Taxonomy Database - mariehoffmann/isPCR GitHub Wiki

Schema

Node

extracted from nodes.dmp

Attributes	Constraint	Comment
tax_id	PRIMARY KEY	node id in GenBank taxonomy database
parent_tax_id		parent node id in GenBank taxonomy database
rank		rank of this node (superkingdom, kingdom, ...)

Names

All known names assigned to a tax_id are listed in the table. If there exists multiple names for a tax_id, there will be as many entries with the same tax_id. Rows are extracted from names.dmp.

Attributes	Constraint	Comment
tax_id	PRIMARY KEY, FOREIGN KEY	the id of node associated with this name
name_txt	PRIMARY KEY	name itself
unique_name		the unique variant of this name if name not unique

Lineage

For each taxonomic node identified by its unique tax_id, a list of ancestors is stored from most far to closest one. Data is extracted per default from NCBI's taxidlineage.dmp.

Attributes	Constraint	Comment
tax_id	PRIMARY KEY, FOREIGN KEY
lineage		list of tax_ids

Accessions

This table contains a pre-processed tax_id to accession number resolution, such that we are able to retrieve all existing accessions given a tax_id. Data is extracted per default from NCBI's nt(.fast) file and Node and Names tables.

Attributes	Constraint	Comment
tax_id	PRIMARY KEY, FOREIGN KEY	only unique in combination with accession
accession	PRIMARY KEY