Plant Reactome Tools

Configuration File: plant_reactome_tools.json Tool Type: Local Tools Count: 5

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_get_pathway_participants (Type: PlantReactomeTool)

List the gene/protein/molecule participants of a Plant Reactome pathway or reaction (the macromol…

PlantReactome_get_pathway_participants tool specification

Tool Information:

  • Name: PlantReactome_get_pathway_participants

  • Type: PlantReactomeTool

  • Description: List the gene/protein/molecule participants of a Plant Reactome pathway or reaction (the macromolecules that are IN the pathway), with UniProt accessions and gene names. PlantReactome_get_pathway returns only pathway metadata and ‘hasEvent’ sub-event IDs, not the participant gene products; use this tool to get the actual genes/proteins. Each participant carries its refEntities, where ‘identifier’ is the UniProt accession and ‘gene_names’ lists the gene symbols. Example: R-OSA-1119263 (Arginine biosynthesis, rice) returns 36 participants; the first refEntity is UniProt Q10MK5 with gene names including LOC_OS03G19280. No API key required.

Parameters:

  • pathway_id (string) (required) Plant Reactome stable identifier of a pathway or reaction. Format: R-{species_code}-{number}. Example: ‘R-OSA-1119263’ (Arginine biosynthesis in rice).

Example Usage:

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

PlantReactome_get_species_pathway_tree (Type: PlantReactomeTool)

Retrieve the full hierarchical pathway/event tree for a plant species (top-level pathways down to…

PlantReactome_get_species_pathway_tree tool specification

Tool Information:

  • Name: PlantReactome_get_species_pathway_tree

  • Type: PlantReactomeTool

  • Description: Retrieve the full hierarchical pathway/event tree for a plant species (top-level pathways down to reactions) in a single call, keyed by NCBI taxonomy id. Lets an agent browse or enumerate the complete pathway catalog for one crop, which keyword search (PlantReactome_search_pathways) and single-pathway fetch (PlantReactome_get_pathway) cannot do. Returns a list of top-level pathways, each with ‘stId’, ‘name’, ‘type’, and nested ‘children’. Example: taxId 4530 (Oryza sativa) returns 6 top-level pathways, e.g. ‘Cellular processes’ (R-OSA-2894886) with nested Cell cycle (R-OSA-9640670). taxId 4577 = maize. No API key required.

Parameters:

  • tax_id ([‘string’, ‘integer’]) (required) NCBI taxonomy id of the plant species. Examples: 4530 (Oryza sativa / rice), 4577 (Zea mays / maize), 3702 (Arabidopsis thaliana).

Example Usage:

query = {
    "name": "PlantReactome_get_species_pathway_tree",
    "arguments": {
        "tax_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)