3 Performing Taxonomically Informed Metabolite Annotation • tima

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
#> Welcome to tima
#> To cite tima in publications use:  Rutz A, Allard P (2024). _tima: Taxonomically Informed Metabolite
#>   Annotation_. doi:10.5281/zenodo.5797920
#>   <https://doi.org/10.5281/zenodo.5797920>, R package, version 2.11.0.  Adriano Rutz; Miwa Dounoue-Kubo; et al. (25 October 2019).
#>   Taxonomically Informed Scoring Enhances Confidence in Natural
#>   Products Annotation. Frontiers in Plant Science. 10: 1329.
#>   doi:10.3389/FPLS.2019.01329. issn:1664-462X. pmc:PMC6824209.
#>   pmid:1708947. qid:Q91218352.To see these entries in BibTeX format, use 'format(<citation>,
#> bibtex=TRUE)', or 'toBibtex(.)'.
#> ✔ par_def_wei_ann completed [0.026 seconds, 4.976 kilobytes]
#> + par_usr_wei_ann dispatched
#> TRACE [2025-04-03 12:49:36] Loading default params
#> TRACE [2025-04-03 12:49:36] All params
#> TRACE [2025-04-03 12:49:36] Small params
#> TRACE [2025-04-03 12:49:36] Advanced params
#> TRACE [2025-04-03 12:49:36] Changing params
#> TRACE [2025-04-03 12:49:36] Changing filenames
#> TRACE [2025-04-03 12:49:37] Exporting params
#> → 126 targets ■■■■■■■■■■■■■■■■                 61 done [1.8s]
#> ✔ par_usr_wei_ann completed [1.339 seconds, 1.739 kilobytes]
#> → 126 targets ■■■■■■■■■■■■■■■■                 61 done [1.8s]+ par_wei_ann dispatched
#> → 126 targets ■■■■■■■■■■■■■■■■                 61 done [1.8s]✔ par_wei_ann completed [0.001 seconds, 922 bytes]
#> → 126 targets ■■■■■■■■■■■■■■■■                 61 done [1.8s]+ ann_pre dispatched
#> → 126 targets ■■■■■■■■■■■■■■■■                 61 done [1.8s]TRACE [2025-04-03 12:49:38] Loading files ...
#> TRACE [2025-04-03 12:49:38] ... components
#> TRACE [2025-04-03 12:49:38] ... edges
#> TRACE [2025-04-03 12:49:38] ... structure-organism pairs
#> TRACE [2025-04-03 12:49:52] ... canopus
#> TRACE [2025-04-03 12:49:52] ... formula
#> TRACE [2025-04-03 12:49:53] ... annotations
#> TRACE [2025-04-03 12:49:54] Initial annotations:
#> INFO [2025-04-03 12:49:54]  candidate_library      n
#>           TIMA MS1 216540
#>    ISDB - Wikidata   4556
#>             SIRIUS    479
#>             merlin    156
#>               gnps    139
#>           massbank     31
#> TRACE [2025-04-03 12:49:54] Re-arranging annotations
#> TRACE [2025-04-03 12:49:56] Adding biological organism metadata
#> TRACE [2025-04-03 12:49:57] Performing taxonomically informed scoring
#> TRACE [2025-04-03 12:49:59] Calculating biological score at all levels ...
