openapi: 3.0.1
info:
  title: Pathway Analysis Service database entities 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: entities
  description: 'Reactome Data: PhysicalEntity queries'
paths:
  /data/complex/{id}/subunits:
    get:
      tags:
      - entities
      summary: A list with the entities contained in a given complex
      description: Retrieves the list of subunits that constitute any given complex. In case the complex comprises other complexes, this method recursively traverses the content returning each contained PhysicalEntity. Contained complexes and entity sets can be excluded setting the 'excludeStructures' optional parameter to 'true'
      operationId: getComplexSubunits
      parameters:
      - name: id
        in: path
        description: The complex for which subunits are requested
        required: true
        schema:
          type: string
        example: R-HSA-5674003
      - name: excludeStructures
        in: query
        description: Specifies whether contained complexes and entity sets are excluded in the response
        required: false
        schema:
          type: boolean
          default: false
        example: 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:
        '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/complexes/{resource}/{identifier}:
    get:
      tags:
      - entities
      summary: A list of complexes containing the pair (identifier, resource)
      description: Retrieves the list of complexes that contain a given (identifier, resource). The method deconstructs the complexes into all its participants to do so.
      operationId: getComplexesFor
      parameters:
      - name: resource
        in: path
        description: The resource of the identifier for complexes are requested
        required: true
        schema:
          type: string
        example: UniProt
      - name: identifier
        in: path
        description: The identifier for which complexes are requested
        required: true
        schema:
          type: string
        example: P00533
      - 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: Pair (identifier, resource) 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/entity/{id}/componentOf:
    get:
      tags:
      - entities
      summary: A list of larger structures containing the entity
      description: Retrieves the list of structures (Complexes and Sets) that include the given entity as their component. It should be mentioned that the list includes only simplified entries (type, names, ids) and not full information about each item.
      operationId: getComponentsOf
      parameters:
      - name: id
        in: path
        required: true
        schema:
          type: string
        example: R-HSA-199420
      - 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/ComponentOf'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/ComponentOf'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/ComponentOf'
  /data/entity/{id}/in-depth:
    get:
      tags:
      - entities
      operationId: getPhysicalEntityInDepth
      parameters:
      - name: id
        in: path
        description: The complex for which subunits are requested
        required: true
        schema:
          type: string
        example: R-HSA-5674003
      - name: maxDepth
        in: query
        description: Specify the depth needed for the given entity. If negative, fetches everything. If not, fetches the specified amount of nesting
        required: false
        schema:
          type: integer
          format: int32
          default: 1
      - name: attributes
        in: query
        description: Specify the attributes to load for each level of the entity
        required: false
        schema:
          type: string
          default: species,compartment
        example: species,compartment
      - 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: object
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: object
  /data/entity/{id}/otherForms:
    get:
      tags:
      - entities
      summary: All other forms of a PhysicalEntity
      description: Retrieves a list containing all other forms of the given PhysicalEntity. These other forms are PhysicalEntities that share the same ReferenceEntity identifier, e.g. PTEN H93R[R-HSA-2318524] and PTEN C124R[R-HSA-2317439] are two forms of PTEN.
      operationId: getOtherFormsOf
      parameters:
      - name: id
        in: path
        description: DbId or StId of a PhysicalEntity
        required: true
        schema:
          type: string
        example: R-HSA-199420
      - 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:
    ComponentOf:
      type: object
      properties:
        names:
          type: array
          items:
            type: string
        schemaClasses:
          type: array
          items:
            type: string
        species:
          type: array
          items:
            type: string
        stIds:
          type: array
          items:
            type: string
        type:
          type: string