NCBI provides taxonomy dump files for users who need a local copy of the taxonomy database through its public Taxonomy FTP site. To download the complete taxonomy database, choose one of the following:  

• Legacy taxonomy dump 
• Expanded taxonomy dump 

Both archives contain the core taxonomy files, including: 

• nodes.dmp 
• names.dmp 
• merged.dmp 
• delnodes.dmp 

Do not use NCBI Datasets command-line tools REST API to download the entire taxonomy. 

Use NCBI Datasets command-line tools and REST API to retrieve the full lineage (parents and children) for one or more taxids or taxonomic names. For installation instructions, command syntax, and examples, see the following: 

• NCBI Datasets how to: Get taxonomy metadata 
• NCBI Datasets command-line reference: Datasets summary taxonomy
• NCBI Datasets command-line reference: Datasets download taxonomy 
• NCBI Datasets v2 REST API reference 

Legacy Taxonomy Dump 

Choose the legacy taxonomy dump option when your workflow only needs the basic taxonomy tree and names. 

wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip 

Extract 

unzip taxdmp.zip  

Expanded Taxonomy Dump (recommended) 

Choose the expanded taxonomy dump to download all of the core taxonomy files included in the legacy dump along with additional information such as lineage, type material, and host information. 

wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.zip 

Extract 

 unzip new_taxdump.zip 

More Information 

For details about the files and format, see the New Tax Dump Read Me.  

To track updates and changes over time, see the monthly Tax Dump Archive (from 2014 onwards).