openapi: 3.0.1
info:
  title: Pathway Analysis Service database pathways 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: pathways
  description: 'Reactome Data: Pathway related queries'
paths:
  /data/pathway/{id}/containedEvents:
    get:
      tags:
      - pathways
      summary: All the events contained in the given event
      description: Events are the building blocks used in Reactome to represent all biological processes, and they include pathways and reactions. Typically, an event can contain other events. For example, a pathway can contain smaller pathways and reactions. This method recursively retrieves all the events contained in any given event.
      operationId: getContainedEvents
      parameters:
      - name: id
        in: path
        description: The event for which the contained events are requested
        required: true
        schema:
          type: string
        example: R-HSA-5673001
      - 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: No contained events found in the given event
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
  /data/pathway/{id}/containedEvents/{attributeName}:
    get:
      tags:
      - pathways
      summary: A single property for each event contained in the given event
      description: Events are the building blocks used in Reactome to represent all biological processes, and they include pathways and reactions. Typically, an event can contain other events. For example, a pathway can contain smaller pathways (subpathways) and reactions.<br> This method recursively retrieves a single attribute for each of the events contained in the given event.
      operationId: getContainedEvents_1
      parameters:
      - name: id
        in: path
        description: The event for which the contained events are requested
        required: true
        schema:
          type: string
        example: R-HSA-5673001
      - name: attributeName
        in: path
        description: Attribute to be filtered
        required: true
        schema:
          type: string
        example: stId
      - 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: No contained events found in the given event or invalid attribute name
          content:
            text/plain:
              schema:
                type: string
        '500':
          description: Internal Server Error
          content:
            text/plain:
              schema:
                type: string
  /data/pathways/low/diagram/entity/{id}:
    get:
      tags:
      - pathways
      summary: A list of lower level pathways with diagram containing a given entity or event
      description: This method traverses the event hierarchy and retrieves the list of all lower level pathways that have a diagram and contain the given PhysicalEntity or Event.
      operationId: getPathwaysWithDiagramFor
      parameters:
      - name: id
        in: path
        description: The entity that has to be present in the pathways
        required: true
        schema:
          type: string
        example: R-HSA-199420
      - name: species
        in: query
        description: 'The species for which the pathways are requested. Taxonomy identifier (eg: 9606) or species name (eg: ''Homo sapiens'')'
        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: Identifier is not present in any pathways with diagram
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
  /data/pathways/low/diagram/entity/{id}/allForms:
    get:
      tags:
      - pathways
      summary: A list of lower level pathways with diagram containing any form of a given entity
      description: This method traverses the event hierarchy and retrieves the list of all lower level pathways that have a diagram and contain the given PhysicalEntity in any of its variant forms. These variant forms include for example different post-translationally modified versions of a single protein, or the same chemical in different compartments.
      operationId: getPathwaysWithDiagramForAllFormsOf
      parameters:
      - name: id
        in: path
        description: The entity (in any of its forms) that has to be present in the pathways
        required: true
        schema:
          type: string
        example: R-HSA-199420
      - name: species
        in: query
        description: 'The species for which the pathways are requested. Taxonomy identifier (eg: 9606) or species name (eg: ''Homo sapiens'')'
        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: Identifier (in any of its forms) is not present in any pathways with diagram
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
  /data/pathways/low/entity/{id}:
    get:
      tags:
      - pathways
      summary: A list of lower level pathways containing a given entity or event
      description: This method traverses the event hierarchy and retrieves the list of all lower level pathways that contain the given PhysicalEntity or Event.
      operationId: getPathwaysFor
      parameters:
      - name: id
        in: path
        description: The entity that has to be present in the pathways
        required: true
        schema:
          type: string
        example: R-HSA-199420
      - name: species
        in: query
        description: 'The species for which the pathways are requested. Taxonomy identifier (eg: 9606) or species name (eg: ''Homo sapiens'')'
        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: Identifier is not present in any pathways
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
  /data/pathways/low/entity/{id}/allForms:
    get:
      tags:
      - pathways
      summary: A list of lower level pathways containing any form of a given entity
      description: This method traverses the event hierarchy and retrieves the list of all lower level pathways that contain the given PhysicalEntity in any of its variant forms. These variant forms include for example different post-translationally modified versions of a single protein, or the same chemical in different compartments.
      operationId: getPathwaysForAllFormsOf
      parameters:
      - name: id
        in: path
        description: The entity (in any of its forms) that has to be present in the pathways
        required: true
        schema:
          type: string
        example: R-HSA-199420
      - name: species
        in: query
        description: 'The species for which the pathways are requested. Taxonomy identifier (eg: 9606) or species name (eg: ''Homo sapiens'')'
        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: Identifier (in any of its forms) is not present in any pathways
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
  /data/pathways/top/{species}:
    get:
      tags:
      - pathways
      summary: All Reactome top level pathways
      description: This method retrieves the list of top level pathways for the given species
      operationId: getTopLevelPathways
      parameters:
      - name: species
        in: path
        description: 'Specifies the species by the taxonomy identifier (eg: 9606) or species name (eg: ''Homo+sapiens'')'
        required: true
        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: No TopLevelPathways were found for species
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object