openapi: 3.0.1
info:
  title: Pathway Analysis Service database participants 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: participants
  description: 'Reactome Data: Queries related to participants'
paths:
  /data/participants/{id}:
    get:
      tags:
      - participants
      summary: A list of participants for a given event
      description: Participants contains a PhysicalEntity (dbId, displayName) and a collection of ReferenceEntities (dbId, name, identifier, url)
      operationId: getParticipants
      parameters:
      - name: id
        in: path
        description: DbId or StId of an Event
        required: true
        schema:
          type: string
        example: 5205685
      - 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 in current data
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Participant'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Participant'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Participant'
  /data/participants/{id}/participatingPhysicalEntities:
    get:
      tags:
      - participants
      summary: A list of participating PhysicalEntities for a given event
      description: This method retrieves all the PhysicalEntities that take part in a given event. It is worth mentioning that because a pathway can contain smaller pathways (subpathways), the method also recursively retrieves the PhysicalEntities from every constituent pathway.
      operationId: getParticipatingPhysicalEntities
      parameters:
      - name: id
        in: path
        description: The event for which the participating PhysicalEntities are requested
        required: true
        schema:
          type: string
        example: R-HSA-5205685
      - 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 in current data
          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
  /data/participants/{id}/referenceEntities:
    get:
      tags:
      - participants
      summary: A list of participating ReferenceEntities for a given event
      description: PhysicalEntity instances that represent, e.g., the same chemical in different compartments, or different post-translationally modified forms of a single protein, share numerous invariant features such as names, molecular structure and links to external databases like UniProt or ChEBI.<br>To enable storage of this shared information in a single place, and to create an explicit link among all the variant forms of what can also be seen as a single chemical entity, Reactome creates instances of the separate ReferenceEntity class. A ReferenceEntity instance captures the invariant features of a molecule.<br>This method retrieves the ReferenceEntities of all PhysicalEntities that take part in a given event. It is worth mentioning that because a pathway can contain smaller pathways (subpathways), this method also recursively retrieves the ReferenceEntities for all PhysicalEntities in every constituent pathway.
      operationId: getParticipatingReferenceEntities
      parameters:
      - name: id
        in: path
        description: The event for which the participating ReferenceEntities are requested
        required: true
        schema:
          type: string
        example: 5205685
      - 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 in current data
          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
components:
  schemas:
    Participant:
      type: object
      properties:
        displayName:
          type: string
        peDbId:
          type: integer
          format: int64
        refEntities:
          type: array
          items:
            $ref: '#/components/schemas/ParticipantRefEntities'
        schemaClass:
          type: string
    ParticipantRefEntities:
      type: object
      properties:
        dbId:
          type: integer
          format: int64
        displayName:
          type: string
        icon:
          type: string
        identifier:
          type: string
        schemaClass:
          type: string
        stId:
          type: string
        url:
          type: string