ncbi_taxonomy.categories

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	category	species_id	taxon_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	Bacteria	100	100
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	Bacteria	100000	100000
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	Bacteria	1000000	1000000
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	Bacteria	1000001	1000001
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	Bacteria	1000002	1000002

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 3 of 4 columns)
   category | species_id | taxon_id
   -------- | ---------- | --------
0  Bacteria | 100        | 100
1  Bacteria | 100000     | 100000
2  Bacteria | 1000000    | 1000000
3  Bacteria | 1000001    | 1000001
4  Bacteria | 1000002    | 1000002

Description

NCBI’s broad category and species-level mapping, 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.
category	TEXT	Broad NCBI category — Archaea, Bacteria, Eukaryota, Viruses and Viroids, Unclassified, or Other.
species_id	TEXT	Species-level taxonomy ID containing this taxon.
taxon_id	TEXT	Taxonomy ID for this taxon.