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bedrock.bio

ncbi_gene.interactions

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources first_interactant_taxon_id first_interactant_gene_id first_interactant_accession first_interactant_name interaction_phrase second_interactant_taxon_id second_interactant_id second_interactant_id_type second_interactant_accession second_interactant_name complex_id complex_id_type complex_name pubmed_ids updated_at text interaction_id interaction_id_type
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... 358 1224321 NP_059802.1 hypothetical protein pTi_130 None NaN NaN NaN AE008690.1 Agrobacterium tumefaciens str. C58 Ti plasmid,... None None None [15155952] 2005-01-18 14:45:00 VirB4 interacts with T-DNA. 134324 BIND
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... 358 1224322 NP_059803.1 hypothetical protein pTi_131 None NaN NaN NaN AE008690.1 Agrobacterium tumefaciens str. C58 Ti plasmid,... None None None [15155952] 2005-01-18 14:45:00 VirB5 interacts with T-DNA. 134323 BIND
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... 358 1224323 NP_059804.1 hypothetical protein pTi_132 None NaN NaN NaN AE008690.1 Agrobacterium tumefaciens str. C58 Ti plasmid,... None None None [15155952] 2005-01-18 14:45:00 VirB6 interacts with T-DNA. 134329 BIND
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... 358 1224324 NP_059805.1 hypothetical protein pTi_133 None 358 1224326 GeneID NP_059807.1 hypothetical protein pTi_135 None None None [9171381] 2005-05-16 15:52:00 VirB7 interacts with VirB9. This interaction w... 196356 BIND
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/gene/Ge... 358 1224324 NP_059805.1 hypothetical protein pTi_133 None 358 1224326 GeneID NP_059807.1 hypothetical protein pTi_135 None None None [15155952] 2005-01-18 14:45:00 VirB7 interacts with VirB9. 134325 BIND

Description

Section titled “Description”

Source-attributed molecular interaction records with up to two interactants and an optional resulting complex.

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 interaction report.
first_interactant_taxon_id TEXT NCBI taxonomy identifier for the first, GeneID-associated interactant.
first_interactant_gene_id TEXT NCBI Gene identifier for the first interactant.
first_interactant_accession TEXT Versioned accession for the first interactant, if supplied.
first_interactant_name TEXT Name of the first interactant, if supplied.
interaction_phrase TEXT Short source-supplied phrase describing the interaction, if supplied.
second_interactant_taxon_id TEXT NCBI taxonomy identifier for the second interactant, if supplied.
second_interactant_id TEXT Source identifier for the second interactant, if supplied.
second_interactant_id_type TEXT Namespace of second_interactant_id, if supplied.
second_interactant_accession TEXT Versioned accession for the second interactant, if supplied.
second_interactant_name TEXT Name of the second interactant, if supplied.
complex_id TEXT Source identifier for the resulting complex, if supplied.
complex_id_type TEXT Namespace of complex_id, if supplied.
complex_name TEXT Name of the resulting complex, if supplied.
pubmed_ids TEXT[] PubMed citation identifiers associated with the interaction.
updated_at TIMESTAMPTZ Timestamp when NCBI last updated the interaction record; the source does not provide a timezone.
text TEXT Source-supplied GeneRIF interaction text, if supplied.
interaction_id TEXT Source-specific interaction identifier, if supplied.
interaction_id_type TEXT Namespace of interaction_id, if supplied.