biocontext_kb.core.reactome

biocontext_kb.core.reactome#

Attributes#

core_mcp

Functions#

get_reactome_info_by_identifier(identifier[, ...])

Query the Reactome API identifier endpoint.

Package Contents#

biocontext_kb.core.reactome.core_mcp#
biocontext_kb.core.reactome.get_reactome_info_by_identifier(identifier, base_url='https://reactome.org/AnalysisService', interactors=False, species=None, page_size=20, page=1, sort_by='ENTITIES_PVALUE', order='ASC', resource='TOTAL', p_value=1.0, include_disease=True, min_entities=None, max_entities=None, importable_only=False, timeout=30)#

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.

Parameters:

  • 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:

API response data or error information

Return type:

dict

Contents