Reactome references API
Reactome xRefs: ReferenceEntity queries
Operations 3
Documentation
Documentation
https://reactome.org/dev/content-service
Documentation
https://reactome.org/dev/analysis
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OpenAPI Specification
openapi: 3.2.0
info:
title: Pathway Analysis Service database References 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: references
description: 'Reactome xRefs: ReferenceEntity queries'
paths:
/references/mapping/xrefs:
post:
tags:
- references
summary: All cross references and physical entities associated with a list of given identifiers
description: Retrieves a paginated list containing cross references and physical entities associated with the matching reference entities identifiers
operationId: getCrossReferencesForList
parameters:
- name: dbFilter
in: query
description: Database filter to apply to results
required: false
schema:
type: string
- name: page
in: query
description: Page to process, starting from 0
required: false
schema:
type: integer
format: int32
default: 0
- name: pageSize
in: query
description: Page size to process, an element being one of the submitted identifiers
required: false
schema:
type: integer
format: int32
default: 100
- 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
requestBody:
description: A comma separated list of identifiers
content:
text/plain:
schema:
type: string
example: P36897, Q5S007
required: true
responses:
'404':
description: Identifier does not match with any reference entity
content:
application/json:
schema:
$ref: '#/components/schemas/PageMapStringCollectionCrossReferenceResult'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
$ref: '#/components/schemas/PageMapStringCollectionCrossReferenceResult'
'500':
description: Internal Server Error
content:
application/json:
schema:
$ref: '#/components/schemas/PageMapStringCollectionCrossReferenceResult'
/references/mapping/{identifier}:
get:
tags:
- references
summary: All ReferenceEntities for a given identifier
description: Retrieves a list containing all the reference entities for a given identifier.
operationId: getReferenceEntitiesFor
parameters:
- name: identifier
in: path
description: Identifier for a given entity
required: true
schema:
type: string
example: 15377
- 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 reference entity
content:
application/json:
schema:
type: array
items:
type: object
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
type: object
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
type: object
/references/mapping/{identifier}/xrefs:
get:
tags:
- references
summary: All cross references and physical entities associated with a given identifier
description: Retrieves a list containing cross references and physical entities associated with the matching reference entities identifier
operationId: getCrossReferencesFor
parameters:
- name: identifier
in: path
description: Identifier for a given entity
required: true
schema:
type: string
example: P36897
- name: dbFilter
in: query
description: Database filter to apply to results
required: false
schema:
type: string
- 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 reference entity
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/CrossReferenceResult'
'406':
description: Not acceptable according to the accept headers sent in the request
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/CrossReferenceResult'
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/CrossReferenceResult'
components:
schemas:
Sort:
type: object
properties:
empty:
type: boolean
sorted:
type: boolean
unsorted:
type: boolean
PageMapStringCollectionCrossReferenceResult:
type: object
properties:
content:
type: array
items:
type: object
additionalProperties:
type: array
items:
$ref: '#/components/schemas/CrossReferenceResult'
empty:
type: boolean
first:
type: boolean
last:
type: boolean
number:
type: integer
format: int32
numberOfElements:
type: integer
format: int32
pageable:
$ref: '#/components/schemas/PageableObject'
size:
type: integer
format: int32
sort:
$ref: '#/components/schemas/Sort'
totalElements:
type: integer
format: int64
totalPages:
type: integer
format: int32
CrossReferenceResult:
type: object
properties:
crossReferences:
type: array
items:
$ref: '#/components/schemas/ShortCrossReference'
physicalEntities:
type: array
items:
type: string
reference:
type: string
PageableObject:
type: object
properties:
offset:
type: integer
format: int64
pageNumber:
type: integer
format: int32
pageSize:
type: integer
format: int32
paged:
type: boolean
sort:
$ref: '#/components/schemas/Sort'
unpaged:
type: boolean
ShortCrossReference:
type: object
properties:
databaseName:
type: string
identifier:
type: string
url:
type: string