Virus report

Virus record metadata

Virus report

Virus record metadata

The downloaded virus package contains a virus data report inJSON Linesformat in the file:

ncbi_dataset/data/data_report.jsonl

Each line of the virus data report file is a hierarchicalJSONobject that represents a single virus record. The schema of the virus record is defined in the tables below whereeach row describes a single field in the report or a sub-structure, which is a collection of fields.The outermost structure of the report isVirusAssembly.

Table fields that include aTable Field Mnemonic can be used with thedataformat command-line tool's--fields option. Refer to thedataformat CLI tool reference to seehow 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":"Betacoronavirus pandemicum","taxId":3418604      },      {"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`	Indicates whether the viral nucleotide sequence represents a complete or partial genome
`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`	SARS-CoV-2 only, indicates whether the sequence was collected randomly for epedimiology studies
`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
`segment`	`segment`	Segment	`string`	The virus segment

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 nameshttps://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`	Sequence start position
`end`	`stop`	Stop	`uint64`	Sequence stop position
`orientation`	`orientation`	Orientation	`Orientation`	Direction relative to the genome
`order`	`order`	Order	`uint32`	The position of this sequence in a group of sequences
`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 December 12, 2025

Movatterモバイル変換

Virus report

Virus report

Sample report

VirusAssembly Structure

InfraspecificNames Structure

Isolate Structure

LineageOrganism Structure

Organism Structure

Range Structure

SeqRangeSetFasta Structure

VirusAssembly.CollectionLocation Structure

VirusAssembly.SubmitterInfo Structure

Orientation Enumeration

PurposeOfSampling Enumeration

VirusAssembly.Completeness Enumeration

Scalar Value Types