Reactome Interactors Tools#

Configuration File: reactome_interactors_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

ReactomeInteractors_get_entity_pathways (Type: ReactomeInteractorsTool)#

Find Reactome biological pathways that contain a specific molecular entity. Returns pathway stabl…

ReactomeInteractors_get_entity_pathways tool specification

Tool Information:

  • Name: ReactomeInteractors_get_entity_pathways

  • Type: ReactomeInteractorsTool

  • Description: Find Reactome biological pathways that contain a specific molecular entity. Returns pathway stable IDs, names, and whether they are disease-associated. Use Reactome stable IDs (e.g., R-HSA-199420 for PTEN) obtained from ReactomeInteractors_search_entity. Example: R-HSA-199420 (PTEN) participates in 10 pathways including PI3K/AKT signaling, PTEN regulation, and TCR signaling.

Parameters:

  • entity_id (string) (required) Reactome stable identifier for the entity. Use ReactomeInteractors_search_entity to find IDs. Examples: ‘R-HSA-199420’ (PTEN), ‘R-HSA-69541’ (TP53 tetramer), ‘R-HSA-8869337’ (TP53).

  • species ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID for species filter (default: 9606 for human). Examples: 9606 (human), 10090 (mouse).

Example Usage:

query = {
    "name": "ReactomeInteractors_get_entity_pathways",
    "arguments": {
        "entity_id": "example_value"
    }
}
result = tu.run(query)

ReactomeInteractors_get_protein_interactors (Type: ReactomeInteractorsTool)#

Get protein-protein interaction partners for a specific protein from Reactome’s IntAct-derived in…

ReactomeInteractors_get_protein_interactors tool specification

Tool Information:

  • Name: ReactomeInteractors_get_protein_interactors

  • Type: ReactomeInteractorsTool

  • Description: Get protein-protein interaction partners for a specific protein from Reactome’s IntAct-derived interaction data. Returns interactor accessions, gene names, confidence scores, and evidence counts, plus the true total number of interactors (‘total_interactors’) and how many were returned on this page (‘returned_interactors’); when ‘truncated’ is true, re-run with a larger page_size to get them all. Interactions are curated from experimental data with molecular interaction (MI) scores. Example: P04637 (TP53) has 249 interactors including MDM2 (score 0.995, 119 evidences), EP300 (score 0.976), BRCA1 (score 0.944); Q04206 (NF-kB p65/RELA) has 106; P42345 (MTOR) has 22.

Parameters:

  • accession (string) (required) UniProt accession number for the query protein. Examples: ‘P04637’ (TP53), ‘Q04206’ (NF-kB p65), ‘P00533’ (EGFR), ‘P38398’ (BRCA1).

  • page_size ([‘integer’, ‘null’]) (optional) Maximum number of interactors to return on this page (default: 20). Not capped - pass a value >= total_interactors (e.g. 300 for P04637) to retrieve every interactor in one call.

Example Usage:

query = {
    "name": "ReactomeInteractors_get_protein_interactors",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

ReactomeInteractors_search_entity (Type: ReactomeInteractorsTool)#

Search Reactome for biological entities (proteins, complexes, reactions, pathways) by name or ide…

ReactomeInteractors_search_entity tool specification

Tool Information:

  • Name: ReactomeInteractors_search_entity

  • Type: ReactomeInteractorsTool

  • Description: Search Reactome for biological entities (proteins, complexes, reactions, pathways) by name or identifier. Returns Reactome stable IDs, entity names, types, and species. Use this to find Reactome IDs for proteins before querying their interactors or pathways. Results are grouped by entity type (Protein, Complex, Reaction, Pathway). Example: search ‘TP53’ returns TP53 protein entities with stable IDs like R-HSA-69488; search ‘apoptosis’ returns apoptosis-related reactions and pathways.

Parameters:

  • query (string) (required) Search query - gene name, protein name, pathway name, or Reactome ID. Examples: ‘TP53’, ‘BRCA1’, ‘apoptosis’, ‘insulin signaling’, ‘cell cycle’.

  • species ([‘string’, ‘null’]) (optional) Species name filter (default: ‘Homo sapiens’). Examples: ‘Homo sapiens’, ‘Mus musculus’, ‘Rattus norvegicus’.

  • types ([‘string’, ‘null’]) (optional) Entity type filter. Options: ‘Protein’, ‘Complex’, ‘Reaction’, ‘Pathway’, ‘SmallMolecule’. If null, returns all types.

Example Usage:

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