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 from Reactome’s IntAct-derived data. Returns the authori…

ReactomeInteractors_get_protein_interactors tool specification

Tool Information:

  • Name: ReactomeInteractors_get_protein_interactors

  • Type: ReactomeInteractorsTool

  • Description: Get protein-protein interaction partners from Reactome’s IntAct-derived data. Returns the authoritative total plus a pageable set of interactors; when has_more is true pass next_page as page with the same accession and page_size. Interactions include confidence scores and evidence counts.

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.

  • page (integer) (optional) One-based Reactome interactor page. Continue with next_page while has_more is true.

Example Usage:

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

ReactomeInteractors_search_entity (Type: ReactomeInteractorsTool)#

Search and page through Reactome biological entities by name or identifier. Reactome groups resul…

ReactomeInteractors_search_entity tool specification

Tool Information:

  • Name: ReactomeInteractors_search_entity

  • Type: ReactomeInteractorsTool

  • Description: Search and page through Reactome biological entities by name or identifier. Reactome groups results by entity type and applies limit/offset independently inside every group: limit=2 can therefore return up to two Proteins, two Complexes, two Pathways, etc., not two records globally. Metadata reports aggregate numberOfMatches, actual returned count, per-group totals, rows_per_group, and next_offset.

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.

  • limit (integer) (optional) Rows to request per Reactome result-type group, not a global response maximum.

  • offset (integer) (optional) Zero-based start row applied independently within every result-type group. Continue with metadata.next_offset.

Example Usage:

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