hgnc.families

Python

In [1]:

import bedrock_bio as bb

rel = bb.load_table('hgnc.families')

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

Out[1]:

	sources	family_id	abbreviation	name	external_note	pubmed_ids	description	description_label	description_source	description_go_id	typical_gene_symbol
0	[{'url': 'https://storage.googleapis.com/publi...	10	VNN	Vanin family	None	[22155241]	NaN	NaN	NaN	None	VNN1
1	[{'url': 'https://storage.googleapis.com/publi...	100	UBA	Ubiquitin like modifier activating enzymes	None	[]	Ubiquitin-activating enzymes, also known as E1...	Ubiquitin-activating enzymes	Wikipedia|http://en.wikipedia.org/wiki/Ubiquit...	None	UBA1
2	[{'url': 'https://storage.googleapis.com/publi...	1000	CYP1	Cytochrome P450 family 1	None	[]	NaN	NaN	NaN	None	NaN
3	[{'url': 'https://storage.googleapis.com/publi...	1001	CYP2	Cytochrome P450 family 2	None	[]	NaN	NaN	NaN	None	NaN
4	[{'url': 'https://storage.googleapis.com/publi...	1002	CYP3	Cytochrome P450 family 3	None	[]	NaN	NaN	NaN	None	NaN

R

In [1]:

library(bedrockbio)

lf <- load_table("hgnc.families")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 11 columns)
   family_id | abbreviation | name                     | external_note | description              | description_label        | description_source       | description_go_id
   --------- | ------------ | ------------------------ | ------------- | ------------------------ | ------------------------ | ------------------------ | -----------------
0  10        | VNN          | Vanin family             | —             | —                        | —                        | —                        | —
1  100       | UBA          | Ubiquitin like modifier… | —             | Ubiquitin-activating en… | Ubiquitin-activating en… | Wikipedia|http://en.wik… | —
2  1000      | CYP1         | Cytochrome P450 family 1 | —             | —                        | —                        | —                        | —
3  1001      | CYP2         | Cytochrome P450 family 2 | —             | —                        | —                        | —                        | —
4  1002      | CYP3         | Cytochrome P450 family 3 | —             | —                        | —                        | —                        | —

Description

HGNC gene families, one row per HGNC gene-family identifier.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the HGNC gene-family family.csv file.
family_id	TEXT	HGNC gene-family identifier.
abbreviation	TEXT	HGNC gene-family abbreviation, if supplied.
name	TEXT	HGNC gene-family name.
external_note	TEXT	HGNC note about the gene family, if supplied.
pubmed_ids	TEXT[]	PubMed identifiers associated with the gene family; empty when HGNC does not supply one.
description	TEXT	HGNC gene-family description, if supplied.
description_label	TEXT	HGNC label for description, if supplied.
description_source	TEXT	Source cited by HGNC for description, if supplied.
description_go_id	TEXT	Gene Ontology identifier associated with the description, if supplied.
typical_gene_symbol	TEXT	Typical member gene symbol supplied by HGNC, if supplied.