NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)

Metagenomic tools like Kraken2, Centrifuge and KMCP support NCBI taxonomy in format of NCBI taxdump files.

While for virus, ICTV (International Committee on Taxonomy of Viruses) has its own taxonomy data.

A TaxonKit command, taxonkit create-taxdump is created to create NCBI-style taxdump files for any taxonomy dataset, including GTDB and ICTV.

Related projects:

• gtdb-taxdump: GTDB taxonomy taxdump files with trackable TaxIds
• taxid-changelog: NCBI taxonomic identifier (taxid) changelog
• taxonkit: A Practical and Efficient NCBI Taxonomy Toolkit

Table of Contents

• Download
• Method
  • Taxonomic hierarchy
  • Generation of TaxIds
  • Data and tools
  • Steps
• Results
  • Summary
  • SARS-COV-2
  • Taxa with same names
• Citation
• Contributing
• License

Download

The release page contains taxdump files.

Method

Taxonomic hierarchy

Virus Metadata Resource (VMR) provides taxonomy data of each release. Most viruses have the seven-ranks (Kingdom, Phylum, Class, Order, Family, Genus, Species), and each has a name.

Optionally, we assign the virus name a TaxId with the rank of "subspecies" below the species rank. Therefore, we can also track the changes of these assemblies via the TaxId later.

Generation of TaxIds

We just hash the taxon name (in lower case) of each taxon node to uint64 using xxhash and convert it to int32.

Taxa from different parents may have the same name. We assign different TaxIds to them. E.g., many viruses from different species have the same names.

Species             Virus name(s)
Jerseyvirus SETP3   Salmonella phage SETP7
Jerseyvirus SETP7   Salmonella phage SETP7

$ grep 'Salmonella phage SETP7' ictv-taxdump-with-subspecies/taxid.map 
Salmonella phage SETP7  2451596205,2451596206

$ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map \
    | csvtk unfold -Ht -f 2 -s , \
    | taxonkit reformat -f 'genus: {g}, species: {s}, subspecies: {S}' \
    --data-dir ictv-taxdump-with-subspecies/ -I 2
Salmonella phage 3-29   3010875164      genus: Epseptimavirus, species: Epseptimavirus ev329, subspecies: Salmonella phage 3-29
Salmonella phage 3-29   3010875165      genus: Epseptimavirus, species: Salmonella virus 329, subspecies: Salmonella phage 3-29

Data and tools

The taxonomy data is released as a .xlsx file at https://talk.ictvonline.org/taxonomy/vmr/.

TaxonKit v0.12.0 or a later version is needed. v0.14.0 or a later version is preferred. Since v0.14.0, taxonkit create-taxdump stores TaxIds in int32 following BLAST and DIAMOND, rather than uint32 in previous versions.

Steps

# download here: https://talk.ictvonline.org/taxonomy/vmr/
file="VMR_19-250422_MSL37.xlsx"

# conver xlsx to tsv
csvtk xlsx2csv "$file" \
    | csvtk csv2tab \
    > ictv.tsv

# remove M-BM- characters.
# https://askubuntu.com/questions/357248/how-to-remove-special-m-bm-character-with-sed
sed -i 's/\xc2\xa0/ /g' ictv.tsv

# remove leading and tailing blanks. e.g., "Escherichia phage PhaxI\t"
# remove a newline character and a space introduced by accident
csvtk replace -t -F -f "*" -p "^\s+|\s+$" ictv.tsv \
    | csvtk replace -t -F -f "*" -p "\n " -r "" \
    > ictv.clean.tsv

# choose columns, rename, and remove duplicates
csvtk cut -t -f "Realm,Subrealm,Kingdom,Subkingdom,Phylum,Subphylum,Class,Subclass,Order,Suborder,Family,Subfamily,Genus,Subgenus,Species,Virus name(s)" ictv.clean.tsv \
    | csvtk rename -t -f 1-16 -n "realm,subrealm,kingdom,subkingdom,phylum,subphylum,class,subclass,order,suborder,family,subfamily,genus,subgenus,species,subspecies" \
    | csvtk uniq   -t -f 1-16 \
    > ictv.taxonomy.tsv
    
# ------------------- create-taxdump -----------------------

# Option A: the lowest rank is species
taxonkit create-taxdump -A 16 --field-accession-re "^(.+)$" \
    ictv.taxonomy.tsv --out-dir ictv-taxdump/


# Option B: treat "Virus name(s)" as subspecies
taxonkit create-taxdump -A 16 --field-accession-re "^(.+)$" \
    ictv.taxonomy.tsv --out-dir ictv-taxdump-with-subspecies/ \
    --field-accession-as-subspecies

