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.