Connection-classes: Database Connections

In gschofl/ncbi: Retrieve data from NCBI.

Description

‘TaxonDBConnection’: A connection to an SQLite database containing the NCBI taxonomy organised in two tables:

Usage

  new_TaxonDBConnection(...)

  new_GeneidDBConnection(...)

Details

nodes with fields:

• tax_id CHAR(10) Primary key

• parent_id CHAR(10)

• rank VARCHAR(50)

• embl_code CHAR(2)

• division_id CHAR(2)

names with fields:

• tax_id CHAR(10) Primary key

• tax_name VARCHAR(200)

• unique_name VARCHAR(100)

• class VARCHAR(50)

‘GeneidDBConnection’: A connection to an SQLite database linking NCBI Gene IDs to Taxids.

See Also

The constructors taxonDBConnect, geneidDBConnect.

gschofl/ncbi documentation built on May 17, 2019, 8:53 a.m.