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. Results are paged: ‘count’ is how many entries came back, ‘total_results’ is how many matched in Reactome overall, and ‘has_more’ flags that the list is a slice – use ‘rows’ and ‘start’ to page through the rest.

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’.

  • rows ([‘integer’, ‘null’]) (optional) Number of results to return per page (1-1000). Omit to use Reactome’s default page of 10. Queries often match far more than that (‘DNA repair’ in Homo sapiens matches 455 pathways), so raise this to see beyond the first page. Compare the returned ‘count’ against ‘total_results’ to know how much you are holding.

  • start ([‘integer’, ‘null’]) (optional) Zero-based offset of the first result to return, for paging through large result sets. Use together with ‘rows’ (e.g. rows=50 with start=0, then start=50). Omit to start at the first result.

Example Usage:

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