ncbi_gene.omim_medgen_relationships

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	omim_number	gene_id	medgen_cui	assertions
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100050	NaN	C3149220	[]
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100070	NaN	C1853365	[]
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100100	1131	C0033770	[{'source': 'GeneMap', 'comment': None}]
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100200	NaN	C4551519	[]
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	100300	57514	C4551482	[{'source': 'GeneMap', 'comment': None}]

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 3 of 5 columns)
   omim_number | gene_id | medgen_cui
   ----------- | ------- | ----------
0  100050      | —       | C3149220
1  100070      | —       | C1853365
2  100100      | 1131    | C0033770
3  100200      | —       | C4551519
4  100300      | 57514   | C4551482

Description

Curated relationships from OMIM phenotype entries to MedGen clinical-genetics concepts and, when known, associated NCBI Gene records.

Each relationship combines the distinct source assertions and qualifier comments reported for it.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Source provenance for the row.
omim_number	TEXT	Six-digit identifier for an OMIM phenotype entry.
gene_id	TEXT	NCBI Gene identifier associated with the phenotype, if known.
medgen_cui	TEXT	MedGen/UMLS concept unique identifier for the phenotype, if supplied.
assertions	STRUCT(source TEXT, comment TEXT)[]	Source assertions for this OMIM, MedGen, and NCBI Gene relationship, each with a source and optional qualifier comment; empty when none is supplied.