Core Project Schema Extensions - giffordlabcvr/Parvovirus-GLUE GitHub Wiki

At the heart of each GLUE project is a relational database with an extensible schema.

Parvovirus-GLUE extends GLUE's core schema with additional tables and data fields. These schema extensions are defined in this project build file.

Sequence table extensions

The sequence table of GLUE's core schema was extended to include the following additional fields:

Parameter	Type	Definition
full_name	VARCHAR	Full name of the virus this sequence is derived from
name	VARCHAR	Abbreviated name of the virus this sequence is derived from
gb_create_date	GenBank	GenBank creation date of the sequence
gb_update_date	VARCHAR	Date of most recent GenBank update
subfamily	VARCHAR	Taxonomy - virus subfamily
genus	VARCHAR	Taxonomy - virus genus
clade	VARCHAR	Taxonomy - virus clade
length	INTEGER	Length of the sequence
pubmed_id	INTEGER	PubMed ID of manuscript associated with GenBank entry

Isolate table

A custom table was defined to capture isolate-associated information, as follows:

Parameter	Type	Definition
isolate	VARCHAR	Name of the isolate
host_sci_name	VARCHAR	Scientific name of the isolation species
country	VARCHAR	Country where virus was isolated
country_iso	VARCHAR	ISO code of country where virus was isolated
place_sampled	VARCHAR	Location of sampling (state, region, or city)
collection_year	INTEGER	Year virus was isolated
collection_month	VARCHAR	Month virus was isolated
collection_month_day	INTEGER	Day of month virus was isolated