Taxonomy names report

Detailed information about names associated with a taxonomic identifier

Taxonomy names report

Detailed information about names associated with a taxonomic identifier

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

ncbi_dataset/data/names_report.jsonl

Each line of the taxonomy names data report file is a hierarchical JSON object that represents a single taxonomic record. The schema of the taxonomic 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 TaxonomyNamesDescriptor.

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 taxonomy name data reports from JSON Lines to tabular formats.

Sample report

{
  "taxonomy": {
    "taxId": "9606",
    "rank": "SPECIES",
    "currentScientificName": {
      "name": "Homo sapiens",
      "authority": "Linnaeus, 1758"
    },
    "groupName": "primates",
    "curatorCommonName": "human",
    "currentScientificNameIsFormal": true
  },
  "query": [
    "9606"
  ]
}

TaxonomyNamesDescriptor Structure

Taxonomic node object.

Contains taxonomic names information for a single query.

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`taxId`	coming soon	coming soon	`uint64`	NCBI Taxonomy identifier	`9606`
`rank`			`RankType`	The taxonomic rank of the taxonomic node.	`kingdom`
`currentScientificName`			`NameAndAuthority`	The currently accepted name chosen out of all synonyms for the taxonomic node.	`Wickerhamiella versatilis (Etchells & T.A. Bell) de Vega & Lachance, 2017`
`groupName`	coming soon	coming soon	`string`	Group name for the species.	`even-toed ungulates`
`curatorCommonName`	coming soon	coming soon	`string`	The canonical common name.	`sweet orange`
`otherCommonNames repeated`	coming soon	coming soon	`string`	Informal names in common usage.	`Valencia orange`
`generalNotes repeated`	coming soon	coming soon	`string`	Any general, unstructured notes for this taxonomy node.
`linksFromType`	coming soon	coming soon	`string`	TBD
`citations repeated`			`TaxonomyNamesDescriptor.Citation`	Citations that are associated with this tax id.
`currentScientificNameIsFormal`	coming soon	coming soon	`bool`

NameAndAuthority Structure

Name and authority object.

Contains information on the taxonomic node’s name, authority, publications, basionym, synonyms, etc.

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`name`	coming soon	coming soon	`string`	This could be the scientific name, common name, synonym, etc. depending on the context.
`authority`	coming soon	coming soon	`string`	The authority that this name was created by. The authority is typically representedby the author(s) name and the year in which it was published.
`typeStrains repeated`			`TaxonomyTypeMaterial`	Any type materials for this entry.
`curatorSynonym`	coming soon	coming soon	`string`	The primary synonym of the scientific name.	`Leptosphaeria maculans`
`homotypicSynonyms repeated`			`NameAndAuthority`	(Taxonomy names report only) Names generated after the basionym (e.g. by moving it to a different genus), but sharing the same type. Usually these are the results of genus changes. Also known as objective synonym, nomenclatural synonym.	`Candida versatilis (Etchells & T.A. Bell) S.A. Mey. & Yarrow, 1978`
`heterotypicSynonyms repeated`			`NameAndAuthority`	(Taxonomy names report only) List of heterotypic synonyms associated with this entry.
`otherSynonyms repeated`			`NameAndAuthority`	List of other (not listed as heterotypic or homotypic) synonyms associated with this entry.
`informalNames repeated`	coming soon	coming soon	`string`	List of informal names for the entry.	`cow, spider`
`basionym`			`NameAndAuthority`	The originally described name, no longer in use. Attached to the type material and species description.	`Brettanomyces versatilis Etchells & T.A. Bell, 1950`
`publications repeated`			`NameAndAuthority.Publication`	Contains a list of publication objects related to this species.
`notes repeated`			`NameAndAuthority.Note`	Contains a list of note objects related to this species.
`formal`	coming soon	coming soon	`bool`	Indicates whether the name is formal (i.e. compliant)

NameAndAuthority.Note Structure

Note object

Contains information related to this specific entry.