# ictv-taxdump/ is a subset of ictv-taxdump-with-subspecies/


# set the environmental variable for taxonkit,
# so we don't need specifiy "--data-dir ictv-taxdump" for each taxonkit command.
export TAXONKIT_DB=ictv-taxdump

Results

Set the environmental variable for taxonkit, so we don't need specifiy --data-dir ictv-taxdump for each taxonkit command.

export TAXONKIT_DB=ictv-taxdump-with-subspecies

Check more TaxonKit commands and usages

Summary

1. Count of all ranks (version: Virus Metadata Repository number 19, April 25 2022; MSL37)

    $ taxonkit list --ids 1 \
        | taxonkit lineage -L -r \
        | csvtk freq -H -t -f 2 -n \
        | csvtk pretty -H -t            
    no rank      1
    subphylum    2
    realm        6
    suborder     8
    kingdom      10
    phylum       17
    class        39
    order        65
    subgenus     84
    subfamily    168
    family       233
    genus        2606
    species      10434
    subspecies   10539
   

SARS-COV-2

1. The TaxId

    $ grep 'severe acute respiratory syndrome coronavirus 2' ictv-taxdump-with-subspecies/taxid.map 
    severe acute respiratory syndrome coronavirus 2        216305222
   

2. Complete lineage

    $ echo 216305222 | taxonkit lineage
    216305222      Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;severe acute respiratory syndrome coronavirus 2
   
    # another format
    $ echo 216305222 \
        | taxonkit lineage -t \
        | csvtk cut -Ht -f 3 \
        | csvtk unfold -Ht -f 1 -s ";" \
        | taxonkit lineage -r -n -L \
        | csvtk cut -Ht -f 1,3,2 \
        | csvtk pretty -Ht
    492247681    realm        Riboviria
    104708768    kingdom      Orthornavirae
    1506901452   phylum       Pisuviricota
    1091693597   class        Pisoniviricetes
    37745009     order        Nidovirales
    242661632    suborder     Cornidovirineae
    738421640    family       Coronaviridae
    1428506634   subfamily    Orthocoronavirinae
    906833049    genus        Betacoronavirus
    605136173    subgenus     Sarbecovirus
    1015862491   species      Severe acute respiratory syndrome-related coronavirus
    216305222    subspecies   severe acute respiratory syndrome coronavirus 2
   
    # in NCBI taxonomy
    $ echo 2697049 \
        | taxonkit lineage -t --data-dir ~/.taxonkit \
        | csvtk cut -Ht -f 3 \
        | csvtk unfold -Ht -f 1 -s ";" \
        | taxonkit lineage -r -n -L --data-dir ~/.taxonkit \
        | csvtk cut -Ht -f 1,3,2 \
        | csvtk pretty -Ht
    10239     superkingdom   Viruses
    2559587   clade          Riboviria
    2732396   kingdom        Orthornavirae
    2732408   phylum         Pisuviricota
    2732506   class          Pisoniviricetes
    76804     order          Nidovirales
    2499399   suborder       Cornidovirineae
    11118     family         Coronaviridae
    2501931   subfamily      Orthocoronavirinae
    694002    genus          Betacoronavirus
    2509511   subgenus       Sarbecovirus
    694009    species        Severe acute respiratory syndrome-related coronavirus
    2697049   no rank        Severe acute respiratory syndrome coronavirus 2
   

Taxa with same names

For examples species Epseptimavirus ev329 and Salmonella virus 329 both have a "Virus name" Salmonella phage 3-29.

    $ cat ictv.taxonomy.tsv \
        | csvtk grep -t -f subspecies -p 'Salmonella phage 3-29' \
        | csvtk cut -t -f genus,species,subspecies \
        | csvtk pretty -t
    genus            species                subspecies
    --------------   --------------------   ---------------------
    Epseptimavirus   Epseptimavirus ev329   Salmonella phage 3-29
    Epseptimavirus   Salmonella virus 329   Salmonella phage 3-29
    

They are assigned with different TaxIds and can be queried in taxid.map:

    $ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map 
    Salmonella phage 3-29   863391516,863391517
    
    $ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map \
        | csvtk unfold -Ht -f 2 -s , \
        | taxonkit lineage --data-dir ictv-taxdump-with-subspecies/ -i 2 
    Salmonella phage 3-29   863391516       Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Demerecviridae;Markadamsvirinae;Epseptimavirus;Epseptimavirus ev329;Salmonella phage 3-29
    Salmonella phage 3-29   863391517       Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Demerecviridae;Markadamsvirinae;Epseptimavirus;Salmonella virus 329;Salmonella phage 3-29

Citation

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit, Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

Contributing

We welcome pull requests, bug fixes and issue reports.

License

MIT License