openapi: 3.0.1
info:
  title: Pathway Analysis Service database query 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: query
  description: 'Reactome Data: Common data retrieval'
paths:
  /data/query/enhanced/v2/{id}:
    get:
      tags:
      - query
      summary: More information on an entry in Reactome knowledgebase
      description: Based on the given identifier, i.e. stable id or database id, this method queries for an entry in Reactome knowledgebase providing more information. In particular, the retrieved database object has all its properties and direct relationships (relationships of depth 1) filled, while it also includes any second level relationships regarding regulations and catalysts.
      operationId: findEnhancedObjectById
      parameters:
      - name: id
        in: path
        description: DbId or StId of the requested database object
        required: true
        schema:
          type: string
        example: R-HSA-60140
      - name: fetchIncomingRelationships
        in: query
        description: Whether incoming relationships should be fetched
        required: false
        schema:
          type: boolean
          default: true
        example: true
      - name: summariseReferenceEntity
        in: query
        description: Whether ReferenceEntity should be summarising its physical entities
        required: false
        schema:
          type: boolean
          default: false
        example: false
      - name: includeDisease
        in: query
        description: Whether disease specific data should be fetched
        required: false
        schema:
          type: boolean
          default: true
        example: true
      - 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/json:
              schema:
                $ref: '#/components/schemas/DatabaseObject'
  /data/query/enhanced/{id}:
    get:
      tags:
      - query
      summary: More information on an entry in Reactome knowledgebase
      description: Based on the given identifier, i.e. stable id or database id, this method queries for an entry in Reactome knowledgebase providing more information. In particular, the retrieved database object has all its properties and direct relationships (relationships of depth 1) filled, while it also includes any second level relationships regarding regulations and catalysts.
      operationId: findOldEnhancedObjectById
      parameters:
      - name: id
        in: path
        description: DbId or StId of the requested database object
        required: true
        schema:
          type: string
        example: R-HSA-60140
      - 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/json:
              schema:
                $ref: '#/components/schemas/DatabaseObject'
  /data/query/ids:
    post:
      tags:
      - query
      summary: A list of entries in Reactome knowledgebase
      description: This method queries for a set of entries in Reactome knowledgebase based on the given list of identifiers. The provided list of identifiers can include stable ids, database ids or a mixture of both. It should be underlined that any duplicated ids are eliminated while only requests containing up to 20 ids are processed.
      operationId: findByIds
      parameters:
      - 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
      requestBody:
        description: A comma separated list of identifiers
        content:
          text/plain:
            schema:
              type: string
            example: R-HSA-1640170, R-HSA-109581, 199420
        required: true
      responses:
        '404':
          description: Identifier does not match with any in current data or invalid attribute name
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/DatabaseObject'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/DatabaseObject'
  /data/query/ids/map:
    post:
      tags:
      - query
      summary: A list of entries with their mapping to the provided identifiers
      description: This method queries for a set of entries in Reactome knowledgebase based on the given list of identifiers. The provided list of identifiers can include stable ids, database ids, old stable ids or a mixture of all. It should be underlined that any duplicated ids are eliminated while only requests containing up to 20 ids are processed.<br>This method is particularly useful for users that still rely on the previous version of stable identifiers to query this API. Please note that those are no longer part of the retrieved objects.
      operationId: findByIdsMap
      parameters:
      - 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
      requestBody:
        description: A comma separated list of identifiers
        content:
          text/plain:
            schema:
              type: string
            example: R-HSA-1640170, R-HSA-109581, 199420
        required: true
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                type: object
                additionalProperties:
                  $ref: '#/components/schemas/DatabaseObject'
  /data/query/{id}:
    get:
      tags:
      - query
      summary: An entry in Reactome knowledgebase
      description: This method queries for an entry in Reactome knowledgebase based on the given identifier, i.e. stable id or database id. It is worth mentioning that the retrieved database object has all its properties and direct relationships (relationships of depth 1) filled.
      operationId: findById
      parameters:
      - name: id
        in: path
        description: DbId or StId of the requested database object
        required: true
        schema:
          type: string
        example: R-HSA-1640170
      - 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 (depth 1)
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DatabaseObject'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DatabaseObject'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DatabaseObject'
  /data/query/{id}/{attributeName}:
    get:
      tags:
      - query
      summary: A single property of an entry in Reactome knowledgebase
      description: This method queries for a specific property of an entry in Reactome knowledgebase based on the given identifier, i.e. stable id or database id.
      operationId: findById_1
      parameters:
      - name: id
        in: path
        description: DbId or StId of the requested database object
        required: true
        schema:
          type: string
        example: R-HSA-1640170
      - name: attributeName
        in: path
        description: Attribute to be filtered
        required: true
        schema:
          type: string
        example: displayName
      - 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 or invalid attribute name
          content:
            text/plain:
              schema:
                type: string
        '500':
          description: Internal Server Error
          content:
            text/plain:
              schema:
                type: string
components:
  schemas:
    DatabaseObject:
      type: object
      properties:
        className:
          type: string
        created:
          type: object
        dbId:
          type: integer
          format: int64
        displayName:
          type: string
        modified:
          type: object
        schemaClass:
          type: string
        stId:
          type: string
        stIdVersion:
          type: string