Field	Table Field Mnemonic	Table Column Name	Type	Description
`name`	coming soon	coming soon	`string`	Name of the notation.
`note`	coming soon	coming soon	`string`	Note text.
`noteClassifier`			`NameAndAuthority.NoteClassifier`	Note classification

NameAndAuthority.Publication Structure

Publication object

Contains information about the publication such as the name and the citation.

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`name`	coming soon	coming soon	`string`	Name of the publication (article, book, etc.).
`citation`	coming soon	coming soon	`string`	Citation to the publication.

TaxonomyNamesDescriptor.Citation Structure

Field	Table Field Mnemonic	Table Column Name	Type
`fullCitation`	coming soon	coming soon	`string`
`shortCitation`	coming soon	coming soon	`string`
`pmid`	coming soon	coming soon	`uint64`

TaxonomyTypeMaterial Structure

Type Material object.

Metadata pertaining to the original voucher used to describe the species.

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`typeStrainName`	coming soon	coming soon	`string`	The strain name of the type material.	`ATCC:43971`
`typeStrainId`	coming soon	coming soon	`string`	The strain ID of the type material.	`ATCC`
`bioCollectionId`	coming soon	coming soon	`string`	The biocollection ID of the type material.	`4278`
`bioCollectionName`	coming soon	coming soon	`string`	The biocollection name of the type material.	`ATCC`
`collectionType repeated`			`CollectionType`	Type of collection for the type material.	`collection_culture_collection`
`typeClass`	coming soon	coming soon	`string`	Type material classification.	`type strain`

CollectionType Enumeration

Name	Number	Description
`no_collection_type`	`0`
`collection_culture_collection`	`1`
`specimen_voucher`	`2`

NameAndAuthority.NoteClassifier Enumeration

Class of authority

If the authority has any special classification, such as having been effectively and validly published or having been included in an approved list.

Name	Number	Description
`no_authority_classifier`	`0`	No specific classification.
`effective_name`	`1`	Has been effectively and validly published (i.e. in the “International Code of Nonemclature of Prokaryotes”).
`nomen_approbbatum`	`2`	Has been included in an approved list (such as the “Approved List of Bacterial Names”).
`ictv_accepted`	`3`	Has been ICTV accepted

RankType Enumeration

Rank level

Name	Number	Description
`NO_RANK`	`0`
`SUPERKINGDOM`	`1`
`KINGDOM`	`2`
`SUBKINGDOM`	`3`
`SUPERPHYLUM`	`4`
`SUBPHYLUM`	`5`
`PHYLUM`	`6`
`CLADE`	`31`
`SUPERCLASS`	`7`
`CLASS`	`8`
`SUBCLASS`	`9`
`INFRACLASS`	`10`
`COHORT`	`11`
`SUBCOHORT`	`12`
`SUPERORDER`	`13`
`ORDER`	`14`
`SUBORDER`	`15`
`INFRAORDER`	`16`
`PARVORDER`	`17`
`SUPERFAMILY`	`18`
`FAMILY`	`19`
`SUBFAMILY`	`20`
`GENUS`	`21`
`SUBGENUS`	`22`
`SPECIES_GROUP`	`23`
`SPECIES_SUBGROUP`	`24`
`SPECIES`	`25`
`SUBSPECIES`	`26`
`TRIBE`	`27`
`SUBTRIBE`	`28`
`FORMA`	`29`
`VARIETAS`	`30`
`STRAIN`	`320`
`SECTION`	`330`
`SUBSECTION`	`340`
`PATHOGROUP`	`350`
`SUBVARIETY`	`360`
`GENOTYPE`	`370`
`SEROTYPE`	`380`
`ISOLATE`	`390`
`MORPH`	`400`
`SERIES`	`410`
`FORMA_SPECIALIS`	`420`
`SEROGROUP`	`430`
`BIOTYPE`	`440`

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 June 25, 2024