bc_get_reactome_info_by_identifier

Retrieve Reactome pathways associated with a specific identifier by querying the Reactome API. Filter results by species, p-value, and entity count to analyze biological pathways efficiently.

Instructions

Query the Reactome API identifier endpoint.

Use this endpoint to retrieve pathways associated with a given identifier. Always provide the species parameter to ensure the correct protein is returned.

Args: identifier (str): The identifier of the element to be retrieved base_url (str): Base URL for the Reactome API interactors (bool): Include interactors species (str or list): List of species to filter the result (accepts taxonomy ids, species names and dbId) page_size (int): Pathways per page page (int): Page number sort_by (str): Field to sort results by (e.g., "ENTITIES_PVALUE", "ENTITIES_FDR") order (str): Sort order ("ASC" or "DESC") resource (str): Resource to filter by (TOTAL includes all molecule types) p_value (float): P-value threshold (only pathways with p-value <= threshold will be returned) include_disease (bool): Set to False to exclude disease pathways min_entities (int): Minimum number of contained entities per pathway max_entities (int): Maximum number of contained entities per pathway importable_only (bool): Filter to only include importable resources timeout (int): Request timeout in seconds

Returns: dict: API response data or error information

Input Schema

Name	Required	Description	Default
`base_url`	No	Base URL for the Reactome API	https://reactome.org/AnalysisService
`identifier`	Yes	The identifier of the element to be retrieved
`importable_only`	No	Filter to only include importable resources
`include_disease`	No	Set to False to exclude disease pathways
`interactors`	No	Include interactors
`max_entities`	No	Maximum number of contained entities per pathway
`min_entities`	No	Minimum number of contained entities per pathway
`order`	No	Sort order ('ASC' or 'DESC')	ASC
`p_value`	No	P-value threshold (only pathways with p-value <= threshold will be returned)
`page`	No	Page number
`page_size`	No	Pathways per page
`resource`	No	Resource to filter by (TOTAL includes all molecule types)	TOTAL
`sort_by`	No	Field to sort results by (e.g., 'ENTITIES_PVALUE', 'ENTITIES_FDR')	ENTITIES_PVALUE
`species`	No	List of species to filter the result (accepts taxonomy ids, species names and dbId)
`timeout`	No	Request timeout in seconds

Input Schema (JSON Schema)

{
  "properties": {
    "base_url": {
      "default": "https://reactome.org/AnalysisService",
      "description": "Base URL for the Reactome API",
      "title": "Base Url",
      "type": "string"
    },
    "identifier": {
      "description": "The identifier of the element to be retrieved",
      "title": "Identifier",
      "type": "string"
    },
    "importable_only": {
      "default": false,
      "description": "Filter to only include importable resources",
      "title": "Importable Only",
      "type": "boolean"
    },
    "include_disease": {
      "default": true,
      "description": "Set to False to exclude disease pathways",
      "title": "Include Disease",
      "type": "boolean"
    },
    "interactors": {
      "default": false,
      "description": "Include interactors",
      "title": "Interactors",
      "type": "boolean"
    },
    "max_entities": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Maximum number of contained entities per pathway",
      "title": "Max Entities"
    },
    "min_entities": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Minimum number of contained entities per pathway",
      "title": "Min Entities"
    },
    "order": {
      "default": "ASC",
      "description": "Sort order ('ASC' or 'DESC')",
      "title": "Order",
      "type": "string"
    },
    "p_value": {
      "default": 1,
      "description": "P-value threshold (only pathways with p-value <= threshold will be returned)",
      "maximum": 1,
      "minimum": 0,
      "title": "P Value",
      "type": "number"
    },
    "page": {
      "default": 1,
      "description": "Page number",
      "minimum": 1,
      "title": "Page",
      "type": "integer"
    },
    "page_size": {
      "default": 20,
      "description": "Pathways per page",
      "minimum": 1,
      "title": "Page Size",
      "type": "integer"
    },
    "resource": {
      "default": "TOTAL",
      "description": "Resource to filter by (TOTAL includes all molecule types)",
      "title": "Resource",
      "type": "string"
    },
    "sort_by": {
      "default": "ENTITIES_PVALUE",
      "description": "Field to sort results by (e.g., 'ENTITIES_PVALUE', 'ENTITIES_FDR')",
      "title": "Sort By",
      "type": "string"
    },
    "species": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of species to filter the result (accepts taxonomy ids, species names and dbId)",
      "title": "Species"
    },
    "timeout": {
      "default": 30,
      "description": "Request timeout in seconds",
      "minimum": 1,
      "title": "Timeout",
      "type": "integer"
    }
  },
  "required": [
    "identifier"
  ],
  "type": "object"
}

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