How to search NCBI by taxa

I'm currently trying to get NCBI to return all virus taxa at a specific rank with a single search query.

Currently, my query:

Genus[Rank] AND virus

in the Taxonomy database is returning few results, where I would expect around 120 hits corresponding to the rough number of known virus genera.

ncbi taxonomy

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updated 4.8 years ago by shenwei356

• written 4.8 years ago by charlieclark1ee •

As far as I see there are no Genus level classification for viruses. For example a query like this using EntrezDirect:

$ esearch -db taxonomy -query "viruses [orgn]" | esummary

give us the following (one example)

<DocumentSummary><Id>2858412</Id>
    <Status>active</Status>
    <Rank>species</Rank>
    <Division>viruses</Division>
    <ScientificName>Blueberry virus T</ScientificName>
    <CommonName></CommonName>
    <TaxId>2858412</TaxId>
    <AkaTaxId>0</AkaTaxId>
    <Genus></Genus>
    <Species></Species>
    <Subsp></Subsp>
    <ModificationDate>2021/07/27 00:00</ModificationDate>
    <GenBankDivision>Viruses</GenBankDivision>
</DocumentSummary>

So the Rank is set to species for all records in taxonomy db. So you can extract the information above to get

$ esearch -db taxonomy -query "viruses [orgn]" | esummary | xtract -pattern DocumentSummary -element Rank,Division,ScientificName

species viruses Vibrio phage 11E33.1
species viruses Erwinia phage pEa_SNUABM_54
species viruses Erwinia phage pEa_SNUABM_49
species viruses Erwinia phage pEa_SNUABM_48

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written 4.8 years ago by GenoMax

The complete lineage from Taxonomy browser shows the genus rank is Tepovirus. esummary's bug?

$ esearch -db taxonomy -query "viruses [orgn] Tepovirus" | esummary | xtract -pattern DocumentSummary -element Rank,Division,ScientificName
genus   viruses Tepovirus

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written 4.8 years ago by shenwei356

1 answer

You can use a local tool taxonkit to list all virus taxIds, filter these at genus rank, and print lineage information:

$ time taxonkit list --ids 10239 \
    | taxonkit filter --equal-to genus \
    | taxonkit lineage --show-rank --show-name \
    > virus.genus.tsv

real    0m1.842s
user    0m8.335s
sys     0m0.619s

$ head -n 5 virus.genus.tsv 
10473   Viruses;Plasmaviridae;Plasmavirus       Plasmavirus     genus
10475   Viruses;Fuselloviridae;Alphafusellovirus        Alphafusellovirus       genus
1299307 Viruses;Fuselloviridae;Betafusellovirus Betafusellovirus        genus
10483   Viruses;Polydnaviridae;Ichnovirus       Ichnovirus      genus
10485   Viruses;Polydnaviridae;Bracovirus       Bracovirus      genus

$ wc -l virus.genus.tsv 
2193 virus.genus.tsv

So, there are 2193 viral genera ( taxdump 2021-10-01).

The results may be different, because the NCBI Taxonomy changes every day.

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written 4.8 years ago by shenwei356