openapi: 3.0.1
info:
  title: Pathway Analysis Service database schema 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: schema
  description: 'Reactome Data: Schema class queries'
paths:
  /data/schema/model:
    get:
      tags:
      - schema
      summary: A list of Reactome data model
      description: This method retrieves a full specification of all Reactome classes.
      operationId: getSchemaModel
      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
      responses:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SchemaNode'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SchemaNode'
  /data/schema/{className}:
    get:
      tags:
      - schema
      summary: A list of entries corresponding to a given schema class
      description: This method retrieves the list of entries in Reactome that belong to the specified schema class. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity. Additionally, paging is required, while a maximum of 25 entries can be returned per request.
      operationId: getDatabaseObjectsForClassName
      parameters:
      - name: className
        in: path
        description: Schema class name
        required: true
        schema:
          type: string
        example: Pathway
      - name: species
        in: query
        description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
        required: false
        schema:
          type: string
        example: 9606
      - name: page
        in: query
        description: Page to be returned
        required: true
        schema:
          type: integer
          format: int32
        example: 1
      - name: offset
        in: query
        description: Number of rows returned. Maximum = 25
        required: true
        schema:
          type: integer
          format: int32
        example: 25
      - 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: Schema class does not match with any current data
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/DatabaseObject'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          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/schema/{className}/count:
    get:
      tags:
      - schema
      summary: Number of entries belonging to the specified schema class
      description: This method counts the total number of entries in Reactome that belong to the specified schema class. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity.
      operationId: countEntries
      parameters:
      - name: className
        in: path
        description: Schema class name
        required: true
        schema:
          type: string
        example: Pathway
      - name: species
        in: query
        description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
        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: Schema class does not match with any current data
          content:
            application/json:
              schema:
                type: integer
                format: int64
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: integer
                format: int64
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: integer
                format: int64
  /data/schema/{className}/min:
    get:
      tags:
      - schema
      summary: A list of simplified entries corresponding to a given schema class
      description: This method retrieves the list of simplified entries in Reactome that belong to the specified schema class. A simplified entry may be considered as a minimised version of the full database object that includes its database id, stable id, displayName and type. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity. Also, paging is required, while a maximum of 20000 entries can be returned per request.
      operationId: getSimpleDatabaseObjectByClassName
      parameters:
      - name: className
        in: path
        description: Schema class name
        required: true
        schema:
          type: string
        example: Pathway
      - name: species
        in: query
        description: 'Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)'
        required: false
        schema:
          type: string
        example: 9606
      - name: page
        in: query
        description: Page to be returned
        required: true
        schema:
          type: integer
          format: int32
        example: 1
      - name: offset
        in: query
        description: Number of rows returned. Maximum = 20000
        required: true
        schema:
          type: integer
          format: int32
        example: 20000
      - 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: Schema class does not match with any current data
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/SimpleDatabaseObject'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/SimpleDatabaseObject'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/SimpleDatabaseObject'
  /data/schema/{className}/reference:
    get:
      tags:
      - schema
      summary: A list of simplified reference objects corresponding to a given schema class
      description: This method retrieves the list of simplified reference objects that belong to the specified schema class. A reference object includes its database id, external identifier, and external database name. Please take into account that schema class needs to be an instance of ReferenceEntity or ExternalOntology. Also, paging is required, while a maximum of 20000 entries can be returned per request.
      operationId: getSimpleReferencesObjectsByClassName
      parameters:
      - name: className
        in: path
        description: Schema class name. Class needs to an instance of ReferenceEntity or ExternalOntology
        required: true
        schema:
          type: string
        example: ReferenceMolecule
      - name: page
        in: query
        description: Page to be returned
        required: true
        schema:
          type: integer
          format: int32
        example: 1
      - name: offset
        in: query
        description: Number of rows returned. Maximum = 20000
        required: true
        schema:
          type: integer
          format: int32
        example: 20000
      - 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: Schema class does not match with any current data
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/SimpleReferenceObject'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/SimpleReferenceObject'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/SimpleReferenceObject'
components:
  schemas:
    SimpleReferenceObject:
      type: object
      properties:
        databaseName:
          type: string
        dbId:
          type: integer
          format: int64
        identifier:
          type: string
    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
    SimpleDatabaseObject:
      type: object
      properties:
        dbId:
          type: integer
          format: int64
        displayName:
          type: string
        labels:
          type: array
          writeOnly: true
          items:
            type: string
        schemaClass:
          type: string
        stId:
          type: string
    SchemaNode:
      type: object
      properties:
        children:
          uniqueItems: true
          type: array
          items:
            $ref: '#/components/schemas/SchemaNode'
        className:
          type: string
        count:
          type: integer
          format: int32