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 species 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: species
description: Species comparison
paths:
/species/homoSapiens/{species}:
get:
tags:
- species
summary: Compares Homo sapiens to the specified species
description: Use page and pageSize to reduce the amount of data retrieved. Use sortBy and order to sort the result by your preferred option. The resource field will filter the results to show only those corresponding to the preferred molecule type (TOTAL includes all the different molecules type)
operationId: compareHomoSapiensTo
parameters:
- name: species
in: path
description: The dbId of the species to compare to
required: true
schema:
type: integer
format: int64
- name: pageSize
in: query
description: pathways per page
required: false
schema:
type: integer
format: int32
example: 20
- name: page
in: query
description: page number
required: false
schema:
type: integer
format: int32
example: 1
- name: sortBy
in: query
required: false
schema:
type: string
description: how to sort the result
example: ENTITIES_PVALUE
enum:
- NAME
- TOTAL_ENTITIES
- TOTAL_INTERACTORS
- TOTAL_REACTIONS
- FOUND_ENTITIES
- FOUND_INTERACTORS
- FOUND_REACTIONS
- ENTITIES_RATIO
- ENTITIES_PVALUE
- ENTITIES_FDR
- REACTIONS_RATIO
- name: order
in: query
required: false
schema:
type: string
description: specifies the order
example: ASC
enum:
- ASC
- DESC
- name: resource
in: query
required: false
schema:
type: string
description: the resource to sort
example: TOTAL
enum:
- TOTAL
- UNIPROT
- ENSEMBL
- CHEBI
- IUPHAR
- MIRBASE
- NCBI_PROTEIN
- EMBL
- COMPOUND
- PUBCHEM_COMPOUND
- name: pValue
in: query
description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
required: false
schema:
type: number
format: double
default: 1.0
example: 1
- name: min
in: query
description: minimum number of contained entities per pathway (takes into account the resource)
required: false
schema:
type: integer
format: int32
- name: max
in: query
description: maximum number of contained entities per pathway (takes into account the resource)
required: false
schema:
type: integer
format: int32
- name: importableOnly
in: query
description: Filters resources to only includes importable ones
required: false
schema:
type: boolean
default: false
responses:
'404':
description: Species identifier does not match with any of the species in the current data
content:
application/json:
schema:
$ref: '#/components/schemas/AnalysisResult'
/data/species/all:
get:
tags:
- species
summary: The list of all species in Reactome
description: This method retrieves the list of all species in Reactome knowledgebase, sorted by name.
operationId: getAllSpecies
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:
type: array
items:
type: object
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
type: object
/data/species/main:
get:
tags:
- species
summary: The list of main species in Reactome
description: This method retrieves the list of main species in Reactome knowledgebase, sorted by name, but having 'Homo sapiens' as the first one. It should be mentioned that for Reactome, main species are considered those have either manually curated or computationally inferred pathways.
operationId: getSpecies
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:
type: array
items:
type: object
'500':
description: Internal Server Error
content:
application/json:
schema:
type: array
items:
type: object
components:
schemas:
AnalysisResult:
type: object
properties:
expression:
$ref: '#/components/schemas/ExpressionSummary'
identifiersNotFound:
type: integer
format: int32
pathways:
type: array
items:
$ref: '#/components/schemas/PathwaySummary'
pathwaysFound:
type: integer
format: int32
resourceSummary:
type: array
items:
$ref: '#/components/schemas/ResourceSummary'
speciesSummary:
type: array
items:
$ref: '#/components/schemas/SpeciesSummary'
summary:
$ref: '#/components/schemas/AnalysisSummary'
warnings:
type: array
items:
type: string
PathwaySummary:
type: object
properties:
dbId:
type: integer
format: int64
entities:
$ref: '#/components/schemas/EntityStatistics'
inDisease:
type: boolean
llp:
type: boolean
name:
type: string
reactions:
$ref: '#/components/schemas/ReactionStatistics'
species:
$ref: '#/components/schemas/SpeciesSummary'
stId:
type: string
AnalysisSummary:
type: object
properties:
fileName:
type: string
gsaMethod:
type: string
gsaToken:
type: string
includeDisease:
type: boolean
interactors:
type: boolean
projection:
type: boolean
sampleName:
type: string
species:
type: integer
format: int64
text:
type: boolean
token:
type: string
type:
type: string
ResourceSummary:
type: object
properties:
filtered:
type: integer
format: int32
pathways:
type: integer
format: int32
resource:
type: string
SpeciesSummary:
type: object
properties:
dbId:
type: integer
format: int64
filtered:
type: integer
format: int32
name:
type: string
pathways:
type: integer
format: int32
taxId:
type: string
EntityStatistics:
type: object
properties:
curatedFound:
type: integer
format: int32
curatedTotal:
type: integer
format: int32
exp:
type: array
items:
type: number
format: double
fdr:
type: number
format: double
found:
type: integer
format: int32
getpValue:
type: number
format: double
interactorsFound:
type: integer
format: int32
interactorsTotal:
type: integer
format: int32
ratio:
type: number
format: double
resource:
type: string
total:
type: integer
format: int32
ReactionStatistics:
type: object
properties:
found:
type: integer
format: int32
ratio:
type: number
format: double
resource:
type: string
total:
type: integer
format: int32
ExpressionSummary:
type: object
properties:
columnNames:
type: array
items:
type: string
max:
type: number
format: double
min:
type: number
format: double