ncbi_gene.neighbors

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('ncbi_gene.neighbors')

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

Out[1]:

	sources	taxon_id	gene_id	genomic_accession	genomic_geninfo_id	gene_start	gene_end	gene_is_forward_strand	chromosome	left_gene_ids	left_distance	right_gene_ids	right_distance	overlapping_gene_ids	assembly_name
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	9770	807607	NC_001321.1	5819095	8389	9069	True	MT	[807612, 807613]	234	[807610]	854	[807608, 807611]	None
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	9770	807608	NC_001321.1	5819095	9069	9854	True	MT	[807611, 807612]	650	[807610, 807616, 807617]	69	[807607]	None
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	9770	807609	NC_001321.1	5819095	4355	5398	True	MT	[807618]	209	[807612, 807613]	384	[]	None
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	9770	807610	NC_001321.1	5819095	9923	10268	True	MT	[807607, 807608, 807611]	69	[807614, 807615, 807616, 807617]	71	[]	None
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	9770	807611	NC_001321.1	5819095	8228	8419	True	MT	[807612, 807613]	73	[807608, 807610]	650	[807607]	None

R

In [1]:

library(bedrockbio)

lf <- load_table("ncbi_gene.neighbors")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 15 columns)
   taxon_id | gene_id | genomic_accession | genomic_geninfo_id | gene_start | gene_end | gene_is_forward_strand | chromosome
   -------- | ------- | ----------------- | ------------------ | ---------- | -------- | ---------------------- | ----------
0  9770     | 807607  | NC_001321.1       | 5819095            | 8389       | 9069     | true                   | MT
1  9770     | 807608  | NC_001321.1       | 5819095            | 9069       | 9854     | true                   | MT
2  9770     | 807609  | NC_001321.1       | 5819095            | 4355       | 5398     | true                   | MT
3  9770     | 807610  | NC_001321.1       | 5819095            | 9923       | 10268    | true                   | MT
4  9770     | 807611  | NC_001321.1       | 5819095            | 8228       | 8419     | true                   | MT

Description

Genomic placements and nearby NCBI Gene records for genes on top-level or curated genomic sequences.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI Gene neighbor file.
taxon_id	TEXT	NCBI taxonomy identifier for the gene’s species or strain.
gene_id	TEXT	NCBI Gene identifier.
genomic_accession	TEXT	Versioned genomic nucleotide accession containing the placement.
genomic_geninfo_id	TEXT	Legacy NCBI GenInfo identifier for the genomic accession, if supplied.
gene_start	BIGINT	One-based inclusive genomic gene start position.
gene_end	BIGINT	One-based inclusive genomic gene end position.
gene_is_forward_strand	BOOLEAN	Whether the gene is on the forward strand — true for source + and false for source -.
chromosome	TEXT	NCBI chromosome name, if supplied.
left_gene_ids	TEXT[]	Nearest non-overlapping genes to the left, including overlapping neighbors of those genes.
left_distance	BIGINT	Distance to the nearest gene on the left, if one is supplied.
right_gene_ids	TEXT[]	Nearest non-overlapping genes to the right, including overlapping neighbors of those genes.
right_distance	BIGINT	Distance to the nearest gene on the right, if one is supplied.
overlapping_gene_ids	TEXT[]	Genes that overlap this placement.
assembly_name	TEXT	NCBI assembly name for the placement, if supplied.