ncbi_taxonomy.nodes

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	parent_taxon_id	rank	embl_code	division_id	inherits_division	genetic_code_id	inherits_genetic_code	mitochondrial_genetic_code_id	inherits_mitochondrial_genetic_code	is_genbank_hidden	is_hidden_subtree_root	comment	plastid_genetic_code_id	inherits_plastid_genetic_code	has_specified_species	hydrogenosome_genetic_code_id	inherits_hydrogenosome_genetic_code
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1	1	no rank	NaN	8	False	1	False	0	False	False	False	NaN	None	<NA>	False	0	False
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	10	1706371	genus	NaN	0	True	11	True	0	True	False	False	code compliant	None	<NA>	False	0	True
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100	99	species	AA	0	True	11	True	0	True	True	False	code compliant; specified	None	<NA>	True	0	True
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	100000	2624150	species	HS	0	True	11	True	0	True	True	False	NaN	None	<NA>	False	0	True
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax...	1000000	2609290	species	MS	0	True	11	True	0	True	True	False	NaN	None	<NA>	False	0	True

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 19 columns)
   taxon_id | parent_taxon_id | rank    | embl_code | division_id | inherits_division | genetic_code_id | inherits_genetic_code
   -------- | --------------- | ------- | --------- | ----------- | ----------------- | --------------- | ---------------------
0  1        | 1               | no rank | —         | 8           | false             | 1               | false
1  10       | 1706371         | genus   | —         | 0           | true              | 11              | true
2  100      | 99              | species | AA        | 0           | true              | 11              | true
3  100000   | 2624150         | species | HS        | 0           | true              | 11              | true
4  1000000  | 2609290         | species | MS        | 0           | true              | 11              | true

Description

NCBI Taxonomy node hierarchy and inherited classification settings, 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 this node.
parent_taxon_id	TEXT	Taxonomy ID for this node’s parent.
rank	TEXT	Taxonomic rank, such as species, genus, family, or no rank.
embl_code	TEXT	EMBL locus name prefix, if assigned.
division_id	TEXT	NCBI Taxonomy division ID.
inherits_division	BOOLEAN	Whether the node inherits its division from its parent.
genetic_code_id	TEXT	NCBI genetic code ID.
inherits_genetic_code	BOOLEAN	Whether the node inherits its genetic code from its parent.
mitochondrial_genetic_code_id	TEXT	NCBI mitochondrial genetic code ID.
inherits_mitochondrial_genetic_code	BOOLEAN	Whether the node inherits its mitochondrial genetic code from its parent.
is_genbank_hidden	BOOLEAN	Whether the node name is suppressed in a GenBank entry lineage.
is_hidden_subtree_root	BOOLEAN	Whether the node roots a subtree with no sequence data.
comment	TEXT	Free text NCBI comments and citations, if supplied.
plastid_genetic_code_id	TEXT	NCBI plastid genetic code ID, if supplied.
inherits_plastid_genetic_code	BOOLEAN	Whether the node inherits its plastid genetic code from its parent, if supplied.
has_specified_species	BOOLEAN	Whether the species in the node’s lineage has a formal name.
hydrogenosome_genetic_code_id	TEXT	NCBI hydrogenosome genetic code ID, if supplied.
inherits_hydrogenosome_genetic_code	BOOLEAN	Whether the node inherits its hydrogenosome genetic code from its parent.