Core Project Extensions

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

Schema extensions for Lentivirus-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
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
length	INTEGER	Length of the sequence
pubmed_id	INTEGER	PubMed ID of manuscript associated with sequence
genus	VARCHAR	Taxonomy - virus genus
clade	VARCHAR	Taxonomy - virus clade

Fields included in 'isolate_data' table

The isolate_data table is linked to the main 'sequence' table via the sequence ID field. It contains information pertaining to viral isolates, e.g., species sampled, date, and location of sample.

Parameter	Type	Definition
isolate_name	VARCHAR	Name of the virus isolate this sequence is derived from
isolate_source	VARCHAR	Source material from which virus isolate was obtained
host_sci_name	VARCHAR	Species (Latin binomial) virus was isolated from
host_name	VARCHAR	Species (common name) virus was isolated from
country	VARCHAR	Country in which virus was isolated
country_iso	VARCHAR	Country in which virus was isolated (M49 standard)
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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