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 exporter 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: exporter
description: 'Reactome Data: Format Exporter'
paths:
/exporter/diagram/{identifier}.{ext}:
get:
tags:
- exporter
summary: Exports a given pathway diagram to the specified image format (png, jpg, jpeg, svg, gif)
description: This method accepts identifiers for <a href="/content/schema/Event" target="_blank">Event class</a> instances.<br/>When a diagrammed pathway is provided, the diagram is exported to the specified format.<br/>When a subpathway is provided, the diagram for the parent is exported and the events that are part of the subpathways are selected.<br/>When a reaction is provided, the diagram containing the reaction is exported and the reaction is selected.<br/><br/>Find out more about this method <a href="/dev/content-service/diagram-exporter" target="_blank">here</a>
operationId: diagramImage_1
parameters:
- name: identifier
in: path
description: Event identifier (it can be a pathway with diagram, a subpathway or a reaction)
required: true
schema:
type: string
example: R-HSA-177929
- name: ext
in: path
description: File extension (defines the image format)
required: true
schema:
type: string
enum:
- png
- jpg
- jpeg
- svg
- gif
example: png
- name: quality
in: query
description: Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)
required: false
schema:
type: integer
format: int32
default: 5
example: 5
- name: flg
in: query
description: Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
required: false
schema:
type: string
- name: flgInteractors
in: query
description: Defines whether to take into account interactors for the flagging
required: false
schema:
type: boolean
default: true
- name: sel
in: query
description: Highlight element(s) selection in the diagram. CSV line.
required: false
schema:
type: array
items:
type: string
- name: title
in: query
description: Sets whether the name of the pathway is shown below
required: false
schema:
type: boolean
default: true
example: true
- name: margin
in: query
description: Defines the image margin between [0 - 20] (Default 15)
required: false
schema:
type: integer
format: int32
default: 15
example: 15
- name: ehld
in: query
description: Defines whether textbook-like illustration are taken into account
required: false
schema:
type: boolean
default: true
example: true
- name: diagramProfile
in: query
description: Diagram Color Profile
required: false
schema:
type: string
enum:
- Modern
- Standard
example: Modern
- 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 diagram
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: analysisProfile
in: query
description: Analysis Color Profile
required: false
schema:
type: string
enum:
- Standard
- Strosobar, Copper%20Plus
example: Standard
- name: expColumn
in: query
description: Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay
required: false
schema:
type: integer
format: int32
- 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:
'200':
description: OK
content:
image/gif: {}
image/jpeg: {}
image/jpg: {}
image/png: {}
image/svg+xml: {}
'404':
description: Stable Identifier does not match with any of the available diagrams.
'500':
description: Could not deserialize diagram file.
/exporter/document/event/{identifier}.pdf:
get:
tags:
- exporter
summary: Exports the content of a given event (pathway or reaction) to a PDF document
description: 'This method accepts identifiers for <a href="/content/schema/Event" target="_blank">Event class</a> instances.<br/>The generated document contains the details for the given event and, optionally, its children (see level parameter). These details include:<br/> - A diagram image<br/> - Summation<br/> - Literature references<br/> - Edit history<br/> - Other details: type, location, compartments, diseases<br/><br/>Documents can also be overlaid with <a href=''/dev/analysis'' target="_blank">pathway analysis results</a>'
operationId: eventPdf
parameters:
- name: identifier
in: path
description: Event identifier (it can be a pathway with diagram, a subpathway or a reaction)
required: true
schema:
type: string
example: R-HSA-177929
- name: level [0 - 1]
in: query
description: Number of levels to explore down in the pathways hierarchy [0 - 1]
required: false
schema:
type: integer
format: int32
default: 1
example: 1
- name: diagramProfile
in: query
description: Diagram Color Profile
required: false
schema:
type: string
enum:
- Modern
- Standard
example: Modern
- 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 diagram
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: importableOnly
in: query
description: Filters resources to only includes importable ones
required: false
schema:
type: boolean
default: false
- name: expColumn
in: query
description: Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay
required: false
schema:
type: integer
format: int32
- name: analysisProfile
in: query
description: Analysis Color Profile
required: false
schema:
type: string
enum:
- Standard
- Strosobar
- Copper%20Plus
example: Standard
- 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:
'200':
description: OK
content:
application/pdf: {}
'404':
description: Stable Identifier does not match with any of the available diagrams.
'500':
description: Could not deserialize diagram file.
'503':
description: Service was unable to export to Power Point.
