Biogrid Tools#

Configuration File: biogrid_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the biogrid_tools.json configuration file.

Available Tools#

BioGRID_get_chemical_interactions (Type: BioGRIDRESTTool)#

Query experimentally validated interactions for specific genes/proteins from BioGRID, filtered fo…

BioGRID_get_chemical_interactions tool specification

Tool Information:

  • Name: BioGRID_get_chemical_interactions

  • Type: BioGRIDRESTTool

  • Description: Query experimentally validated interactions for specific genes/proteins from BioGRID, filtered for potential chemical relevance, with recoverable official start/max pagination through offset and metadata.next_offset. Important limitation: The BioGRID REST API does not support chemical-only queries — you MUST provide gene_names. The chemicalList parameter is unreliable. For drug-protein interaction queries, prefer ChEMBL_search_mechanisms or DGIdb_get_drug_gene_interactions instead. Prerequisites: Requires BIOGRID_API_KEY environment variable (free academic API key at https://webservice.thebiogrid.org/).

Parameters:

  • gene_names (array) (optional) List of gene names to query for chemical interactions (e.g., [‘TP53’, ‘EGFR’, ‘AKT1’]). Leave empty to search by chemical only.

  • chemical_names (array) (optional) List of chemical compound names (e.g., [‘Aspirin’, ‘Metformin’, ‘Imatinib’]). Leave empty to search by gene only.

  • organism (string) (optional) NCBI taxonomy ID (e.g., ‘9606’ for human, ‘10090’ for mouse). Default: 9606

  • interaction_action (string) (optional) Filter by interaction action type (e.g., ‘inhibitor’, ‘activator’, ‘antagonist’, ‘agonist’). Leave empty for all actions.

  • limit (integer) (optional) Maximum upstream interactions on this page (default: 100, max: 9999).

  • offset (integer) (optional) Zero-based BioGRID upstream record offset. Continue with metadata.next_offset.

  • include_evidence (boolean) (optional) Include detailed evidence and publication information (default: true)

Example Usage:

query = {
    "name": "BioGRID_get_chemical_interactions",
    "arguments": {
    }
}
result = tu.run(query)

BioGRID_get_interactions (Type: BioGRIDRESTTool)#

Query experimentally validated protein and genetic interactions from BioGRID. Results use the off…

BioGRID_get_interactions tool specification

Tool Information:

  • Name: BioGRID_get_interactions

  • Type: BioGRIDRESTTool

  • Description: Query experimentally validated protein and genetic interactions from BioGRID. Results use the official start/max pagination: begin with offset=0 and continue with metadata.next_offset while metadata.has_more is true. For physical/genetic client-side filters, offset advances through upstream records and a page may contain fewer than limit matching records. Requires a free BIOGRID_API_KEY.

Parameters:

  • gene_names (array) (optional) List of gene names or protein identifiers (e.g., [‘TP53’, ‘BRCA1’, ‘MYC’]). Accepts official gene symbols.

  • gene_name (string) (optional) Alias for gene_names: single gene symbol (e.g., ‘TP53’). Converted to gene_names list automatically.

  • organism (string) (optional) Organism name (e.g., ‘Homo sapiens’, ‘Mus musculus’) or NCBI taxonomy ID (e.g., ‘9606’ for human, ‘10090’ for mouse). Default: 9606 (human)

  • interaction_type (string) (optional) Type of interaction: ‘physical’ (protein-protein), ‘genetic’ (epistasis, synthetic lethality), ‘both’ (all interactions)

  • evidence_types (array) (optional) Filter by evidence types (e.g., [‘Affinity Capture-MS’, ‘Two-hybrid’] for physical, [‘Synthetic Lethality’, ‘Dosage Rescue’] for genetic). Leave empty for all evidence types.

  • limit (integer) (optional) Maximum upstream interactions to scan on this page (default: 100, max: 9999; one extra record is fetched to prove whether another page exists).

