Virus report

Virus record metadata

Virus report

Virus record metadata

The downloaded virus package contains a virus data report in JSON Lines format in the file:

ncbi_dataset/data/data_report.jsonl

Each line of the virus data report file is a hierarchical JSON object that represents a single virus record. The schema of the virus record is defined in the tables below where each row describes a single field in the report or a sub-structure, which is a collection of fields. The outermost structure of the report is VirusAssembly.

Table fields that include a Table Field Mnemonic can be used with the dataformat command-line tool's --fields option. Refer to the dataformat CLI tool reference to see how you can use this tool to transform virus data reports from JSON Lines to tabular formats.

Sample report

{
  "accession": "NC_045512.2",
  "bioprojects": [
    "PRJNA485481"
  ],
  "completeness": "COMPLETE",
  "geneCount": 11,
  "host": {
    "lineage": [
      {
        "name": "cellular organisms",
        "taxId": 131567
      },
      {
        "name": "Eukaryota",
        "taxId": 2759
      },
      {
        "name": "Opisthokonta",
        "taxId": 33154
      },
      {
        "name": "Metazoa",
        "taxId": 33208
      },
      {
        "name": "Eumetazoa",
        "taxId": 6072
      },
      {
        "name": "Bilateria",
        "taxId": 33213
      },
      {
        "name": "Deuterostomia",
        "taxId": 33511
      },
      {
        "name": "Chordata",
        "taxId": 7711
      },
      {
        "name": "Craniata",
        "taxId": 89593
      },
      {
        "name": "Vertebrata",
        "taxId": 7742
      },
      {
        "name": "Gnathostomata",
        "taxId": 7776
      },
      {
        "name": "Teleostomi",
        "taxId": 117570
      },
      {
        "name": "Euteleostomi",
        "taxId": 117571
      },
      {
        "name": "Sarcopterygii",
        "taxId": 8287
      },
      {
        "name": "Dipnotetrapodomorpha",
        "taxId": 1338369
      },
      {
        "name": "Tetrapoda",
        "taxId": 32523
      },
      {
        "name": "Amniota",
        "taxId": 32524
      },
      {
        "name": "Mammalia",
        "taxId": 40674
      },
      {
        "name": "Theria",
        "taxId": 32525
      },
      {
        "name": "Eutheria",
        "taxId": 9347
      },
      {
        "name": "Boreoeutheria",
        "taxId": 1437010
      },
      {
        "name": "Euarchontoglires",
        "taxId": 314146
      },
      {
        "name": "Primates",
        "taxId": 9443
      },
      {
        "name": "Haplorrhini",
        "taxId": 376913
      },
      {
        "name": "Simiiformes",
        "taxId": 314293
      },
      {
        "name": "Catarrhini",
        "taxId": 9526
      },
      {
        "name": "Hominoidea",
        "taxId": 314295
      },
      {
        "name": "Hominidae",
        "taxId": 9604
      },
      {
        "name": "Homininae",
        "taxId": 207598
      },
      {
        "name": "Homo",
        "taxId": 9605
      },
      {
        "name": "Homo sapiens",
        "taxId": 9606
      }
    ],
    "organismName": "Homo sapiens",
    "taxId": 9606
  },
  "isAnnotated": true,
  "isolate": {
    "collectionDate": "2019-12",
    "name": "Wuhan-Hu-1"
  },
  "length": 29903,
  "location": {
    "geographicLocation": "China",
    "geographicRegion": "Asia"
  },
  "maturePeptideCount": 26,
  "nucleotide": {
    "sequenceHash": "A926D55E"
  },
  "proteinCount": 12,
  "releaseDate": "2020-01-13T00:00:00Z",
  "sourceDatabase": "RefSeq",
  "submitter": {
    "affiliation": "National Center for Biotechnology Information, NIH",
    "country": "USA",
    "names": [
      "Wu,F.",
      "Zhao,S.",
      "Yu,B.",
      "Chen,Y.M.",
      "Wang,W.",
      "Song,Z.G.",
      "Hu,Y.",
      "Tao,Z.W.",
      "Tian,J.H.",
      "Pei,Y.Y.",
      "Yuan,M.L.",
      "Zhang,Y.L.",
      "Dai,F.H.",
      "Liu,Y.",
      "Wang,Q.M.",
      "Zheng,J.J.",
      "Xu,L.",
      "Holmes,E.C.",
      "Zhang,Y.Z.",
      "Baranov,P.V.",
      "Henderson,C.M.",
      "Anderson,C.B.",
      "Gesteland,R.F.",
      "Atkins,J.F.",
      "Howard,M.T.",
      "Robertson,M.P.",
      "Igel,H.",
      "Baertsch,R.",
      "Haussler,D.",
      "Ares,M. Jr.",
      "Scott,W.G.",
      "Williams,G.D.",
      "Chang,R.Y.",
      "Brian,D.A.",
      "Chen,Y.-M.",
      "Song,Z.-G.",
      "Tao,Z.-W.",
      "Tian,J.-H.",
      "Pei,Y.-Y.",
      "Zhang,Y.-L.",
      "Dai,F.-H.",
      "Wang,Q.-M.",
      "Zheng,J.-J.",
      "Zhang,Y.-Z."
    ]
  },
  "updateDate": "2020-07-18T00:00:00Z",
  "virus": {
    "lineage": [
      {
        "name": "Viruses",
        "taxId": 10239
      },
      {
        "name": "Riboviria",
        "taxId": 2559587
      },
      {
        "name": "Orthornavirae",
        "taxId": 2732396
      },
      {
        "name": "Pisuviricota",
        "taxId": 2732408
      },
      {
        "name": "Pisoniviricetes",
        "taxId": 2732506
      },
      {
        "name": "Nidovirales",
        "taxId": 76804
      },
      {
        "name": "Cornidovirineae",
        "taxId": 2499399
      },
      {
        "name": "Coronaviridae",
        "taxId": 11118
      },
      {
        "name": "Orthocoronavirinae",
        "taxId": 2501931
      },
      {
        "name": "Betacoronavirus",
        "taxId": 694002
      },
      {
        "name": "Sarbecovirus",
        "taxId": 2509511
      },
      {
        "name": "Severe acute respiratory syndrome-related coronavirus",
        "taxId": 694009
      },
      {
        "name": "Severe acute respiratory syndrome coronavirus 2",
        "taxId": 2697049
      }
    ],
    "organismName": "Severe acute respiratory syndrome coronavirus 2",
    "pangolinClassification": "B",
    "taxId": 2697049
  }
}

