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Core Project Schema Extensions

Robert J. Gifford edited this page Sep 30, 2024 · 4 revisions

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
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