.15    compiler_4.1.0         httr_1.4.2            
#>  [31] tictoc_1.0.1           backports_1.2.1        assertthat_0.2.1      
#>  [34] Matrix_1.3-3           fastmap_1.1.0          ontologyIndex_2.7     
#>  [37] cli_2.5.0              tweenr_1.0.2           htmltools_0.5.1.1     
#>  [40] tools_4.1.0            igraph_1.2.6           gtable_0.3.0          
#>  [43] glue_1.4.2             fastmatch_1.1-0        Rcpp_1.0.6            
#>  [46] lexicon_1.2.1          cellranger_1.1.0       jquerylib_0.1.4       
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#>  [52] xfun_0.23              ps_1.6.0               rvest_1.0.0           
#>  [55] lifecycle_1.0.0        MASS_7.3-54            scales_1.1.1          
#>  [58] ipred_0.9-11           tidygraph_1.2.0        vroom_1.4.0           
#>  [61] clisymbols_1.2.0       hms_1.1.0              parallel_4.1.0        
#>  [64] yaml_2.2.1             memoise_2.0.0          gridExtra_2.3         
#>  [67] sass_0.4.0             rpart_4.1-15           stringi_1.6.2         
#>  [70] RSQLite_2.2.7          highr_0.9              e1071_1.7-6           
#>  [73] BiocParallel_1.26.0    lava_1.6.9             ada_2.0-5             
#>  [76] systemfonts_1.0.2      rlang_0.4.11           pkgconfig_2.0.3       
#>  [79] evaluate_0.14          lattice_0.20-44        labeling_0.4.2        
#>  [82] bit_4.0.4              tidyselect_1.1.1       magrittr_2.0.1        
#>  [85] bookdown_0.22          R6_2.5.0               magick_2.7.2          
#>  [88] generics_0.1.0         DBI_1.1.1              pillar_1.6.1          
#>  [91] haven_2.4.1            withr_2.4.2            survival_3.2-11       
#>  [94] nnet_7.3-16            modelr_0.1.8           crayon_1.4.1          
#>  [97] utf8_1.2.1             rmarkdown_2.8          viridis_0.6.1         
#> [100] syuzhet_1.0.6          grid_4.1.0             readxl_1.3.1          
#> [103] data.table_1.14.0      blob_1.2.1             webshot_0.5.2         
#> [106] reprex_2.0.0           digest_0.6.27          xtable_1.8-4          
#> [109] ff_4.0.4               munsell_0.5.0          viridisLite_0.4.0     
#> [112] bslib_0.2.5.1

References

Castellano-Escuder, Pol, Raúl González-Domı́nguez, David S Wishart, Cristina Andrés-Lacueva, and Alex Sánchez-Pla. 2020. “FOBI: An Ontology to Represent Food Intake Data and Associate It with Metabolomic Data.” Database 2020.

Dooley, Damion M, Emma J Griffiths, Gurinder S Gosal, Pier L Buttigieg, Robert Hoehndorf, Matthew C Lange, Lynn M Schriml, Fiona SL Brinkman, and William WL Hsiao. 2018. “FoodOn: A Harmonized Food Ontology to Increase Global Food Traceability, Quality Control and Data Integration.” Npj Science of Food 2 (1): 1–10.