Reactome Tools¶
Configuration File: reactome_tools.json
Tool Type: Local
Tools Count: 20
This page contains all tools defined in the reactome_tools.json configuration file.
Available Tools¶
Reactome_get_complex (Type: ReactomeRESTTool)¶
Get detailed information about a protein complex by its Stable ID. Returns comprehensive complex …
Reactome_get_complex tool specification
Tool Information:
Name:
Reactome_get_complexType:
ReactomeRESTToolDescription: Get detailed information about a protein complex by its Stable ID. Returns comprehensive complex data including subunits, compartments, and related information. Uses the unified query endpoint that works for all entity types.
Parameters:
stId(string) (required) Complex Stable ID (e.g., ‘R-HSA-XXXXX’). To find complex IDs, use Reactome_get_participants with a reaction ID to see complexes participating in that reaction.
Example Usage:
query = {
"name": "Reactome_get_complex",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_database_version (Type: ReactomeRESTTool)¶
Get Reactome database version information. Returns version number as integer.
Reactome_get_database_version tool specification
Tool Information:
Name:
Reactome_get_database_versionType:
ReactomeRESTToolDescription: Get Reactome database version information. Returns version number as integer.
Parameters:
No parameters required.
Example Usage:
query = {
"name": "Reactome_get_database_version",
"arguments": {
}
}
result = tu.run(query)
Reactome_get_diseases (Type: ReactomeRESTTool)¶
Get list of disease pathways or DOIDs (Disease Ontology IDs) annotated in Reactome. Returns disea…
Reactome_get_diseases tool specification
Tool Information:
Name:
Reactome_get_diseasesType:
ReactomeRESTToolDescription: Get list of disease pathways or DOIDs (Disease Ontology IDs) annotated in Reactome. Returns disease-related pathway information including database identifiers, definitions, and names.
Parameters:
No parameters required.
Example Usage:
query = {
"name": "Reactome_get_diseases",
"arguments": {
}
}
result = tu.run(query)
Reactome_get_entity_compartment (Type: ReactomeRESTTool)¶
Get compartment information for an entity. Returns TSV-formatted compartment data parsed into str…
Reactome_get_entity_compartment tool specification
Tool Information:
Name:
Reactome_get_entity_compartmentType:
ReactomeRESTToolDescription: Get compartment information for an entity. Returns TSV-formatted compartment data parsed into structured JSON. The API returns tab-separated values (ID, name, type) which are automatically converted to JSON format.
Parameters:
stId(string) (required) Entity Stable ID (e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways. To find reaction IDs, use Reactome_get_pathway_reactions. To find entity IDs, use Reactome_get_participants.
Example Usage:
query = {
"name": "Reactome_get_entity_compartment",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_entity_events (Type: ReactomeRESTTool)¶
Get events (reactions/subpathways) associated with an entity. Returns TSV-formatted event data pa…
Reactome_get_entity_events tool specification
Tool Information:
Name:
Reactome_get_entity_eventsType:
ReactomeRESTToolDescription: Get events (reactions/subpathways) associated with an entity. Returns TSV-formatted event data parsed into structured JSON. The API returns tab-separated values (ID, name, type) which are automatically converted to JSON format.
Parameters:
stId(string) (required) Entity Stable ID (pathway, e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
Example Usage:
query = {
"name": "Reactome_get_entity_events",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_event_ancestors (Type: ReactomeRESTTool)¶
Get ancestor events (parent pathways) for a reaction or pathway.
Reactome_get_event_ancestors tool specification
Tool Information:
Name:
Reactome_get_event_ancestorsType:
ReactomeRESTToolDescription: Get ancestor events (parent pathways) for a reaction or pathway.
Parameters:
stId(string) (required) Event Stable ID (pathway or reaction, e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways. To find reaction IDs, use Reactome_get_pathway_reactions with a pathway ID.
Example Usage:
query = {
"name": "Reactome_get_event_ancestors",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_events_hierarchy (Type: ReactomeRESTTool)¶
Get the full event hierarchy (pathways and reactions) for a specific species. Returns complete ne…
Reactome_get_events_hierarchy tool specification
Tool Information:
Name:
Reactome_get_events_hierarchyType:
ReactomeRESTToolDescription: Get the full event hierarchy (pathways and reactions) for a specific species. Returns complete nested hierarchy structure with top-level pathways and their children (subpathways and reactions). Note: Use taxonomy ID (e.g., ‘9606’) for best results.
Parameters:
species(string) (required) Species taxonomy ID (e.g., ‘9606’ for Homo sapiens) or species name. Taxonomy ID is recommended. To find available species and their taxonomy IDs, use Reactome_list_species.