VirusAssembly Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`accession`	`accession`	Accession	`string`	The accession.version of the viral nucleotide sequence. Includes both GenBank and RefSeq accessions	`NC_045512.2`
`isAnnotated`	`is-annotated`	Is Annotated	`bool`	The viral genome has been annotated by either the submitter (GenBank) or by NCBI (RefSeq)
`isolate`	`isolate-`	Isolate	`Isolate`
`sourceDatabase`	`sourcedb`	Source database	`string`	Indicates if the source of the viral nucleotide record is from a GenBank submitter or from NCBI-derived curation (RefSeq)	`RefSeq` `GenBank`
`proteinCount`	`protein-count`	Protein count	`uint32`	The total count of annotated proteins including both proteins and polyproteins but not processed mature peptides
`host`	`host-`	Host	`Organism`	Taxon from which the virus sample was isolated
`virus`	`virus-`	Virus	`Organism`	Viral taxon
`bioprojects repeated`	`bioprojects`	BioProjects	`string`	Associated BioProject accessions, when available	`PRJNA485481`
`location`	`geo-`	Geographic	`VirusAssembly.CollectionLocation`
`updateDate`	`update-date`	Update date	`string`	Date the viral nucleotide accession was last updated in NCBI Virus
`releaseDate`	`release-date`	Release date	`string`	Date the viral nucleotide accession was first released in NCBI Virus
`completeness`	`completeness`	Completeness	`VirusAssembly.Completeness`
`length`	`length`	Length	`uint32`	Length of the viral nucleotide sequence
`geneCount`	`gene-count`	Gene count	`uint32`	Total count of genes annotated on the viral nucleotide sequence
`maturePeptideCount`	`matpeptide-count`	Mature peptide count	`uint32`	Total count of processed mature peptides annotated on the viral nucleotide sequence
`biosample`	`biosample-acc`	BioSample accession	`string`	Associated Biosample accessions	`SAMN15394129`
`molType`	`mol-type`	Molecule type	`string`	ICTV (International Committee on Taxonomy of Viruses) viral classification based on nucleic acid composition, strandedness and method of replication
`nucleotide`			`SeqRangeSetFasta`	The whole genomic nucleotide record of the CDS feature.
`purposeOfSampling`	`purpose-of-sampling`	Purpose of Sampling	`PurposeOfSampling`
`sraAccessions repeated`	`sra-accs`	SRA Accessions	`string`	SRA accessions linked to the genbank genome
`submitter`	`submitter-`	Submitter	`VirusAssembly.SubmitterInfo`	Name, affiliation, and country of the submitter(s)
`labHost`	`lab-host`	Lab Host	`string`	This sequence is from viruses passaged in this host
`isLabHost`	`is-lab-host`	Is Lab Host	`bool`	If true, this sequence is from viruses passaged in a laboratory
`isVaccineStrain`	`is-vaccine-strain`	Is Vaccine Strain	`bool`	If true, this sequence is derived from a virus used as a vaccine or potential vaccine

InfraspecificNames Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`breed`	`breed`	Breed	`string`	A homogenous group of animals within a domesticated species	`Hereford` `boxer`
`cultivar`	`cultivar`	Cultivar	`string`	A variety of plant within a species produced and maintained by cultivation	`B73`
`ecotype`	`ecotype`	Ecotype	`string`	A population or subspecies occupying a distinct habitat	`Alpine`
`isolate`	`isolate`	Isolate	`string`	The individual isolate from which the sequences in the genome assembly were derived	`L1 Dominette 01449 registration number 42190680` `Pmale09`
`sex`	`sex`	Sex	`string`	Male or female	`female`
`strain`	`strain`	Strain	`string`	A genetic variant, subtype or culture within a species	`SE11`

