ncbi_taxonomy.type_material_exclusions

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	taxon_name	type_material_status	voucher_or_strain_id
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1049583	Kocuria indica	not considered type	CCTCC:AA 209050
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1049583	Kocuria indica	not considered type	CCTCC AA 209050
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1049583	Kocuria indica	not considered type	CCTCC-AA 209050
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1049583	Kocuria indica	not considered type	CCTCCAA 209050
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1056496	Pseudomonas nosocomialis	not considered type	CECT:9981

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 4 of 5 columns)
   taxon_id | taxon_name               | type_material_status | voucher_or_strain_id
   -------- | ------------------------ | -------------------- | --------------------
0  1049583  | Kocuria indica           | not considered type  | CCTCC:AA 209050
1  1049583  | Kocuria indica           | not considered type  | CCTCC AA 209050
2  1049583  | Kocuria indica           | not considered type  | CCTCC-AA 209050
3  1049583  | Kocuria indica           | not considered type  | CCTCCAA 209050
4  1056496  | Pseudomonas nosocomialis | not considered type  | CECT:9981

Description

Strains and vouchers NCBI determined are not verified type material, one row per excluded record.

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 associated with the excluded strain or voucher.
taxon_name	TEXT	Organism name to which NCBI assigns the excluded material.
type_material_status	TEXT	NCBI exclusion status — not considered type or not verified as type.
voucher_or_strain_id	TEXT	Strain or voucher identifier.