Example Usage:
query = {
"name": "Reactome_get_events_hierarchy",
"arguments": {
"species": "example_value"
}
}
result = tu.run(query)
Reactome_get_interactor (Type: ReactomeRESTTool)¶
Get detailed information about an interactor (protein, complex, or small molecule) by its Stable …
Reactome_get_interactor tool specification
Tool Information:
Name:
Reactome_get_interactorType:
ReactomeRESTToolDescription: Get detailed information about an interactor (protein, complex, or small molecule) by its Stable ID. Returns comprehensive interactor data including reference entities, compartments, and related pathways. Uses the unified query endpoint that works for all entity types.
Parameters:
stId(string) (required) Interactor Stable ID. To find interactor IDs, use Reactome_get_participants with a reaction ID, or Reactome_map_uniprot_to_pathways/Reactome_map_uniprot_to_reactions if you have a UniProt protein ID.
Example Usage:
query = {
"name": "Reactome_get_interactor",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_participant_reference_entities (Type: ReactomeRESTTool)¶
Get reference entities for participants of a reaction or event. Returns list of reference entitie…
Reactome_get_participant_reference_entities tool specification
Tool Information:
Name:
Reactome_get_participant_reference_entitiesType:
ReactomeRESTToolDescription: Get reference entities for participants of a reaction or event. Returns list of reference entities (UniProt proteins, ChEBI chemicals, etc.) associated with the participants, including database identifiers and names.
Parameters:
stId(string) (required) Event Stable ID (reaction or pathway, e.g., ‘R-HSA-111289’). To find reaction IDs, use Reactome_get_pathway_reactions with a pathway ID. To find pathway IDs, use Reactome_list_top_pathways.
Example Usage:
query = {
"name": "Reactome_get_participant_reference_entities",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_participants (Type: ReactomeRESTTool)¶
Get all participants (physical entities) of a reaction or event. Returns list of physical entitie…
Reactome_get_participants tool specification
Tool Information:
Name:
Reactome_get_participantsType:
ReactomeRESTToolDescription: Get all participants (physical entities) of a reaction or event. Returns list of physical entities (proteins, complexes, small molecules) participating in the event, including their reference entities.
Parameters:
stId(string) (required) Event Stable ID (reaction or pathway, e.g., ‘R-HSA-111289’). To find reaction IDs, use Reactome_get_pathway_reactions with a pathway ID. To find pathway IDs, use Reactome_list_top_pathways.
Example Usage:
query = {
"name": "Reactome_get_participants",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_pathway (Type: ReactomeRESTTool)¶
Get detailed information about a specific pathway by its Stable ID. Returns comprehensive pathway…
Reactome_get_pathway tool specification
Tool Information:
Name:
Reactome_get_pathwayType:
ReactomeRESTToolDescription: Get detailed information about a specific pathway by its Stable ID. Returns comprehensive pathway data including metadata, compartments, literature references, orthologous events, and related pathways. Uses the unified query endpoint that works for all entity types.
Parameters:
stId(string) (required) Pathway Stable ID (e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
Example Usage:
query = {
"name": "Reactome_get_pathway",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_pathway_hierarchy (Type: ReactomeRESTTool)¶
Get the hierarchy (parent pathways) for a pathway. Returns list of parent pathways.
Reactome_get_pathway_hierarchy tool specification
Tool Information:
Name:
Reactome_get_pathway_hierarchyType:
ReactomeRESTToolDescription: Get the hierarchy (parent pathways) for a pathway. Returns list of parent pathways.
Parameters:
stId(string) (required) Pathway Stable ID (e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
Example Usage:
query = {
"name": "Reactome_get_pathway_hierarchy",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_pathway_reactions (Type: ReactomeRESTTool)¶
Query all reactions and subpathways contained under a Pathway using Pathway Stable ID. Returns li…
Reactome_get_pathway_reactions tool specification
Tool Information:
Name:
Reactome_get_pathway_reactionsType:
ReactomeRESTToolDescription: Query all reactions and subpathways contained under a Pathway using Pathway Stable ID. Returns list of events (reactions and subpathways) contained in the pathway, including their metadata and relationships.
Parameters:
stId(string) (required) Pathway Stable ID (e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways to get top-level pathways, or Reactome_map_uniprot_to_pathways if you have a UniProt protein ID.
Example Usage:
query = {
"name": "Reactome_get_pathway_reactions",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_get_pathways_low_entity (Type: ReactomeRESTTool)¶
Get low-level pathways (most specific pathways) containing a specific entity. Returns pathways at…
Reactome_get_pathways_low_entity tool specification
Tool Information:
Name:
Reactome_get_pathways_low_entityType:
ReactomeRESTToolDescription: Get low-level pathways (most specific pathways) containing a specific entity. Returns pathways at the lowest level of the hierarchy.
Parameters:
id(string) (required) Entity Stable ID (pathway, reaction, or physical entity, e.g., ‘R-HSA-73817’). To find pathway IDs, use Reactome_list_top_pathways. To find reaction IDs, use Reactome_get_pathway_reactions. To find entity IDs, use Reactome_get_participants.
