# install.packages("BiocManager")
BiocManager::install("fobitools")

library(fobitools)

library(dplyr)
library(kableExtra)

# select 300 random metabolites from FOBI
idx_universe <- sample(nrow(fobitools::idmap), 300, replace = FALSE)
metaboliteUniverse <- fobitools::idmap %>%
  dplyr::slice(idx_universe) %>%
  pull(FOBI)

# select 10 random metabolites from metaboliteUniverse that are associated with 'Red meat' (FOBI:0193), 
# 'Lean meat' (FOBI:0185) , 'egg food product' (FOODON:00001274), 
# or 'grape (whole, raw)' (FOODON:03301702)
fobi_subset <- fobitools::fobi %>% # equivalent to `parse_fobi()`
  filter(FOBI %in% metaboliteUniverse) %>%
  filter(id_BiomarkerOf %in% c("FOBI:0193", "FOBI:0185", "FOODON:00001274", "FOODON:03301702")) %>%
  dplyr::slice(sample(nrow(.), 10, replace = FALSE))

metaboliteList <- fobi_subset %>%
  pull(FOBI)

fobitools::ora(metaboliteList = metaboliteList, 
               metaboliteUniverse = metaboliteUniverse, 
               subOntology = "food", 
               pvalCutoff = 0.01)

terms <- fobi_subset %>%
  pull(id_code)

# create the associated graph
fobitools::fobi_graph(terms = terms, 
                      get = "anc",
                      labels = TRUE,
                      legend = TRUE)

sessionInfo()
#> R version 4.6.0 (2026-04-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [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       
#> 
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] kableExtra_1.4.0 lubridate_1.9.5  forcats_1.0.1    stringr_1.6.0   
#>  [5] dplyr_1.2.1      purrr_1.2.2      readr_2.2.0      tidyr_1.3.2     
#>  [9] tibble_3.3.1     ggplot2_4.0.3    tidyverse_2.0.0  fobitools_1.20.0
#> [13] BiocStyle_2.40.0
#> 
#> loaded via a namespace (and not attached):
#>   [1] DBI_1.3.0              qdapRegex_0.7.10       gridExtra_2.3         
#>   [4] rlang_1.2.0            magrittr_2.0.5         e1071_1.7-17          
#>   [7] compiler_4.6.0         RSQLite_3.53.1         systemfonts_1.3.2     
#>  [10] vctrs_0.7.3            pkgconfig_2.0.3        crayon_1.5.3          
#>  [13] fastmap_1.2.0          labeling_0.4.3         ggraph_2.2.2          
#>  [16] rmarkdown_2.31         prodlim_2026.03.11     tzdb_0.5.0            
#>  [19] bit_4.6.0              xfun_0.57              cachem_1.1.0          
#>  [22] jsonlite_2.0.0         blob_1.3.0             tictoc_1.2.1          
#>  [25] BiocParallel_1.46.0    tweenr_2.0.3           syuzhet_1.0.7         
#>  [28] parallel_4.6.0         R6_2.6.1               bslib_0.11.0          
#>  [31] stringi_1.8.7          RColorBrewer_1.1-3     textclean_0.9.7       
#>  [34] parallelly_1.47.0      rpart_4.1.27           jquerylib_0.1.4       
#>  [37] Rcpp_1.1.1-1.1         knitr_1.51             future.apply_1.20.2   
#>  [40] clisymbols_1.2.0       timechange_0.4.0       Matrix_1.7-5          
#>  [43] splines_4.6.0          nnet_7.3-20            igraph_2.3.1          
#>  [46] tidyselect_1.2.1       rstudioapi_0.18.0      yaml_2.3.12           
#>  [49] viridis_0.6.5          codetools_0.2-20       listenv_0.10.1        
#>  [52] lattice_0.22-9         withr_3.0.2            S7_0.2.2              
#>  [55] evaluate_1.0.5         ontologyIndex_2.12     future_1.70.0         
#>  [58] survival_3.8-6         proxy_0.4-29           polyclip_1.10-7       
#>  [61] xml2_1.5.2             pillar_1.11.1          BiocManager_1.30.27   
#>  [64] lexicon_1.2.1          generics_0.1.4         vroom_1.7.1           
#>  [67] hms_1.1.4              scales_1.4.0           ff_4.5.2              
#>  [70] globals_0.19.1         xtable_1.8-8           class_7.3-23          
#>  [73] glue_1.8.1             RecordLinkage_0.4-12.6 maketools_1.3.2       
#>  [76] tools_4.6.0            sys_3.4.3              data.table_1.18.4     
#>  [79] fgsea_1.38.0           buildtools_1.0.0       graphlayouts_1.2.3    
#>  [82] fastmatch_1.1-8        tidygraph_1.3.1        cowplot_1.2.0         
#>  [85] grid_4.6.0             ipred_0.9-15           ggforce_0.5.0         
#>  [88] cli_3.6.6              evd_2.3-7.1            textshaping_1.0.5     
#>  [91] viridisLite_0.4.3      svglite_2.2.2          lava_1.9.1            
#>  [94] gtable_0.3.6           sass_0.4.10            digest_0.6.39         
#>  [97] ggrepel_0.9.8          farver_2.1.2           memoise_2.0.1         
#> [100] htmltools_0.5.9        lifecycle_1.0.5        bit64_4.8.2           
#> [103] MASS_7.3-65