ncbi_gene.go_annotations

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	taxon_id	gene_id	go_id	evidence	qualifier	go_term	pubmed_ids	category
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	2711	102577933	GO:0004449	IEA	enables	isocitrate dehydrogenase (NAD+) activity	[30032202]	Function
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	2711	102577933	GO:0005739	IEA	located_in	mitochondrion	[30032202]	Component
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	2711	102577933	GO:0006099	IEA	involved_in	tricarboxylic acid cycle	[22301074, 30032202]	Process
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	2711	102577933	GO:0006102	IEA	involved_in	isocitrate metabolic process	[30032202]	Process
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/DA...	2711	102577934	GO:0004497	IEA	enables	monooxygenase activity	[22301074]	Function

R

In [1]:

library(bedrockbio)

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

head(df)

Out[1]:

Sample output (5 rows, showing 7 of 9 columns)
   taxon_id | gene_id   | go_id      | evidence | qualifier   | go_term                  | category
   -------- | --------- | ---------- | -------- | ----------- | ------------------------ | ---------
0  2711     | 102577933 | GO:0004449 | IEA      | enables     | isocitrate dehydrogenas… | Function
1  2711     | 102577933 | GO:0005739 | IEA      | located_in  | mitochondrion            | Component
2  2711     | 102577933 | GO:0006099 | IEA      | involved_in | tricarboxylic acid cycle | Process
3  2711     | 102577933 | GO:0006102 | IEA      | involved_in | isocitrate metabolic pr… | Process
4  2711     | 102577934 | GO:0004497 | IEA      | enables     | monooxygenase activity   | Function

Description

Gene Ontology annotations reported by NCBI Gene, one row per GeneID, GO term, and representative evidence code.

Partitions

Not partitioned.

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Provenance for the NCBI Gene GO annotation file.
taxon_id	TEXT	NCBI taxonomy identifier for the gene’s species or strain.
gene_id	TEXT	NCBI Gene identifier.
go_id	TEXT	Gene Ontology identifier.
evidence	TEXT	GO evidence code.
qualifier	TEXT	GO relationship qualifier, if supplied.
go_term	TEXT	Name of the associated GO term.
pubmed_ids	TEXT[]	PubMed identifiers reported as annotation evidence.
category	TEXT	GO category, such as Function, Process, or Component.