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The Taxonomy Identifier

The Taxonomy ID (TaxID or taxon number) is a stable unique identifier for each taxonomic group in the NCBI Taxonomy Browser. The TaxID is seen in the GenBank records under feature source. For example,

  db_xref="taxon:170187"

is the TaxID for Streptococcus pneumoniae TIGR4.

In NMPDR, a genome is identified by a Genome ID that consists of the taxonomy ID as assigned by NCBI, followed by a version number. TaxID numbers usually correspond to a specific strain of a bacterial species. For example, 170187 corresponds to strain TIGR4 of Streptococcus pneumoniae. Sometimes genome sequences are made available for annotation by NMPDR and SEED prior to listing them with NCBI. In that case, there would be no TaxID specific to the strain. However, there is a TaxID corresponding to the species level. So, for example, the 1313 in the genome ID 1313.4 indicates Streptococcus pneumoniae and the 4 indicates the INV200 strain. Genome ID 1313.5, which differs only in the version number, is the OXC141 strain. Neither strain is listed at NCBI. On occasion, a new version of a genome will be put into the system that represents a more accurate sequencing of a genome already in NMPDR. When this happens, the new version replaces the old one, and the old genome ID gets a new version number.