3 Performing Taxonomically Informed Metabolite Annotation

This vignette describes how Taxonomically Informed Metabolite Annotation is performed. If you followed all previous steps successfully, this should be a piece of cake, you deserve it!
targets::tar_make(names = tidyselect::matches("ann_pre$"))
#> ✔ skipping targets (1 so far)...
#> ▶ dispatched target par_def_wei_ann
#> ● completed target par_def_wei_ann [0 seconds, 4.96 kilobytes]
#> ▶ dispatched target lib_spe_is_lot_neg
#> File already exists. Skipping.
#> ● completed target lib_spe_is_lot_neg [0 seconds, 168.722 megabytes]
#> ▶ dispatched target lib_spe_is_lot_pos
#> File already exists. Skipping.
#> ● completed target lib_spe_is_lot_pos [0 seconds, 221.809 megabytes]
#> ▶ dispatched target lib_sop_lot
#> A file with the same size is already present. Skipping
#> ● completed target lib_sop_lot [2.031 seconds, 92.98 megabytes]
#> ✔ skipping targets (46 so far)...
#> ▶ dispatched target par_usr_wei_ann
#> 2025-01-16 07:44:57 Loading default params 
#> 2025-01-16 07:44:57 All params 
#> 2025-01-16 07:44:57 Small params 
#> 2025-01-16 07:44:57 Changing params 
#> 2025-01-16 07:44:57 Changing filenames 
#> 2025-01-16 07:44:57 Exporting params ... 
#> ● completed target par_usr_wei_ann [0.299 seconds, 1.739 kilobytes]
#> ▶ dispatched target par_wei_ann
#> ● completed target par_wei_ann [0 seconds, 921 bytes]
#> ▶ dispatched target ann_pre
#> 2025-01-16 07:44:57 Loading files ... 
#> 2025-01-16 07:44:57 ... components 
#> 2025-01-16 07:44:57 ... edges 
#> 2025-01-16 07:44:57 ... structure-organism pairs 
#> 2025-01-16 07:45:01 ... canopus 
#> 2025-01-16 07:45:01 ... formula 
#> 2025-01-16 07:45:01 ... annotations 
#> 2025-01-16 07:45:03 Got c("ISDB", "MassBank - 2024.06", "TIMA MS1") initial annotations 
#>  2025-01-16 07:45:03 Got c(976, 59, 289567) initial annotations 
#> 2025-01-16 07:45:04 Re-arranging annotations 
#> 2025-01-16 07:45:05 adding biological organism metadata 
#> 2025-01-16 07:45:06 performing taxonomically informed scoring 
#> 2025-01-16 07:45:06 filtering top  3  candidates and keeping only MS1 candidates with minimum 
#>  0  biological score 
#>  OR 0 chemical score 
#>  
#> 2025-01-16 07:45:06 adding "notClassified" 
#>  
#> 2025-01-16 07:45:06 calculating biological score at all levels ... 
#>  
#> 2025-01-16 07:45:06 ... domain 
#>  
#> 2025-01-16 07:45:06 ... kingdom 
#>  
#> 2025-01-16 07:45:06 ... phylum 
#>  
#> 2025-01-16 07:45:06 ... class 
#>  
#> 2025-01-16 07:45:06 ... order 
#>  
#> 2025-01-16 07:45:06 ... family 
#>  
#> 2025-01-16 07:45:06 ... tribe 
#>  
#> 2025-01-16 07:45:06 ... genus 
#>  
#> 2025-01-16 07:45:06 ... species 
#>  
#> 2025-01-16 07:45:07 ... varietas 
#>  
#> 2025-01-16 07:45:07 ... keeping best biological score 
#>  
#> 2025-01-16 07:45:08 ... calculating weighted biological score 
#>  
#> 2025-01-16 07:45:09 taxonomically informed scoring led to 
#>  47466 annotations reranked at the kingdom level, 
#>  47003 annotations reranked at the phylum level, 
#>  39312 annotations reranked at the class level, 
#>  11411 annotations reranked at the order level, 
#>  9388 annotations reranked at the family level, 
#>  1538 annotations reranked at the tribe level, 
#>  1220 annotations reranked at the genus level, 
#>  464 annotations reranked at the species level, 
#>  and 0 annotations reranked at the variety level. 
