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Adding a custom synonym file to the ensembleTax workflow

D Catlett 8/26/2020

Overview

This vignette demonstrates how to use a custom collection of taxonomic synonyms with taxmapper. The file in this repo called "tax_synonyms_FINAL.csv" contains taxonomic synonyms for eukaryotes compiled by the ensembleTax authors, and these are the default synonyms searched by taxmapper in the event that no matches are found when mapping a particular taxonomic name. This list is not comprehensive and contributed additions to this list are welcome.

Example synonym data

Here we'll read in the file and how it looks so you can use a custom file with taxmapper if you'd like.

syn <- utils::read.csv("~/Documents/R/amplicon_bioinformatics/taxonomy_pipeline/tax_table_mapping/tax_synonyms_FINAL.csv")
class(syn)
## [1] "data.frame"

typeof(syn)
## [1] "list"

head(syn)
##              Name_1          Name_2 Name_3 Name_4 Name_5 Name_6 Name_7
## 1       Neoceratium       Ceratium    <NA>   <NA>   <NA>   <NA>   <NA>
## 2     Siphonophorae    Siphonophora   <NA>   <NA>   <NA>   <NA>   <NA>
## 3    Mamiellales_fa     Mamiellales   <NA>   <NA>   <NA>   <NA>   <NA>
## 4        Eurotiales Elaphomycetales   <NA>   <NA>   <NA>   <NA>   <NA>
## 5 Gymnodinium_clade     Gymnodinium   <NA>   <NA>   <NA>   <NA>   <NA>
## 6 Gymnodiniphycidae   Gymnodinoidia   <NA>   <NA>   <NA>   <NA>   <NA>
##                                                                                                                                                  References
## 1                                                                          https://img.algaebase.org/pdf/C13170E01dfb92CEDCGWI1A1AD34/gomez_neoceratium.pdf
## 2 https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=42759&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock
## 3                                                                                                                                       dylans common sense
## 4  https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=5042&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock
## 5                                                                                                                                       dylans common sense
## 6                                                                                                       https://mmbr.asm.org/content/mmbr/57/4/953.full.pdf
##   Notes.References X                                                    X.1
## 1                                                                          
## 2                                                                          
## 3                                                                          
## 4                                                                          
## 5                                                                          
## 6                    http://faculty.une.edu/cas/lfritz/old_pages/notes8.htm

...that's it. That's what it is. You can have as many Name_x and reference/note columns as you want in there. The important part is that the taxonomic synonyms are found in columns with names that start with "Name". When taxmapper can't find an exact match for a particular taxonomic name, it finds the row in the synonym.file containing that name, and compiles all the other values in that row (excluding NA) that are found in columns with "Name" in their name.