ncbi_gene.gene_rifs
import bedrock_bio as bb
rel = bb.load_table('ncbi_gene.gene_rifs')
df = rel.limit(5).pl() # Polars
df = rel.limit(5).df() # Pandas
df.head()| sources | taxon_id | gene_id | pubmed_ids | updated_at | text | |
|---|---|---|---|---|---|---|
| 0 | [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... | 7 | 5692769 | [27190162] | 2017-11-18 13:38:00 | we investigated how Azorhizobium caulinodans r... |
| 1 | [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... | 7 | 5692769 | [29150498] | 2019-02-02 11:27:00 | We identified a CheZ-like protein among Alphap... |
| 2 | [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... | 7 | 5692769 | [32002604] | 2020-11-28 13:15:00 | Azorhizobium caulinodans c-di-GMP phosphodiest... |
| 3 | [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... | 14 | 6951813 | [33242495] | 2021-06-12 12:57:00 | Crystal structure of Dictyoglomus thermophilum... |
| 4 | [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... | 14 | 6951813 | [34649692] | 2021-10-23 11:12:00 | Improvements in xylose stability and thermalst... |
library(bedrockbio)
lf <- load_table("ncbi_gene.gene_rifs")
df <- head(lf, 5) |> collect()
head(df)Sample output (5 rows, showing 4 of 6 columns) taxon_id | gene_id | updated_at | text -------- | ------- | ------------------- | ------------------------ 0 7 | 5692769 | 2017-11-18 13:38:00 | we investigated how Azo… 1 7 | 5692769 | 2019-02-02 11:27:00 | We identified a CheZ-li… 2 7 | 5692769 | 2020-11-28 13:15:00 | Azorhizobium caulinodan… 3 14 | 6951813 | 2021-06-12 12:57:00 | Crystal structure of Di… 4 14 | 6951813 | 2021-10-23 11:12:00 | Improvements in xylose …
Description
Section titled “Description”Literature-backed Gene Reference Into Function (GeneRIF) statements for individual NCBI Gene records.
Partitions
Section titled “Partitions”Not partitioned.
Schema
Section titled “Schema”| Column | Type | Description |
|---|---|---|
sources |
STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] |
Provenance for the NCBI GeneRIF report. |
taxon_id |
TEXT |
NCBI taxonomy identifier for the gene’s species or strain. |
gene_id |
TEXT |
NCBI Gene identifier. |
pubmed_ids |
TEXT[] |
PubMed citation identifiers associated with the statement. |
updated_at |
TIMESTAMPTZ |
Timestamp when NCBI last updated the GeneRIF statement; the source does not provide a timezone. |
text |
TEXT |
GeneRIF functional statement text. |