#> TRACE [2025-04-03 12:49:59] ... domain
#> TRACE [2025-04-03 12:49:59] ... kingdom
#> TRACE [2025-04-03 12:49:59] ... phylum
#> TRACE [2025-04-03 12:49:59] ... class
#> TRACE [2025-04-03 12:49:59] ... order
#> TRACE [2025-04-03 12:49:59] ... family
#> TRACE [2025-04-03 12:49:59] ... tribe
#> TRACE [2025-04-03 12:49:59] ... genus
#> TRACE [2025-04-03 12:49:59] ... species
#> TRACE [2025-04-03 12:50:00] ... varietas
#> TRACE [2025-04-03 12:50:00] Keeping best biological score
#> INFO [2025-04-03 12:50:01] Taxonomically informed metabolite annotation led to 
#> 39239 annotations reranked at the kingdom level, 
#> 38878 annotations reranked at the phylum level, 
#> 33524 annotations reranked at the class level, 
#> 9538 annotations reranked at the order level, 
#> 7699 annotations reranked at the family level, 
#> 1169 annotations reranked at the tribe level, 
#> 921 annotations reranked at the genus level, 
#> 374 annotations reranked at the species level, and 
#> 0 annotations reranked at the variety level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT! (for later predictions)
#> TRACE [2025-04-03 12:50:01] Calculating chemical consistency of features with at least 2 neighbors
#> TRACE [2025-04-03 12:50:01] Among all edges
#> TRACE [2025-04-03 12:50:01] ... at the (classyfire) kingdom level
#> TRACE [2025-04-03 12:50:01] ... at the (NPC) pathway level
#> TRACE [2025-04-03 12:50:01] ... at the (classyfire) superclass level
#> TRACE [2025-04-03 12:50:01] ... at the (NPC) superclass level
#> TRACE [2025-04-03 12:50:03] ... at the (classyfire) class level
#> TRACE [2025-04-03 12:50:03] ... at the (NPC) class level
#> TRACE [2025-04-03 12:50:04] ... at the (classyfire) parent level
#> TRACE [2025-04-03 12:50:05] Splitting already computed predictions
#> TRACE [2025-04-03 12:50:05] Joining all except -1 together
#> TRACE [2025-04-03 12:50:06] Adding already computed predictions back
#> TRACE [2025-04-03 12:50:07] Calculating chemical score at all levels ...
#> TRACE [2025-04-03 12:50:07] ... (classyfire) kingdom
#> TRACE [2025-04-03 12:50:07] ... (NPC) pathway
#> TRACE [2025-04-03 12:50:07] ... (classyfire) superclass
#> TRACE [2025-04-03 12:50:07] ... (NPC) superclass
#> TRACE [2025-04-03 12:50:07] ... (classyfire) class
#> TRACE [2025-04-03 12:50:07] ... (NPC) class
#> TRACE [2025-04-03 12:50:07] ... (classyfire) parent
#> TRACE [2025-04-03 12:50:08] ... keeping best chemical score
#> INFO [2025-04-03 12:50:09] Chemically informed scoring led to 
#> 35288 annotations reranked at the (classyfire) kingdom level, 
#> 24287 annotations reranked at the (NPC) pathway level, 
#> 18183 annotations reranked at the (classyfire) superclass level, 
#> 10370 annotations reranked at the (NPC) superclass level, 
#> 18183 annotations reranked at the (classyfire) class level, 
#> 10370 annotations reranked at the (NPC) class level, and 
#> 10358 annotations reranked at the (classyfire) parent level. 
#> WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!
#> INFO [2025-04-03 12:50:09] Filtering top 1 candidates and keeping only MS1 candidates with minimum 0 biological score OR 0 chemical score 
#> TRACE [2025-04-03 12:50:09] Keeping high confidence candidates only
#> INFO [2025-04-03 12:50:09] Removed 220469 low confidence candidates out of the 222528 total ones.
#> INFO [2025-04-03 12:50:09] 2059 high confidence candidates remaining.
#> TRACE [2025-04-03 12:50:10] Adding initial metadata (RT, etc.) and simplifying columns
#> TRACE [2025-04-03 12:50:15] Selecting columns to export
#> TRACE [2025-04-03 12:50:15] Adding consensus again to droped candidates
#> INFO [2025-04-03 12:50:16] Directory data/processed/20250403_125016_example created.
#> INFO [2025-04-03 12:50:16] ... path to used parameters is data/processed/20250403_125016_example
#> INFO [2025-04-03 12:50:16] ... path to used parameters is data/processed/20250403_125016_example
#> INFO [2025-04-03 12:50:16] ... path to export is data/processed/20250403_125016_example/example_results.tsv
#> → 126 targets ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■  126 done [41s]
#> ✔ ann_pre completed [38.786 seconds, 2.165 megabytes]
#> → 126 targets ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■  126 done [41s]✔ ended pipeline [41.957 seconds, 4 completed, 122 skipped]
The final exported file is formatted in order to be easily imported in Cytoscape to further explore your data!
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