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 events contained within a Reactome pathway. Returns every resolved sub-pathway plus an explic…

ReactomeContent_get_contained_events tool specification

Tool Information:

  • Name: ReactomeContent_get_contained_events

  • Type: ReactomeContentTool

  • Description: Get events contained within a Reactome pathway. Returns every resolved sub-pathway plus an explicitly pageable reaction list with true event/pathway/reaction counts and a next offset, so large pathways do not silently stop at 50 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).

  • reaction_limit (integer) (optional) Maximum contained reactions to return on this page.

  • reaction_offset (integer) (optional) Zero-based offset into contained reactions.

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 the complete curated description and complet…

ReactomeContent_get_enhanced_pathway tool specification

Tool Information:

  • Name: ReactomeContent_get_enhanced_pathway

  • Type: ReactomeContentTool

  • Description: Get enhanced pathway details from Reactome including the complete curated description and complete direct literature-reference list, GO biological process terms, and direct sub-events. Reports summary character and literature counts; it does not silently cut summaries at 2,000 characters or references at 20.

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. With grouped (cluster) results, ‘rows’ applies to each type group; continue with start=next_offset while has_more is true.

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). Default 30. 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.

  • limit (integer) (optional) Alias for rows, used when rows is not given.

  • offset (integer) (optional) Alias for start, used when start is not given.

Example Usage:

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