Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
2
0
Entering edit mode
3.3 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 • 2.2k views
ADD COMMENT
2
Entering edit mode
3.3 years ago

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
0
Entering edit mode

Thanks a lot for the answer!

ADD REPLY
2
Entering edit mode
3.3 years ago
GenoMax 123k

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
ADD COMMENT
0
Entering edit mode

Thank you for the answer!

ADD REPLY

Login before adding your answer.

Traffic: 1365 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6