ncbi_taxonomy.type_materials

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	taxon_name	type_material_type	collection_identifier
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	Microcyclus aquaticus	type strain	ATCC:25396
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	Microcyclus aquaticus	type strain	ATCC 25396
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	Microcyclus aquaticus	type strain	CCUG:1820
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	Microcyclus aquaticus	type strain	CCUG 1820
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	Microcyclus aquaticus	type strain	CCUG:30551

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 4 of 5 columns)
   taxon_id | taxon_name            | type_material_type | collection_identifier
   -------- | --------------------- | ------------------ | ---------------------
0  100      | Microcyclus aquaticus | type strain        | ATCC:25396
1  100      | Microcyclus aquaticus | type strain        | ATCC 25396
2  100      | Microcyclus aquaticus | type strain        | CCUG:1820
3  100      | Microcyclus aquaticus | type strain        | CCUG 1820
4  100      | Microcyclus aquaticus | type strain        | CCUG:30551

Description

NCBI type material collection records associated with taxonomy nodes, one row per 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 type material.
taxon_name	TEXT	Organism name to which NCBI assigns the type material.
type_material_type	TEXT	NCBI type material type.
collection_identifier	TEXT	Identifier in the type material collection.