#>  WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! (for later predictions) 
#> 2025-01-16 07:45:09 calculating chemical consistency
#>               features with at least 2 neighbors ... 
#>  
#> 2025-01-16 07:45:09 ... among all edges ... 
#>  
#> 2025-01-16 07:45:09 ... at the (classyfire) kingdom level 
#>  
#> 2025-01-16 07:45:09 ... at the (NPC) pathway level 
#>  
#> 2025-01-16 07:45:09 ... at the (classyfire) superclass level 
#>  
#> 2025-01-16 07:45:10 ... at the (NPC) superclass level 
#>  
#> 2025-01-16 07:45:10 ... at the (classyfire) class level 
#>  
#> 2025-01-16 07:45:11 ... at the (NPC) class level 
#>  
#> 2025-01-16 07:45:12 ... at the (classyfire) parent level 
#>  
#> 2025-01-16 07:45:13 splitting already computed predictions 
#>  
#> 2025-01-16 07:45:14 joining all except -1 together 
#>  
#> 2025-01-16 07:45:15 adding dummy consistency for features
#>               with less than 2 neighbors 
#>  
#> 2025-01-16 07:45:15 adding already computed predictions back 
#>  
#> 2025-01-16 07:45:16 calculating chemical score at all levels ... 
#>  
#> 2025-01-16 07:45:16 ... (classyfire) kingdom 
#>  
#> 2025-01-16 07:45:16 ... (NPC) pathway 
#>  
#> 2025-01-16 07:45:17 ... (classyfire) superclass 
#>  
#> 2025-01-16 07:45:17 ... (NPC) superclass 
#>  
#> 2025-01-16 07:45:17 ... (classyfire) class 
#>  
#> 2025-01-16 07:45:17 ... (NPC) class 
#>  
#> 2025-01-16 07:45:17 ... (classyfire) parent 
#>  
#> 2025-01-16 07:45:17 ... keeping best chemical score 
#>  
#> 2025-01-16 07:45:17 ... calculating weighted chemical score 
#>  
#> 2025-01-16 07:45:18 chemically informed scoring led to 
#>  36534 annotations reranked at the (classyfire) kingdom level, 
#>  24014 annotations reranked at the (NPC) pathway level, 
#>  17629 annotations reranked at the (classyfire) superclass level, 
#>  10188 annotations reranked at the (NPC) superclass level, 
#>  17629 annotations reranked at the (classyfire) class level, 
#>  9871 annotations reranked at the (NPC) class level, and 
#>  9388 annotations reranked at the (classyfire) parent level. 
#>  WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! 
#> 2025-01-16 07:45:18 Keeping high confidence candidates only... 
#> 2025-01-16 07:45:18 Removed 289280 low confidence candidates out of the 291312 total ones. 
#> 2025-01-16 07:45:18 2032 high confidence candidates remaining. 
#> 2025-01-16 07:45:19 adding initial metadata (RT, etc.) and simplifying columns 
#>  
#> 2025-01-16 07:45:19 adding references 
#>  
#> 2025-01-16 07:45:20 selecting columns to export 
#>  
#> 2025-01-16 07:45:20 adding consensus again to droped candidates 
#>  
#> 2025-01-16 07:45:22 Exporting ... 
#> Directory data/processed/250116_074522_example created.
#> 2025-01-16 07:45:22 ... path to used parameters is data/processed/250116_074522_example 
#> 2025-01-16 07:45:22 ... path to used parameters is data/processed/250116_074522_example 
#> 2025-01-16 07:45:22 ... path to export is data/processed/250116_074522_example/example_results.tsv 
#> ● completed target ann_pre [24.665 seconds, 2.332 megabytes]
#> ▶ ended pipeline [29.086 seconds]
#>
The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!
We hope you enjoyed using TIMA and are pleased to hear from you!
For any remark or suggestion, please fill an issue or feel free to contact us directly.
Adriano Rutz

2025-01-16
