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 schema 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: schema
description: 'Reactome Data: Schema class queries'
paths:
/data/schema/model:
get:
tags:
- schema
summary: A list of Reactome data model
description: This method retrieves a full specification of all Reactome classes.
operationId: getSchemaModel
parameters:
- 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:
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
$ref: '#/components/schemas/SchemaNode'
'500':
description: Internal Server Error
content:
application/json:
schema:
$ref: '#/components/schemas/SchemaNode'
/data/schema/{className}:
get:
tags:
- schema
summary: A list of entries corresponding to a given schema class
description: This method retrieves the list of entries in Reactome that belong to the specified schema class. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity. Additionally, paging is required, while a maximum of 25 entries can be returned per request.
operationId: getDatabaseObjectsForClassName
parameters:
- name: className
in: path
description: Schema class name
required: true
schema:
type: string
example: Pathway
- name: species
in: query
description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
required: false
schema:
type: string
example: 9606
- name: page
in: query
description: Page to be returned
required: true
schema:
type: integer
format: int32
example: 1
- name: offset
in: query
description: Number of rows returned. Maximum = 25
required: true
schema:
type: integer
format: int32
example: 25
- 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: Schema class does not match with any current data
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/DatabaseObject'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/DatabaseObject'
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/DatabaseObject'
/data/schema/{className}/count:
get:
tags:
- schema
summary: Number of entries belonging to the specified schema class
description: This method counts the total number of entries in Reactome that belong to the specified schema class. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity.
operationId: countEntries
parameters:
- name: className
in: path
description: Schema class name
required: true
schema:
type: string
example: Pathway
- name: species
in: query
description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
required: false
schema:
type: string
example: 9606
- 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: Schema class does not match with any current data
content:
application/json:
schema:
type: integer
format: int64
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: integer
format: int64
'500':
description: Internal Server Error
content:
application/json:
schema:
type: integer
format: int64
/data/schema/{className}/min:
get:
tags:
- schema
summary: A list of simplified entries corresponding to a given schema class
description: This method retrieves the list of simplified entries in Reactome that belong to the specified schema class. A simplified entry may be considered as a minimised version of the full database object that includes its database id, stable id, displayName and type. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity. Also, paging is required, while a maximum of 20000 entries can be returned per request.
operationId: getSimpleDatabaseObjectByClassName
parameters:
- name: className
in: path
description: Schema class name
required: true
schema:
type: string
example: Pathway
- name: species
in: query
description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
required: false
schema:
type: string
example: 9606
- name: page
in: query
description: Page to be returned
required: true
schema:
type: integer
format: int32
example: 1
- name: offset
in: query
description: Number of rows returned. Maximum = 20000
required: true
schema:
type: integer
format: int32
example: 20000
- 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: Schema class does not match with any current data
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/SimpleDatabaseObject'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/SimpleDatabaseObject'
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/SimpleDatabaseObject'
/data/schema/{className}/reference:
get:
tags:
- schema
summary: A list of simplified reference objects corresponding to a given schema class
description: This method retrieves the list of simplified reference objects that belong to the specified schema class. A reference object includes its database id, external identifier, and external database name. Please take into account that schema class needs to be an instance of ReferenceEntity or ExternalOntology. Also, paging is required, while a maximum of 20000 entries can be returned per request.
operationId: getSimpleReferencesObjectsByClassName
parameters:
- name: className
in: path
description: Schema class name. Class needs to an instance of ReferenceEntity or ExternalOntology
required: true
schema:
type: string
example: ReferenceMolecule
- name: page
in: query
description: Page to be returned
required: true
schema:
type: integer
format: int32
example: 1
- name: offset
in: query
description: Number of rows returned. Maximum = 20000
required: true
schema:
type: integer
format: int32
example: 20000
- 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: Schema class does not match with any current data
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/SimpleReferenceObject'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/SimpleReferenceObject'
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/SimpleReferenceObject'
components:
schemas:
SimpleReferenceObject:
type: object
properties:
databaseName:
type: string
dbId:
type: integer
format: int64
identifier:
type: string
DatabaseObject:
type: object
properties:
className:
type: string
created:
type: object
dbId:
type: integer
format: int64
displayName:
type: string
modified:
type: object
schemaClass:
type: string
stId:
type: string
stIdVersion:
type: string
SimpleDatabaseObject:
type: object
properties:
dbId:
type: integer
format: int64
displayName:
type: string
labels:
type: array
writeOnly: true
items:
type: string
schemaClass:
type: string
stId:
type: string
SchemaNode:
type: object
properties:
children:
uniqueItems: true
type: array
items:
$ref: '#/components/schemas/SchemaNode'
className:
type: string
count:
type: integer
format: int32