Taxonomy report

General information about a taxonomic identifier

Taxonomy report

General information about a taxonomic identifier

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

ncbi_dataset/data/taxonomy_report.jsonl

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

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 data reports from JSON Lines to tabular formats.

Sample report

{
  "taxonomy": {
    "taxId": 9606,
    "rank": "SPECIES",
    "currentScientificName": {
      "name": "Homo sapiens",
      "authority": "Linnaeus, 1758"
    },
    "curatorCommonName": "human",
    "groupName": "primates",
    "classification": {
      "superkingdom": {
        "name": "Eukaryota",
        "id": 2759
      },
      "kingdom": {
        "name": "Metazoa",
        "id": 33208
      },
      "phylum": {
        "name": "Chordata",
        "id": 7711
      },
      "class": {
        "name": "Mammalia",
        "id": 40674
      },
      "order": {
        "name": "Primates",
        "id": 9443
      },
      "family": {
        "name": "Hominidae",
        "id": 9604
      },
      "genus": {
        "name": "Homo",
        "id": 9605
      },
      "species": {
        "name": "Homo sapiens",
        "id": 9606
      }
    },
    "parents": [
      1,
      131567,
      2759,
      33154,
      33208,
      6072,
      33213,
      33511,
      7711,
      89593,
      7742,
      7776,
      117570,
      117571,
      8287,
      1338369,
      32523,
      32524,
      40674,
      32525,
      9347,
      1437010,
      314146,
      9443,
      376913,
      314293,
      9526,
      314295,
      9604,
      207598,
      9605
    ],
    "children": [
      741158,
      63221
    ],
    "counts": [
      {
        "type": "COUNT_TYPE_ASSEMBLY",
        "count": 1689
      },
      {
        "type": "COUNT_TYPE_GENE",
        "count": 193360
      },
      {
        "type": "COUNT_TYPE_tRNA",
        "count": 701
      },
      {
        "type": "COUNT_TYPE_rRNA",
        "count": 785
      },
      {
        "type": "COUNT_TYPE_snRNA",
        "count": 166
      },
      {
        "type": "COUNT_TYPE_scRNA",
        "count": 4
      },
      {
        "type": "COUNT_TYPE_snoRNA",
        "count": 1201
      },
      {
        "type": "COUNT_TYPE_PROTEIN_CODING",
        "count": 20621
      },
      {
        "type": "COUNT_TYPE_ncRNA",
        "count": 22103
      },
      {
        "type": "COUNT_TYPE_BIOLOGICAL_REGION",
        "count": 128261
      },
      {
        "type": "COUNT_TYPE_OTHER",
        "count": 844
      }
    ],
    "genomicMoltype": "dsDNA",
    "currentScientificNameIsFormal": true
  },
  "query": [
    "9606"
  ]
}

TaxonomyNode Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`taxId`	coming soon	coming soon	`uint32`	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`
`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`
`curatorCommonName`	coming soon	coming soon	`string`	The canonical common name.	`sweet orange`
`groupName`	coming soon	coming soon	`string`	A common name describing large, well-known taxa.	`even-toed ungulates`
`hasTypeMaterial`	coming soon	coming soon	`bool`	A boolean that indicates whether or not type material is available for the species.
`classification`			`Classification`	A subset of parent nodes including well-established ranks.
`parents repeated`	coming soon	coming soon	`uint32`	Taxids of all parents, ordered from most specific (immediate parent), to most general.
`children repeated`	coming soon	coming soon	`uint32`	Taxids of children.
`counts repeated`			`TaxonomyNode.CountByType`
`genomicMoltype`	coming soon	coming soon	`string`	Genomic molecule type (dsDNA, ssDNA, ssDNA(-), ssRNA)
`currentScientificNameIsFormal`	coming soon	coming soon	`bool`
`secondaryTaxIds repeated`	coming soon	coming soon	`uint32`

Classification Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`superkingdom`			`TaxData`
`kingdom`			`TaxData`
`phylum`			`TaxData`
`class`			`TaxData`
`order`			`TaxData`
`family`			`TaxData`
`genus`			`TaxData`
`species`			`TaxData`

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.

TaxData Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`name`	coming soon	coming soon	`string`	Taxonomic name
`id`	coming soon	coming soon	`uint32`	NCBI Taxonomy identifier

TaxonomyNode.CountByType Structure

Count of various attributes, summed up for above species ranks.

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`type`			`CountType`
`count`	coming soon	coming soon	`uint32`

CollectionType Enumeration

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

CountType Enumeration

Name	Number	Description
`COUNT_TYPE_UNSPECIFIED`	`0`
`COUNT_TYPE_ASSEMBLY`	`1`
`COUNT_TYPE_GENE`	`2`
`COUNT_TYPE_tRNA`	`3`
`COUNT_TYPE_rRNA`	`4`
`COUNT_TYPE_snRNA`	`5`
`COUNT_TYPE_scRNA`	`6`
`COUNT_TYPE_snoRNA`	`7`
`COUNT_TYPE_PROTEIN_CODING`	`8`
`COUNT_TYPE_PSEUDO`	`9`
`COUNT_TYPE_TRANSPOSON`	`10`
`COUNT_TYPE_miscRNA`	`11`
`COUNT_TYPE_ncRNA`	`12`
`COUNT_TYPE_BIOLOGICAL_REGION`	`13`
`COUNT_TYPE_OTHER`	`14`
`COUNT_TYPE_ORGANELLE`	`15`

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 November 25, 2024