Example Usage:
query = {
"name": "Reactome_get_pathways_low_entity",
"arguments": {
"id": "example_value"
}
}
result = tu.run(query)
Reactome_get_reaction (Type: ReactomeRESTTool)¶
Get detailed information about a specific reaction/event by its Stable ID. Returns comprehensive …
Reactome_get_reaction tool specification
Tool Information:
Name:
Reactome_get_reactionType:
ReactomeRESTToolDescription: Get detailed information about a specific reaction/event by its Stable ID. Returns comprehensive reaction data including inputs, outputs, regulation, literature references, and participants. Uses the unified query endpoint. Use Reactome_get_pathway_reactions to get valid reaction IDs first.
Parameters:
stId(string) (required) Reaction Stable ID (e.g., ‘R-HSA-111289’). To find reaction IDs, use Reactome_get_pathway_reactions with a pathway ID to get all reactions in that pathway.
Example Usage:
query = {
"name": "Reactome_get_reaction",
"arguments": {
"stId": "example_value"
}
}
result = tu.run(query)
Reactome_list_species (Type: ReactomeRESTTool)¶
List all species available in Reactome database.
Reactome_list_species tool specification
Tool Information:
Name:
Reactome_list_speciesType:
ReactomeRESTToolDescription: List all species available in Reactome database.
Parameters:
No parameters required.
Example Usage:
query = {
"name": "Reactome_list_species",
"arguments": {
}
}
result = tu.run(query)
Reactome_list_top_pathways (Type: ReactomeRESTTool)¶
List top-level pathways for a specific species. Returns pathways that have no parent pathways, in…
Reactome_list_top_pathways tool specification
Tool Information:
Name:
Reactome_list_top_pathwaysType:
ReactomeRESTToolDescription: List top-level pathways for a specific species. Returns pathways that have no parent pathways, including their metadata and basic information.
Parameters:
species(string) (required) Species name or taxonomy ID (e.g., ‘Homo sapiens’ or ‘9606’). To find available species and their taxonomy IDs, use Reactome_list_species.
Example Usage:
query = {
"name": "Reactome_list_top_pathways",
"arguments": {
"species": "example_value"
}
}
result = tu.run(query)
Reactome_map_uniprot_to_pathways (Type: ReactomeRESTTool)¶
Map a UniProt protein identifier to Reactome pathways. Returns all pathways that contain this pro…
Reactome_map_uniprot_to_pathways tool specification
Tool Information:
Name:
Reactome_map_uniprot_to_pathwaysType:
ReactomeRESTToolDescription: Map a UniProt protein identifier to Reactome pathways. Returns all pathways that contain this protein.
Parameters:
id(string) (required) UniProt protein identifier (e.g., ‘P04637’)
Example Usage:
query = {
"name": "Reactome_map_uniprot_to_pathways",
"arguments": {
"id": "example_value"
}
}
result = tu.run(query)
Reactome_map_uniprot_to_reactions (Type: ReactomeRESTTool)¶
Map a UniProt protein identifier to Reactome reactions. Returns all reactions that involve this p…
Reactome_map_uniprot_to_reactions tool specification
Tool Information:
Name:
Reactome_map_uniprot_to_reactionsType:
ReactomeRESTToolDescription: Map a UniProt protein identifier to Reactome reactions. Returns all reactions that involve this protein.
Parameters:
id(string) (required) UniProt protein identifier (e.g., ‘P04637’)
Example Usage:
query = {
"name": "Reactome_map_uniprot_to_reactions",
"arguments": {
"id": "example_value"
}
}
result = tu.run(query)
Reactome_query_by_ids (Type: ReactomeRESTTool)¶
Query Reactome by providing a list of Reactome stable identifiers (R-HSA-*). Returns detailed inf…
Reactome_query_by_ids tool specification
Tool Information:
Name:
Reactome_query_by_idsType:
ReactomeRESTToolDescription: Query Reactome by providing a list of Reactome stable identifiers (R-HSA-*). Returns detailed information about pathways, reactions, or other entities. Note: This endpoint requires Reactome stable IDs, not external IDs (UniProt, ChEBI). Use mapping endpoints first to convert external IDs to Reactome IDs.
Parameters:
ids(array) (required) List of Reactome stable identifiers (e.g., ‘R-HSA-73817’, ‘R-HSA-111289’). Must be Reactome stable IDs, not external IDs. To find pathway IDs, use Reactome_list_top_pathways. To find reaction IDs, use Reactome_get_pathway_reactions. To convert external IDs (UniProt) to Reactome IDs, first use Reactome_map_uniprot_to_pathways or Reactome_map_uniprot_to_reactions.species(string) (optional) Optional: Filter by species (e.g., ‘Homo sapiens’)types(array) (optional) Optional: Filter by types (e.g., [‘Pathway’, ‘Reaction’])
Example Usage:
query = {
"name": "Reactome_query_by_ids",
"arguments": {
"ids": ["item1", "item2"]
}
}
result = tu.run(query)