Data Sources

Currently, VirJenDB incorporates the following data sources:

ICTV attempts to introduce order into the bewildering variety of viruses:
- develop an internationally agreed taxonomy for viruses
- develop internationally agreed names for these taxa
- communicate taxonomic decisions to the international community of virologists
- maintain an index of virus names
BV-BRC release v3.32.13a,
provides integrated data, advanced bioinformatics tools, and workflows to support the scientific community in understanding and combating infectious diseases.
The National Center for Biotechnology Information (NCBI) advances science and health by providing access to biomedical and genomic information.
- NCBI Virus version from 12.11.23
  Community portal for viral sequence data from RefSeq, GenBank and other NCBI repositories.
- PubMed comprises more than 38 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.
- Taxonomy is a curated classification and nomenclature for all of the organisms in the public sequence databases.
ViralZone is a web resource for all viral genera and families that provides general molecular and epidemiological information, along with virion and genome figures.
IMG/VR aggregates the largest publicly available collection of UViGs by identifying viral sequences in IMG assemblies.
Phage & Host Daily provides a daily updated catalog of known interactions between viruses and prokaryotic host species, allowing users to select viruses targeting specific bacterial and archaeal taxa of interest.

To read about our sources of metadata and descriptions of the fields, please go to the Metadata docs page.

Field Mappings

VirJenDB Field	Type	Source	Source Field Name
BV-BRC Sequence	boolean	VJDB	-
Cluster Representative	boolean	VJDB	-
GenBank Sequence	boolean	NCBI Virus	GenBank_RefSeq
ICTV Exemplar	boolean	ICTV	-
RefSeq Sequence	boolean	NCBI Virus BVBRC	GenBank_RefSeq Reference
Unique Representative	boolean	VJDB	-
Collection Date	date	NCBI Virus BVBRC	Collection_Date Collection Date
Host Collection Date	date	IMG/VR PhiSpy PhD	- - -
Release Date	date	NCBI Virus	Release_Date
Average Depth	float	BVBRC	Sequencing Depth
GC Content	float	BVBRC	GC Content
Host Average Sequence Depth	float	IMG/VR PhiSpy PhD	- - -
Host Age	integer	BVBRC	Host Age
Sequence Length	integer	NCBI Virus BVBRC	Length Size
VirJenDB Accession	integer	VJDB	-
VirJenDB Metadata Version	integer	VJDB	-
NCBI Lineage IDs	integer list	BVBRC	Taxon Lineage IDs
Accession	keyword	NCBI Virus BVBRC	Accession GenBank Accessions
Assembly Accession	keyword	NCBI Virus BVBRC	Assembly Assembly Accession
BV-BRC Accession	keyword	BVBRC	Genome ID
BV-BRC Host Age	keyword	BVBRC	Host Age
BV-BRC Host Group	keyword	BVBRC	Host Group
Bioproject Accession	keyword	NCBI Virus BVBRC	BioProject BioProject Accession
Biosample Accession	keyword	NCBI Virus BVBRC	BioSample BioSample Accession
Collection Geo Location	keyword	NCBI Virus BVBRC	Geo_Location Geographic Location
Collection Source Host Tissue	keyword	NCBI Virus	Tissue_Specimen_Source
Country	keyword	NCBI Virus BVBRC	Country Isolation Country
Genome Completeness	keyword	NCBI Virus	Nuc_Completeness
Genotype	keyword	NCBI Virus	Genotype
Host Accession	keyword	VJDB	-
Host Assembly Accession	keyword	IMG/VR PhiSpy PhD	- - -
Host BioProject Accession	keyword	IMG/VR PhiSpy PhD	- - -
Host Biosample Accession	keyword	IMG/VR PhiSpy PhD	- - -
Host Common Name	keyword	NCBI Virus BVBRC	Host Host Common Name
Host Country	keyword	IMG/VR PhiSpy PhD	- - -
Host GTDB Species Name	keyword	IMG/VR PhiSpy PhD	- - -
Host IMGM Taxon OID	keyword	IMG/VR PhiSpy PhD	- - -
Host NCBI Tax ID	keyword	GTDB	-
Host Sequencing Platform	keyword	IMG/VR PhiSpy PhD	- - -
Host Sex	keyword	BVBRC	Host Gender
Host Species	keyword	BVBRC	Host Name
ICTV Class	keyword	ICTV	Class
ICTV Family	keyword	ICTV	Family
ICTV Genus	keyword	ICTV	Genus
ICTV Host Group	keyword	ICTV	Host source
ICTV Kingdom	keyword	ICTV	Kingdom
ICTV Lineage Names	keyword	VJDB	-
ICTV Order	keyword	ICTV	Order
ICTV Phylum	keyword	ICTV	Phylum
ICTV Realm	keyword	ICTV	Realm
ICTV Species	keyword	ICTV	Species
ICTV Subfamily	keyword	ICTV	Subfamily
ICTV Subgenus	keyword	ICTV	Subgenus
ICTV Suborder	keyword	ICTV	Suborder
ICTV Subphylum	keyword	ICTV	Subphylum
Isolate	keyword	NCBI Virus	Isolate
Molecule Type	keyword	NCBI Virus	Molecule_type
NCBI Class	keyword	BVBRC	Class
NCBI Family	keyword	NCBI Virus BVBRC	Family Family
NCBI Genus	keyword	NCBI Virus BVBRC	Genus Genus
NCBI Kingdom	keyword	BVBRC	Kingdom
NCBI Lineage Names	keyword	BVBRC	Taxon Lineage Names
NCBI Order	keyword	BVBRC	Order
NCBI Phylum	keyword	BVBRC	Phylum
NCBI Realm	keyword	NCBI Taxonomy	-
NCBI Species	keyword	NCBI Virus BVBRC	Species Species
NCBI SpeciesTax ID	keyword	BVBRC	NCBI Taxon ID
NCBI Subfamily	keyword	NCBI Taxonomy	-
NCBI Subgenus	keyword	NCBI	-
NCBI Suborder	keyword	NCBI Taxonomy	-
NCBI Subphylum	keyword	NCBI Taxonomy	-
Organism Name	keyword	NCBI Virus	Organism_Name
Pangolin Lineage	keyword	NCBI Virus BVBRC	- Lineage
Platform	keyword	BVBRC	Sequencing Platform
SRA Accession	keyword	NCBI Virus BVBRC	SRA_Accession SRA Accession
Segment Name	keyword	NCBI Virus	Segment
Sequence Source	keyword	VJDB	-
Sequencing Center	keyword	BVBRC	Sequencing Center
Strain	keyword	BVBRC	Strain
Submitter	keyword	NCBI Virus	Submitters
Submitter Country	keyword	NCBI Virus	Org_location
Submitter Organization	keyword	NCBI Virus	Organization
Submitter Region	keyword	NCBI Virus	-
Predicted	list	IMG/VR PhiSpy PhD	- - -
Cluster Reference	nan	VJDB	-
Unique Reference	nan	VJDB	-

Documentation

Data Sources

Field Mappings

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