openapi: 3.0.1
info:
  title: Pathway Analysis Service database orthology 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: orthology
  description: 'Reactome Data: Orthology related queries'
paths:
  /data/orthologies/ids/species/{speciesId}:
    post:
      tags:
      - orthology
      summary: The orthologies of a given set of events or entities
      description: Reactome uses the set of manually curated human reactions to computationally infer reactions in twenty evolutionarily divergent eukaryotic species for which high-quality whole-genome sequence data are available, and hence a comprehensive and high-quality set of protein predictions exists. Thus, this method retrieves the orthologies for any given set of events or entities in the specified species. <a href="/documentation/inferred-events/" target="_blank">Here</a> you can find more information about the computationally inferred events.
      operationId: getOrthologies
      parameters:
      - name: speciesId
        in: path
        description: The species for which the orthology is requested
        required: true
        schema:
          type: integer
          format: int64
        example: 49633
      - 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: The <b>events</b> or <b>entities</b> for which the orthology is requested
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '404':
          description: Species does not match with any in current data
          content:
            application/json:
              schema:
                type: object
                additionalProperties:
                  $ref: '#/components/schemas/DatabaseObject'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: object
                additionalProperties:
                  $ref: '#/components/schemas/DatabaseObject'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: object
                additionalProperties:
                  $ref: '#/components/schemas/DatabaseObject'
  /data/orthology/{id}/species/{speciesId}:
    get:
      tags:
      - orthology
      summary: The orthology for a given event or entity
      description: Reactome uses the set of manually curated human reactions to computationally infer reactions in twenty evolutionarily divergent eukaryotic species for which high-quality whole-genome sequence data are available, and hence a comprehensive and high-quality set of protein predictions exists. Thus, this method retrieves the orthology for any given event or entity in the specified species. <a href="//www.reactome.org/pages/documentation/electronically-inferred-events/" target="_blank">Here</a> you can find more information about the computationally inferred events.
      operationId: getOrthology
      parameters:
      - name: id
        in: path
        description: The event for which the orthology is requested
        required: true
        schema:
          type: string
        example: R-HSA-6799198
      - name: speciesId
        in: path
        description: The species for which the orthology is requested
        required: true
        schema:
          type: integer
          format: int64
        example: 49633
      - 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: Species does not match with any in current data
          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'
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