Reactome Content Tools

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

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

Available Tools

ReactomeContent_get_contained_events (Type: ReactomeContentTool)

Get all events (sub-pathways and reactions) contained within a Reactome pathway. Decomposes a top…

ReactomeContent_get_contained_events tool specification

Tool Information:

  • Name: ReactomeContent_get_contained_events

  • Type: ReactomeContentTool

  • Description: Get all events (sub-pathways and reactions) contained within a Reactome pathway. Decomposes a top-level pathway into its complete hierarchy of sub-pathways and individual biochemical reactions. Returns counts and lists of both pathways and reactions. Example: R-HSA-109581 (Apoptosis) contains 177 events total: 4 major sub-pathways (extrinsic, intrinsic, execution, regulation) plus 173 individual reactions.

Parameters:

  • identifier (string) (required) Reactome pathway stable identifier. Examples: ‘R-HSA-109581’ (Apoptosis, 177 events), ‘R-HSA-69278’ (Cell Cycle), ‘R-HSA-73857’ (RNA Polymerase II Transcription), ‘R-HSA-1640170’ (Cell Cycle Checkpoints).

Example Usage:

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

ReactomeContent_get_enhanced_pathway (Type: ReactomeContentTool)

Get enhanced pathway details from Reactome including description, literature references, GO biolo…

ReactomeContent_get_enhanced_pathway tool specification

Tool Information:

  • Name: ReactomeContent_get_enhanced_pathway

  • Type: ReactomeContentTool

  • Description: Get enhanced pathway details from Reactome including description, literature references, GO biological process terms, and direct sub-events. Provides richer information than basic pathway lookup by including curated summaries, PubMed references, and Gene Ontology annotations. Example: R-HSA-109581 (Apoptosis) returns a detailed summation, GO:0006915 annotation, 4 sub-pathways (extrinsic, intrinsic, execution, regulation), and key literature references.

Parameters:

  • identifier (string) (required) Reactome pathway stable identifier. Examples: ‘R-HSA-109581’ (Apoptosis), ‘R-HSA-6804757’ (Regulation of TP53 Degradation), ‘R-HSA-69278’ (Cell Cycle), ‘R-HSA-168256’ (Immune System).

Example Usage:

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

ReactomeContent_search (Type: ReactomeContentTool)

Search Reactome for pathways, reactions, and biological entities by keyword. Performs free-text s…

ReactomeContent_search tool specification

Tool Information:

  • Name: ReactomeContent_search

  • Type: ReactomeContentTool

  • Description: Search Reactome for pathways, reactions, and biological entities by keyword. Performs free-text search across Reactome’s knowledge base of biological pathways. Supports filtering by species and entity type. Example: searching ‘apoptosis’ in Homo sapiens returns pathways like R-HSA-109581 (Apoptosis), R-HSA-169911 (Regulation of Apoptosis), R-HSA-9635465 (Suppression of apoptosis). Use this to discover relevant pathways before querying their details.

Parameters:

  • query (string) (required) Search query. Examples: ‘apoptosis’, ‘TP53’, ‘cell cycle’, ‘DNA repair’, ‘insulin signaling’.

  • species (string) (optional) Species name for filtering results. Default: ‘Homo sapiens’. Other options: ‘Mus musculus’, ‘Rattus norvegicus’, ‘Danio rerio’, ‘Drosophila melanogaster’.

  • types (string) (optional) Entity type to search. Options: ‘Pathway’, ‘Reaction’, ‘Complex’, ‘Protein’, ‘SmallMolecule’. Default: ‘Pathway’.

Example Usage:

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