ncbi_taxonomy.taxon_id_lineages

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	ancestor_taxon_ids
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1	[]
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	10	[131567, 2, 3379134, 1224, 1236, 1706369, 1706...
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	[131567, 2, 3379134, 1224, 28211, 356, 335928,...
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100000	[131567, 2, 3379134, 1224, 28216, 80840, 75682...
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000000	[131567, 2, 1783272, 201174, 1760, 85006, 8502...

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 1 of 3 columns)
   taxon_id
   --------
0  1
1  10
2  100
3  100000
4  1000000

Description

Full NCBI Taxonomy ID lineages, 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.
ancestor_taxon_ids	TEXT[]	Ancestor taxonomy IDs, split from NCBI’s space-delimited lineage in order from the root to the parent. Empty for root nodes.