Documentation
Documentation
https://reactome.org/dev/content-service
Documentation
https://reactome.org/dev/analysis
OpenAPI Specification
openapi: 3.0.1
info:
title: Pathway Analysis Service database events API
description: Provides an API for pathway over-representation and expression analysis as well as species comparison tool.
termsOfService: /license
contact:
name: Reactome
url: https://reactome.org
email: help@reactome.org
license:
name: Creative Commons Attribution 3.0 Unsupported License
url: https://creativecommons.org/licenses/by/3.0/legalcode
version: '2.0'
servers:
- url: /AnalysisService
tags:
- name: events
description: 'Reactome Data: Queries related to events'
paths:
/data/event/{id}/ancestors:
get:
tags:
- events
summary: The ancestors of a given event
description: The Reactome definition of events includes pathways and reactions. Although events are organised in a hierarchical structure, a single event can be in more than one location, i.e. a reaction can take part in different pathways while, in the same way, a sub-pathway can take part in many pathways. Therefore, this method retrieves a list of all possible paths from the requested event to the top level pathway(s).
operationId: getEventAncestors
parameters:
- name: id
in: path
description: The event for which the ancestors are requested
required: true
schema:
type: string
example: R-HSA-5673001
- name: view
in: query
description: Global parameter - Customise the view to be more concise and/or aggregate relationships
required: false
schema:
type: string
default: flatten
enum:
- flatten
- nested
- nested-aggregated
example: null
- name: includeRef
in: query
description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
required: false
schema:
type: boolean
default: false
example: null
responses:
'404':
description: Identifier does not match with any in current data
content:
application/json:
schema:
type: array
items:
type: array
items:
$ref: '#/components/schemas/EventProjection'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
type: array
items:
$ref: '#/components/schemas/EventProjection'
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
type: array
items:
$ref: '#/components/schemas/EventProjection'
/data/event/{id}/in-depth:
get:
tags:
- events
operationId: getEventInDepth
parameters:
- name: id
in: path
description: The complex for which subunits are requested
required: true
schema:
type: string
example: R-HSA-9612973
- name: maxDepth
in: query
description: Specify the depth needed for the given entity. If negative, fetches everything. If not, fetches the specified amount of nesting
required: false
schema:
type: integer
format: int32
default: 1
- name: attributes
in: query
description: Specify the attributes to load for each level of the entity
required: false
schema:
type: string
default: species,compartment
example: species,compartment
- name: view
in: query
description: Global parameter - Customise the view to be more concise and/or aggregate relationships
required: false
schema:
type: string
default: flatten
enum:
- flatten
- nested
- nested-aggregated
example: null
- name: includeRef
in: query
description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
required: false
schema:
type: boolean
default: false
example: null
responses:
'404':
description: Identifier does not match with any in current data
content:
application/json:
schema:
type: object
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: object
'500':
description: Internal Server Error
content:
application/json:
schema:
type: object
/data/eventsHierarchy/{species}:
get:
tags:
- events
summary: The full event hierarchy for a given species
description: Events (pathways and reactions) in Reactome are organised in a hierarchical structure for every species. By following all 'hasEvent' relationships, this method retrieves the full event hierarchy for any given species. The result is a list of tree structures, one for each TopLevelPathway. Every event in these trees is represented by a PathwayBrowserNode. The latter contains the stable identifier, the name, the species, the url, the type, and the diagram of the particular event.
operationId: getEventHierarchy
parameters:
- name: species
in: path
description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
required: true
schema:
type: string
example: 9606
- name: pathwaysOnly
in: query
description: Only get pathways
required: false
schema:
type: boolean
default: false
example: false
- name: token
in: query
description: The <a href="/dev/analysis" target="_blank">analysis</a> token with the results to be overlaid on top of the given pathways overview
required: false
schema:
type: string
- name: resource
in: query
description: The <a href="/dev/analysis" target="_blank">analysis</a> resource for which the results will be overlaid on top of the given pathways overview
required: false
schema:
type: string
default: TOTAL
- name: interactors
in: query
description: Include interactors
required: false
schema:
type: boolean
default: false
example: false
- name: importableOnly
in: query
description: Filters resources to only includes importable ones
required: false
schema:
type: boolean
default: false
- name: view
in: query
description: Global parameter - Customise the view to be more concise and/or aggregate relationships
required: false
schema:
type: string
default: flatten
enum:
- flatten
- nested
- nested-aggregated
example: null
- name: includeRef
in: query
description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
required: false
schema:
type: boolean
default: false
example: null
responses:
'404':
description: Species does not match with any in current data
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/PathwayBrowserNode'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/PathwayBrowserNode'
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/PathwayBrowserNode'
components:
schemas:
EventProjection:
type: object
properties:
category:
type: string
dbId:
type: integer
format: int64
definition:
type: string
diagramHeight:
type: integer
format: int32
diagramWidth:
type: integer
format: int32
displayName:
type: string
doi:
type: string
hasDiagram:
type: boolean
hasEHLD:
type: boolean
inDisease:
type: boolean
inferred:
type: boolean
isCanonical:
type: string
name:
type: array
items:
type: string
oldStId:
type: string
releaseDate:
type: string
releaseStatus:
type: string
schemaClass:
type: string
speciesName:
type: string
stId:
type: string
stIdVersion:
type: string
PathwayBrowserNode:
type: object
properties:
children:
uniqueItems: true
type: array
items:
$ref: '#/components/schemas/PathwayBrowserNode'
diagram:
type: boolean
name:
type: string
species:
type: string
stId:
type: string
type:
type: string
url:
type: string