  • offset (integer) (optional) Zero-based BioGRID upstream record offset. Continue with metadata.next_offset.

  • throughput (string) (optional) Filter by throughput: ‘low’ (low-throughput studies), ‘high’ (high-throughput screens), or leave empty for all

Example Usage:

query = {
    "name": "BioGRID_get_interactions",
    "arguments": {
    }
}
result = tu.run(query)

BioGRID_get_ptms (Type: BioGRIDRESTTool)#

Retrieve post-translational-modification interaction records for proteins from BioGRID with recov…

BioGRID_get_ptms tool specification

Tool Information:

  • Name: BioGRID_get_ptms

  • Type: BioGRIDRESTTool

  • Description: Retrieve post-translational-modification interaction records for proteins from BioGRID with recoverable official start/max pagination. Begin at offset=0 and continue with metadata.next_offset while metadata.has_more is true. Requires a free BIOGRID_API_KEY.

Parameters:

  • gene_names (array) (required) List of gene names to query for PTMs (e.g., [‘TP53’, ‘AKT1’, ‘EGFR’, ‘ERK1’]). Accepts official gene symbols.

  • organism (string) (optional) NCBI taxonomy ID (e.g., ‘9606’ for human, ‘10090’ for mouse). Default: 9606

  • ptm_type (array) (optional) Filter by PTM types (e.g., [‘Phosphorylation’, ‘Ubiquitination’, ‘Acetylation’, ‘Methylation’, ‘Sumoylation’]). Leave empty for all PTM types.

  • residue (string) (optional) Filter by specific amino acid residue (e.g., ‘S’ for serine, ‘T’ for threonine, ‘Y’ for tyrosine). Leave empty for all residues.

  • include_enzymes (boolean) (optional) Include information about enzymes responsible for the PTM (kinases, ligases, etc.). Default: true

  • include_evidence (boolean) (optional) Include experimental evidence and publication details. Default: true

  • limit (integer) (optional) Maximum upstream PTM interaction records on this page (default: 500, max: 9999).

  • offset (integer) (optional) Zero-based BioGRID upstream record offset. Continue with metadata.next_offset.

Example Usage:

query = {
    "name": "BioGRID_get_ptms",
    "arguments": {
        "gene_names": ["item1", "item2"]
    }
}
result = tu.run(query)

BioGRID_search_by_pubmed (Type: BioGRIDRESTTool)#

Retrieve BioGRID interactions curated from PubMed studies with recoverable official start/max pag…

BioGRID_search_by_pubmed tool specification

Tool Information:

  • Name: BioGRID_search_by_pubmed

  • Type: BioGRIDRESTTool

  • Description: Retrieve BioGRID interactions curated from PubMed studies with recoverable official start/max pagination. Begin at offset=0 and continue with metadata.next_offset while metadata.has_more is true; a large paper is no longer silently limited to its first page. Requires a free BIOGRID_API_KEY.

Parameters:

  • pubmed_ids (array) (required) List of PubMed IDs to query (e.g., [‘12345678’, ‘87654321’]). Can be numeric or string format.

  • organism (string) (optional) NCBI taxonomy ID to filter interactions by organism (e.g., ‘9606’ for human, ‘559292’ for S. cerevisiae). Leave empty for all organisms.

  • interaction_type (string) (optional) Type of interaction: ‘physical’, ‘genetic’, ‘both’. Default: ‘both’

  • include_evidence (boolean) (optional) Include detailed evidence information (experimental systems, methods). Default: true

  • limit (integer) (optional) Maximum upstream interactions on this page (default: 1000, max: 9999).

  • offset (integer) (optional) Zero-based BioGRID upstream record offset. Continue with metadata.next_offset.

Example Usage:

query = {
    "name": "BioGRID_search_by_pubmed",
    "arguments": {
        "pubmed_ids": ["item1", "item2"]
    }
}
result = tu.run(query)