Paleovirus Schema Extensions

The paleovirus component of Flavivirid-GLUE extends GLUE's core schema to allow the capture of EFV-specific data.

These schema extensions are defined in this file and comprise two additional tables: 'locus_data' and 'refcon_data'.

The 'locus_data' table contains EFV locus information: e.g. species, assembly, scaffold, location coordinates.

The 'refcon_data' table contains summary information for individual EFV insertions. It refers to the reference sequences constructed to represent each insertion, which reflect our best efforts to reconstruct progenitor virus sequences as they might have looked when they initially integrated into the germline of ancestral species.

Both these custom tables are linked to the main 'sequence' table via the 'sequenceID' field.

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

Parameter	Type	Definition
refcon_data	LINK	Link to the refcon_data table containing consensus/reference sequence data
locus_data	LINK	Link to the locus_data table containing locus-specific information

The project-specific extensions comprise two custom tables:

1. locus_data: contains EVE locus information: e.g. species, assembly, scaffold, location coordinates.

2. refcon_data: contains summary information for individual EVE insertions. It refers to the reference sequences constructed to represent each insertion, which reflect our best efforts to reconstruct progenitor virus sequences as they might have looked when they initially integrated into the germline of ancestral species.

Refcon Data table

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A custom table was defined to capture reference/consensus sequence-associated information, as follows:

Parameter	Type	Definition
reftype	VARCHAR	Type of reference (e.g., consensus or reference sequence)
host_group_taxlevel	VARCHAR	Taxonomic level of the host group (e.g., genus, species)
host_group_name	VARCHAR	Scientific name of the host group
host_group_common_name	VARCHAR	Common name of the host group
num_copies	INTEGER	Number of endogenous viral element copies
locus_id	VARCHAR	Identifier for the corresponding locus

Locus Data table

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A custom table was defined to capture information associated with individual EVE loci, as follows:

Parameter	Type	Definition
locus_id	VARCHAR	Identifier for the EVE locus
duplicate_id	INTEGER	Identifier for duplicates within the same locus
organism	VARCHAR	Host organism containing the locus
scaffold	VARCHAR	Scaffold or chromosome on which the locus resides
start	INTEGER	Start position of the locus on the scaffold
end	INTEGER	End position of the locus on the scaffold
orientation	VARCHAR	Orientation of the locus (plus or minus strand)
length	INTEGER	Length of the locus in nucleotides

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