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. Interactions are curated from experimental data with molecular interaction (MI) scores. Example: get interactors for P04637 (TP53) returns 248 interactors including MDM2 (score 0.995, 119 evidences), EP300 (score 0.976), BRCA1 (score 0.944); for Q04206 (NF-kB p65/RELA) returns 105 interactors.

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 (default: 20, max: 100).

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)