ncbi_taxonomy.ranked_lineages

Python
R

import bedrock_bio as bb

rel = bb.load_table('ncbi_taxonomy.ranked_lineages')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

	sources	taxon_id	scientific_name	species_name	genus_name	family_name	order_name	class_name	phylum_name	kingdom_name	domain_or_realm_name
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1	root	None	NaN	NaN	NaN	NaN	NaN	NaN	NaN
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	10	Cellvibrio	None	NaN	Cellvibrionaceae	Cellvibrionales	Gammaproteobacteria	Pseudomonadota	Pseudomonadati	Bacteria
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	Ancylobacter aquaticus	None	Ancylobacter	Xanthobacteraceae	Hyphomicrobiales	Alphaproteobacteria	Pseudomonadota	Pseudomonadati	Bacteria
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100000	Herbaspirillum sp. BA12	None	Herbaspirillum	Oxalobacteraceae	Burkholderiales	Betaproteobacteria	Pseudomonadota	Pseudomonadati	Bacteria
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000000	Microbacterium sp. 6.11-VPa	None	Microbacterium	Microbacteriaceae	Micrococcales	Actinomycetes	Actinomycetota	Bacillati	Bacteria

library(bedrockbio)

lf <- load_table("ncbi_taxonomy.ranked_lineages")
df <- head(lf, 5) |> collect()

head(df)

Sample output (5 rows, showing 8 of 11 columns)
   taxon_id | scientific_name          | species_name | genus_name     | family_name       | order_name       | class_name          | phylum_name
   -------- | ------------------------ | ------------ | -------------- | ----------------- | ---------------- | ------------------- | --------------
0  1        | root                     | —            | —              | —                 | —                | —                   | —
1  10       | Cellvibrio               | —            | —              | Cellvibrionaceae  | Cellvibrionales  | Gammaproteobacteria | Pseudomonadota
2  100      | Ancylobacter aquaticus   | —            | Ancylobacter   | Xanthobacteraceae | Hyphomicrobiales | Alphaproteobacteria | Pseudomonadota
3  100000   | Herbaspirillum sp. BA12  | —            | Herbaspirillum | Oxalobacteraceae  | Burkholderiales  | Betaproteobacteria  | Pseudomonadota
4  1000000  | Microbacterium sp. 6.11… | —            | Microbacterium | Microbacteriaceae | Micrococcales    | Actinomycetes       | Actinomycetota

Description

Selected NCBI Taxonomy ancestor names at established taxonomic ranks, one row per taxon.

Partitions

Not partitioned.

Schema

Column	Type	Description
`sources`	`STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]`	Source provenance for the row.
`taxon_id`	`TEXT`	Taxonomy ID for the node.
`scientific_name`	`TEXT`	Scientific name of the node.
`species_name`	`TEXT`	Species ancestor name, if available.
`genus_name`	`TEXT`	Genus ancestor name, if available.
`family_name`	`TEXT`	Family ancestor name, if available.
`order_name`	`TEXT`	Order ancestor name, if available.
`class_name`	`TEXT`	Class ancestor name, if available.
`phylum_name`	`TEXT`	Phylum ancestor name, if available.
`kingdom_name`	`TEXT`	Kingdom ancestor name, if available.
`domain_or_realm_name`	`TEXT`	Domain or realm ancestor name, if available.