Question

Mapping NCBI Genome Accessions - NCBI Taxonomy IDs

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5.3 years ago

mar.ark.parr ▴ 40

Hi all,

I have list of NCBI genome accessions (SAMN02441064, NC_014374, NZ_ACYB00000000 ...) and would like to know taxonomic IDs of the species that they belong to.

Is there a mapping file somewhere? Or how can I find their taxonomic IDs programmatically?

Thanks in advance, Marina

genome taxonomy GenBank NCBI • 3.2k views

ADD COMMENT • link updated 5.3 years ago by GenoMax 147k • written 5.3 years ago by mar.ark.parr ▴ 40

score 2 · Answer 1 · 2019-08-14

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5.3 years ago

Andrzej Zielezinski 11k

The directory ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ provides mapping files between the accession.version (from a nucleotide, protein, WGS or TSA sequence record) and a taxonomy ID.

ADD COMMENT • link 5.3 years ago by Andrzej Zielezinski 11k

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Thanks a lot for the answer!

ADD REPLY • link 5.3 years ago by mar.ark.parr ▴ 40

score 2 · Answer 2 · 2019-08-14

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5.3 years ago

GenoMax 147k

If these are all nucleotide accessions then you can also use NCBI EntrezDirect:

$ esearch -db nuccore -query "SAMN02441064" | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element TaxId
1052825
$ esearch -db nuccore -query "NC_014374" | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element TaxId
666510