ncbi_taxonomy.merged_nodes

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	old_taxon_id	new_taxon_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000	107401
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100031	2153283
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000424	52477
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000427	193300
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000431	97029

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 2 of 3 columns)
   old_taxon_id | new_taxon_id
   ------------ | ------------
0  1000         | 107401
1  100031       | 2153283
2  1000424      | 52477
3  1000427      | 193300
4  1000431      | 97029

Description

NCBI Taxonomy nodes merged into replacement nodes, one row per superseded taxon ID.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Source provenance for the row.
old_taxon_id	TEXT	Taxonomy ID that was merged.
new_taxon_id	TEXT	Replacement taxonomy ID.