Get virus genome metadata

View, save or create a tabular ouput of virus metadata. For an overview of all available metadata, see our virus report schemas

Use the datasets command-line tool (CLI) to get metadata for all virus genomes in NCBI Virus. The summary command can be used to access primary and annotation metadata. The output can be printed to the screen, redirected to a file, or piped to dataformat to generate a customized table. All metadata files are delivered in JSON or JSON-Lines format.

Get virus primary metadata for by taxon

Get virus genome metadata using the organism name or NCBI Taxonomy ID.

datasets summary virus genome taxon monkeypox

Get virus primary metadata by accession.

For virus genomes, use Genbank nucleotide accessions instead of genome assembly accessions (which start with GCA or GCF).

datasets summary virus genome accession NC_063383.1

Get virus annotation metadata by taxon

Retrieve an annotation report using the flag --report annotation.

datasets summary virus genome taxon monkeypox --report annotation

Create a tsv output of virus primary metadata using dataformat

datasets summary virus genome taxon monkeypox --as-json-lines | dataformat tsv virus-genome --fields accession,release-date | head

Output:

Accession       Release date
AY223478.1      2004-05-12T00:00:00Z
AY223477.1      2004-05-12T00:00:00Z
AY160189.1      2003-03-18T00:00:00Z
AY160188.1      2003-03-18T00:00:00Z
AY160187.1      2003-03-18T00:00:00Z
AY160186.1      2003-03-18T00:00:00Z
AY102986.1      2003-10-31T00:00:00Z
AY102985.1      2003-10-31T00:00:00Z
AJ404663.1      2000-07-08T00:00:00Z

Related information

• NCBI Datasets Virus Data Package