Isolate Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`name`	`lineage`	Lineage	`string`	BioSample harmonized attribute names https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
`source`	`lineage-source`	Lineage source	`string`	Source material from which the viral specimen was isolated	`blood` `feces` `lung`
`collectionDate`	`collection-date`	Collection date	`string`	The collection date for the sample from which the viral nucleotide sequence was derived

LineageOrganism Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`taxId`	coming soon	coming soon	`uint32`	NCBI Taxonomy identifier	`11118`
`name`	coming soon	coming soon	`string`	Scientific name	`Coronaviridae`

Organism Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`taxId`	`tax-id`	Taxonomic ID	`uint32`	NCBI Taxonomy identifier	`9606` `2697049`
`organismName`	`name`	Name	`string`	Scientific name	`Homo sapiens` `Severe acute respiratory syndrome coronavirus 2`
`commonName`	`common-name`	Common Name	`string`	Common name	`human` `pangolin` `MERS` `SARS2`
`lineage repeated`			`LineageOrganism`	Lineage ordered from superkingdom level to increasingly more specific taxonomic entries
`pangolinClassification`	`pangolin`	Pangolin Classification	`string`		`B.1.1.7`
`infraspecificNames`	`infraspecific-`	Infraspecific Names	`InfraspecificNames`

Range Structure

A 1-based range on a sequence record.

Field	Table Field Mnemonic	Table Column Name	Type	Description
`begin`	`start`	Start	`uint64`
`end`	`stop`	Stop	`uint64`
`orientation`	`orientation`	Orientation	`Orientation`
`order`	`order`	Order	`uint32`
`ribosomalSlippage`	coming soon	coming soon	`int32`	When ribosomal slippage is desired, fill out slippage amount between this and previous range.

SeqRangeSetFasta Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description
`seqId`	`seq-id`	Sequence ID	`string`	Seq_id may include location info in addition to a sequence accession
`accessionVersion`	`accession`	Accession	`string`	Accession and version of the viral nucleotide sequence
`title`	`title`	Title	`string`
`sequenceHash`	`hash`	Hash	`string`	Unique identifier for identical sequences
`range repeated`	`range-`	Range	`Range`	Series of intervals on above accession_version

VirusAssembly.CollectionLocation Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`geographicLocation`	`location`	Location	`string`	Country of virus specimen collection	`USA` `France`
`geographicRegion`	`region`	Region	`string`	Region of virus specimen collection	`Asia` `North America`
`usaState`	`state`	State	`string`	Two letter abbreviation of the state of the virus specifime collection (if United States)	`NY` `VA`

VirusAssembly.SubmitterInfo Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`names repeated`	`names`	Names	`string`	List of submitters or authors of the virus assembly	`Jane D` `John S`
`affiliation`	`affiliation`	Affiliation	`string`	The submitter’s organization and/or institution	`Centers for Disease Control and Prevention, Respiratory Viruses Branch, Division of Viral Diseases` `Public Health Directorate, Communicable Disease Laboratory`
`country`	`country`	Country	`string`	The country representing the submitter’s affilation	`USA` `China`

Orientation Enumeration

Name	Number	Description
`none`	`0`
`plus`	`1`
`minus`	`2`

PurposeOfSampling Enumeration

Name	Number	Description
`PURPOSE_OF_SAMPLING_UNKNOWN`	`0`
`PURPOSE_OF_SAMPLING_BASELINE_SURVEILLANCE`	`1`

VirusAssembly.Completeness Enumeration

Name	Number	Description
`UNKNOWN`	`0`
`COMPLETE`	`1`
`PARTIAL`	`2`

Scalar Value Types

Protocol buffers type	Notes	C++	Python	Java	Go
`double`		`double`	`float`	`double`	`float64`
`float`		`float`	`float`	`float`	`float32`
`int32`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.	`int32`	`int`	`int`	`int32`
`int64`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.	`int64`	`int/long`	`long`	`int64`
`uint32`	Uses variable-length encoding.	`uint32`	`int/long`	`int`	`uint32`
`uint64`	Uses variable-length encoding.	`uint64`	`int/long`	`long`	`uint64`
`sint32`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.	`int32`	`int`	`int`	`int32`
`sint64`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.	`int64`	`int/long`	`long`	`int64`
`fixed32`	Always four bytes. More efficient than uint32 if values are often greater than 2^28.	`uint32`	`int`	`int`	`uint32`
`fixed64`	Always eight bytes. More efficient than uint64 if values are often greater than 2^56.	`uint64`	`int/long`	`long`	`uint64`
`sfixed32`	Always four bytes.	`int32`	`int`	`int`	`int32`
`sfixed64`	Always eight bytes.	`int64`	`int/long`	`long`	`int64`
`bool`		`bool`	`boolean`	`boolean`	`bool`
`string`	A string must always contain UTF-8 encoded or 7-bit ASCII text.	`string`	`str/unicode`	`String`	`string`
`bytes`	May contain any arbitrary sequence of bytes.	`string`	`str`	`ByteString`	`[]byte`

Generated November 25, 2024