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$"))
#> + par_def_wei_ann dispatched
#> ✔ par_def_wei_ann completed [29ms, 5.05 kB]
#> + par_usr_wei_ann dispatched
#> TRACE [2025-05-09 13:25:46] Loading default params
#> TRACE [2025-05-09 13:25:46] All params
#> TRACE [2025-05-09 13:25:46] Small params
#> TRACE [2025-05-09 13:25:46] Advanced params
#> TRACE [2025-05-09 13:25:46] Changing params
#> TRACE [2025-05-09 13:25:46] Changing filenames
#> TRACE [2025-05-09 13:25:48] Exporting params
#> ✔ par_usr_wei_ann completed [1.5s, 1.76 kB]
#> + par_wei_ann dispatched
#> ✔ par_wei_ann completed [2ms, 931 B]
#> + ann_pre dispatched
#> TRACE [2025-05-09 13:25:48] Loading files ...
#> TRACE [2025-05-09 13:25:48] ... components
#> TRACE [2025-05-09 13:25:48] ... edges
#> TRACE [2025-05-09 13:25:48] ... structure-organism pairs
#> TRACE [2025-05-09 13:26:02] ... canopus
#> TRACE [2025-05-09 13:26:02] ... formula
#> TRACE [2025-05-09 13:26:03] ... annotations
#> TRACE [2025-05-09 13:26:04] Initial annotations:
#> INFO [2025-05-09 13:26:04]  candidate_library      n
#>           TIMA MS1 161108
#>    ISDB - Wikidata   4556
#>             SIRIUS    479
#>             merlin    156
#>               gnps    139
#>           massbank     31
#> TRACE [2025-05-09 13:26:04] Re-arranging annotations
#> TRACE [2025-05-09 13:26:06] Adding biological organism metadata
#> TRACE [2025-05-09 13:26:06] Performing taxonomically informed scoring
#> TRACE [2025-05-09 13:26:09] Calculating biological score at all levels ...
#> TRACE [2025-05-09 13:26:09] ... domain
#> TRACE [2025-05-09 13:26:09] ... kingdom
#> TRACE [2025-05-09 13:26:09] ... phylum
#> TRACE [2025-05-09 13:26:09] ... class
#> TRACE [2025-05-09 13:26:09] ... order
#> TRACE [2025-05-09 13:26:09] ... family
#> TRACE [2025-05-09 13:26:09] ... tribe
#> TRACE [2025-05-09 13:26:09] ... genus
#> TRACE [2025-05-09 13:26:09] ... species
#> TRACE [2025-05-09 13:26:09] ... varietas
#> TRACE [2025-05-09 13:26:09] Keeping best biological score
#> INFO [2025-05-09 13:26:10] Taxonomically informed metabolite annotation led to 
#> 31594 annotations reranked at the kingdom level, 
#> 31336 annotations reranked at the phylum level, 
#> 26178 annotations reranked at the class level, 
#> 7503 annotations reranked at the order level, 
#> 6043 annotations reranked at the family level, 
#> 1020 annotations reranked at the tribe level, 
#> 812 annotations reranked at the genus level, 
#> 348 annotations reranked at the species level, and 
#> 0 annotations reranked at the variety level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! (for later predictions)
#> TRACE [2025-05-09 13:26:10] Calculating chemical consistency of features with at least 2 neighbors
#> TRACE [2025-05-09 13:26:10] Among all edges
#> TRACE [2025-05-09 13:26:10] ... at the (classyfire) kingdom level
#> TRACE [2025-05-09 13:26:10] ... at the (NPC) pathway level
#> TRACE [2025-05-09 13:26:10] ... at the (classyfire) superclass level
#> TRACE [2025-05-09 13:26:10] ... at the (NPC) superclass level
#> TRACE [2025-05-09 13:26:11] ... at the (classyfire) class level
#> TRACE [2025-05-09 13:26:11] ... at the (NPC) class level
#> TRACE [2025-05-09 13:26:11] ... at the (classyfire) parent level
#> TRACE [2025-05-09 13:26:11] Splitting already computed predictions
#> TRACE [2025-05-09 13:26:12] Joining all except -1 together
#> TRACE [2025-05-09 13:26:13] Adding already computed predictions back
#> TRACE [2025-05-09 13:26:14] Calculating chemical score at all levels ...
#> TRACE [2025-05-09 13:26:14] ... (classyfire) kingdom
#> TRACE [2025-05-09 13:26:14] ... (NPC) pathway
#> TRACE [2025-05-09 13:26:14] ... (classyfire) superclass
#> TRACE [2025-05-09 13:26:14] ... (NPC) superclass
#> TRACE [2025-05-09 13:26:14] ... (classyfire) class
#> TRACE [2025-05-09 13:26:14] ... (NPC) class
#> TRACE [2025-05-09 13:26:14] ... (classyfire) parent
#> TRACE [2025-05-09 13:26:14] ... keeping best chemical score
#> INFO [2025-05-09 13:26:14] Chemically informed scoring led to 
#> 13010 annotations reranked at the (classyfire) kingdom level, 
#> 9000 annotations reranked at the (NPC) pathway level, 
#> 6832 annotations reranked at the (classyfire) superclass level, 
#> 4475 annotations reranked at the (NPC) superclass level, 
#> 6832 annotations reranked at the (classyfire) class level, 
#> 4475 annotations reranked at the (NPC) class level, and 
#> 4464 annotations reranked at the (classyfire) parent level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!
#> INFO [2025-05-09 13:26:14] Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score 
#> TRACE [2025-05-09 13:26:14] Keeping high confidence candidates only
#> INFO [2025-05-09 13:26:14] Removed 165620 low confidence candidates out of the 167433 total ones.
#> INFO [2025-05-09 13:26:14] 1813 high confidence candidates remaining.
#> TRACE [2025-05-09 13:26:15] Processing full results
#> TRACE [2025-05-09 13:26:15] Adding initial metadata (RT, etc.) and simplifying columns
#> TRACE [2025-05-09 13:26:20] Selecting columns to export
#> TRACE [2025-05-09 13:26:20] Adding consensus again to droped candidates
#> TRACE [2025-05-09 13:26:21] Processing filtered results
#> TRACE [2025-05-09 13:26:21] Adding initial metadata (RT, etc.) and simplifying columns
#> TRACE [2025-05-09 13:26:25] Selecting columns to export
#> TRACE [2025-05-09 13:26:25] Adding consensus again to droped candidates
#> INFO [2025-05-09 13:26:27] Directory data/processed/20250509_132627_example created.
#> INFO [2025-05-09 13:26:27] ... path to used parameters is data/processed/20250509_132627_example
#> INFO [2025-05-09 13:26:27] ... path to used parameters is data/processed/20250509_132627_example
#> INFO [2025-05-09 13:26:27] ... path to export is data/processed/20250509_132627_example/example_results_filtered.tsv
#> INFO [2025-05-09 13:26:27] ... path to export is data/processed/20250509_132627_example/example_results.tsv
#> ✔ ann_pre completed [39s, 3.73 MB]
#> ✔ ended pipeline [42.4s, 4 completed, 122 skipped]
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

2025-05-09
