Database Schema Extensions

Flu-GLUE extends GLUE's core schema through the incorporation of additional fields in the sequence table, as well as several custom tables.

Schema extensions for Flu-GLUE are defined in this project build file.

Fields added to 'sequence' table

Parameter	Type	Definition
full_name	VARCHAR	Full name of the virus this sequence is derived from
gb_primary_accession	VARCHAR	Primary GenBank accession number
gb_accession_version	VARCHAR	GenBank accession number with version
gb_create_date	DATE	GenBank creation date of the sequence
gb_update_date	DATE	Date of the most recent GenBank update
length	INTEGER	Length of the sequence
pubmed_id	VARCHAR	PubMed ID of the manuscript associated with this sequence
species	VARCHAR	Virus species
gb_segment	INTEGER	GenBank segment number
rec_segment	VARCHAR	Recognized segment, as assigned in Flu-GLUE
rec_subtype	VARCHAR	Recognized subtype specific to the segment
variation_present	BOOLEAN	Indicates if variations are present in the sequence

Fields included in 'isolate' table

The isolate table is linked to the main 'sequence' table via the sequence ID field. It contains information related to viral isolates, such as the species sampled, date, and location of sample.

Parameter	Type	Definition
isolate_id	VARCHAR	Identifier for the virus isolate
iso_host	VARCHAR	Scientific name of the host from which the virus was isolated
iso_source	VARCHAR	Source material from which the isolate was obtained
iso_country	VARCHAR	Country where the virus was isolated
iso_region	VARCHAR	Region within the country where the virus was isolated
iso_year	INTEGER	Year when the virus was isolated
iso_month	VARCHAR	Month when the virus was isolated
iso_day	INTEGER	Day when the virus was isolated
lab_host	VARCHAR	Laboratory host used for propagation
cg_subtype	VARCHAR	Subtype determined by computational genotyping
gb_subtype	VARCHAR	Subtype assigned in GenBank
complete_genome	BOOLEAN	Indicates if the isolate contains a complete genome

Fields included in 'flu_replacement' table

The flu_replacement table contains data on amino acid replacements. Each row represents a specific replacement, along with its biochemical properties.

Parameter	Type	Definition
display_name	VARCHAR	Display name of the amino acid replacement
codon_label	VARCHAR	Codon label (position) where the replacement occurs
codon_label_int	INTEGER	Codon position as an integer
reference_aa	VARCHAR	Reference amino acid
reference_nt	INTEGER	Nucleotide position corresponding to the codon
replacement_aa	VARCHAR	Amino acid after the replacement
num_seqs	INTEGER	Number of sequences containing the replacement
radical_hanada_category_i	BOOLEAN	Hanada classification category I (true if radical)
radical_hanada_category_ii	BOOLEAN	Hanada classification category II (true if radical)
radical_hanada_category_iii	BOOLEAN	Hanada classification category III (true if radical)
grantham_distance_double	DOUBLE	Grantham distance between the reference and replacement amino acids
grantham_distance_int	INTEGER	Grantham distance as an integer
miyata_distance	DOUBLE	Miyata biochemical distance between the amino acids
parent_feature	VARCHAR	Parent feature where the replacement is located
parent_codon_label	VARCHAR	Codon label of the parent feature

Fields included in 'host' table

The host table stores information about the host organisms from which the influenza viruses were isolated.

Parameter	Type	Definition
taxon_name	VARCHAR	Scientific taxon name of the host
taxonomic_level	VARCHAR	Taxonomic level (e.g., species, genus)
common_name	VARCHAR	Common name of the host

Links between tables

Flu-GLUE extends the core schema by linking several tables to represent relationships between sequences, isolates, hosts, and amino acid replacements:

Link	From Table	To Table	Type
variation	sequence	flu_replacement_sequence	ONE_TO_MANY
flu_replacement_sequence	flu_replacement	flu_replacement_sequence	ONE_TO_MANY
isolate	isolate	sequence	ONE_TO_MANY
host	isolate	host	ONE_TO_ONE

---