Plant Reactome Tools

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

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

Available Tools

PlantReactome_get_pathway (Type: PlantReactomeTool)

Get detailed information about a specific Plant Reactome pathway by stable ID. Returns pathway na…

PlantReactome_get_pathway tool specification

Tool Information:

  • Name: PlantReactome_get_pathway

  • Type: PlantReactomeTool

  • Description: Get detailed information about a specific Plant Reactome pathway by stable ID. Returns pathway name, species, sub-events (reactions), compartments, GO annotations, and cross-references. Example: ‘R-OSA-1119312’ returns the Photorespiration pathway in Oryza sativa.

Parameters:

  • pathway_id (string) (required) Plant Reactome stable identifier. Format: R-{species_code}-{number}. Examples: ‘R-OSA-1119312’ (Photorespiration in rice), ‘R-OSA-1119519’ (Calvin cycle in rice).

Example Usage:

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

PlantReactome_list_species (Type: PlantReactomeTool)

List all plant species available in Plant Reactome with their taxonomy IDs. Returns the complete …

PlantReactome_list_species tool specification

Tool Information:

  • Name: PlantReactome_list_species

  • Type: PlantReactomeTool

  • Description: List all plant species available in Plant Reactome with their taxonomy IDs. Returns the complete catalog of 140+ plant species including model organisms and major crop species. Useful for discovering which species have curated pathway data available.

Parameters:

No parameters required.

Example Usage:

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

PlantReactome_search_pathways (Type: PlantReactomeTool)

Search for plant biological pathways in Plant Reactome (Gramene). Plant Reactome is a curated res…

PlantReactome_search_pathways tool specification

Tool Information:

  • Name: PlantReactome_search_pathways

  • Type: PlantReactomeTool

  • Description: Search for plant biological pathways in Plant Reactome (Gramene). Plant Reactome is a curated resource for plant metabolic and regulatory pathways, covering model and crop species including rice (Oryza sativa), Arabidopsis thaliana, maize, wheat, and 140+ plant species. Returns pathways matching the query with their stable IDs and species. Example: ‘photosynthesis’ finds photosynthesis-related pathways.

Parameters:

  • query (string) (required) Search query for plant pathways. Examples: ‘photosynthesis’, ‘Calvin cycle’, ‘flavonoid biosynthesis’, ‘nitrogen fixation’, ‘auxin signaling’.

  • species ([‘string’, ‘null’]) (optional) Species name to filter results. Examples: ‘Oryza sativa’, ‘Arabidopsis thaliana’, ‘Zea mays’. Default: all species.

Example Usage:

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