Uppsala Multidisciplinary Center for Advanced Computational Science

NCBI taxonomy databases

Uppmax maintains local copies of the full set of NCBI Taxonomy databases (https://www.ncbi.nlm.nih.gov/guide/taxonomy/). Note that:

  • The local copies are found at /sw/data/uppnex/ncbi_taxonomy/latest
  • This also contains the subdirectories accession2taxid and biocollections containing those databases, see the tables below for their contents
  • latest is a symbolic link to a directory named from the date of the most recent update
  • There is also a subdirectory download containing the files as downloaded from NCBI
  • The installation of new versions begins the first day of each month at 00.10. The update may take several minutes up to an hour, depending on network speeds.
  • When new versions are successfully installed, the latest/ symbolic link is updated to point to the new dated directory
  • The previous version of the taxonomy databases are removed when the new versions have completed installation

See the links for each database for specifics on file format and contents. Many tools know how to make use of these databases; follow each tool's specific instructions. The files can be found in the indicated directories.

The databases available within /sw/data/uppnex/ncbi_taxonomy/latest are below. For more on each, see the links.

Name Source Notes
taxdump NCBI NCBI taxonomic database, in multiple .dmp files (see link)
taxcat NCBI NCBI taxonomic categories, in categories.dmp (see link)
gi_taxid_nucl.dmp NCBI Mappings of nucleotide GI to taxid (DEPRECATED)
gi_taxid_nucl_diff.dmp NCBI Differences between this and previous gi_taxid_nucl.dmp (DEPRECATED)
gi_taxid_prot.dmp NCBI Mappings of protein GI to taxid (DEPRECATED)
gi_taxid_prot_diff.dmp NCBI Differences between this and previous gi_taxid_prot.dmp (DEPRECATED)

The databases available within /sw/data/uppnex/ncbi_taxonomy/latest/accession2taxid are below. The dead_ files contain accession-to-TaxID mappings for dead (suppressed or withdrawn) sequence records. For more on each, see the links.

Name Source Notes
nucl_est.accession2taxid NCBI TaxID mapping for nucleotide records of type EST
nucl_gss.accession2taxid NCBI TaxID mapping for nucleotide records of type GSS
nucl_wgs.accession2taxid NCBI TaxID mapping for nucleotide records of type WGS or TSA
nucl_gb.accession2taxid NCBI TaxID mapping for nucleotide records not of the above types
prot.accession2taxid NCBI TaxID mapping for protein records
pdb.accession2taxid NCBI TaxID mapping for PDB protein records
dead_nucl.accession2taxid NCBI TaxID mapping for dead nucleotide records
dead_prot.accession2taxid NCBI TaxID mapping for dead protein records
dead_wgs.accession2taxid NCBI TaxID mapping for dead WGS or TSA records

The biocollections databases contain collections location information. coll_dump.txt is located within the /sw/data/uppnex/ncbi_taxonomy/latest directory. Those marked biocollections are located within the /sw/data/uppnex/ncbi_taxonomy/latest/biocollections directory.

Name Source Notes
coll_dump.txt NCBI
Collection_codes.txt NCBI biocollections
Institution_codes.txt NCBI biocollections
Unique_institution_codes.txt NCBI biocollections