dbsnp.clinvar_diseases

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('dbsnp.clinvar_diseases')
rel = rel.filter("assembly_accession = 'GCF_000001405.25' AND chromosome = '1'")

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

Out[1]:

	sources	build	assembly_accession	assembly_name	chromosome	position	ref_allele	alt_allele	rsid	clinvar_accession	clinvar_disease_name
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248058987	C	T	rs372830127	RCV002771534.2	not_provided
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248112835	C	T	rs150695367	RCV004255005.1	not_specified
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059078	G	T	rs61752499	RCV003115385.4	not_provided
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059087	T	G	rs755632283	RCV002590247.2	not_provided
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/snp/arc...	b157	GCF_000001405.25	GRCh37.p13	1	248059161	C	G	rs1195966877	RCV003553873.1	not_provided

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("dbsnp.clinvar_diseases")
df <- filter(lf, assembly_accession == "GCF_000001405.25", chromosome == "1") |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 11 columns)
   assembly_accession | chromosome | build | assembly_name | position  | ref_allele | alt_allele | rsid
   ------------------ | ---------- | ----- | ------------- | --------- | ---------- | ---------- | ------------
0  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248058987 | C          | T          | rs372830127
1  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248112835 | C          | T          | rs150695367
2  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059078 | G          | T          | rs61752499
3  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059087 | T          | G          | rs755632283
4  GCF_000001405.25   | 1          | b157  | GRCh37.p13    | 248059161 | C          | G          | rs1195966877

Description

Condition names associated with ClinVar records.

not_provided and not_specified are source placeholders, not condition names.

Condition identifiers are in clinvar_disease_xrefs.

Partitions

• assembly_accession
  • 'GCF_000001405.25'
  • 'GCF_000001405.40'
• chromosome
  • '1'
  • '10'
  • '11'
  • '12'
  • '13'
  • '14'
  • '15'
  • '16'
  • '17'
  • '18'
  • '19'
  • '2'
  • '20'
  • '21'
  • '22'
  • '3'
  • '4'
  • '5'
  • '6'
  • '7'
  • '8'
  • '9'
  • 'MT'
  • 'X'
  • 'Y'

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Source provenance for the row.
build	TEXT	dbSNP build version (e.g. b157).
assembly_accession	TEXT	Partition column. Versioned RefSeq assembly accession (GCF) for the variant coordinates.
assembly_name	TEXT	Exact NCBI assembly name, including its patch release (for example, GRCh38.p14).
chromosome	TEXT	Partition column. Chromosome on which the variant is located (1-22, X, Y, MT).
position	INT	Variant position within the chromosome (1-based).
ref_allele	TEXT	Reference allele.
alt_allele	TEXT	Alternate allele.
rsid	TEXT	NCBI RefSNP identifier.
clinvar_accession	TEXT	ClinVar RCV accession with version.
clinvar_disease_name	TEXT	ClinVar condition name, with underscores in place of spaces.