/exporter/event/{identifier}.sbgn:
get:
tags:
- exporter
summary: Exports a given pathway or reaction to SBGN
operationId: eventSBGN
parameters:
- name: identifier
in: path
description: DbId or StId of the requested pathway or reaction
required: true
schema:
type: string
example: R-HSA-5205682
- 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 not found
'422':
description: Identifier does not correspond to a pathway or reaction
'500':
description: Internal Server Error
/exporter/event/{identifier}.sbml:
get:
tags:
- exporter
summary: Exports a given pathway or reaction to SBML
operationId: eventSBML
parameters:
- name: identifier
in: path
description: DbId or StId of the requested pathway or reaction
required: true
schema:
type: string
example: R-HSA-68616
- 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 not found
'422':
description: Identifier does not correspond to a pathway or reaction
'500':
description: Internal Server Error
/exporter/fireworks/{species}.{ext}:
get:
tags:
- exporter
summary: Exports a given pathway overview to the specified image format (png, jpg, jpeg, svg, gif)
operationId: diagramImage
parameters:
- name: species
in: path
description: Species identifier (it can be the taxonomy id, species name or dbId)
required: true
schema:
type: string
example: 9606
- name: ext
in: path
description: File extension (defines the image format)
required: true
schema:
type: string
enum:
- png
- jpg
- jpeg
- svg
- gif
example: svg
- name: quality
in: query
description: Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)
required: false
schema:
type: integer
format: int32
default: 5
example: 5
- name: flg
in: query
description: Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
required: false
schema:
type: string
- name: flgInteractors
in: query
description: Defines whether to take into account interactors for the flagging
required: false
schema:
type: boolean
default: true
- name: sel
in: query
description: Highlight element(s) selection in the diagram. CSV line.
required: false
schema:
type: array
items:
type: string
- name: title
in: query
description: Sets whether the name of the pathway is shown below
required: false
schema:
type: boolean
default: true
example: true
- name: margin
in: query
description: Defines the image margin between [0 - 20] (Default 15)
required: false
schema:
type: integer
format: int32
default: 15
example: 15
- name: diagramProfile
in: query
description: Diagram Color Profile
required: false
schema:
type: string
enum:
- Copper
- Copper plus
- Barium Lithium
- Calcium Salts
example: Copper
- 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: expColumn
in: query
description: Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay
required: false
schema:
type: integer
format: int32
- name: coverage
in: query
description: Set to 'true' to overlay analysis coverage values
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:
'200':
description: OK
content:
image/gif: {}
image/jpeg: {}
image/jpg: {}
image/png: {}
image/svg+xml: {}
'404':
description: Species does not match with any of the available.
'500':
description: Could not deserialize pathways overview file.
/exporter/reaction/{identifier}.{ext}:
get:
tags:
- exporter
summary: Exports a given reaction to the specified image format (png, jpg, jpeg, svg, gif)
description: This method accepts identifiers for <a href="/content/schema/ReactionLikeEvent" target="_blank">ReactionLikeEvent class</a> instances.
operationId: reactionImage
parameters:
- name: identifier
in: path
description: Reaction identifier
required: true
schema:
type: string
example: R-HSA-6787403
- name: ext
in: path
description: File extension (defines the image format)
required: true
schema:
type: string
enum:
- png
- jpg
- jpeg
- svg
- gif
example: png
- name: quality
in: query
description: Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)
required: false
schema:
type: integer
format: int32
default: 5
example: 5
- name: flg
in: query
description: Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
required: false
schema:
type: string
- name: flgInteractors
in: query
description: Defines whether to take into account interactors for the flagging
required: false
schema:
type: boolean
default: true
- name: sel
in: query
description: Highlight element selection in the diagram.
required: false
schema:
type: array
items:
type: string
- name: title
in: query
description: Sets whether the name of the reaction is shown below
required: false
schema:
type: boolean
default: true
example: true
- name: margin
in: query
description: Defines the image margin between [0 - 20] (Default 15)
required: false
schema:
type: integer
format: int32
default: 15
example: 15
- name: diagramProfile
in: query
description: Diagram Color Profile
required: false
schema:
type: string
enum:
- Modern
- Standard
example: Modern
- 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 reaction
required: false
schema:
type: string
- name: analysisProfile
in: query
description: Analysis Color Profile
required: false
schema:
type: string
enum:
- Standard
- Strosobar, Copper%20Plus
example: Standard
- 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: expColumn
in: query
description: Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay
required: false
schema:
type: integer
format: int32
- 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:
'200':
description: OK
content:
image/gif: {}
image/jpeg: {}
image/jpg: {}
image/png: {}
image/svg+xml: {}
'404':
description: Stable Identifier does not match with any of the reactions.
'500':
description: Could not deserialize diagram file.