Database Schema Extensions - giffordlabcvr/Hepadnaviridae-GLUE GitHub Wiki
Overview
Hepadnavirus-GLUE extends GLUE's core schema through the incorporation of additional fields in the sequence table, and a custom table: isolate_data.
These schema extensions are defined here.
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.
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
| Parameter | Type | Definition |
|---|---|---|
| isolate_name | VARCHAR | Name of the virus isolate this sequence is derived from |
| host_sci_name | VARCHAR | Species (Latin binomial) virus was isolated from |
| host_name | VARCHAR | Species (common name) virus was isolated from |
| country | VARCHAR | Country where virus was isolated |
| collection_year | INTEGER | Year virus was isolated |
| collection_month | VARCHAR | Month virus was isolated |
| collection_month_day | INTEGER | Day of month virus was isolated |